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At least 955 records · Page 53Linked to original sources
PubMed2003

Vesicle trafficking: pleasure and pain from SM genes.

Most cells contain a variety of transport vesicles traveling to different destinations. Although many specific transport routes exist, the underlying molecular principles appear to be rather similar and conserved in evolution. It has become evident that formation of protein complexes named SNARE complexes between vesicle and target membrane is a central aspect of the final fusion reaction in many, if not all, routes and that SNARE complexes in different routes and species form in a similar manner. It is also evident that a second gene family, the Sec1/Munc18 genes (SM genes), plays a prominent role in vesicle trafficking. But, in contrast to the consensus and clarity about SNARE proteins, recent data on SM proteins in different systems produce an uncomfortable heterogeneity of ideas about their exact role, their site of action and their relation to SNARE proteins. This review examines whether a universal principle for the molecular function of SM genes exists and whether the divergence in SM gene function can be related to the unique characteristics of different transport routes.

Animals↗
PubMed1993

Cloning, sequencing and phylogenetic analysis of a human 5-hydroxytryptamine 1D receptor pseudogene.

A third member of the human 5HT1D gene family has been identified using a combination of homology cloning and DNA sequence analysis. This human gene is most related to the 5HT1D alpha subtype (77% shared identity) and is a pseudogene, based on the lack of an open reading frame (ORF) caused by multiple in-frame stop codons and nucleotide (nt) deletions relative to the functional 5HT1D alpha gene (encoding the 5-hydroxytryptamine 1D alpha receptor). The 5HT1D pseudogene also contained an insertion that shares 87% identity to the Alu consensus sequence. Phylogenetic analysis of the three human genes in this family reveals that although the two functional genes, 5HT1D alpha and 5HT1D beta, are detected in all mammalian species examined, the 5HT1D pseudogene is only detected in a subset of primates (catarrhines) that evolved approximately 35-45 million years (Myr) ago. Alternatively, based on the 23% divergence between the functional 5HT1D alpha gene and the 5HT1D pseudogene, we estimate that these two genes began to diverge approximately 50 Myr ago.

Amino Acid Sequence↗
PubMed2003

Divergent promoter organization may be a preferred structure for gene control in Escherichia coli.

The prokaryote possesses intriguing promoter arrangements called divergent promoters, which transcribe adjacent genes in opposite directions. The genome analysis in Escherichia coli revealed the occurrence of a large number of divergent promoters, whose total number was estimated to be about 1.6-fold larger than that of single promoters. Surprisingly, more than 65% divergent promoters transcribe functionally unrelated genes. Transcription from one promoter has been proposed and demonstrated to influence that from the other promoter via change in superhelicity in the divergent promoter region. Therefore, the organism may have acquired divergent promoters as a common structure for ingenious gene controls including transcription coupling.

Escherichia coli↗
PubMed1996

Divergent effects of Fc gamma RIIIA ligands on the functional activities of human natural killer cells in vitro.

The Fc gamma receptor (R)IIIA (CD 16) plays an important role in regulating the cytotoxic and non-cytotoxic functions of human natural killer (NK) cells. Some anti-CD 16 monoclonal antibodies (mAb) have been shown to stimulate NK activity, while human monomeric (m) IgG induces dose-dependent inhibition of NK activity. To explore further these interactions mediated via Fc gamma RIIIA, purified NK cells were cultured for 2-3 days in the presence of mIgG, 3G8 mAb, interleukin-2 (IL-2) or a combination of mIgG or 3G8 with IL-2. Binding of mIgG or 3G8 to Fc gamma RIIIA induced divergent effects of functions of cultured NK cells: 3G8 mAb + IL-2 induced dose-dependent inhibition of proliferation attributable to apoptosis; in contrast, mIgG + IL-2 significantly increased NK cell proliferation. Incubation of NK cells in the presence of mIgG up-regulated expression of surface activation markers (CD69, IL-2R alpha, ICAM-1), cytotoxicity, cytokine production (IL-1 beta, IFN-gamma and TNF-alpha) and release of soluble IL-2R. Thus, mIgG binding to Fc gamma RIIIA induced stimulatory signals in human NK cells, leading to up-regulation of IL-2R alpha expression, cell proliferation and cytokine release.

Antigens, CD↗
PubMed2006

Divergence in spatial expression patterns and in response to stimuli of tandem-repeat paralogues encoding a novel class of proline-rich proteins in Oryza sativa.

Gene duplication has been recognized as a major route to supply raw sequences for genome novelty in evolution, but the mechanism underlying the retention of duplicate genes is not fully understood yet. Divergence in spatial expression patterns was investigated here and in response to stimuli of the four members of a rice proline-rich protein gene family (OsPRP1), which encode a class of proline-rich proteins. The four paralogues are tandemly organized within a 20 kbp range of chromosome 10 without any interval of other open reading frames and with a median K(S) value of 0.474. These paralogues showed little similarity in their regulatory regions but high conservation in coding regions. Search of an intergenomic cis-element database predicted their promoter regions with divergent cis-element fingerprints. Further expression analyses involving different tissues/organs and nine types of stimuli by a promoter::GUS-fusion strategy revealed that the four paralogues were expressed mainly in vascular cylinders of different organs and showed diversity in tissue/organ specificity and in response to these stimuli, with some overlapping expression. Furthermore, these data show that OsPRP1.2 appeared to inherit most of the functions from their multifunctional progenitor, whereas the other three genes diverged after duplication events. Thus, the retention of paralogues in a multigene family seems to require a more complicated diversification process than originally thought. In addition, the promoter::GUS strategy is a powerful way to explore function divergence of a tandem-repeat gene family.

Amino Acid Sequence↗
PubMed2002

Correlated evolutionary divergence of egg size and a mitochondrial protein across the Isthmus of Panama.

An explicit assumption of studies that employ a mitochondrial DNA (mtDNA) molecular clock is that mtDNA evolves independently of morphology. Here we report a very strong correlation between egg size divergence and cytochrome c oxidase-1 (CO1) amino acid sequence divergence among sister species of bivalve molluscs separated by the Central American Isthmus (i.e., "geminate" species). Analyses of the molecular data reveal that CO1 sequences likely did not diverge as a function of time or evolve in response to positive natural selection. Given that an excess of CO1 amino acid polymorphism exists within species (as expected if most mutations are only slightly deleterious), a third hypothesis is that reductions in effective population size could simultaneously increase the fixation rate of nearly neutral mtDNA polymorphisms and in some way also facilitate egg size evolution. The remarkable strength of the relationship between egg size and CO1 amino acid sequence demonstrates that, even in the absence of an obvious functional relationship or clock-like evolution, the amounts of molecular and morphological change can be tightly correlated, and therefore may reflect common processes. Accordingly, the assumption that the evolutionary divergence of molecules and morphology are independent must always be carefully examined.

Animals↗
PubMed1993

Comparative analysis of the pC194 group of rolling circle plasmids.

pC194-type plasmids have been isolated from widely divergent species of bacteria: Gram positive, Proteobacteria, Spirochaetes and Cyanobacteria. We have examined the three essential replication elements of these plasmids, i.e., the Rep protein, and the origins of double and single stranded synthesis. Comparative analysis of Rep protein sequences from these plasmids indicates that they are highly divergent. Those isolated from Gram positive species fall into five groups: a Bacillus group, a Lactobacillus group, a Streptococcus group and two Staphylococcus aureus groups. The two S. aureus clusters are quite separate, suggesting that there has been at least one plasmid transfer between divergent Gram positive species. The double stranded origin of replication and the active site of the Rep protein display similarities across species indicating that these motifs can function in very divergent hosts. In contrast the single stranded origin of replication is typical of the host from which the plasmid is isolated. This is exemplified by (i) pKYM where the single stranded origins are similar to the minus origins found on the single-stranded coliphages, and (ii) pTD1 (isolated from a Spirochaete), pNostoc, pMA1 and pRF1 (all isolated from Cyanobacteria) which have no sequence homology to the minus origins identified in Gram positive or Gram negative species. This points to the single stranded origin as a feature critical to the determination of the host range of the plasmid.

Amino Acid Sequence↗
PubMed2004

Highly conserved non-coding sequences are associated with vertebrate development.

In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH), in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development.

Animals↗
PubMed1997

Recovery of function after sciatic nerve crush lesion in rats selected for diverging locomotor activity in the open field.

The relation between recovery of function following a sciatic nerve crush lesion and an individual behavioural characteristic, the locomotor activity in an open field, was investigated in rats. Ten high-active (HA) and ten low-active (LA) rats were selected from a stock of sixty male, random-bred Wistar rats, by measuring travelled distance in an open field. Subsequently, both HA and LA rats underwent an unilateral sciatic nerve crush. Recovery of motor function revealed no significant differences between both groups, whereas recovery of sensory function in HA rats was significantly more rapid than in the LA rats (P < 0.01). These observations suggest the existence of a relationship between individual behavioural characteristics, and the sensory recovery of nerve function following crush lesion in rats.

Adrenal Glands↗
PubMed2006

The role of AtMSH2 in homologous recombination in Arabidopsis thaliana.

During homologous recombination (HR), a heteroduplex DNA is formed as a consequence of strand invasion. When the two homologous strands differ in sequence, a mismatch is generated. Earlier studies showed that mismatched heteroduplex often triggers abortion of recombination and that a pivotal component of this pathway is the mismatch repair Msh2 protein. In this study, we analysed the roles of AtMSH2 in suppression of recombination in Arabidopsis. We report that AtMSH2 has a broad range of anti-recombination effects: it suppresses recombination between divergent direct repeats in somatic cells or between homologues from different ecotypes during meiosis. This is the first example of a plant gene that affects HR as a function of sequence divergence and that has an anti-recombination meiotic effect. We discuss the implications of these results for plant improvement by gene transfer across species.

Arabidopsis↗
PubMed2005

Asymmetric evolution of duplicate genes encoding the CCAAT-binding factor NF-Y in plant genomes.

NF-Y is a ubiquitous CCAAT-binding factor composed of NF-YA, NF-YB and NF-YC. Multiple genes encoding NF-Y subunits have been identified in plant genomes. It remains unclear whether the duplicate genes underwent different evolutionary patterns. Likelihood-ratio tests were used to examine whether the amino acid substitution rates are the same between duplicate genes. The influences of selection on evolution were evaluated by comparing the conservative and radical amino acid substitution rates, as well as maximum-likelihood analysis. Some NF-YB and NF-YC duplicates showed significant evidence of asymmetric evolution but not the NF-YA duplicates. Most amino acid replacements in the NF-YB and NF-YC duplicates result in changes in hydropathy, polar requirement and polarity. The physicochemical changes in the sequences of NF-YB seem to be coupled to asymmetric divergence in gene function. Plant NF-Y genes have evolved in different patterns. Relaxed selective constraints following gene duplication are most likely responsible for the unequal evolutionary rates and distinct divergence patterns of duplicate NF-Y genes. Positive selection may have promoted amino acid hydropathy changes in the NF-YC duplicates.

Amino Acid Substitution↗
PubMed1998

Molecular evolution of Hox gene regulation: cloning and transgenic analysis of the lamprey HoxQ8 gene.

The mammalian Hox clusters arose by duplication of a primordial cluster. The duplication of Hox clusters created redundancy within cognate groups, allowing for change in function over time. The lamprey, Petromyzon marinus, occupies an intermediate position within the chordates, both in terms of morphologic complexity and possibly cluster number. To determine the extent of divergence among Hox genes after duplication events within vertebrates, we analyzed Hox genes belonging to cognate group 8. Here we report characterization of the HoxQ8 gene, which shows conservation with mammalian genes in its amino-terminal, homeobox and hexapeptide sequences, and in the position of its splice sites. A beta-galactosidase reporter gene was introduced in the HoxQ8 genomic region by targeted recombinational cloning using a yeast-bacteria shuttle vector, pClasper. These reporter gene constructs were tested for their ability to direct region-specific expression patterns in transgenic mouse embryos. Lamprey enhancers direct expression to posterior neural tube but not to mesoderm, suggesting conservation of neuronal enhancers. In the presence of the mouse heat shock promoter, lamprey enhancers could also direct expression to the posterior mesoderm suggesting that there has been some divergence in promoter function. Our results suggest that comparative studies on Hox gene structure and analysis of regulatory elements may provide insights into changes concomitant with Hox cluster duplications in the chordates.

Amino Acid Sequence↗
PubMed2005

Quantum gas-liquid condensation in an attractive Bose gas.

Gas-liquid condensation (GLC) in an attractive Bose gas is studied on the basis of statistical mechanics. Using some results in combinatorial mathematics, the following are derived. (1) With decreasing temperature, the Bose-statistical coherence grows in the many-body wave function, which gives rise to the divergence of the grand partition function prior to Bose-Einstein condensation. It is a quantum-mechanical analogue to the GLC in a classical gas (quantum GLC). (2) This GLC is triggered by the bosons with zero momentum. Compared with the classical GLC, an incomparably weaker attractive force creates it. For the system showing the quantum GLC, we discuss a cold helium 4 gas at sufficiently low pressure.

Journal Article↗
PubMed1995

Validation of the Cumulative Illness Rating Scale in a geriatric residential population.

OBJECTIVE: To evaluate the validity of the Cumulative Illness Rating Scale (CIRS) in a geriatric institutional population by examining its associations with mortality, hospitalization, medication usage, laboratory findings and disability. DESIGN: A validation of the CIRS using self- and physician-report surveys, with archival data drawn from medical charts and facility records. SETTING: Long-term care facility with skilled nursing and congregate apartments. PARTICIPANTS: Four hundred thirty-nine facility residents selected on the basis of completeness of self-report data and physician ratings. PRIMARY MEASURES: Composite measures of illness severity and comorbidity, based on physicians' CIRS ratings; time to death or acute hospitalization after assessment; medication use, drawn from pharmacy records; medical chart data on laboratory tests; self-reported functional disability. RESULTS: CIRS illness severity and comorbidity indices, as well as individual CIRS items, were significantly associated with mortality, acute hospitalization, medication usage, laboratory test results, and functional disability. The CIRS showed good divergent validity vis a vis functional disability in predicting mortality and hospitalization. CONCLUSIONS: The CIRS appears to be a valid indicator of health status among frail older institution residents. The illness severity and comorbidity composites performed equally well in predicting longitudinal outcomes. Item-level analyses suggest that the CIRS may be useful in developing differential illness profiles associated with mortality, hospitalization, and disability.

Activities of Daily Living↗
PubMed1990

The human genome contains a single processed pseudogene for alpha enolase located on chromosome 1.

We have isolated and characterized human genomic clones containing an alpha enolase pseudogene which lacks introns and has the hallmarks of having been generated by reverse transcription. Two in-frame termination codons renders its coding region incapable of producing a functional protein. An Alu-like sequence is present in the region homologous to the 3' untranslated of the alpha enolase mRNA. Comparison of the two sequences shows that the pseudogene diverged from its functional counterpart about 14 million years ago and interestingly it is the only alpha enolase pseudogene present in the human genome. Chromosomal mapping locates the processed pseudogene to human chromosome 1, the same chromosome where the functional gene has been mapped.

Base Sequence↗
PubMed2004

Patterns of gene divergence and VL promoter activity in immunoglobulin light chain clusters of the channel catfish.

The structure and genomic organization of V, J, and C segments in multiple gene clusters of the G class of catfish light (L) chain were determined to study evolutionary patterns of cluster divergence and regulatory function. The results showed that the organizational pattern is conserved; two VL segments reside in opposite transcriptional orientation to a pseudogene JL segment (psiJ), a functional JL segment, and a CL segment. Structures within the central V-psiJ-J-C regions indicate that cluster duplication occurred after the V-V-psiJ-J-C organization became fixed. VL divergence in gene clusters subsequently occurred by mechanisms that principally targeted complementarity-determining regions. The sequence of the VL-flanking regions, which contained regulatory octamer, TATA, and Pax-5 (BSAP) binding site motifs, was conserved during G cluster duplication and within VL-flanking regions in divergent lineages of bony fish. Reporter assays of catfish B cells transfected with a 742-bp VL-flanking fragment showed promoter activity in the absence of enhancer elements. The promoter's activity doubled when coupled with the catfish IgH enhancer. A 136-bp fragment containing the motifs conserved in bony fish phylogeny and located between the leader initiation codon and the initiation sites of sterile transcripts served as a minimal promoter and provided the highest B-cell activity. These constructs, however, did not act as promoters in catfish non-lymphoid cells or mammalian BJA-B B cells or fibroblasts. These results indicate that the structure and function of VL promoter regions in the regulation and tissue specificity of L-chain gene expression evolved early in phylogeny.

Amino Acid Sequence↗
PubMed2006

Adaptive divergence and power for improving connectivity in free-space optical mobile networks.

A significant challenge for free-space optical (FSO) links is the restrictive alignment requirements, especially when the transceivers are moving. For moderate distances and rapid unpredictable motion, the receiver's field of view and the positioning system's dynamics become factors. We explore the use of adaptive transmitter power and beam divergence to improve the likelihood of maintaining a mobile FSO link by using Gaussian beam propagation theory and link budgets. We calculate the allowable misalignment between the transceivers' optical axes as a function of power, divergence, and transceiver distance. The maximum allowable error is independent of the distance, except when the field of view is a limiting factor. Certain combinations of divergence and power, while suboptimal for one distance, provide a relaxed misalignment limit for many distances. Based on the calculations, we make initial suggestions for system design.

Journal Article↗
PubMed2004

Divergent cell cycle kinetics underlie the distinct functional capacity of mucosal T cells in Crohn's disease and ulcerative colitis.

BACKGROUND: Different abnormalities of T cell effector function distinguish Crohn's disease (CD) from ulcerative colitis (UC). Because cell cycling determines effector function, pathogenic events in CD and UC may depend on cell cycle changes unique to each condition. METHODS: Cell cycle kinetics, cycle regulatory molecule expression, apoptosis, caspase and telomerase activity, and cellular expansion were evaluated in CD2 and CD3 activated control, CD, and UC lamina propria T cells. RESULTS: Compared with normal cells, CD T cells cycle faster, express increased phosphorylated Rb and decreased phosphorylated p53 levels, display less caspase activity but more telomerase activity, die less, and undergo vigorous cellular expansion. In contrast, UC T cells cycle slower, express normal levels of phosphorylated Rb and p53, display more caspase activity but have no telomerase activity, die more, and have a limited capacity to expand. CONCLUSIONS: T cell cycle abnormalities in CD indicate a state of hyperreactivity compatible with loss of tolerance, but a hyporeactive state compatible with anergy in UC. Thus distinct and divergent T cell cycle characteristics underlie the pathogenesis of the two main forms of inflammatory bowel disease.

Adolescent↗