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  • 1
    ISSN: 1432-0428
    Keywords: Genetics ; haplotype ; HLA-A ; HLA-DQ ; HLA-DR ; tumour necrosis factor ; diabetes mellitus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In Finland the haplotype A2, Cw1, B56, DR4, DQ8 is the third most common haplotype in insulin-dependent diabetic (IDDM) patients and has the highest haplotype-specific absolute risk for IDDM. Cw1, B56, DR4, DQ8 haplotypes containing HLA-A alleles other than A2 are infrequent in the population and are not associated with IDDM. Comparison of the A2 and non-A2 haplotypes at the DNA level showed that they were identical at HLA-B,-DR, and -DQ loci. Evidence that class I alleles confer susceptibility to IDDM was obtained from the two HLA-C, -B, -DR and -DQ haplotypes most frequently found in IDDM patients in Finland. A24, A3 and A2 on the Cw3, B62, DR4, DQ8 haplotype, and A28, A2 and A1 on the Cw7, B8, DR3, DQ2 were all found to be associated with IDDM. In Finland these seven haplotypes, including A2, Cw1, B56, DR4, DQ8, account for 33% of diabetic haplotypes and 10.3% of non-diabetic haplotypes (p〈0.00001). The contribution of the class I region to IDDM susceptibility was also apparent in those IDDM patients lacking the disease-predisposing class II alleles. Significantly more non-DR3/non-DR4 IDDM patients (47 of 55) possessed two of the IDDM-associated HLA-A alleles compared to non-DR3/non-DR4 control subjects (40 of 58; p=0.038). Moreover, IDDM patients confirmed by oligotyping as unable to form a ‘diabetes-susceptibility’ DQ heterodimer, tended to possess two diabetes-associated HLA-A alleles (12 of 13) compared to control subjects (12 of 20; p=0.056).
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  • 2
    ISSN: 1432-0428
    Keywords: Genetics ; diabetes mellitus ; mitochondria ; maternal ; deafness
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Non-insulin-dependent diabetes mellitus (NIDDM) has a strong genetic component and maternal factors have recently been implicated in disease inheritance. The mitochondrial myopathies are a group of diseases which often show maternal inheritance as a result of mtDNA defects; some patients have impaired glucose tolerance. Occasional families with maternally inherited diabetes and deafness associated with a deletion or point mutation of mtDNA have been reported. To assess the importance of mitochondrial gene defects in NIDDM, 150 unrelated diabetic subjects from Wales, UK and 68 unrelated patients with diabetes and at least one affected sibling from England, UK were studied. Southern blot analysis did not show any large mtDNA deletions or duplications. One patient had a mutation in the mitochondrial tRNAleu(UUR) gene at bp 3243. This mutation is commonly associated with the syndrome of mitochondrial encephalomyopathy, lactic acidosis and stroke like episodes (MELAS). Study of this patient and his siblings showed a distinct form of late-onset diabetes associated with nerve deafness but no clinical features of the MELAS syndrome. No diabetic subject was shown to have the mtDNA mutation at position 8344 (tRNAlys) which has previously been described in the syndrome of mitochondrial encephalomyopathy and red-ragged fibres (MERRF). The role of other mitochondrial gene defects in diabetes and the pathophysiological basis of glucose intolerance in patients with the MELAS mutation requires further elucidation.
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  • 3
    ISSN: 1432-0533
    Keywords: Amyotrophic lateral sclerosis ; Neuropathology ; Posterior column involvement ; Genetics ; Superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Several missense mutations within exons 1, 2, 4 and 5 of the gene for Cu/Zn-binding superoxide dismutase (SOD1) have been discovered to be involved in the development of chromosome 21q-linked familial amyotrophic lateral sclerosis (FALS). We describe here an autopsied patient with FALS, in whom we have recently identified a novel missense mutation in exon 1 of the SOD1 gene. The neuropathological findings were compatible with those described previously in patients with FALS with posterior column involvement. This suggests that mutations of the SOD1 gene may be responsible for this form of FALS.
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  • 4
    ISSN: 1432-0533
    Keywords: Key words: Amyotrophic lateral sclerosis ; Neuropathology ; Posterior column involvement ; Genetics ; Superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Several missense mutations within exons 1, 2, 4 and 5 of the gene for Cu/Zn-binding superoxide dismutase (SOD1) have been discovered to be involved in the development of chromosome 21q-linked familial amyotrophic lateral sclerosis (FALS). We describe here an autopsied patient with FALS, in whom we have recently identified a novel missense mutation in exon 1 of the SOD1 gene. The neuropathological findings were compatible with those described previously in patients with FALS with posterior column involvement. This suggests that mutations of the SOD1 gene may be responsible for this form of FALS.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular medicine 72 (1994), S. 409-413 
    ISSN: 1432-1440
    Keywords: Myotonic dystrophy ; Limb girdle muscular dystrophy ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract A family is reported in which a 29-year-old woman showed the clinical features of myotonic dystrophy while her 26-year-old brother presented with the clinical picture of limb girdle syndrome. In the affected female, direct genetic testing for the specific myotonic dystrophy mutation on chromosome 19 revealed abnormal expansion of a repeat unit containing the three nucleotides cytosine, thymine, and guanine (CTG) — typical for myotonic dystrophy — while her diseased brother displayed two normal alleles. This supports the hypothesis of the extremely rare occurrence of two clinically and genetically different myopathies in one family. Genetic analysis of six other family members showed that the father of the diseased siblings as well as all of his three brothers and sisters had a pathological CTG repeat expansion, and that the other two family members tested had a normal allelic pattern. The number of CTG repeats in the diseased women was approximately tenfold higher than in her asymptomatic relatives who revealed an abnormal allelic pattern. The increase in CTG repeats with transmission to a subsequent generation in this family was paralleled by a dramatic increase in the severity of myotonic dystrophy.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 153 (1994), S. 372-377 
    ISSN: 1432-1076
    Keywords: Epilepsy ; Absences ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Clinical and EEG family data of 140 cases with early childhood epilepsy with absences are presented. The aim of the study was to evaluate, whether the occurrence of generalized tonic clonic seizures (GTCS) as a presenting symptom might correlate with family data, i.e. whether there are indications of heterogeneity. One hundred and forty cases were selected from the epilepsy family data base of the Neuropaediatric Department. The selection parameter was epilepsy with absences manifesting between the 1 st and 5th year of age. The incidence of seizures was evaluated in siblings, parents and parents' siblings. EEG records were available from 103 parents and 106 siblings. The analysis supports the assumption of heterogeneity within early childhood absence epilepsy. Parents and their sibs of cases manifesting with GTCS had seizures twice as often than parents and their sibs in the non-GTCS group. In the affected relatives of the GTCS group early onset GTCS prevailed, whereas in the relatives of the non-GTCS group absences were found more frequently. The EEG of relatives showed elevated incidences of spikes and waves and photosensitivity in both groups, indicating common genetic factors. In parents of the non-GTCS group, however, EEG pathology was significantly more frequent than in parents of the GTCS group. Comparing EEG pathology in parents with seizure risk in siblings, evidence for maternal preponderance in transmission of the seizure liability was found. Mothers' EEG seems to be the best predictor of the seizure risk in probands' siblings. Early childhood epilepsy with absences can be regarded as an intermediate type, showing overlap with early onset GTCS and myoclonic astatic epilepsy on the one side and with childhood absence epilepsy on the other.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    European journal of epidemiology 10 (1994), S. 317-324 
    ISSN: 1573-7284
    Keywords: Epidemiology ; Genetics ; Oral clefts ; Registers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Epidemiological and genetic variables for oral clefts were analysed for the years 1981–1989 in a case-control study of congenital malformations in the Emilia Romagna, Veneto, and Friuli regions, and in the Trento and Bolzano hospitals. Birth prevalence for all cases of cleft lip with or without cleft palate (CL(P)) was 8.2 per 10,000 births, and that for cleft palate only (CP) was 6.1 per 10,000. Coexisting abnormalities were found in 23% of CL(P) cases and in 43% of CP. No clusters in time or space were detected. For isolated clefts, a predominance of males among CL(P) and of females among CP was found; epilepsy was the only maternal risk factor correlated with clefts, and an association between clefting and consanguinity was found. Empirical recurrence risks were calculated in both isolated CL(P) and CP.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomedical science 1 (1994), S. 201-203 
    ISSN: 1423-0127
    Keywords: Hypertension ; Eicosanoid ; Rat ; Genetics ; Kidney
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The present paper reviews the evidence for a possible involvement of renal eicosanoids in the pathophysiology of high blood pressure in genetically hypertensive rats of the Lyon strain. Both in vivo and in vitro experiments suggest that an increased ability to synthesize the vasoconstrictor prostaglandin H2 and/or thromboxane A2 in renal vessels (1) acts as an autocrine amplifier of pressor agents and (2) may contribute to resetting the pressure natriuresis curve which is a prerequisite for the development and maintenance of hypertension.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Comparative clinical pathology 4 (1994), S. 146-151 
    ISSN: 1433-2981
    Keywords: Biochemistry ; Development ; Haematology ; Koala
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Haematology and biochemistry of captive pouch young and back young koalas from 165 days to one year old were studied. Distinct changes with age were observed. Packed cell volume, haemoglobin, erythrocyte count, MCV and total plasma protein where lowest in the youngest animals less than 180 days old. Reticulocytes were highest in this age group. Haematological values differed from those of adult animals. Lymphocytosis occurred, especially between 210–330 days of age. Intense erythropoiesis was indicated by reticulocytosis and the presence of erythrocyte granular inclusions, anisocytosis and poikilocytosis on blood films, particularly up to 330 days of age. Microcytosis present on blood films throughout the study period could not be explained by iron deficiency.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    European archives of psychiatry and clinical neuroscience 244 (1994), S. 138-140 
    ISSN: 1433-8491
    Keywords: Parity ; Genetics ; Diathesis-stress model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract As part of a follow-up and family study of post-partum psychoses, this episode of illness being the first leading to psychiatric hospitalisation, patients with puerperal episodes (PE) and nonpuerperal episodes (NPE) of illness in the long-term course (n=79) were compared to patients with PE only (n=40). Few differences were found. Relatives of patients with PE only had a lower morbidity risk for functional psychoses than relatives of patients with PE and NPE. A favourable course of illness in the presence of a low genetic predisposition may be expected, according to the diathesis-stress model of functional psychoses.
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  • 11
    ISSN: 1432-1459
    Keywords: PGAM deficiency ; Myopathy ; Biochemistry ; Muscle culture ; 31P-MR spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Muscle phosphoglycerate mutase (PGAM) deficiency has been so far identified in only six patients, five of these being African Americans. We report the results of clinical, morphological, biochemical, muscle culture and31P-MR spectroscopy studies in the first Caucasian patient with muscle PGAM deficiency. A 23-year-old man had a 10-year history of cramps after physical exertion with one episode of pigmenturia. Neurological examination and EMG study were normal. ECG and echocardiography revealed hypertrophy of the interventricular septum and slight dilatation of the left chambers of the heart. Muscle biopsy revealed increased glycogen content and some accumulation of mitochondria. Muscle PGAM activity was markedly decreased (6.5% and 9.7% of control value in two different biopsies). Citrate synthase and other mitochondrial respiratory chain enzyme activities were much higher than normal. In contrast to the marked decrease of PGAM activity observed in muscle biopsy, total enzyme activity in the patient's aneural muscle culture was normal, being represented exclusively by BB isoenzyme. The deficiency of PGAM-MM isoenzyme was reproduced in the patient's innervated muscle culture. Muscle31P-MR spectroscopy showed accumulation of phosphomonoesters only on fast “glycolytic” exercise. On “aerobic” exercise, Vmax, calculated from the work-energy cost transfer function, showed an increase consistent with the morphological and biochemical evidence of mitochondrial proliferation. This might represent a sort of compensatory aerobic effort in an attempt to restore muscle power.
    Type of Medium: Electronic Resource
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  • 12
    ISSN: 1432-1459
    Keywords: Multiple sclerosis Epidemiology ; Immigrants Environment ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The incidence and prevalence of multiple sclerosis (MS) were compared, controlling for age, in native-born Israelis of different origins and in immigrants to Israel. This comparison was carried out in two populations, countrywide and in Jerusalem. In the countrywide population, ascertainment was based mainly on hospitalizations; it included 252 patients who were native-born and 150 who had immigrated from Africa-Asia (AA immigrants). The 89 MS patients of Jerusalem also included patients diagnosed in outpatient clinics. In native-born Israelis whose father was born in Europe-America (I-EA), the incidence and prevalence of MS were found to be as high as or even higher than that found previously in immigrants from Europe-America. Among native-born Israelis whose father was born in Africa or Asia (I-AA), the yearly age-adjusted incidence and prevalence rates were found to be 1.4- to 1.8-fold higher than among AA immigrants, pointing to environmental factors. The incidence and prevalence rates in the I-EA were 1.2- to 1.6-fold higher than in the I-AA, pointing to genetic factors. These results seem to point to both environmental and genetic factors in the aetiology of MS. Further research is needed, however, to disentangle the genetic factors from possible environmental differences in the two ethnic groups.
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Journal of neurology 241 (1994), S. 487-491 
    ISSN: 1432-1459
    Keywords: Juvenile absence epilepsy ; Valproate ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Fifteen patients aged 11–25 years (mean 15.37, SD 3.89) suffering from juvenile absence epilepsy are presented. Only 3 (20%) had absences (AS) as the only seizure type, 12 (80%) had associated generalized tonic-clinic seizures (GTCS) and in the remaining 3 with absences and GTCS there was also sporadic myoclonus. We found a higher frequency of AS in our patients by clinical history and video-EEG than has been previously reported. In our patients the mean age of onset in years was 11.4, SD 1.24 for AS, 13.12, SD 2.31 for GTCS and 12.5, SD 2.18 for myoclonus. The correct diagnosis was not made on referrals for any of the patients. It took an average of 3–5.5 years from the onset of the AS (range: 6–120 months) and 2 years from the occurrence of GTCS (average: 1–72 months) to make the correct diagnosis and institute proper treatment, which was valproic acid (VPA). The GTCS were controlled in all patients whereas AS continued in 6 (40%), but to a significantly lesser degree. The frequency and the duration of the GTCS before the start of VPA treatment seemed to have an adverse effect on AS control. We documented no circadian rhythm in either AS or the GTCS, except in 2 patients who had AS and GTCS mainly when they awoke in the morning. The sample size was too small to perform a proper genetic study, though a positive history of epilepsies of mixed types was obtained in 35.7% of the parents and the siblings of the probands.
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  • 14
    ISSN: 1432-0533
    Keywords: Key words     Primitive neuroepithelial tumor ; Desmoplastic small cell tumor ; Brain tumor of infancy ; Immunocytochemistry ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract      We describe a case of a desmoplastic brain tumor which was initially resected from the right fronto-temporal region in a 2 year-old boy. This nodular, calcified tumor was vascularized by the internal carotid artery and the middle meningeal artery branches. Grossly, it contained several mucoid cysts. Light microscopy showed cords or nests of small cuboidal cells surrounded by a loose connective tissue and desmoplasic areas containing fibers and spindle cells. The cuboidal cells expressed epithelial, neuronal and neuroendocrine markers. Some foci of spindle cells showed glial differentiation. The tumor recurred 16 months later and displayed some characteristics of the small cell neuroepithelial component, mitoses being conspicuous. Electron microscopy revealed undifferentiated clear cells, some containing neurosecretory granules. Karyotyping demonstrated the following formula: 〈 15 〉 46, t(8;11) (q13; q11). The chromosome 11 breakpoint was different from that described in Ewing's sarcoma. This isolated translocation has not been previously reported to our knowledge. These unusual features lead us to report this case and to discuss its pathogenesis.
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  • 15
    Electronic Resource
    Electronic Resource
    Springer
    Pediatric cardiology 15 (1994), S. 198-200 
    ISSN: 1432-1971
    Keywords: Subaortic stenosis ; Congenital heart disease ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The first case of multiple family members with discrete subaortic membrane and no other congenital defects is presented. One family member presents with findings suggesting a forme fruste of this disease. Increased surveillance of family members of individuals with discrete subaortic membrane is warranted, as the clinical findings of mild subaortic obstruction may be indistinguishable from those of an innocent flow murmur.
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Pediatric cardiology 15 (1994), S. 201-203 
    ISSN: 1432-1971
    Keywords: Tricuspid atresia ; Tricuspid hypoplasia ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Occurrence of a similar cardiac malformation in multiple family members has been reported for many lesions. Neither tricuspid atresia nor tricuspid annular hypoplasia and tricuspid atresia and one case of tricuspid annular hypoplasia with an atrial septal defect in siblings. The findings in this family suggest an autosomal recessive pattern of inheritance for abnormal tricuspid valve morphogenesis.
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  • 17
    ISSN: 1432-2072
    Keywords: Risperidone ; Antipsychotics ; 5-HT2 antagonism ; D2 antagonism ; Pharmacology ; Receptor binding ; Biochemistry ; Review
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract This review reports on the pharmacodynamics of the new antipsychotic risperidone. The primary action of risperidone is serotonin 5-HT2 receptor blockade as shown by displacement of radioligand binding (Ki: 0.16 nM), activity on isolated tissues (EC50:0.5 nM), and antagonism of peripherally (ED50: 0.0011 mg/kg) and centrally (ED50:0.014 mg/kg) acting 5-HT2 receptor agonists in rats. Risperidone is at least as potent as the specific 5-HT2 receptor antagonist ritanserin in these tests. Risperidone is also a potent dopamine D2 receptor antagonist as indicated by displacement of radioligand binding (Ki: 1.4 nM), activity in isolated striatal slices (IC50: 0.89 nM), and antagonism of peripherally (ED50: 0.0057 mg/kg in dogs) and centrally acting D2 receptor agonists (ED50: 0.056–0.15 mg/kg in rats). Risperidone shows all effects common to D2 antagonists, including enhancement of prolactin release. However, some central effects such as catalepsy and blockade of motor activity occur at high doses only. Risperidone is 4–10 times less potent than haloperidol as a central D2 antagonist in rats and it differs from haloperidol by the following characteristics: predominant 5-HT2 antagonism; LSD antagonism; effects on sleep; smooth dose-response curves for D2 antagonism; synergism of combined 5-HT2/D2 antagonism; pronounced effects on amphetamine-induced oxygen consumption; increased social interaction; and pronounced effects on dopamine (DA) turnover. Risperidone displays similar activity at pre- and postsynaptic D2 receptors and at D2 receptors from various rat brain regions. The binding affinity for D4 and D3 receptors is 5 and 9 times weaker, respectively, than for D2 receptors; interaction with D1 receptors occurs only at very high concentrations. The pharmacological profile of risperidone includes interaction with histamine H1 and α-adrenergic receptors but the compound is devoid of significant interaction with cholinergic and a variety of other types of receptors. Risperidone has excellent oral activity, a rapid onset, and a 24-h duration of action. Its major metabolite, 9-hydroxyrisperidone, closely mimics risperidone in pharmacodynamics. Risperidone can be characterized as a potent D2 antagonist with predominant 5HT2 antagonistic activity and optimal pharmacokinetic properties.
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  • 18
    ISSN: 1432-2242
    Keywords: Maize ; Restriction fragment length polymorphisms (RFLPs) ; Qualitative and quantitative inheritance ; Plant breeding ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Restriction fragment length polymorphisms (RFLPs) and one morphological marker were used to investigate quantitative trait loci (QTL) for morphological and physiological traits evaluated on 150 F2∶3 maize (Zea mays L.) lines derived from the cross of elite U.S. Corn Belt inbreds Mo17 and H99. F2∶3 lines were grown in a replicated experiment and evaluated for plant and ear heights and flowering traits. QTL were identified for each trait, and genetic effects were determined. Estimated gene action for the flowering traits was predominantly overdominance. Both parents contributed toward increased values for anthesis and silk emergence. QTL for increased plant and ear heights were usually contributed by the taller parent, Mo17. Estimated gene action for these traits was mainly partial to overdominance. QTL for plant height were located in the vicinity of loci defined by alleles with qualitative effects on plant height.
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  • 19
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 89 (1994), S. 959-963 
    ISSN: 1432-2242
    Keywords: Sugarcane ; Polyploidy ; Genetics ; Evolution ; Breeding ; DNA markers ; Arbitrarily primed PCR ; RAPD markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Recent work has revealed random chromosome pairing and assortment in Saccharum spontaneum L., the most widely distributed, and morphologically and cytologically variable of the species of Saccharum. This conclusion was based on the analysis of a segregating population from across between S. spontaneum ‘SES 208’ and a spontaneously-doubled haploid of itself, derived from anther culture. To determine whether polysomic inheritance is common in Saccharum and whether it is observed in a typical biparental cross, we studied chromosome pairing and assortment in 44 progeny of a cross between euploid, meiotically regular, 2n=80 forms of Saccharum officinarum ‘LA Purple’ and Saccharum robustum ‘ Mol 5829’. Papuan 2n=80 forms of S. robustum have been suggested as the immediate progenitor species for cultivated sugarcane (S. officinarum). A total of 738 loci in LA Purple and 720 loci in Mol 5829 were amplified and typed in the progeny by arbitrarily primed PCR using 45 primers. Fifty and 33 single-dose polymorphisms were identified in the S. officinarum and S. robustum genomes, respectively (χ 2 at 98%). Linkage analysis of single-dose polymorphisms in both genomes revealed linkages in repulsion and coupling phases. In the S. officinarum genome, a map hypothesis gave 7 linkage groups with 17 linked and 33 unlinked markers. Four of 13 pairwise linkages were in repulsion phase and 9 were in coupling phase. In the S. robustum genome, a map hypothesis gave 5 linkage groups, defined by 12 markers, with 21 markers unlinked, and 2 of 9 pairwise linkages were in repulsion phase. Therefore, complete polysomic inheritance was not observed in either species, suggesting that chromosomal behavior is different from that observed by linkage analysis of over 500 markers in the S. spontaneum map. Implications of this finding for evolution and breeding are discussed.
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  • 20
    ISSN: 1432-2242
    Keywords: Breeding ; Helminthosporium turcicum ; RFLP ; QTLs ; Disease-resistance ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RFLPs were used to investigate components of host-plant response to Exserohilum turcicum in 150 unselected F2∶3 lines of a B52/Mo17 maize population. Following inoculation with spore suspensions of the pathogen (race 0), components of disease development were measured and then quantitative trait mapping was performed to identify the location and effects of quantitative trait loci (QTLs) determining host-plant response. Components of interest were the average number of lesions per leaf, the average percent leaf tissue diseased (severity) and the average size of lesions (cm2). Based on a LOD threshold of 2.31 (P〈0.05), the number of lesions appears to be associated with QTLs on chromosomes 1S, 3L, 5S. Severity was associated with analogous regions and, in addition, QTLs on chromosomes 7L and 8L. Most QTLs, for either of these two components, involve additive gene action and partial dominance or overdominance. In contrast, lesion size was associated with QTLs on chromosomes 7L and 5L; recessive gene action may be involved at 7L.
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  • 21
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 88 (1994), S. 754-758 
    ISSN: 1432-2242
    Keywords: Potato breeding ; Potato leaf roll virus ; Virus resistance ; Major gene resistance ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The concentration of potato leaf roll virus (PLRV), as measured by a quantitative enzyme-linked immunosorbent assay, in the foliage of potato plants (Solanum tuberosum) of cv ‘Maris Piper’ with secondary infection was 2900 ng/g leaf, whereas in clones G7445(1) and G7032(5) it was 180 ng/g leaf and 120 ng/g leaf, respectively. To examine the genetic control of resistance to PLRV multiplication, reciprocal crosses were made between the susceptible cultivar ‘Maris Piper’ and the two resistant clones, and the three parents were selfed. Seedling progenies of these families were grown to generate tubers of individual genotypes (clones). Clonally propagated plants were graft-inoculated, and their daughter tubers were collected and used to grow plants with secondary infection in which PLRV concentration was estimated. The expression of resistance to PLRV multiplication had a bimodal distribution in progenies from crosses between ‘Maris Piper’ and either resistant clone, and also in progeny from selfing the resistant parents, with genotypes segregating into high and low virus titre groups. Only the progeny obtained from selfing ‘Maris Piper’ did not segregate, all genotypes being susceptible to PLRV multiplication. The pattern of segregation obtained from these progenies fits more closely with the genetical hypothesis that resistance to PLRV multiplication is controlled by two unlinked dominant complementary genes, both of which are required for resistance, than with the simpler hypothesis that resistance is conferred by a single dominant gene, as published previously.
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  • 22
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 89 (1994), S. 313-317 
    ISSN: 1432-2242
    Keywords: Genetics ; Rice ; Phosphorousefficiency ; Diallel analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The inheritance of phosphorous (P) — deficiency tolerance in rice was investigated by a sevenparent diallel. The parent materials involved were four P-efficient (IR20, IR54, IR28, and Mahsuri), one moderately P-efficient (TN1), and two P-inefficient (IR31406333-1 and IR34686-179-1-2-1), genotypes. Relative tilering ability (RTA) under P-deficient and P-supplemented soil conditions was the parameter used in determining the tolerance level of the different genotypes. Diallel graph analysis revealed that tolerant parents have an excess of recessive genes, while moderate and susceptible parents possess more dominant genes. Genetic-component analysis suggested that both additive and dominance gene effects are involved in the inheritance of P-deficiency tolerance in rice. The trait exhibited over doiminance as confirmed by the graphical analysis. Narrow-sense heritability of the trait was moderate (0.50) and environmental effects were low. Both the general combining ability (GCA) and the specific combining ability (SCA) were significant, but GCA was more prevalent than SCA. Tolerant parents exhibited a high GCA whereas susceptibles have a very poor GCA, suggesting that tolerant parents were mostly enriched in additive genes and susceptible parents in non-additive genes. Crosses involving two high general combiners showed low SCA effects whereas crosses between poor general combiners manifested highly-significant SCA values.
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  • 23
    ISSN: 1432-2242
    Keywords: Genetics ; Disease resistance ; Monocots
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An F2 oat population was produced by crossing the diploid (n=7) species Avena strigosa (CI 3815) with A. wiestii (CI 1994), resistant and susceptible, respectively, to 40 isolates of Puccinia coronata, the causal agent of crown rust. Eighty-eight F2 individuals were used to construct an RFLP linkage map representing the A genome of cultivated hexaploid oat. Two hundred and eight RFLP loci have been placed into 10 linkage groups. This map covers 2416 cM, with an average of 12 cM between RFLP loci. Eighty-eight F3 lines, derived from F2 individuals used to construct the map, were screened for resistance to 9 isolates of P. coronata. One locus, Pca, was found to confer a dominant resistance phenotype to isolates 203, 258, 263, 264B, 290, 298, 325A, and 345. Pca also conferred resistance to isolate 276; however, an unlinked second gene may also be involved.
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  • 24
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    Sexual plant reproduction 7 (1994), S. 290-296 
    ISSN: 1432-2145
    Keywords: Secale cereale ; Polyembryony ; Chromosome mosaics ; Rye ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have obtained one plant regenerated from rye tissue culture which showed a high percentage of polyembryonic seeds in its progeny. The mutation inducing the development of extra embryos is also influencing erroneous cell division, mitosis and meiosis. The genetic analysis indicated that the aptitude for polyembryonic seed formation is a heritable trait controlled by a dominant gene. However, for expression of the phenotype the female parent should have a specific cytoplasm.
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  • 25
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    Cellular and molecular life sciences 50 (1994), S. 429-437 
    ISSN: 1420-9071
    Keywords: Genetics ; ecology ; DNA-transfer ; conjugation ; transformation ; transduction ; transposons ; dormant cells ; epilithon ; microbial colonisation ; symbiosis ; virus resistance ; biosafety ; release of genes ; insults to humanity ; evolution ; biodiversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Genetic ecology is the extension of our modern knowledge in molecular genetics to studies of viability, gene expression and gene movements in natural environments like soils, aquifers and digestive tracts. In such milieux, the horizontal transfer of plasmid-borne genes between phylogenetically distant species has already been found to be much more frequent than had been expected from laboratory experience. For the study of exchanges involving chromosomally-located genes, more has to be learned about the behaviour of transposons in such environments. The results expected from studies in genetic ecology are relevant for considerations of evolution, biodiversity and biosafety. The role of this new field of research in restoring popular confidence in science and in its biotechnological applications is stressed.
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  • 26
    ISSN: 1530-0358
    Keywords: Desmoids ; Genetics ; Chemotherapy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract PURPOSE: The aim of this study was to describe the natural history and management of surgically unresectable intra-abdominal desmoid tumors in two patients with Gardner's syndrome from two unrelated families, where each had failed on conventional therapy. METHODS: Two patients with Gardner's syndrome were placed on a chemotherapy regimen which included doxorubicin (90 mg/m2) and dacarbazine (900 mg/m2) in divided doses over four days of continuous infusion. Their progress on chemotherapy was assessed by abdominal computerized tomography and laparoscopy. RESULTS: The computerized abdominal tomography scans proved difficult to interpret because of adhesions and matted small bowel resulting from the patients original colectomies. These findings made it difficult to differentiate postoperative changes from residual desmoid tumor. Second-look laparotomy in such patients was contraindicated as this may predispose to further desmoid production. Laparoscopy disclosed a complete response to this chemotherapy. Nevertheless, we had an iatrogenic small bowel perforation in one of these patients. Each patient showed a complete response to chemotherapy. CONCLUSION: Surgical resection remains the first-line treatment of intra-abdominal desmoid tumors. However, doxorubicin/ dacarbazine chemotherapy on a clinical trial basis may be indicated in patients whose intra-abdominal desmoid is unresectable, or who have failed to respond to treatment with hormones (tamoxifen, Toremifene), steroids (prednisone), and nonsteroidal anti-inflammatory agents (Clinoril®; Merck & Co., Inc., West Point, PA).
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  • 27
    ISSN: 1437-160X
    Keywords: Systemic lupus erythematosus ; Recombinant U1-nRNP proteins ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract To investigate a possible involvement of HLA-class II alleles in the genetic predisposition for the formation of anti-U1-nRNP antibody in systemic lupus erythematosus (SLE), genomic DNA of 178 patients was typed for the DRB1, DQA1 and DQB1 alleles using a polymerase chain reaction (PCR) and non-radioactive-oligonucleotide typing. Antibodies against recombinant U1-nRNP proteins (U1-A- U1-C-and 70K-protein) were determined by ELISA. Anti-U1-C antibody was found in 26 (14.7%), anti-U1-A in 34 (19.2%) and anti-70K in 17 (9.6%) patients. A joint occurrence was observed for these antibodies against the recombinant U1-nRNP proteins: anti-U1-C and anti-U1-A antibodies occurred together more frequently than alone and than together with anti-U1-70K antibodies. The frequency of DRB1 * 04 was slightly increased in the patients with anti-U1-C as compared to the patients without anti-U1-C (P〈0.05, Pcorr=n.s., RR=2.4). The DQA1 * 0301 allele, which is in linkage disequilibrium with DRB1 * 04, is found more frequently in anti-U1-C-positive than in antibody-negative patients. The DQB1 * 0303 allele, detected in 12 of 176 SLE patients, was absent in the patients with any of the antibodies against the U1-nRNP proteins. All these deviations may be due to chance alone. We concluded that the presence of antibodies against recombinant U1-nRNP proteins was not significantly associated with any HLA DRB1, DQA1 and DQB1 allele in our group of SLE patients.
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  • 28
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    Metabolic brain disease 9 (1994), S. 105-131 
    ISSN: 1573-7365
    Keywords: Alcoholism ; Genetics ; Endorphins ; Enkephalins ; Dynorphins ; Opioid ; Receptors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract At the present time alcoholism is recognized as a metabolic disease exhibiting the clinical features of craving for alcohol, loss of control over drinking, tolerance and physical dependence on alcohol, while both epidemiological and experimental studies have demonstrated that genetic factors may be important in determining whether an individual has a high or low vulnerability to develop alcoholism. Evidence also indicates that alcoholism is not characterized by a single gene single allele inheritance. Instead it seems that multiple genes and environmental factors interact to increase or decrease an individual's vulnerability to become an alcoholic. Current research is aimed at investigating whether certain behavioral, physiological and biochemical markers are highly associated with the incidence of alcoholism. Among the biochemical markers currently under investigation is the endogenous opioid system and its implication in mediating the reinforcing effects of ethanol. It is the objective of this manuscript to review current research on: (a) the interactions of ethanol with the endogenous opioid system at the molecular level; (b) the existence of genetically determined differences in the response of the endogenous opioid system to ethanol between subjects at high and low risk for excessive ethanol consumption, as well as between lines of animals showing preference or aversion for ethanol solutions; (c) the decrease of alcohol consumption following pretreatment with opioid antagonists; and (d) the possible use of specific opioid receptor antagonists together with behavioral therapy to modify drinking behavior, to control craving and to prevent relapse.
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  • 29
    ISSN: 1617-4623
    Keywords: Gene regulation ; Ribozyme ; npt-gene ; Transgenic tobacco ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A chimeric gene encoding a ribozyme under the control of the cauliflower mosaic virus (CaMV) 35S promoter was introduced into transgenic tobacco plants. In vivo activity of this ribozyme, which was designed to cleave npt mRNA, was previously demonstrated by transient expression assays in plant protoplasts. The ribozyme gene was transferred into transgenic tobacco plants expressing an rbcS-npt chimeric gene as an indicator. Five double transformants out of sixteen exhibited a reduction in the amount of active NPT enzyme. To measure the amount of ribozyme produced, in the absence of its target, the ribozyme and target genes were separated by genetic segregation. The steady-state concentrations of ribozyme and target RNA were shown to be similar in the resulting single transformants. Direct evidence for a correlation between reduced npt gene expression and ribozyme expression was provided by crossing a plant containing only the ribozyme gene with a transgenic plant expressing the npt gene under control of the 35S promoter, i.e. the same promoter used to direct ribozyme expression. The expression of npt was reduced in all progeny containing both transgenes. Both steady-state levels of npt mRNA and amounts of active NPT enzyme are decreased. In addition, our data indicate that, at least in stable transformants, a large excess of ribozyme over target is not a prerequisite for achieving a significant reduction in target gene expression.
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  • 30
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    Developmental Genetics 15 (1994), S. 7-18 
    ISSN: 0192-253X
    Keywords: Tribolium ; engrailed ; embryogenesis ; segmentation ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have cloned and sequenced the single Tribolium homolog of the Drosophila engrailed gene. The predicted protein contains a homeobox and several domains conserved among all engrailed genes identified to date. In addition it contains several features specific to the invected homologs of Bombyx and Drosophila, indicating that these features most likely were present in the ancestral gene in the common ancestor of holometabolous insects. We used the cross-reacting monoclonal antibody, 4D9, to follow the expression of the Engrailed protein during segmentation in Tribolium embryos. As in other insects, Engrailed accumulates in the nuclei of cells along the posterior margin of each segment. The first Engrailed stripe appears as the embryonic rudiment condenses. Then as the rudiment elongates into a germ band, Engrailed stripes appear in an anterior to posterior progression, just prior to morphological evidence of the formation of each segment. As in Drosophila (a long germ insect), expression of engrailed in Tribolium (classified as a short germ insect) is preceeded by the expression of several homologous segmentation genes, suggesting that similar genetic regulatory mechanisms are shared by diverse developmental types. © 1994 Wiley-Liss, Inc.
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  • 31
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    Developmental Genetics 15 (1994), S. 1-6 
    ISSN: 0192-253X
    Keywords: Evolution ; homeobox gene ; body plan ; comparative method ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
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  • 32
    ISSN: 0192-253X
    Keywords: Homeobox ; Ultrabithorax ; abdominal-A ; short germ development ; grasshopper ; evolution ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: To investigate what role homeotic genes may play in morphological evolution, we are comparing homeotic gene expression in two very different insects, Drosophila (Diptera) and Schistocerca (Orthoptera). In this paper we describe a monoclonal antibody, FP6.87, that recognizes the products of both the Ultrabithorax (Ubx) and abdominal-A (abd-A) genes in Drosophila, via an epitope common to the carboxy terminal region of these two proteins. This antibody recognizes nuclear antigens present in the posterior thorax and abdomen of Schistocerca. We infer that it recognizes the Schistocerca homolog of UBX protein, and probably also of ABD-A. As the distribution of Schistocerca ABD-A protein is already known, we can use this reagent to map the expression of Schistocerca UBX in the thorax and anterior abdomen, where ABD-A is not expressed. Both the general domain, and many of the details, of UBX exp ression are remarkably conserved compared with Drosophila. Thus UBX expression extends back from T2 in the ectoderm (including the CNS), but only from A1 in the mesoderm. As noted for other bithorax complex genes in Schistocerca, expression begins in the abdomen, at or shortly before the time of segmentation. It only later spreads anteriorly to the thorax. For much of embryogene-sis, the expression of UBX in the thoracic epidermis is largely restricted to the T3 limb. Inthis limb, UBX is strikingly regulated, in a complex pattern that reflects limb segmentation.Reviewing these and earlier observations, we conclude that evolutionary changes affect both the precise regulation of homeotic genes within segments, and probably also the spectrum of downstream genes that respond to homeotic gene expression in a given tissue. Overall domains of homeotic gene expression appear to be well conserved between different insect groups, though a change in the extent and timing of homeotic gene expression may underlie the modification of the posterior abdomen in different insect groups. © 1994 Wiley-Liss, Inc.
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  • 33
    ISSN: 0192-253X
    Keywords: C/EBP ; thyroid hormone ; metamorphosis ; gene expression ; Rana cafesbeiana ; bZlP proteins ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Tissue-specific changes in gene expression occur in the liver of Rana cafesbeiana tadpoles undergoing metamorphosis. Many of these changes can be induced precociously by administration of thyroid hormone (TH) to a tadpole or to cultured tadpole liver. While the precise molecular means by which TH exerts a tissue-specific response is unknown, recent studies suggest that the expression of genes which are liver-specific and characteristic of the adult liver phenotype may rely on TH-induction of tissue-specific transcription factors, as well as the thyroid hormone receptor proteins. Guided by this notion, we screened our Rana catesbeiana liver cDNA library and isolated clones, RcC/EBP-1 and -2, encoding Rana homologues of a mammalian transcription factor, C/EBP (CCAAT/enhancer core binding protein), implicated in the expression of liver-specific genes and terminal differentiation of hepatocytes. Gel mobility shift assays demonstrate that the proteins synthesized from these cDNAs bind specifically to the consensus binding site for C/EBP-related proteins. Characterization of the amino acid sequence in the bZlP DNA-binding domains of these proteins suggests that RcC/EBP-1 and -2 encode Rana homologues of C/EBPα and δ, respectively. Hybridization analyses demonstrate that the amount of RcC/EBP-2 mRNAs in tadpole liver remains constant throughout metamorphosis, whereas RcC/EBP-1 mRNAs are up-regulated during both spontaneous and TH-induced metamorphosis. The TH-induced up-regulation of RcC/ EBP-1 mRNAs precedes the up-regulation of liver-specific urea cycle enzyme mRNAs by 6 to 12 hours. These results, coupled with in situ hybridization studies, suggest that RcC/EBP-1 mRNAs encode a transcription factor which may play an early role(s) in the terminal differentiation and/or reprogramming of gene expression in this tadpole's liver cells during both spontaneous and TH-induced metamorphosis. ©1994 WiIey-Liss, Inc.
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  • 34
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    Developmental Genetics 15 (1994), S. 155-171 
    ISSN: 0192-253X
    Keywords: Sex determination ; epistasis ; floral development ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The tassel seed mutations of maize cause sex reversal of the florets of the tassel, such that the normally staminate florets develop pistils. Although these mutations have been recognized for many years, little is known about how they act. We have tested the hypothesis that the tassel seed genes interact directly with each other and with other genes controlling sex determination in a single genetic pathway by the construction and analysis of double mutants. On the basis of the phenotypes of the double mutants, the tassel seed mutations were placed into two groups: ts1, ts2, Ts5 and ts4, Ts6. Both groups of tassel seed mutations were additive with the masculinizing mutation dwarf, indicating independent modes of action. Interactions of tassel seed mutations with silkless varied, allowing the ordering of the action of the various tassel seed mutations relative to silkless. Both groups of tassel seed mutations were epistatic with regard to sex expression to mutations that alter both architecture of the plant and distribution of male and female florets, Teopod 1, terminal ear, and teosinte branched. Thus, there are at least two separate genetic pathways that control the sex of florets in maize tassels. In addition, analysis of double mutants revealec that all tassel seed genes tested play a role in the regulation of flower morphogenesis as well as pistil suppression. © 1994 Wiley-Liss, Inc.
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  • 35
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    Developmental Genetics 15 (1994), S. 201-204 
    ISSN: 0192-253X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
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  • 36
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    Developmental Genetics 15 (1994), S. 214-230 
    ISSN: 0192-253X
    Keywords: Sex determination ; angiosperms ; genetics ; white campion ; sex chromosomes ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Most flowering plant species are hermaphroditic, but a small number of species in most plant families are unisexual (i.e., an individ-ual will produce only male or female gametes). Because species with unisexual flowers have evolved repeatedly from hermaphroditic progenitors, the mechanisms controlling sex determination in flowering plants are extremely diverse. Sex is most strongly determined by genotype in all species but the mechanisms range from a single controlling locus to sex chromosomes bearing several linked locirequired for sex determination. Plant hormones also influence sex expression with variable effects from species to species. Here, we review the genetic control of sex determination from a number of plant species to illustrate the variety of extant mechanisms. We emphasize species that are now used as models to investigate the molecular biology of sex determination. We also present our own investigations of the structure of plant sex chromosomes of white campion (Silene latifolia - Melan-drium album). The cytogenetic basis of sex determination in white campion is similar to mammals in that it has a male-specific Y-chromosome that carries dominant male determining genes. If one copy of this chromosome is in the genome, the plant is male. Otherwise it is female. Like mammalian Y-chromosomes, the white campion Y-chromosome is rich in repetitive DNA. We isolated repetitive sequences from microdissected Y-chromosomes of white campion to study the distribution of homologous repeated sequences on the Y-chromosome and the other chromosomes. We found the Y to be especially rich in repetitive sequences that were generally dispersed over all the white campion chromosomes. Despite its repetitive character, the Y-chromosome is mainly euchromatic. This may be due to the relatively recent evolution of the white campion sex chromosomes compared to the sex chromosomes of animals. © 1994 Wiley-Liss, Inc.
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  • 37
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    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994) 
    ISSN: 0192-253X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
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  • 38
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    Developmental Genetics 15 (1994), S. 320-331 
    ISSN: 0192-253X
    Keywords: Drosophila melanogaster ; ecdysone ; steroid ; Eip28/29 ; EcREs ; lacZ ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The Eip28/29 gene of Drosophila is an example of a tissue- and stage-specific ecdysone-responsive gene. Its diverse patterns of expression during the third larval instar and a synopsis of those patterns in terms of expression groups have been reported previously. Here we have studied the expression (in transgenic flies) of reporter genes controlled by Eip28/29-derived flanking DNA. During the middle and late third instar, most tissues exhibit normal expression patterns when controlled by one of two classes of regulatory sequences. Class A sequences include only 657 Np of 5′ flanking DNA from Eip28/29. Class B sequences include an extended 3′ flanking region and a minimal (≤93 Np) 5′ flanking region. The class B sequences include all those elements known to be important for ecdvsone induction in cultured cells. They are sufficient to direct the normal premetamorphic induction of Eip28/29 in the lymph glands, hemocytes, proventriculus, and Malpighian tubules. This is consistent with our suggestion that Kc cells are derived from embryonic hematopoietic cells. It is remarkable that the epidermis requires only class A sequences. These are sufficient to up-regulate expression at medinstar and to down-regulate expression at metamorphosis. It follows that the epidermis uses EcREs distinct from those that function in Kc cells. It is possible that the Upstream EcRE, which is nearly silent in Kc cells, is active in the epidermis. © 1994 Wiley-Liss, Inc.
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  • 39
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    Developmental Genetics 15 (1994), S. 356-365 
    ISSN: 0192-253X
    Keywords: Thyroid hormone ; AP-2 ; Xenopus luevis ; metamorphosis ; 63 kDa keratin gene ; epidermal differentiation ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: During amphibian metamorphosis dramatic changes occur in the morphogenesis and differentiation of the epidermis. Concurrently with these changes, the 63 kDa keratin geneis upregulated from low basal levels to high levels. What makes these processes unique is that they are controlled by triiodothyronine (T3) and can be duplicated in cultures of purified epidermal cells. Since there is a 2 day lag period between the addition of T3 and the upregulation of keratin gene expression and terminal differentiation, recent studies have focused on identifying the genes activated during the lag period. We assume that the transcription factors required for upregulation of the keratin gene are induced by T3 during the lag period, and therefore we have cloned the keratin gene so that promoter analyses can be conducted. S1 mapping assays have shown that the same transcription start sites are used during premetamorphosis when the keratin gene is basally expressed, during metamorphosis when it is T3-upregulated, and in the adult epidermis where it is expressed independently of T3. During the early part of the lag period TRP and AP-2 mRNA levels are upregulated in the epidermis by T3. The transcription factor AP-2 is expressed at high levels in the skin of premetamorphic larvae and induced about fivefold by T3 but is not induced in an epithelial cell line (XL-177). Since the keratin mRNA, AP-2 rnRNA, and other genes induced during the lag period are expressed in premetamorphic larvae it appears that T3 functions by upregulating the expression of genes previously activated by a T3-independent process. This preprogramming may account for the tissue specificity of T3 action during metamorphosis. © 1994 WiIey. Liss, Inc.
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  • 40
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    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994) 
    ISSN: 0192-253X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
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  • 41
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    Developmental Genetics 15 (1994), S. 435-442 
    ISSN: 0192-253X
    Keywords: Fertility ; sex-reversal ; XY ovary ; XY oocyte ; mouse ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: When the Y chromosome of a Mus musculus domesticus mouse strain is placed onto the C57BL/6J (B6) inbred background, the XY progeny develop ovaries or ovotestes but never normal testes during fetal life. While some of the hermaphroditic males become fertile, none of the XY females produces litters. Here, we examined the fertility and development of oocytes derived from the XY female mouse. With or without preceding injection of gonadotropins, female mice were mated with normal B6 males, and their embryos were recovered at various developmental stages. In vitro fertilization was performed with the eggs recovered from the oviduct after treatment with go-nadotropins. Development of embryos was examined by both light and electron microscopy. The results indicate that the oocytes released from the B6.YDOM ovary were efficiently fertilized and often initiated the first cell cleavage, but all embryos died during early preimplantation periods. Even when oocytes were fertilized in vitro, minimizing their exposure to the XY oviduct/uterus environment, most embryos died at the 1- or 2-cell stage. A few exceptional embryos reached the 4- or 8-cell stage, but abnormalities were evident in both nuclear and cytoplasmic structures of all embryos. After cleavage, neighbouring blastomeres were only loosely associated, and microvilli were abundant at the intercellular interfaces. We postulate that oocytes of the B.6.YDOM female mouse become defective during XY ovarian differentiation, and, hence, fail to proceed through normal embryonic development. © 1994 Wiley-Liss, Inc.
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  • 42
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    Developmental Genetics 15 (1994), S. 51-63 
    ISSN: 0192-253X
    Keywords: Actin ; ascidian development ; gene expression ; heterochrony ; muscle actin gene ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Adultation is a hetercchronic mode of development in which adult tissues and organs differentiate precociously during the larval phase. We have investigated the expression of an adult muscle actin gene during adultation in the ascidian Molgula citrina. Ascidians contain multiple muscle actin genes which are expressed in the larva, the adult, or during both phases of the life cycle. In ascidian species with conventional larval development, the larval mesenchyme cells, which are believed to be progenitors of the adult mesoderm, remain undifferentiated and do not express the muscle actin genes. In M. citrina, the mesen-chyme cells differentiate precociously during larval development, suggesting a role in adultation. An adult muscle actin gene from M. citrina was obtained by screening a mantle cDNA library with a probe containing the coding region of SpMAl, a Styela plicata adult muscle actin gene. The screen yielded a cDNA clone designated McMAl, which contained virtually the complete coding and 3′ noncoding regions of a muscle actin gene. The deduced McMAl and SpMAl proteins exhibit 97% identity in amino acid sequence and may be encoded by homologous genes. The McMAl gene is expressed in juveniles and adults, but not in larval tail muscle cells, suggesting that it is an adult muscle actin gene. In situ hybridization with a 3′ non-coding region probe was used to determine whether the McMAl gene is expressed during adultation in M. citrina. McMAl mRNA was first detected exclusively in the mesenchyme cells during the late tailbud stage and continued to accumulate in these cells during their migration into the future body cavity and heart primordium in the hatched larva. The McMAl transcripts persisted in mesenchyme cells after larval metamorphosis. It is concluded that an adult muscle actin gene shows a heterochronic shift of expression into the larval phase during adultation in M. citrina.
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  • 43
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    Developmental Genetics 15 (1994) 
    ISSN: 0192-253X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 44
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    Developmental Genetics 15 (1994), S. 176-187 
    ISSN: 0192-253X
    Keywords: Floral development ; floral genetics ; Tunicate maize ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The co-dominant Tunicate (Tu) mutation in maize causes nonreproductive structures in both the male and female inflorescences to be enlarged. This mutation also affects sex determination, permitting the development of pistils in the normally staminate tassel. In order to characterize the role of the normal tu gene product, we have analysed genetic interaction between Tu and other mutations that perturb specific stages of floral development. Synergistic interactions observed suggested that the tu product functions in at least three stages of floral development-determination of spikelet primordia, differentiation of non-reproductive organs and pistil abortion in the tassel. © 1994 Wiley-Liss, Inc.
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  • 45
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    Developmental Genetics 15 (1994), S. 205-213 
    ISSN: 0192-253X
    Keywords: Sex ; sexual reproduction ; recombination ; diploidy ; anisogamy ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Despite the obvious efficiencies of many forms of asexual reproduction, sexual reproduction abounds. Asexual species, for the most part, are relatively short-lived offshoots of sexual ancestors. From the nineteenth century, it has been recognized that, since there is no obvious advantage to the individuals involved, the advantages of sexual reproduction must be evolutionary. Furthermore, the advantage must be substantial; for example, producing males entails a two-fold cost, compared to dispensing with them and reproducing by parthenogenetic females.There are a large number of plausible hypotheses. To me the most convincing of these are two. The first hypothesis, and the oldest, is that sexual reproduction offers the opportunity to produce recombinant types that can make the population better able to keep up with changes in the environment. Although the subject of a great deal of work, and despite its great plausibility, the hypothesis has been very difficult to test by critical observations or experiments.Second, species with recombination can bunch harmful mutations together and eliminate several in a single “genetic death.” Asexual species, can eliminate them only in the same genotype in which they occurred. If the rate of occurrence of deleterious mutations is one or more per zygote, some mechanism for eliminating them efficiently must exist. A test of this mutation load hypothesis for sexual reproduction, then, is to find whether deleterious mutation rates in general are this high-as Drosophila data argue. Unfortunately, although molecular and evolutionary studies can give information on the total mutation rate, they cannot determine what fraction are deleterious.In addition, there are short discussions of the advantages of diploidy, anisogamy, and separate sexes. © 1994 Wiley-Liss, Inc.
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  • 46
    ISSN: 0192-253X
    Keywords: Sex determination ; sexual differentiation ; reptiles ; temperature-dependent sex determination ; behavior ; steroidogenic enzymes ; aromatase ; reductase ; estrogen ; androgen ; steroid hormone receptors ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: In many egg-laying reptiles, the incubation temperature of the egg determines the sex of the offspring, a process known as temperature-dependent sex determination (TSD). In TSD sex determination is an “all or none” process and intersexes are rarely formed. How is the external signal of temperature transduced into a genetic signal that determines gonadal sex and channels sexual development? Studies with the red-eared slider turtle have focused on the physiological, biochemical, and molecular cascades initiated by the temperature signal. Both male and female development are active processes - rather than the crganized/default system characteristic of vertebrates with genotypic sex determination - that require simultaneous activation and suppression of testis- and ovary-determining cascades for normal sex determination. It appears that temperature accomplishes this end by acting on genes encoaing for steroidogenic enzymes and steroid hormone receptors and modifying the endocrine microenvironment in the embryo. The temperature experienced in development also has long-term functional outcomes in addition to sex determination. Research with the leopard gecko indicates that incubation temperature as well as steroid hormones serve as organizers in shaping the adult phenotype, with temperature modulating sex hormone action in sexual differentiation. Finally, practical applications of this research have emerged for the conservation and restoration of endangered egg-laying reptiles as well as the embryonic development of reptiles as biomarkers to monitor the estrogenic effects of common environmental contaminants. © 1994 Wiley-Liss, Inc.
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  • 47
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    Developmental Genetics 15 (1994), S. 523-532 
    ISSN: 0192-253X
    Keywords: Epigenetic ; paramutation ; cosuppression ; pattern elaboration ; flower pigmentation ; plant morphogenesis ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Developmental and physiological factors can impose heritable metastable changes on the plant genome, a fact that was established by maize geneticists during the 1950s and 1960s, largely through the efforts of R. Alexander Brink and Barbara McClintock. This paper describes a transgenic reporter system that monitors genomic impositions as changes in morphogenetically-determined flower color patterns. The observations reported here on the metastable properties of plant transgenes illustrate the proposals of Brink and McClintock that chromosomal impositions occur during normal development as ordered sequences of events which contribute to the elaboration of complex developmental patterns. The relationship between this process and some recent findings about the control of gene expression in transgenic plants is also discussed. © 1994 Wiley-Liss, Inc.
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  • 48
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    Journal of Computational Chemistry 15 (1994), S. 105-123 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The convergence behavior of free energy calculations has been explored in more detail than in any previously reported work, using a model system of two neon atoms in a periodic box of water. We find that for thermodynamic integration-type free energy calculations as much as a nanosecond or more molecular dynamics sampling is required to obtain a fully converged value for a single λ point of the integrand. The concept of “free energy derivatives” with respect to the individual parameters of the force field is introduced. This formalism allows the total convergence of the simulation to be deconvoluted into components. A determination of the statistical “sampling ratio” from these simulations indicates that for window-type free energy calculations carried out in a periodic waterbox of typical size at least 0.6 ps of sampling should be performed at each window (0.7 ps if constraint contributions to the free energy are being determined). General methods to estimate and reduce the error in thermodynamic integration and free energy perturbation calculations are discussed. We show that the difficulty in applying such methods is determining a reliable estimate of the correlation length from a short series of data. © 1994 by John Wiley & Sons, Inc.
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  • 49
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 50
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    Journal of Computational Chemistry 15 (1994), S. 684-703 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The inelastic neutron-scattering experiment of a small globular protein in powder form can present the density of states as a function of the frequency. This characterizes the internal dynamics of the protein, which (especially in the case of low-frequency internal dynamics, 〈 200 cm-1) is required for an improved understanding of protein function. The theoretical frequency distributions of the internal dynamics of a protein have only been calculated in vacuo using the normal mode analysis. Here we show that frequency distributions of the internal motions of a protein in different environments can be provided by changing the magnitude of external force fields acting on the protein. Our test case is bovine pancreatic trypsin inhibitor (BPTI), consisting of 58 amino acid residues. To mimic the effect of intermolecular contacts in powders, external force fields formed by surrounding water molecules are forced to act on the protein. The neutron-derived density of states of BPTI in powders is shown to be reproduced by the external force fields. In addition, the densities of states, shifted to low frequencies, are suggested to represent that of BPTI in solution. © 1994 by John Wiley & Sons, Inc.
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  • 51
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    Journal of Computational Chemistry 15 (1994), S. 704-718 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics (MD) simulation and thermodynamic integration (TI) techniques have been used to study the relative free energies of the 8-methyl-N5-deazapterin and 8-methyl-pterin cations (N3 protonated) in aqueous solution. The MD simulations were performed at constant temperature and volume, and the mutations between the cations were carried out by changing the coupling parameter continuously and linearly with the MD simulation time (continuous coupling or slow growth method). The free energy changes have been calculated using both linear and nonlinear couplings of the potential energy functions. Free energy changes have also been computed using the perturbation method for comparison. After separation into electrostatic and van der Waals mutations, most (ca. 80%) of the total free energy change is found to be due to mutation of the electrostatic terms. The free energy change is found to be sensitive to the cutoff radii for interactions between solvent molecules, but rather insensitive to the cutoff radii for interactions between cation and solvent. The free energy changes have also been calculated using various cation and solvent models. Atomic charges for the cations were derived from the molecular electrostatic potential at the semiempirical AM1 and ab initio self-consistent field (SCF) (3-21G, 6-31G, 6-31G*, 6-311G**) levels using AM1 and 3-21G optimized geometries. The TIP3P and SPC models were adopted for the solvent. For the TIP3P solvent model, the order of the free energy change is 6-31G 〉 3-21G 〉 6-31G* ≈ 6-311G** 〉 AM1, where the difference between 6-31G and AM1 is approximately 1 kcal/mol. The free energies obtained using 3-21G optimized geometries are approximately 0.7 kcal/mol larger than those obtained using AM1 geometries for the cations. The free energy change computed using the TIP3P/6-311G* model is 0.3 kcal/mol larger than that obtained for the SPC/6-311G* model. © 1994 by John Wiley & Sons, Inc.
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  • 52
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    Journal of Computational Chemistry 15 (1994), S. 752-768 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A CFF931 all-atom force field for aromatic polyesters based on ab initio calculations is reported. The force field parameters are derived by fitting to quantum mechanical data which include total energies, first and second derivatives of the total energies, and electrostatic potentials. The valence parameters and the ab initio electrostatic potential (ESP) derived charges are then scaled to correct the systematic errors originating from the truncation of the basis functions and the neglect of electron correlation in the HF/6-31G* calculations. Based on the force field, molecular mechanics calculations are performed for homologues of poly(p-hydroxybenzoic acid) (PHBA) and poly(ethylene terephthalate) (PET). The force field results are compared with available experimental data and the ab initio results. © 1994 by John Wiley & Sons, Inc.
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  • 53
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    Journal of Computational Chemistry 15 (1994), S. 782-790 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have applied the FEM-MP2 method (an implementation of the p-version finite element technique within the framework of second-order Møller-Plesset perturbation theory, [J. Chem. Phys., 98, 5642 (1993), and references therein]) to calculate second-order correlation energies for the atoms Be, Ca, Sr, Ba, Yb, Cd, and Hg and thus to complete our studies on closed-shell elements. The FEM-MP2 method permits the use of virtual orbitals of very high angular momentum (lmax = 12) in combination with radial basis sets which are very close to completeness, in such a way that we are able to obtain results that could be the most accurate published so far and, in some cases, the only values available in the literature. We hope they may be useful as a reference for basis set saturation tests and for new methods to calculate correlation energies. © 1994 by John Wiley & Sons, Inc.
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  • 54
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    Journal of Computational Chemistry 15 (1994), S. 838-846 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A detailed comparison has been made of the performance of molecular dynamics and hybrid Monte Carlo simulation algorithms for calculating thermodynamic properties of 2D Lennard-Jonesium. The hybrid Monte Carlo simulation required an order of magnitude fewer steps than the molecular dynamics simulation to calculate reproducible values of the specific heat. The ergodicity of the two algorithms was compared via the use of intermediate scattering functions. For classical systems the intermediate scattering functions should be real; however, a simple analysis demonstrates that this function will have a significant imaginary component when ergodicity breaks down. For q vectors near the zone boundary, the scattering functions are real for both algorithms. However, for q vectors near the zone center (i.e., harmonic, weakly coupled modes), the scattering function calculated via molecular dynamics had a significantly larger imaginary component than that calculated using hybrid Monte Carlo. Therefore, the hybrid Monte Carlo algorithm is more ergodic and samples phase space more efficiently than molecular dynamics for simulations of 2D Lennard-Jonesium. © 1994 by John Wiley & Sons, Inc.
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  • 55
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Group theoretic methods are presented for the transformations of integrals and the evaluation of matrix elements encountered in multiconfigurational self-consistent field (MCSCF) and configuration interaction (CI) calculations. The method has the advantages of needing only to deal with a symmetry unique set of atomic orbitals (AO) integrals and transformation from unique atomic integrals to unique molecular integrals rather than with all of them. Hamiltonian matrix element is expressed by a linear combination of product terms of many-center unique integrals and geometric factors. The group symmetry localized orbitals as atomic and molecular orbitals are a key feature of this algorithm. The method provides an alternative to traditional method that requires a table of coupling coefficients for products of the irreducible representations of the molecular point group. Geometric factors effectively eliminate these coupling coefficients. The saving of time and space in integral computations and transformations is analyzed. © 1994 by John Wiley & Sons, Inc.
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  • 56
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The consistency of three density functional computational implementations (DMol, DGauss, and deMon) are compared with high-level Hartree-Fock and Møller-Plesset (MP) calculations for triazene (HN=NNH2) and formyl triazene (HN=NNHCOH). Proton affinities on all electronegative sites are investigated as well as the geometries of the neutral and protonated species. Density functional calculations employing the nonlocal gradient corrections show agreement with MP calculations for both proton affinities and geometries of neutral and protonated triazenes. Local spin density approximation DMol calculations using numerical basis sets must employ an extended basis to agree with other density functional codes using analytic Gaussian basis sets. The lowest energy conformation of triazene was found to be nonplanar; however, the degree of nonplanarity, as well as some bond lengths, is dependent on the basis set, electron correlation treatment, and methods used for the calculation. © 1994 by John Wiley & Sons, Inc.This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
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  • 57
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    Journal of Computational Chemistry 15 (1994), S. 925-936 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The semiempirical (MNDO, AM1, and PM3) and ab initio predicted structure of disiloxane is studied with a series of basis sets and inclusion of electron correlation at MP2, MP3, MP4, CCD, CCSD, and CCSD(T) levels. The calculated molecular geometry and barrier to linearization of the Si—O—Si bond angle are compared with previous theoretical and experimental values. Our results show that the calculated barrier to linearization is very sensitive to the number of polarization functions in the basis set. We also investigate the coupling between the Si—O—Si bond angle and the Si—O bond length and calculate the Mulliken and electrostatic potential-derived charges. For comparison purposes we also calculate the molecular geometry, the barrier to linearization of the Si—O—Si bond angle, and the atomic charges in hexamethyldisiloxane. © 1994 by John Wiley & Sons, Inc.
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  • 58
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    Journal of Computational Chemistry 15 (1994), S. 963-980 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Principal component analysis applied to a set of dipeptides illustrates how changes in families of parameters act in concert to produce overall molecular structural changes. Principal component analysis is an eigenvalue-eigenvector analysis whereby the parametric sensitivity coefficient matrix is manipulated to produce weighted principal components, which reveal the variant and invariant directions in the parameter space. This analysis summarizes the sensitivity results by revealing interdependence among the parameter values with regard to their role in controlling the molecular structure. An analysis of the principal components reveals hidden relationships among the parameters. Thus, those parameters, which were thought to be of controlling significance with respect to the molecular structure, may, in fact, not be (or vice versa) due to cooperative parametric interactions; as a result, the parameters of significance in a sequence of dipeptides are identified. In general, for the dipeptides studied, there is mutual exclusion of dominant parameters between the sets of invariant and variant eigenvectors. © 1994 by John Wiley & Sons, Inc.
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  • 59
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    Journal of Computational Chemistry 15 (1994), S. 346-350 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The equilibrium geometries, excitation energies, force constants, and vibrational frequencies of the low-lying electronic states X2B1, 2A1, 2B2, and 2A2 of the PF2 radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated geometry, force constants, and vibrational frequencies for the X2B1 state are in good agreement with experimental data. The electronic transition moments, oscillator strengths for the 2A1 → X2B1 and 2A2 → X2B1 transitions, and radiative lifetimes for the 2A1 and 2A2 states are calculated based on the MRSDCI wave functions. © 1994 by John Wiley & Sons, Inc.
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  • 60
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 61
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    Journal of Computational Chemistry 15 (1994), S. 385-394 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular geometry of 1-fluorosilatrane was optimized fully by restricted Hartree-Fock (HF) calculations using the 3-21G, 3-21G(d) and 6-31G(d) basis sets, with the aim of locating the positions of the local minima on the energy hypersurface. The optimized geometries were compared with available experimental (X-ray and ED) and semiempirical data. The ab initio calculations using polarized basis sets are in good agreement with those of previously reported semiempirical calculations, giving a slightly longer equilibrium Si—N distance (∼ 256 pm) in the case of the endo minimum. However, the exo minimum predicted by the semiempirical methods is not supported. There was no experimental evidence for the existence of this exo minimum, and the present ab initio calculations suggest that it is highly unstable. There is considerable disagreement among the experimental results in the C—N and C—C bond lengths in various silatranes, their differences being as large as 13 pm. The present calculations predict that these differences may appear because the silatrane skeleton is flexible with low-energy, large-amplitude internal motions which introduce considerable uncertainties into the position of ring carbon atoms. © 1994 by John Wiley & Sons, Inc.
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  • 62
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    Journal of Computational Chemistry 15 (1994), S. 424-432 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Systematic MRD-CI calculations using the AM1 Hamiltonian have been carried out for two polyenes and eight aromatic hydrocarbons ranging from benzene to ovalene (C32H14). Twenty singlet-singlet excitation energies in these compounds were calculated and compared with experimental data and ab initio STO-3G results. On an absolute scale, the AM1/MRD-CI approach underestimates the excitation energies to states with dominant covalent character by an average of 1.1 eV, whereas the errors for ionic states are between -1.0 and 1.0 eV. The STO-3G calculated data are much too high by ≈ 1 eV and ≈ 5 eV, respectively. The inclusion of σπ-correlation effects through second-order Epstein-Nesbet perturbation theory combined with the use of localized orbitals leads to a significant improvement of the ab initio calculated state energies. In an analogous AM1 treatment, negligible corrections for the σπ correlations are found, which is attributed to the implicit account in the parameters and approximation of the semiempirical Hamiltonian. The possible error sources of the calculational methods are discussed. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 455-465 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular mechanics force field for studying some beta-lactams was developed from ab initio and experimental data. The optimized parameters allowed accurate calculation of the geometries of both the compounds on which the parametrization was based and others on which the validity of the predictions was checked. © 1994 by John Wiley & Sons, Inc.
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  • 64
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 65
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    Journal of Computational Chemistry 15 (1994), S. 524-531 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.
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  • 66
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    Journal of Computational Chemistry 15 (1994), S. 571-571 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 67
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    Journal of Computational Chemistry 15 (1994), S. 633-643 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure is developed and applied to characterize the global shape of the hydrogen-bonded networks formed in solvent and solute-solvent clusters. The methodology combines elements of geometry and topology of molecular chains, and it provides a description of the compactness and complexity of the entanglements formed by the network of hydrogen bonds between solute and solvent molecules. This approach complements others in the literature, where the hydrogen bonding is described in terms of the spatial distribution of bonds, their energetics and lifetimes, or the length hydrogen-bonded walks in space. The results of the present technique do not depend too strongly on the details of the molecular geometry. Therefore, one can assess the extent to which large-scale architecture is modified by rearrangements in the nuclear configuration, information which is important in molecular dynamics when estimating the persistence of essential structural features along dynamic trajectories. In this article we discuss the methodology and illustrate its application to the study of water clusters and solvated clusters of acetic acid. Expected qualitative features in the change of shape descriptors in actual reorganizations of hydrogen-bonding patterns are discussed briefly. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 1217-1227 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report on an implementation of quantum mechanical density functional calculations carried out in a dielectric medium. The dielectric medium is introduced by integrating the solution of the Poisson-Boltzmann equations into the density functional calculation. The calculations are carried out for a simple amide in vacuum, in the field of an ion, and in the ion field in several dielectric environments. The environment was constructed to include a low dielectric interior embedded in a high dielectric continuum of dielectric 80 (corresponding to aqueous solution). The energies and electron densities of formamide in the ion field were calculated at various configurations in this system, including at the low dielectric-high dielectric interface. The systems were designed to simulate situations which are similar to those that occur in proteins (i.e., the protein constitutes the low dielectric medium surrounded by aqueous solution). The system mimics situations in which charges in such proteins located in various regions interact with other parts of the protein and with ligands which mainly bind to the surface. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 1266-1277 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MECHEM is a computer aid for elucidation of reaction pathways that was developed over the last 5 years. The program searches systematically and comprehensively for the simplest multistep reaction pathways (or mechanisms) that are consistent with the experimental constraints formulated by the experimentalist, any ad hoc assumptions, and the program's internal theory. Previous articles have reported the basic pathway-generation algorithm and another algorithm that tests the structural soundness of individual steps. This article introduces an algorithm to solve another basic problem: Given a multistep pathway containing a mixture of molecular structures and formulas, assign possible structures to the formulas while obeying (and exploiting) the constraint imposed by the pathway steps. With this new algorithm, MECHEM is now approaching competence as an interactive tool for elucidating some catalytic reaction pathways, which is the current chemical focus. © 1994 by John Wiley & Sons, Inc.
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  • 70
    ISSN: 0192-253X
    Keywords: Evolution ; Drosophila ; promoter ; glucose dehydrogenase ; development ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The tissue-specific expression patterns of glucose dehydrogenase (GLD) exhibit a high degree of inter specific variation in the adult reproductive tract among the species in the genus Drosophila. We chose to focus on the evolution of GLD expression and the evolution of the Gld promoter in seven closely related species in the mela-nogaster subgroup as a means of elucidating the relationship of changes in cis-acting regulatory elements in the Gld promoter region with changes in tissue-specific expression. Although little variation in tissue-specific patterns of GLD was found in nonreproductive tissues during development, a surprisingly high level of variation was observed in the expression of GLD in both developing and ma-ture reproductive organs. In some cases this variation is correlated with changes in sequence elements in the Gld promoter which were previously shown to direct tissue-specific expression in the reproductive tract. In particular D. teissieri adult males do not express GLD in their ejaculatory ducts, atypical of the melanogaster subgroup species. The Gld promoter region of D. teissieri specifically lacks all three of the TTAGA regulatory elements present in D. melanogaster. The TTAGA elements were previously shown to direct reporter gene expression to the ejaculatory duct. Together these data suggest the absence or presence of the TTAGA elements may be responsible for variation in the absence or presence of GLD in the ejaculatory duct among species. © 1994 Wiley-Liss, Inc.
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  • 71
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    Developmental Genetics 15 (1994), S. 119-128 
    ISSN: 0192-253X
    Keywords: Embryogenesis ; gene expression ; isozymes ; Pomoxis ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The regulation of gene expression during embryogenesis was investigated in white and black crappie (Pomoxis spp.) and their reciprocal interspecific F1 hybrids. The schedule of morphological development and the timing of isozyme expression were compared among the two species and both reciprocal maternal half-sibling F1 hybrids. Although absolute rates of morphological development differed in response to incubation temperature, relative rates of morphological development (normalized to the onset of retinal pigment deposition) were similar among all crosses. Furthermore, these relative rates were similar to those previously documented for other centrarchid species. To assess differences in ontogenetic patterns of gene expression among the crosses, we examined expression for 39 enzymeencoding loci. Expression was not detected in the embryos for 16 loci due to low or nonexistent activity. Enzymatic activity from eight other loci were continuously detected throughout embryogenesis as a result of maternal enzyme in the egg. However, 15 loci initiated expression during the early development period investigated (fertilization through yolk sac absorption). We observed temporal variability in expression of these 15 loci among the crosses, either in the form of differential expression between parental species or as disturbances in the ontogeny of expression in interspecific hybrids. Such variability in expression suggests that some of the gene regulating mechanisms have diverged since Pomoxis species shared a common ancestral genome. © 1994 Wiley-Liss, Inc.
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  • 72
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    Developmental Genetics 15 (1994), S. 129-138 
    ISSN: 0192-253X
    Keywords: Zinc finger Y ; sex reversed ; epididymis ; sex differentiation ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The presence of the mutation Sex reversed (Sxr), a copy of a Y-chromosomal segment that gets transferred to an X chromosome, causes the resulting XXSxr mice to develop as apparent males. However, several features of male sexual development are abnormal in these animals. The testes are small and aspermatogenic, and the epididymides lack the initial segment. Testes and epididymides show abnormalities of extracellular matrix. In this study we examined transcription of the conserved Y chromosomal gene Zfy, which has an X-chromosomal homologue (Zfx). Northern blotting showed Zfy to be expressed in the testes of XXSxr animals, except for those that carry the coat-marker gene Tabby (Ta), despite the lack of germ cells in XXSxr mice. Reverse transcription polymerase chain reaction (RT-PCR) studies detected Zfy in mRNA in testes even when Ta was present. RT-PCR also demonstrated Zfy transcription in epididymides of normal males, though not in XXSxr mice. Previous authors reported an absence of Zfy transcription in XXSxr testes; Zfy transcription in normal testes has been ascribed to germ cells. Our observation indicates that this idea requires re-evaluation. The occurrence of Zfy transcription in the normal epididymis is similarly a novel finding that may help explain those aspects of epididymal development that occur in the absence of androgen. © 1994 Wiley-Liss, Inc.
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  • 73
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    Developmental Genetics 15 (1994), S. 172-175 
    ISSN: 0192-253X
    Keywords: Paramecium ; DNA synthesis ; sexual pathways ; vegetative pathways ; cell cycle ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The temperature-sensitive mutation cc1 blocks a number of cell cycle processes in Paramecium including macronuclear DNA synthesis, oral morphogenesis, and the later stages of micronuclear mitosis. Oral morphogenesis and micronuclear mitosis also occur in the sexual pathway. This study shows that cc1 cells can proceed through conjugation or autogamy under restrictive conditions; neither stomatogenesis nor micronuclear mitosis is blocked. Fertilization and macronuclear determination occur normally, but DNA synthesis in macronuclear anlagen is blocked. Therefore, this mutation discriminates between oral replacement during meiosis and vegetative prefission stomatogenesis, and between mitotic spindle elongation during the pregamic and postzygotic divisions and spindle elongation during the vegetative cell cycle. These results point to a fundamental regulatory difference between morphogenesis in the vegetative and sexual pathways. © 1994 Wiley-Liss, Inc.
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  • 74
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    Developmental Genetics 15 (1994), S. 265-274 
    ISSN: 0192-253X
    Keywords: Germ cells ; Inductive signals ; Sex determination ; Sex-lethal ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: In Drosophila, the sex of germ cells is determined by autonomous and inductive signals. Somatic inductive signals can drive XX germ cells into oogenesis or into spermatogenesis. An autonomous signal makes XY germ cells male and unresponsive to sex determination by induction. The elements forming the X:A ratio in the soma and the genes tra, tra2, dsx, and ix that determine the sex of somatic cells have no similar role in the germline. The gene Sxl, however, is required for female differentiation of somatic and germ cells. Inductive signals that are dependent on somatic tra and dsx expression already affect the sex-specific development of germ cells of first instar larvae. At this early stage, however, germline expression of Sxl does not appear to affect the sexual characteristics of germ cells. Since inductive signals dependent on tra and dsx nevertheless influence the choice of sex-specific splicing of Sxl, it can be concluded that Sxl is a target of the inductive signal, but that its product is required late for oogenesis. Other genes must therefore control the early sexual dimorphism of larval germ cells. © 1994 Wiley-Liss, Inc.
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  • 75
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    Developmental Genetics 15 (1994), S. 275-296 
    ISSN: 0192-253X
    Keywords: Reproductive behavior ; courtship song ; Sex-specific internal anatomy ; doublesex mutants ; transformer mutants ; intersex mutant ; fruitless mutants ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The function of the central nervous system as it controls sex-specific behaviors in Drosophila has been studied with renewed intensity, in the context of genetic factors that influence the development of sexually differentiated aspects of this insect. Three categories of genetic variations that cause anomalies in courtship and mating behaviors are discussed: (1) mutants isolated with regard to courtship defects, of which putatively courtship-specific variants such as the fruitless mutant are a subset; (2) general behavioral and neurological variants (including sensory and learning mutants), whose defects include subnormal reproductive performance; and (3) mutations of genes within the sex-determination regulatory hierarchy of Drosophila, the analysis of which has included studies of reproductive behavior. Recent studies of mutations in two of these categories have provided new insights into the control of neuronally based aspects of sex-specific behavior. The doublesex gene, the final factor acting in the sex-determination hierarchy, had been previously thought to regulate all aspects of sexual differentiation. Yet, it has been recently shown that doublesex does not control at least one neuronally-determined feature of sex-specific anatomy - a muscle in the male's abdomen, whose normal development is, however, dependent on the action of fruitless. These considerations prompted us to examine further (and in some cases re-examine) the influences exerted by sex-determination hierarchy genes on behavior. Our results - notably those obtained from assessments of doublesex mutations' effects on general reproductive actions and on a particular component of the courtship sequence (male “singing” behavior) - lead to the suggestion that there is a previously unrecognized branch within the sexdetermination hierarchy, which controls the differentiation of the male- and female- specific phenotypes of Drosophila. This new branch separates from the doublesex-related one immediately before the action of that gene (just after fransformer and transformer-2) and appears to control as least some aspects of neuronally determined sexual differentiation of males. © 1994 Wiley-Liss, Inc.
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  • 76
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    Developmental Genetics 15 (1994), S. 64-78 
    ISSN: 0192-253X
    Keywords: Spiralians ; Nemertea ; development ; cell lineage ; evolution ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The Nemertea represent one of a number of invertebrate phyla that display a highly conserved pattern of cell division known as spiral cleavage. The fates of the early blastomeres are known for representatives of some spiralian phyla (i.e., molluscs and annelids) and in these species there appears to be a high degree of conservation in the ultimate fates of particular embryonic cells. The first two cleavage planes bear an invariant relationship to the symmetry properties of the future larval and adult body plan. To investigate whether these properties of spiralian embryo-genesis are shared (conserved) amongst members of other spiralian phyla, individual blastomeres in two- and four-cell embryos of the nemertean, Nemertopsis bivittata, were microinjected with bi-otinylated dextran lineage tracers. N. bivittata is a direct-developing hoplonemertean that forms a nonfeeding larva. When individual blastomeres are injected at the two-cell stage, two sets of complementary labeling patterns (a total of four different patterns) were observed in the ectoderm of the larvae. When cells were injected at the four-cell stage, four different patterns were observed that represented subsets of the four patterns observed in the previous experiment. Unlike the case in the annelids and molluscs, in which the first cleavage plane bears a strict 45° angular relationship to the future dorsoventral axis, the first cleavage plane in N. bivittata can bear one of two different relationships relative to the larval/adult dorsoventral axis. In half the cases examined, the first cleavage plane corresponded roughly to the plane of bilateral symmetry, and in the rest, it lay along a frontal plane. A similar result was observed for the embryos of the indirect-developing heteronemertean, Cerebratutus lacteus. These results indicate that the fates of the four cell quadrants in nemerteans are not directly homologous to those in other spira-lians, such as the annelids and molluscs. For instance, no single cell quadrant appears to contribute a greater share to the formation of ectoderm, as is the case in the formation of the post-trochal region by the D-cell quadrant in annelids and mol-luscs. Rather, two adjacent cell quadrants contribute nearly equally to the formation of dorsal or ventral ectoderm in the larvae. Possible explanations for the determination of dorsoventrality in nemerte-ans, as well as implications of these findings regarding the evolution of spiralian development, are discussed. © 1994 Wiley-Liss, Inc.
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  • 77
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    Developmental Genetics 15 (1994), S. 92-103 
    ISSN: 0192-253X
    Keywords: Developmental quantitative genetics ; development ; epigenetic ; evolution ; genetic models ; effects ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Discussions about evolutionary change in developmental processes or morphological structures are predicated on specific quantitative genetic models whose parameters predict whether evolutionary change can occur, its relative rate and direction, and if correlated change will occur in other related and unrelated structures. The appropriate genetic model should reflect the relevant genetical and developmental biology of the organisms, yet be simple enough in its parameters so that deductions can be made and hypotheses tested. As a consequence, the choice of the most appropriate genetic model for polygenically controlled traits is a complex tissue and the eventual choice of model is often a compromise between completeness of the model and computational expediency. Herein, we discuss several developmental quantitative genetic models for the evolution of development and morphology. The models range from the classical direct effects model to complex epigenetic models. Further, we demonstrate the algebraic equivalency of the Cowley and Atchley epigenetic model and Wagner's developmental mapping model. Finally, we propose a new multivariate model for continuous growth trajectories. The relative efficacy of these various models for understanding evolutionary change in developmental and morphological traits is discussed. © 1994 Wiley-Liss, Inc.
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  • 78
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    Developmental Genetics 15 (1994), S. 401-414 
    ISSN: 0192-253X
    Keywords: Mosaic of cell identities ; knotted leaf ; homeobox gene ; cell fates ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The dominant Knotted-1 mutations in maize alter development of the leaf blade. Sporadic patches of localized growth, or knots, and fringes of ectopic ligule occur along lateral veins of mutant leaf blades. In addition, bundle sheaths do not completely encircle lateral veins on mutant leaf blades. We have compared mutant leaf blades with wild-type leaves to determine the precise nature of the perturbed regions. Our analysis includes characterization of epidermal cell shapes, localization of photosynthetic proteins and histology of the leaf. We show that mutant leaf blades are a mosaic of leaf organ components. Affected regions of mutant leaf blades resemble either sheath or auricle tissue in both external and internal features. This conversion of blade cells represents an acropetal shift of more basal parts of the leaf blade region and correlates with previously identified ectopic expression of the Knotted-1 protein in the leaf blade. We propose that inappropriate expression of Kn1 interferes with the process of establishment of cell identities, resulting in early termination of the normal blade development program or precocious expression of the sheath and auricle development programs. © 1994 Wiley-Liss, Inc.
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  • 79
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    Developmental Genetics 15 (1994), S. 453-457 
    ISSN: 0192-253X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
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  • 80
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    Journal of Computational Chemistry 15 (1994), S. 1-11 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A family of the updated Hessian matrices for locating transition structures is presented. An analysis and improvement of the restricted step algorithm described by Culot et al. is proposed. The efficiency of the latter method is compared with other well-established methods for locating transition structures. © 1994 by John Wiley & Sons, Inc.
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  • 81
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    Journal of Computational Chemistry 15 (1994), S. 28-43 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The fast multipole method proposed by Greengard and Rokhlin (GR) is applied to large biomacromolecular systems. In this method, the system is divided into a hierarchy of cells, and electric field exerted on a particle is decomposed into two parts. The first part is a rapidly varying field due to nearby cells, so that it needs rigorous pairwise calculations. The second part is a slowly varying local field due to distant cells; hence, it allows rapid calculations through a multipole expansion technique. In this work, two additional possibilities for improving the performance are numerically examined. The first is an improvement of the convergence of the expansion by increasing the number of nearby cells, without including higher-order multipole moments. The second is an acceleration of the calculations by the particle-particle and particle-mesh/multipole expansion (PPPM/MPE) method, which uses fast Fourier transform instead of the hierarchy. For this purpose, the PPPM/MPE method originally developed by the authors for a periodic system is extended to a nonperiodic isolated system. The advantages and disadvantages of the GR and PPPM/MPE methods are discussed for both periodic and isolated systems. It is numerically shown that these methods with reasonable costs can reduce the error in potential felt by each particle to 0.1-1 kcal/mol, much smaller than the 30-kcal/mol error involved in conventional simple truncations. © 1994 by John Wiley & Sons, Inc.
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  • 82
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    Journal of Computational Chemistry 15 (1994), S. 61-71 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Zinc ions have been shown to inhibit human immunodeficiency virus type 1 (HIV-1) protease in vitro at neutral pH [Zhang et al. Biochemistry, 36, 8717 (1991)]. Kinetic data from this study support a reversible binding mechanism of zinc in the active site. Preliminary calculations of the ion-protein potential energy based on the geometry of the crystallographic structure [Wlodawer et al. Science, 245, 616 (1989)] are consistent with this proposed mechanism. To examine the structure of HIV-1 protease with zinc bound in the active site, molecular dynamics simulations in the presence and absence of zinc at this site have been carried out to 200 ps. These simulations suggest zinc remains stably bound to the catalytic aspartate residues without disruption of the dimer or significant alteration of the active site structure. These data are consistent with those observed by Zhang et al. (1991), and together give strong evidence that this is the binding site that leads to inactivation. A proposed model of zinc binding at the active site based on quantum mechanical calculations indicates Zn+2 coordination is monodentate with each catalytic aspartate, leaving at least two ligand positions potentially free (occupied by water molecules in the calculations). © 1994 by John Wiley & Sons, Inc.
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  • 83
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 84
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    Journal of Computational Chemistry 15 (1994), S. 374-374 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 85
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    Journal of Computational Chemistry 15 (1994), S. 395-404 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The kinetics and thermodynamics of lactam/lactim tautomerization in 2-pyridone have been investigated, with special attention to direct and assisted proton transfer mechanisms in the ground and first excited electronic state. Specific interactions with a single water molecule strongly enhance the reaction rate and shift the equilibrium toward the lactam form. The effect of bulk solvent is comparatively negligible, although the lactam form is further stabilized. Electron excitation strongly destabilizes the saddle point for proton transfer and, especially, the lactim form with respect to the lactam species. As a consequence, the direct reaction barrier is increased, but the reverse barrier is lowered. Nonpotential energy effects are relatively small and do not modify the aforementioned general trends. © 1994 by John Wiley & Sons, Inc.
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  • 86
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    Journal of Computational Chemistry 15 (1994), S. 446-454 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The cavity used to represent the solute/water interface in Miertus-Scrocco-Tomasi self-consistent reaction field (MST-SCRF) calculations of neutral molecules has been optimized by fitting to experimental data. The study is focused on the refinement of the van der Waals radii of polar and apolar hydrogens and of the van der Waals parameters used to compute the dispersion/repulsion contribution to the total free energy of hydration. When a scaling coefficient of 1.25 is used to build the solute cavity, comparison of 6-31G*/MST results with experimental data demonstrates that the optimum van der Waals radii for hydrogens are around 1.2 Å (apolar) and 0.9 Å (polar). The optimization of the solute cavity and the refinement of the van der Waals parameters lead to root mean square deviations in the computed free energy of hydration of only 0.9 kcal/mol for the 23 molecules considered in this study. © 1994 by John Wiley & Sons, Inc.
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  • 87
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    Journal of Computational Chemistry 15 (1994), S. 466-474 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new code has been written to perform relativistic Dirac-Fock self-consistent field (SCF) calculations on closed-shell molecules of any symmetry. The choice of the basis set allows us to work at different levels of approximation depending on the precision required. Calculations on the H2Po molecule show that accurate results on specific problems like geometry optimization can be obtained by evaluating the two-electron integrals on half the basis spinors. © 1994 by John Wiley & Sons, Inc.
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  • 88
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    Journal of Computational Chemistry 15 (1994), S. 479-487 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effect of correlation energy, basis set size, zero-point energy (ZPE) correction, and solvation on the reaction mechanism of the ketene-imine cycloaddition reaction has been investigated. The electrostatic solvent effect was studied with a self-consistent reaction field method in which the solvation energy is obtained using a multipole expansion of the molecular charge distribution. The ab initio results have been analyzed by means of a theoretical method based on the expansion of the MOs of the supermolecule in terms of those of the reactants and the performance of the configuration analysis. In gas phase, due to the correlation energy and/or the ZPE corrections, the reaction is predicted to be a one-step process. In solution, the stabilization of the charge-transferred configurations results in the occurrence of a very stable, Zwitterionic intermediate giving a two-step mechanism. © 1994 by John Wiley & Sons, Inc.
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  • 89
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    Journal of Computational Chemistry 15 (1994), S. 488-506 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double-energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest-energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side-chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein-folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
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  • 90
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    Journal of Computational Chemistry 15 (1994), S. 532-552 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report the adaptation of the truncated Newton minimization package TNPACK for CHARMM and biomolecular energy minimization. TNPACK is based on the preconditioned linear conjugate-gradient technique for solving the Newton equations. The structure of the problem - sparsity of the Hessian - is exploited for preconditioning. Experience with the new version of TNPACK is presented on a series of molecular systems of biological and numerical interest: alanine dipeptide (N-methyl-alanyl-acetamide), a dimer of N-methyl-acetamide, deca-alanine, mellitin (26 residues), avian pancreatic polypeptide (36 residues), rubredoxin (52 residues), bovine pancreatic trypsin inhibitor (58 residues), a dimer of insulin (99 residues), and lysozyme (130 residues). Detailed comparisons among the minimization algorithms available in CHARMM, particularly those used for large-scale problems, are presented along with new mathematical developments in TNPACK. The new TNPACK version performs significantly better than ABNR, the most competitive minimizer in CHARMM, for all systems tested in terms of CPU time when curvature information (Hessian/vector product) is calculated by a finite-difference of gradients (the numeric option of TNPACK). The remaining derivative quantities are, however, evaluated analytically in TNPACK. The CPU gain is 50% or more (speedup factors of 1.5 to 2.5) for the largest molecular systems tested and even greater for smaller systems (CPU factors of 1 to 4 for small systems and 1 to 5 for medium systems). TNPACK uses curvature information to escape from undesired configurational regions and to ensure the identification of true local minima. It converges rapidly once a convex region is reached and achieves very low final gradient norms, such as of order 10-8, with little additional work. Even greater overall CPU gains are expected for large-scale minimization problems by making the architectures of CHARMM and TNPACK more compatible with respect to the second-derivative calculations. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 91
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 92
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 580-587 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The formation of a charge-transfer complex between carbon dioxide and naphthalene was studied using a molecular modeling program, with the aim of studying the solubility of naphthalene in supercritical carbon dioxide. The orbitals involved in the formation of the complex were studied using MINDO/3 as the semi-empirical method. A solvent cage was constructed, and the maximum number of carbon dioxide molecules to surround naphthalene was found to be 20. The heat of interaction of the complex was obtained using MINDO/3. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 93
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    Journal of Computational Chemistry 15 (1994), S. 596-626 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effects of substituents (X) on the structures and stabilities of CH2X- anions for groups comprised of fourth- and fifth-period main group elements (X = K, CaH, GaH2, GeH3, AsH2, SeH, Br, Rb, SrH, InH2, SnH3, SbH2, TeH, and I) have been investigated by ab initio pseudopotential calculations. Full geometry optimizations have been carried out on the CH2X- anions and the corresponding neutral parent molecules, CH3X, at HF/DZP + and MP2/DZP + levels. Results for substituents from the second (X = Li—F) and third (X = Na—Cl) periods provide comparisons of substituent effects of the main group elements of the first four rows of the periodic table on methyl anions. Frequency calculations characterize the nature of stationary points and show pyramidal CH2X- anion structures to be the most stable unless π acceptor interactions (e.g., with BH2, AlH2, GaH2, and InH2 favor planar geometries. The CH2X- stabilization energies [at QCISD(T)/DZP + /MP2/DZP + + ZPE level for X = K—I and QCISD(T)/6-31 + G*/MP2/6-31 + G* + ZPE level] for X = Li—Cl) also show strong π-stabilizing effects for the same substituents. With the exception of CH3 and NH2, all substituents stabilize methyl anions, although the σ stabilization by OH and F is small. The SiH3—PH2—SH—Cl, GeH3—AsH2—SeH—Br, and SnH3—SbH2—TeH—I sets of substituents give stabilization energies between 19 and 30 kcal/mol. The stability of methyl anions substituted by the halogens and the chalcogens (X = OH, SH, SeH, and TeH) increases down a group in accord with the increasing substituent polarizability, while for π acceptors (BH2, AlH2, GaH2, and InH2) the stability decreases down a group in line with their π-accepting ability. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 94
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    Journal of Computational Chemistry 15 (1994), S. 132-143 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
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  • 95
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    Journal of Computational Chemistry 15 (1994), S. 183-189 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In the forerunner of this article, we described a MNDO modification designed for studies of compounds with intramolecular O—H…O hydrogen bonds. Here, we report the further verification of the modification by means of its application to 14 compounds not considered in its development. Comparison of the calculated structural parameters and proton transfer characteristics with available experimental or ab initio results, and with those obtained using MNDO, AM1, MNDO/H, MNDO/M, and PM3, supports the validity of the new modification for prediction of hydrogen bond characteristics. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 96
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    Journal of Computational Chemistry 15 (1994), S. 200-207 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 97
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    Journal of Computational Chemistry 15 (1994), S. 249-249 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 98
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 233-240 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Rigid inhibitors suffer a smaller loss of conformational entropy when they bind to a macromolecular receptor than their acyclic counterparts. They can also be useful for elucidating pharmacophores due to their reduced conformational space and may be more amenable to synthesis. Computational approaches to rational drug design should therefore take these factors into consideration when suggesting possible compounds. We describe how an acyclic chain which links two parts of a receptor site can be ‘braced’ using ring templates. The acyclic chains may be produced from a number of sources, including lattices or the structures of known inhibitors. The resulting structures contain a rich variety of isolated and fused ring systems, which provide many useful molecular skeletons for subsequent inhibitor design. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 99
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 144-148 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we develop and implement an algorithm for calculating the rovbrational states of diatomic molecules optimized for multiple instructions multiple data computers of distributed memory. The method is based upon the p-version of the finite element method and has been implemented on an INTEL iPSC/2 machine with 16 processors. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
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  • 100
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 155-161 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is described for refining the populations of a set of multiple-solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least-squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1-O-methyl-α-L-iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C4, 4C1, and 2S0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton-proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities. © 1994 by John Wiley & Sons, Inc.
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