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At least 487 records · Page 27Linked to original sources
PubMed1980

Building bacterial flagella.

Most bacterial movement is the result of the action of a subcellular structure, the flagellar organelle. Bacterial flagella propel the cell by rotating, and this rotation is regulated in response to information transmitted by chemoreceptors on the surface of the cell. Rotation is driven by a motor anchored in the cell membrane. To understand such processes as the assembling of flagellar organelles, energy transduction to produce flagellar rotation, and the integration of sensory information necessary for chemotaxis, one prerequisite is the determination of the architecture of flagella. Emphasis is given here to experimental approaches using Escherichia coli and Salmonella in order to identify the flagellar components and to determine how these components are used to construct the functional organelle. The purification of apparently intact organelles has revealed an intricate structure composed to at least 11 polypeptide components. Genetic techniques have been developed which enable the identification of the components of the flagellar system. More than 35 genes which are necessary for flagellar function have been defined in E. coli, and the gene products of 17 of the genes have been identified. From such genetic studies, it is apparent that the flagellar system is complex and includes many elements in addition to those found in the intact flagellar structures purified from the cell membrane. Proteins required for energy and sensory transduction have been identified and located in the cytoplasm and cell membrane. Since these components are not integral parts of the isolated organelle, it is clear that flagellar movement requires the interaction of several functionally distinct and spatially separate systems. The organelle appears to be constructed in discrete stages consisting of the sequential association of individual components. As with bacteriophage assembly, some flagellar proteins function not as structural components, but to regulate the assembly of the organelle. A structural variation is found in Salmonella, which have the ability to alternately express one of two components of the flagellar filament. The unique genetic control mechanism regulating this structural variation is discussed.

Bacterial Physiological Phenomena↗
PubMed1983

Synthesis of analogues of pepstatin. Effect of structure in subsites P1', P2', and P2 on inhibition of porcine pepsin.

A series of pepstatin analogues having structural variations in the P2', P1', and P2 positions have been synthesized and tested for inhibition of porcine pepsin. The standard peptide for this study was Iva-Sta-Val-Ala-Iaa. Structural variations in the P2' and P1' positions have relatively little effect on Ki; however, small variations in the P2 position have a more dramatic effect on Ki and time-dependent inhibition. A series of pepstatin fragments were also synthesized and tested for inhibition of porcine pepsin.

Animals↗
PubMed1976

Volume changes in binding of ligands to methemoglobin and metmyoglobin.

The volume changes for the binding of various ligands to metmyoglobin and methemoglobin have been determined from the effect of pressure on the binding constants (for metmyoglobin) and by direct dilatometry (for methemoglobin). The volume changes associated with the binding of cyanide and azide ions to methemoglobin are pH-dependent. The volume change for the binding reaction is evidently affected by the same subtle structural variations that have been judged to be present from the variation with pH of enthalpy and entropy for the binding reactions in these proteins. Hydration changes and spin state changes which have been postulated to be linked with structural variations in these proteins must be pH-dependent.

Atmospheric Pressure↗
PubMed1980

Effect of mating structure on variation in linkage disequilibrium.

Measurement of linkage disequilibrium involves two sampling processes. First, there is the sampling of gametes in the population to form successive generations, and this generates disequilibrium dependent on the effective population size (Ne) and the mating structure. Second, there is sampling of a finite number (n) of individuals to estimate the population disequilibrium. --Two-locus descent measures are used to describe the mating system and are transformed to disequilibrium moments at the final sampling. Approximate eigenvectors for the transition matrix of descent measures are used to obtain formulae for the variance of the observed disequilibria as a function of N3, mating structure, n, and linkage or recombination parameter. --The variance of disequilibrium is the same for monoecious populations with or without random selfing and for dioecious populations with random pairing for each progeny. With monogamy, the variance is slightly higher, the proportional difference being greater for unlinked loci.

Crosses, Genetic↗
PubMed1978

Anatomic variations of the sella turcica.

Structural variations of the sella turcica occur more often than might be supposed. Some of these may assume technical significance in surgery for intracranial aneurysm.

Humans↗
PubMed1997

Comparative morphology of the gallbladder and biliary tract in vertebrates: variation in structure, homology in function and gallstones.

A review of investigations on the morphology of the gallbladder and biliary tract in fish, reptiles, amphibians, birds, and mammals was performed. Scanning electron microscopy, transmission electron microscopy, and light microscopy observations by the authors were also included. Variations in the presence or absence of a gallbladder, surface epithelium of the gallbladder, and differences in the morphology of the biliary tract in vertebrates were reported. Many differences were diet-related. Despite some dissimilarities observed, analogous functioning of the biliary system was accomplished by its various components, with the biliary ducts performing the function of the gallbladder when this organ was absent. In addition, the occurrence of peculiar parasitism and gallstones among some cases of vertebrates, including humans, was presented.

Amphibians↗
PubMed1996

Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster.

We surveyed sequence variation and divergence for the entire 5972-bp transcriptional unit of the white gene in 15 lines of Drosophila melanogaster and one line of D. simulans. We found a very high degree of haplotypic structuring for the polymorphisms in the 3' half of the gene, as opposed to the polymorphisms in the 5' half. To determine the evolutionary mechanisms responsible for this pattern we sequenced a 1612-bp segment of the white gene from an additional 33 lines of D. melanogaster from a European and a North American population. This 1612-bp segment encompasses an 834-bp region of the white gene in which the polymorphisms form high frequency haplotypes that cannot be explained by a neutral equilibrium model of molecular evolution. The small number of recombinants in the 834-bp region suggests epistatic selection as the cause of the haplotypic structuring, while an investigation of nucleotide diversity supports a directional selection hypothesis. A multi-locus selection model that combines features from both hypotheses and takes the recent history of D. melanogaster into account may be the best explanation for these data.

ATP-Binding Cassette Transporters↗
PubMed2000

Genetic variation and structure in six Rhododendron species (Ericaceae) with contrasting local distribution patterns in Hong Kong, China.

Genetic variability of six rhododendrons with contrasting local distribution patterns in Hong Kong was assessed by starch gel electrophoresis. Rhododendron championiae, R. hongkongense and R. simiarum are locally rare with disjunct distributions, R. moulmainense is restricted and R. farrerae and R. simsii are common. For each species, 13-18 allozyme loci representing 12-16 enzyme systems were scored. The six species showed similar levels of genetic variations (HT ranged from 0.209 to 0.386 and AT ranged from 2.4 to 4.1) which are high compared to plants with similar life history traits. Genetic structure, in contrast, varied greatly between species, with FST ranging from 0.056 to 0.393. The three rarest species had high genetic differentiation (FST and FPT) and distinct geographical patterns, while the other three had low differentiation and little or no geographical structure. These differences are attributed to both present distributions and historical changes following deforestation within the last 1000 years. The conservation implications of these results are discussed.

Alleles↗
PubMed2006

Exon sequencing and high resolution haplotype analysis of ABC transporter genes implicated in drug resistance.

BACKGROUND: The ATP-binding cassette (ABC) proteins are a superfamily of efflux pumps implicated as a mechanism for multidrug resistance in cytotoxic chemotherapy, immunosuppressive therapy, HIV and epilepsy. Genetic variation in P-glycoprotein, the product of the ABCB1 gene, is proposed to mediate de novo drug resistance, but associations between polymorphisms in ABCB1 and pharmacoresistance have produced conflicting results. Potential explanations for the inconsistency of results include inadequate characterization of gene structure, variation and linkage disequilibrium (LD) in ABCB1, as well as overlap in substrate specificity between ABCB1 and the various other drug transporters. METHODS AND RESULTS: We undertook a fundamental analysis of gene structure, variation and LD in ABCB1 and four other drug transporter genes implicated in pharmacoresistance: ABCC1, ABCC2, ABCC5 and ABCB4. Manual annotation of the five genes revealed nine shorter alternative transcripts with new untranslated regions and one novel region of coding sequence, demonstrating that on-line annotations are incomplete. Sequencing of exons in 47 Caucasian individuals identified 75 novel single nucleotide polymorphisms (SNPs) previously undescribed in any public database, including 14 new coding sequence SNPs. Genotyping of 502 SNPs in 842 Caucasian individuals across the five genes revealed large blocks of high LD, and low haplotype diversity across all five genes that could be characterized by between 67 and 114 tagging SNPs, depending on the tagging criteria. CONCLUSION: The study illustrates that publicly available data resources on genomic organization of genes and common variation can have important gaps and limitations, and establishes a comprehensive set of tagging SNPs for future association studies in pharmacoresistance.

ATP-Binding Cassette Transporters↗
PubMed2003

Spatially structured genetic variation in a broadcast spawning bivalve: quantitative vs. molecular traits.

Understanding the origin, maintenance and significance of phenotypic variation is one of the central issues in evolutionary biology. An ongoing discussion focuses on the relative roles of isolation and selection as being at the heart of genetically based spatial variation. We address this issue in a representative of a taxon group in which isolation is unlikely: a marine broadcast spawning invertebrate. During the free-swimming larval phase, dispersal is potentially very large. For such taxa, small-scale population genetic structuring in neutral molecular markers tends to be limited, conform expectations. Small-scale differentiation of selective traits is expected to be hindered by the putatively high gene flow. We determined the geographical distribution of molecular markers and of variation in a shell shape measure, globosity, for the bivalve Macoma balthica (L.) in the western Dutch Wadden Sea and adjacent North Sea in three subsequent years, and found that shells of this clam are more globose in the Wadden Sea. By rearing clams in a common garden in the laboratory starting from the gamete phase, we show that the ecotypes are genetically different; heritability is estimated at 23%. The proportion of total genetic variation that is between sites is much larger for the morphological additive genetic variation (QST = 0.416) than for allozyme (FST = 0.000-0.022) and mitochondrial DNA cytochrome-c-oxidase-1 sequence variation (phiST = 0.017). Divergent selection must be involved and intraspecific spatial genetic differentiation in marine broadcast spawners is apparently not constrained by low levels of isolation.

Analysis of Variance↗
PubMed2001

Electronic fine tuning of the structures of reduced rare-earth metal halides.

Electronic band-structure calculations on Pr3I3Ru and Y3I3Ru have been performed in order to analyze the large structural differences found in these isoelectronic compounds. These constitute two structural extremes within the family of monoclinic Re3I3Ru phases (RE = rare-earth metal) that exhibit distortions ranging from one-dimensional double chains of trans-edge-sharing octahedra (bioctahedral chains, BOH) to one-dimensional chains of trans-edge-sharing square pyramidal units bonded base to base (bisquare pyramidal chains, BSP). The structure of La3I3Ru was established by single-crystal X-ray diffraction (monoclinic, P2(1)/m, Z = 4, a = 9.343(1) A, b = 4.3469(8) A, c = 12.496(3) A, beta = 93.42(2) degrees) and found to be isomorphous with the BOH Pr3I3Ru. It is determined that the structural variation in this RE3I3Z family of materials depends largely on the differences in orbital energies between the corresponding rare-earth metal and the interstitial. These bonding considerations can be generalized to account for structural variations in a variety of other rare-earth halides as well as several group 4 or 5 reduced metal halide cluster phases.

Journal Article↗
PubMed1993

Structure and variations of feline immunodeficiency virus envelope glycoproteins.

We report the characterization of the env gene of a feline immunodeficiency virus isolate from France (FIV Wo). FIV Wo gag and env genes were cloned directly from cat peripheral blood mononuclear cells, using polymerase chain reaction. The env molecular clone was shown to be functional and to express antigenically relevant envelope glycoproteins in vitro. Alignment of FIV Wo sequences with available FIV sequences and application of a regionalization algorithm resulted in delineation of variable and conserved domains of FIV Env. These data were used to build a schematic folding model of FIV envelope glycoproteins. The Env molecular clone, variability map, and structural model constitute helpful tools for future studies of FIV envelope aimed at the determination of structure-function relationships or design of diagnostics or vaccine reagents.

Animals↗
PubMed1984

Antigenic variation during persistent infection by equine infectious anemia virus, a retrovirus.

The recurrent nature of equine infectious anemia has been attributed to relatively rapid antigenic variations in equine infectious anemia virus (EIAV) during persistent infection under selective immune pressures. This model was tested by serological and biochemical analysis of virus isolates recovered from separate febrile episodes in two experimentally infected ponies. Neutralization assays employing immune sera from the experimentally infected ponies demonstrated that distinct antigenic strains of virus predominate during sequential febrile episodes in a single pony. Analysis of the test strains of EIAV by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed varying electrophoretic mobilities for the respective virion glycoproteins gp90 and gp45. Furthermore, peptide mapping comparisons demonstrated structural variations between the gp90 components of the various strains. In contrast, the respective internal proteins of the virus strains displayed identical electrophoretic mobilities in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and, in general, produced identical tryptic peptide maps. The observed differences in glycoprotein electrophoretic mobility and peptide maps were highly reproducible and did not vary with repeated passage of the virus strains in cell culture. Thus, these results demonstrate the occurrence of glycoprotein-specific structural variations during persistent infection by EIAV and support the concept of antigenic variation in this retrovirus. This capacity to alter envelope glycoprotein structure, previously reported for visna virus, may represent an important mechanism of retrovirus persistence in the presence of immune responses by the animal host.

Animals↗
PubMed2000

Functional variant in the DRD2 receptor promoter region and subtypes of alcoholism.

Dopaminergic pathway genes are considered as candidate genes for several neuropsychiatric diseases including severe alcoholism. Since 1990, there have been numerous reports of conflicting association studies of the Taq I A allele of the dopamine D2 receptor (DRD2) gene and alcoholism. Functional and structural variations in candidate genes offer more direct evaluation of their role in the development of a disorder. To determine the role of such variations in the DRD2 gene in the development of alcoholism subtypes, we screened a sample of 173 alcoholics and 88 normal controls with the A-241G and -141C Ins/Del variations in the promoter region and C311G variation in exon 7 of the DRD2 gene. Comparison of alcoholics with normal controls for allele frequency differences of these three variations was negative. Allele frequency differences of the two variations in the promoter region between type II alcoholics, alcoholics with medical complications, and normal controls were not significant. There was linkage disequilibrium only between -141 Ins/Del and Taq I D polymorphisms. We conclude that the functional and structural variations in DRD2 gene do not play a major role in the development of alcoholism subtypes in our sample.

Alcoholism↗
PubMed1996

Three-dimensional distortion correction applied to tomographic reconstructions of sectioned crystals.

Unaveraged tomograms of embedded and sectioned insect flight muscle show not only structural variation within the individual unit cells but also defects in the filament lattice such as lack of straightness of the filaments and wrinkling of the sections. Adaptation of conventional 2D crystal image processing methods usually average out these structural variations and lattice defects thereby reducing the resolution and information content of the 3D reconstructions. We present here a computational method to correct the reconstructed 3D object for these distortions to make it suitable for further analysis. The correction is an extension of conventional 2D cross-correlation techniques applied to a 3D image. These procedures determine the unit cell positions of the distorted crystal and use a spline-fitting approach to calculate a mapping function from the observed positions that is subsequently used to reinterpolate the image onto a regular grid. The resulting reinterpolated image is corrected for both filament straightening as well as section wrinkling.

Animals↗
PubMed1981

Intratypic electrophoretic variation of structural and non-structural polypeptides of human influenza A viruses.

Intratypic electrophoretic mobility differences in high resolution SDS-polyacrylamide gels were detected between corresponding matrix (M) proteins, nucleoproteins (NP), haemagglutinin (HA) and the non-structural polypeptides NS1 and NS2 induced in Vero cells by human influenza A viruses of the antigenic subtypes H1N1 and H3N2. Such phenotypic differences were distinguishable in both H1N1 and H3N2 viruses isolated in single school and city outbreaks. Additional intratypic variation was detected in the biological property of virus plaquing in MDCK cells. Although the biochemical basis is not established, phenotypic variation could represent an additional factor influencing the epidemiology of influenza A viruses.

Disease Outbreaks↗
PubMedDate not supplied

Structure and variation within variant surface glycoproteins of Trypanosoma brucei.

Variant surface glycoproteins of the African trypanosomes are members of a multigene family which show extraordinary amino sequence diversity. The extent of this diversity and the significance of homologies both in the amino acid sequence and in the post-translational modifications are discussed in the light of what is predicted for the structure of these molecules and what is now known from X-ray crystallographic analysis.

Amino Acid Sequence↗