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PubMed1999

Neuromolecular computing: a new approach to human brain evolution.

Evolutionary approaches in human cognitive neurobiology traditionally emphasize macroscopic structures. It may soon be possible to supplement these studies with models of human information-processing of the molecular level. Thin-film, simulation, fluorescence microscopy, and high-resolution X-ray crystallographic studies provide evidence for transiently organized neural membrane molecular systems with possible computational properties. This review article examines evidence for hydrophobic-mismatch molecular interactions within phospholipid microdomains of a neural membrane bilayer. It is proposed that these interactions are a massively parallel algorithm which can rapidly compute near-optimal solutions to complex cognitive and physiological problems. Coupling of microdomain activity to permenant ion movements at ligand-gated and voltage-gated channels permits the conversion of molecular computations into neuron frequency codes. Evidence for microdomain transport of proteins to specific locations within the bilayer suggests that neuromolecular computation may be under some genetic control and thus modifiable by natural selection. A possible experimental approach for examining evolutionary changes in neuromolecular computation is briefly discussed.

Brain Chemistry↗
PubMed1997

p16 tumor suppressor gene mutations in Chinese esophageal carcinomas in Hong Kong.

The frequency and nature of genetic alterations in the p16 tumor suppressor gene in 25 esophageal squamous cell carcinoma specimens from Chinese patients were investigated by PCR-SSCP and DNA sequencing techniques. No gross deletions occurred in either exon 1 and 2 of the gene by PCR amplification. However, genetic changes were observed in three cases. These included a point mutation in codon 12 of exon 1 with a resulting Ala --> Thr amino acid substitution, a point mutation at base 91 in the non-coding region of exon 1, and a 1 base pair insertion in codon 116 of exon 2. The low mutation frequency of 12% is consistent with that of three previous studies involving Japanese and Caucasian patients (8, 16 and 21% frequency: Esteve et al., 1996, Igaki et al., 1995 and Zhou et al., 1994). p16 gene mutations do not appear to play a major role in esophageal carcinogenesis.

Aged↗
PubMed2005

Phylogenetics of eggshell morphogenesis in Antheraea (lepidoptera: saturniidae): unique origin and repeated reduction of the aeropyle crown.

Integrated phylogenetic and developmental analyses should enhance our understanding of morphological evolution and thereby improve systematists' ability to utilize morphological characters, but case studies are few. The eggshell (chorion) of Lepidoptera (Insecta) has proven especially tractable experimentally for such analyses because its morphogenesis proceeds by extracellular assembly of proteins. This study focuses on a morphological novelty, the aeropyle crown, that arises at the end of choriogenesis in the wild silkmoth genus Antheraea. Aeropyle crowns are cylindrical projections, ending in prominent prongs, that surround the openings of breathing tubes (aeropyle channels) traversing the chorion. They occur over the entire egg surface in some species, are localized to a circumferential band in many others, and in some are missing entirely, thus exhibiting variation typical of discrete characters analyzed in morphological phylogenetics. Seeking an integrated developmental-phylogenetic view, we first survey aeropyle crown variation broadly across Antheraea and related genera. We then map these observations onto a robust phylogeny, based on three nuclear genes, to test the adequacy of character codings for aeropyle crown variation and to estimate the frequency and direction of change in those characters. Thirdly, we draw on previous studies of choriogenesis, supplemented by new data on gene expression, to hypothesize developmental-genetic bases for the inferred chorion character transformations. Aeropyle crowns are inferred to arise just once, in the ancestor of Antheraea, but to undergo four or more subsequent reductions without regain, a pattern consistent with Dollo's Law. Spatial distribution shows an analogous trend, though less clear-cut, toward reduction of coverage by aeropyle crowns. These trends suggest either that there is little or no natural selection on the details of the aeropyle crown structure or that evolution toward functional optima is ongoing, although no direct evidence exists for either. Genetic, biochemical, and microscopy studies point to at least two developmental changes underlying the origin of the aeropyle crown, namely, reinitiation of deposition of chorionic lamellae after the end of normal choriogenesis (i.e., heterochrony), and sharply increased production of underlying "filler" proteins that push the nascent final lamellae upward to form the crown (i.e., heteroposy). Identification of a unique putative cis-regulatory element shared by unrelated genes involved in aeropyle crown formation suggests a possible simple mechanism for repeated evolutionary reduction and spatial restriction of aeropyle crowns.

Animals↗
PubMed2005

Inbreeding depression and the evolution of dispersal rates: a multilocus model.

Inbreeding depression is one of the possible reasons organisms disperse. In this article, we present a two-locus model for the evolution of dispersal in the presence of inbreeding depression. The first locus codes for a modifier of the migration rate, while the second locus is a selected locus generating inbreeding depression. We express the change in frequency of the migration modifier as a function of allele frequencies and genetic associations and then use a quasi-equilibrium assumption to express genetic associations as functions of allele frequencies. Our model disentangles two effects of inbreeding depression: it gives an advantage to migrant individuals because their offspring are on average less homozygous, but it also decreases the degree of population structure, thus decreasing the strength of kin selection for dispersal. We then extend our model to include an infinite number of selected loci. When the cost of dispersal is not too high, the model predictions are confirmed by multilocus simulation results and show that inbreeding depression can have a substantial effect on the dispersal rate. For high costs of dispersal, we observe discrepancies between the model and the simulations, probably caused by associations among selected loci, which are neglected in the analysis.

Animal Migration↗
PubMed2003

Polymorphisms of adrenergic receptors: variations on a theme.

Recent studies have revealed that most of the adrenergic receptor genes are polymorphic, leading to changes in the amino sequence of the encoded receptor. The variations occur in multiple functional regions of the receptors, and appear as haplotypes with other coding and noncoding polymorphisms in their genes. The consequences of such genetic variability have been explored in recombinant cell-based systems and in human studies. Adrenergic receptor polymorphisms have been shown to alter receptor binding, G-protein coupling, regulation, and expression compared with their allelic counterparts. Here, the genetic and molecular characterization of these polymorphisms is reviewed, as well as their potential impact on pharmacogenetics, disease risk, and disease modification.

Humans↗
PubMed1982

Characterization of N-type and dually permissive cells segregated from mouse fibroblasts whose Fv-1 phenotype could be modified by another independently segregating gene(s).

Though the inbred DDD mouse strain is essentially of the N type, the primary culture of this strain was about 100-fold more sensitive to B-tropic WN1802B virus than were the typical N-type strains (C3H/He, C57L, etc.). After cloning, DDD mouse cells segregated two types of cells, typical N-type cells and cells lacking in Fv-1 restriction. As both types of cells so far tested retained glucose-6-phosphatase-1 coded by a locus closely linked to Fv-1 and genetic cross experiments indicated the presence of a gene(s) modifying the Fv-1 phenotype, variation in Fv-1 restriction could presumably be brought about by genetic changes in a gene(s) other than Fv-1 itself. N-type and dually permissive cell clones were similarly established from the inbred G mouse. Compositions of polypeptides labeled with [35S]methionine in the N-type and dually permissive cells of DDD and G mouse origins were compared by two-dimensional gel electrophoresis. The polypeptide maps of these cells were similar except for a few spots. Among these dissimilar spots, a spot of about 20,000 daltons with a pI of about 5.5 was always present in N-type cells, whereas it was absent in dually permissive cells. In DDD mouse-derived clones, a proportional relation was observed between the intensity of the spot and the restriction to the B-tropic virus.

Animals↗
PubMed2026

Genomic insights into local adaptation of indigenous chickens.

Indigenous chickens are an essential part of biodiversity and a vital protein resource to humans, yet global warming and environmental changes pose serious threats to their survival and productivity. Therefore, assessing population adaptive capacity under shifting environments is crucial for breeding resilient animals, and guiding conservation strategies. Here, we integrated ecological and whole-genome resequencing data from 1 022 chickens from 44 Chinese indigenous populations to reveal genomic signatures of local adaptation. From 87 agroclimatic variables, we identified eight dominant environmental factors including solar radiation, precipitation, diurnal temperature range, and five landcover variables (cropland areas, water areas, trees coverage, bare ground and shrubs coverage) that shape ecological niches of indigenous chickens. Landscape and comparative genomics analyses revealed both known and novel candidate genes, such as UNC80, PTPRO, NCOR2, CSF2RB, NXT2 and PALLD for the solar radiation, precipitation, diurnal temperature range, cropland areas, trees coverage and bare ground, respectively. Particularly, adaptive non-coding variants harbored in these genes exhibited spatial allelic changes across populations and acted as regulatory elements via chromatin accessibility and DNA methylation, influencing adaptation in a tissue-specific manner. Our findings underscore the rich genetic diversity of Chinese indigenous chickens and provide new insights into genomic mechanisms of local adaptation, offering valuable references for domestic animal breeding, conservation, and climate resilience.

Animals↗
PubMed1999

[Participation of mobile elements in formation of properties of pathogenic bacteria].

Published reports about structural organization of genes coding for pathogenicity factors are reviewed. Many of such genes are often united into "virulence blocks" or "pathogenicity islands" and are surrounded by mobile genetic elements, promoting their transposition between related bacteria genomes and leading to changes in virulence in the course of evolution. Data on the similarity of nucleotide sequences of virulence genes in different bacteria are presented, despite differences in their localization in the relevant genomes. The role of rRNA genes in dissemination of virulence genes among different bacteria during transduction or conjugation is shown.

Bacteria↗
PubMed1988

[Pollution and smoking in pregnant women].

For nine months the pregnant woman, and indirectly her fetus, is exposed to an aerosol composed of different pollutants. With some of these, as for smoking, it has been possible to define objectively and statistically an alteration of the health status and of the satisfactory outcome of pregnancy; with others it has not been possible at present to define a dose relation effect or a threshold of risk. In this study, known connections were studied between pregnancy and smoking (specific risks, perinatal mortality, childhood cancer and breastfeeding), industrial pollution and particularly those related to lead, fertilisers and pesticides, opiates and cannabis derivatives (in particular their effect on reproductive function), radioactivity and its correlation with the genetic code and the risk of cancer and pollution by micro-organisms. If these risks exist, even it they are not all assessable objectively, the short term action of the most benefit is certainly a change in individual behaviour, for example with tobacco consumption.

Air Pollutants↗
PubMed1979

Evolution of human influenza A viruses in nature: sequential mutations in the genomes of new H1N1.

The genetic variation of the new pandemic H1N1 influenza A viruses isolated in 1977 was analyzed by two-dimensional oligonucleotide fingerprinting and RNA sequencing. Differences were observed in the fingerprints of the RNAs of these viruses, and analysis of the changes suggested that sequential mutations occurred in their genomes. Based on these data, a scheme is presented which proposes divergent evolution of strains from a common ancestry. Furthermore, it was found that mutations were not restricted to the genes coding for the hemagglutinin and the neuraminidase, but were scattered throughout the genome, suggesting that selective antibody pressure is not solely responsible for the emergence of genetic variants. Our data also strengthen the hypothesis that the new H1N1 influenza virus strains are derived from strains circulating in 1950.

Antigens, Viral↗
PubMed2002

[Gilbert disease and type I and II Crigler-Najjar syndrome due to mutations in the same UGT1A1 gene locus].

BACKGROUND: Gilbert syndrome and the Crigler-Najjar syndromes Type I and II are disorders of bilirubin conjugation with consecutive indirect hyperbilirubinemia of different severity. Morbus Gilbert is a mild hyperbilirubinemia, which is only of significance in case of drug therapy or differential diagnosis. Crigler-Najjar syndrome II leads to a more serious kind of hyperbilirubinemia. In case of Crigler-Najjar syndrome I patients are suffering from a very severe hyperbilirubinemia, which often causes death during the first months of life. MOLECULAR GENETICS: The molecular defects of these three syndromes have been characterized during the last decade. They are caused by mutations in the UGT1A1 gene locus. This locus codes for the enzyme bilirubin uridine 5'-diphosphate-(UDP-) glucuronosyltransferase (UGT1A1). In the case of Gilbert syndrome two bases are inserted into the promoter of the gene. In Crigler-Najjar syndrome type I and II mutations lead to the exchange of amino acids, changes of the reading frame or to stop codons. CONCLUSION: All three forms of indirect hyperbilirubinemia are caused by mutations in the UGT1A1 gene locus, which codes for the enzyme UDP-glucuronosyltransferase.

Amino Acid Substitution↗
PubMed1999

Identification of mutations contributing to the temperature-sensitive, cold-adapted, and attenuation phenotypes of the live-attenuated cold-passage 45 (cp45) human parainfluenza virus 3 candidate vaccine.

The live-attenuated human parainfluenza virus 3 (PIV3) cold-passage 45 (cp45) candidate vaccine was shown previously to be safe, immunogenic, and phenotypically stable in seronegative human infants. Previous findings indicated that each of the three amino acid substitutions in the L polymerase protein of cp45 independently confers the temperature-sensitive (ts) and attenuation (att) phenotypes but not the cold-adaptation (ca) phenotype (29). cp45 contains 12 additional potentially important point mutations in other proteins (N, C, M, F, and hemagglutinin-neuraminidase [HN]) or in cis-acting sequences (the leader region and the transcription gene start [GS] signal of the N gene), and their contribution to these phenotypes was undefined. To further characterize the genetic basis for the ts, ca, and att phenotypes of this promising vaccine candidate, we constructed, using a reverse genetics system, a recombinant cp45 virus that contained all 15 cp45-specific mutations mentioned above, and found that it was essentially indistinguishable from the biologically derived cp45 on the basis of plaque size, level of temperature sensitivity, cold adaptation, level of replication in the upper and lower respiratory tract of hamsters, and ability to protect hamsters from subsequent wild-type PIV3 challenge. We then constructed recombinant viruses containing the cp45 mutations in individual proteins as well as several combinations of mutations. Analysis of these recombinant viruses revealed that multiple cp45 mutations distributed throughout the genome contribute to the ts, ca, and att phenotypes. In addition to the mutations in the L gene, at least one other mutation in the 3' N region (i.e., including the leader, N GS, and N coding changes) contributes to the ts phenotype. A recombinant virus containing all the cp45 mutations except those in L was more ts than cp45, illustrating the complex nature of this phenotype. The ca phenotype of cp45 also is a complex composite phenotype, reflecting contributions of at least three separate genetic elements, namely, mutations within the 3' N region, the L protein, and the C-M-F-HN region. The att phenotype is a composite of both ts and non-ts mutations. Attenuating ts mutations are located in the L protein, and non-ts attenuating mutations are located in the C and F proteins. The presence of multiple ts and non-ts attenuating mutations in cp45 likely contributes to the high level of attenuation and phenotypic stability of this promising vaccine candidate.

Adaptation, Biological↗
PubMed2005

A 4-bp deletion in the Birt-Hogg-Dubé gene (FLCN) causes dominantly inherited spontaneous pneumothorax.

Primary spontaneous pneumothorax (PSP), a condition in which air enters the pleural space and causes secondary lung collapse, is mostly sporadic but also occurs in families. The precise etiology of PSP remains unknown, although it is associated with emphysemalike changes (bullae) in the lungs of almost all patients. We describe the results of a genetic study of a large Finnish family with a dominantly inherited tendency to PSP. A genomewide scan suggested linkage to chromosome 17p11. Screening of the best candidate gene, FLCN, revealed a 4-bp deletion in the first coding exon, which causes a frameshift that predicts a protein truncation 50 missense amino acids downstream. All carriers of the deletion had bullous lung lesions. Mutations in FLCN are also responsible for Birt-Hogg-Dubé (BHD) syndrome (a dominantly inherited disease characterized by benign skin tumors, PSP, and diverse types of renal cancer) and, rarely, are detected in sporadic renal and colorectal tumors. Unlike other FLCN mutations, the exon 4 deletion seems to be associated with bullous lung changes only with 100% penetrance. These results suggest that changes in FLCN may have an important role in the development of PSP and, more importantly, of emphysema, a chronic pulmonary disease that often leads to formation of bullous lesions and lowered pulmonary function. Additionally, given the strong association of PSP and BHD, the connection between these conditions needs to be investigated further, particularly in patients with familial PSP, who may be at a greater risk of developing renal cancer.

Base Sequence↗
PubMed1997

Real-time measurement of multiple intramolecular distances during protein folding reactions: a multisite stopped-flow fluorescence energy-transfer study of yeast phosphoglycerate kinase.

Understanding the set of rules which dictate how the primary amino acid sequence determines tertiary structure is an unsolved problem in biophysics. If it were possible to simultaneously measure all of the intramolecular distances in a protein (in real time) during a folding reaction, the "second" genetic code problem would be solved. Regrettably, no such technique currently exists. As a first step toward this goal, an optical distance assay system has been developed for a two-domain protein, yeast phosphoglycerate kinase (PGK), using Förster resonance energy transfer [Lillo, M. P., et al. (1997) Biochemistry 36, 11261-11272]. In this study, real-time stopped-flow distance changes are measured using six unique pairs of donor/acceptor fluorescent labels strategically placed throughout the tertiary structure of PGK. These multiple donor/acceptor sites were genetically engineered into PGK by cysteine substitution mutagenesis followed by extrinsic labeling with fluorescent probes, 5-[[[(2-iodoacetyl)amino]ethyl]amino]naphthalenesulfonic acid (as a donor) and 5-iodoacetamidofluorescein (acceptor). The unfolding of PGK is found to be a sequential multistep process (native --> I1 --> I2 --> unfolded) with rate constants of 0.30, 0.16, and 0.052 s-1, respectively (from native to unfolded). Unique to this unfolding study, six intramolecular distance vectors have been resolved for both the I1 and I2 states. With this distance information, it is shown that the transition from the native to I1 state can be modeled as a large hinge-bending motion, in which both domains "swing away" from each other by about 15 A. As the domains move apart, the carboxyl-terminal domain rotates almost 90 degrees about the hinge region connecting the two domains. It is also shown that the amino-terminal domain remains intact during the native --> I1 transition, consistent with our previous site-specific tryptophan fluorescence anisotropy stopped-flow study [Beechem, J. M., et al. (1995) Biochemistry 34, 13943-13948]. Future experiments are proposed which will attempt to resolve in detail the unfolding/refolding transitions in this protein with a resolution of approximately 5-10 A.

Energy Transfer↗
PubMed1988

Genetic variation among geographic isolates of Rift Valley fever virus.

The genetic variation of Rift Valley fever virus (RVFV) was estimated by sequencing a portion of the M segment RNA of 22 isolates from a variety of host species collected over 34 years in 6 African countries. The M segment RNA of the Egyptian isolate, ZH501, which has been molecularly cloned and sequenced, was used as a reference for these comparisons. Specific gene regions, responsible for antigenic determinants presumed to play a role in protection against disease, were emphasized in these investigations. Comparative sequence data revealed that most isolates were very similar to ZH501 at both the nucleic acid and deduced amino acid sequence levels. Nucleic acid sequence variation range was 0-4.5%. Amino acid sequence variation range was 0-2.4%. We identified specific amino acid coding changes which may be involved in virus neutralization and may contribute to the virulence characteristics of RVFV.

Amino Acid Sequence↗
PubMed2000

[Genetic changes and clinical management in familial hypertrophic cardiomyopathy].

Hypertrophic cardiomyopathy (HCM) is phenotypically and genotypically heterogeneous disease of heart. Nine chromosomal loci responsible for this condition have been identified: beta-myosin heavy chain, essential and regulatory myosin light chains, troponin T and I subunits, alpha-tropomosin, cardiac myosin binding protein C, cardiac actin and titin. These genes code for proteins involved in the contraction mechanism or in the control of contraction, therefore HCM has been classified as a disease of cardiac sarcomere. Over 107 mutations have been identified. More then half of them have been detected in the beta-myosin heavy chain gene (beta-MHC). Some mutations in beta-MHC gene are associated with a benign prognosis, other are associated with high incidence of sudden cardiac death (SCD) and severe hypertrophy. Mutations in myosin binding protein C are associated with mild, delayed expression of cardiac hypertrophy and benign prognosis. Mutations in cardiac troponinT are associated with a mild degree of hypertrophy but a high incidence of SCD. Study of genes responsible for HCM will assume role in the context of clinical management of HCM, in particular regarding diagnosis and prognosis patients and families with HCM.

Cardiomyopathy, Hypertrophic↗
PubMed2002

Full-length genome analysis of natural isolates of vesicular stomatitis virus (Indiana 1 serotype) from North, Central and South America.

Most studies on the molecular biology and functional analysis of vesicular stomatitis virus Indiana 1 serotype (VSV-IN1) are based on the only full-length genomic sequence currently deposited in GenBank. This sequence is a composite of several VSV-IN1 laboratory strains passaged extensively in tissue culture over the years and it is not certain that this sequence is representative of strains circulating in nature. We describe here the complete genomic sequence of three natural isolates, each representing a distinct genetic lineage and geographical origin: 98COE (North America), 94GUB (Central America) and 85CLB (South America). Genome structure and organization were conserved, with a 47 nucleotide 3' leader, five viral genes -- N, P, M, G and L -- and a 59 nucleotide 5' trailer. The most conserved gene was N, followed by M, L and G, with the most variable being P. Sequences containing the polyadenylation and transcription stop and start signals were completely conserved among all the viruses studied, but changes were found in the non-transcribed intergenic nucleotides, including the presence of a trinucleotide at the M-G junction of the South American lineage isolate. A 102-189 nucleotide insertion was present in the 5' non-coding region of the G gene only in the viruses within a genetic lineage from northern Central America. These full-length genomic sequences should be useful in designing diagnostic probes and in the interpretation of functional genomic analyses using reverse genetics.

Base Sequence↗