Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “sequence diversity”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 685 records · Page 38Linked to original sources
PubMed2004

The maintenance of extreme amino acid diversity at the disease resistance gene, RPP13, in Arabidopsis thaliana.

We have used the naturally occurring plant-parasite system of Arabidopsis thaliana and its common parasite Peronospora parasitica (downy mildew) to study the evolution of resistance specificity in the host population. DNA sequence of the resistance gene, RPP13, from 24 accessions, including 20 from the United Kingdom, revealed amino acid sequence diversity higher than that of any protein coding gene reported so far in A. thaliana. A significant excess of amino acid polymorphism segregating within this species is localized within the leucine-rich repeat (LRR) domain of RPP13. These results indicate that single alleles of the gene have not swept through the population, but instead, a diverse collection of alleles have been maintained. Transgenic complementation experiments demonstrate functional differences among alleles in their resistance to various pathogen isolates, suggesting that the extreme amino acid polymorphism in RPP13 is maintained through continual reciprocal selection between host and pathogen.

Alleles↗
PubMed2006

Sequence variation among group III F-specific RNA coliphages from water samples and swine lagoons.

Typing of F-specific RNA (FRNA) coliphages has been proposed as a useful method for distinguishing human from animal fecal contamination in environmental samples. Group II and III FRNA coliphages are generally associated with human wastes, but several exceptions have been noted. In the present study, we have genotyped and partially sequenced group III FRNA coliphage field isolates from swine lagoons in North Carolina (NC) and South Carolina (SC), along with isolates from surface waters and municipal wastewaters. Phylogenetic analysis of a region of the 5' end of the maturation protein gene revealed two genetically different group III FRNA subclusters with 36.6% sequence variation. The SC swine lagoon isolates were more closely related to group III prototype virus M11, whereas the isolates from a swine lagoon in NC, surface waters, and wastewaters grouped with prototype virus Q-beta. These results suggest that refining phage genotyping systems to discriminate M11-like phages from Q-beta-like phages would not necessarily provide greater discriminatory power in distinguishing human from animal sources of pollution. Within the group III subclusters, nucleotide sequence diversity ranged from 0% to 6.9% for M11-like strains and from 0% to 8.7% for Q-beta-like strains. It is demonstrated here that nucleotide sequencing of closely related FRNA strains can be used to help track sources of contamination in surface waters. A similar use of phage genomic sequence information to track fecal pollution promises more reliable results than phage typing by nucleic acid hybridization and may hold more potential for field applications.

Animals↗
PubMed1992

Interaction of a common factor with ATF, Sp1, or TATAA promoter elements is required for these sequences to mediate transactivation by the adenoviral oncogene E1a.

The adenovirus protein E1a stimulates transcription of both viral and cellular genes. Unlike most other transcription factors, it induces transactivation through several different promoter elements. The mechanism by which elements of diverse sequence mediate the effect of E1a is the focus of this study. Three E1a-responsive elements (an ATF site, an Sp1 site, and a TATA box containing the sequence TATAA) were studied to determine whether their interaction with a common factor is necessary for transactivation. In transfection assays, each element was used as a competitor against promoter constructs containing the other elements. The elements as competitors had no effect on basal transcription, but each competitor completely inhibited transactivation by E1a. Competitors that were not E1a responsive failed to inhibit transactivation. Therefore, either E1a itself or an E1a-inducible factor interacts with each of the elements to cause transactivation, most likely though an association with each element's specific binding protein.

Activating Transcription Factors↗
PubMed2001

Helicobacter pylori detection in Chinese subjects: a comparison of two common DNA fingerprinting methods.

This study aims to demonstrate DNA diversity in Helicobacter pylori strains obtained from patients with peptic ulcer disease and compare the results from two DNA fingerprinting techniques. H. pylori strains (n = 42), collected from June 1996 to August 1999, were cultured from storage at -80 degrees C. DNA diversity was determined by the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis, and random amplified polymorphic DNA (RAPD)-PCR. Isolates showed a significant DNA sequence diversity by both methods. RAPD-PCR demonstrated 33 distinct strain-specific band patterns, whereas PCR-RFLP demonstrated six distinct restriction patterns. PCR-RFLP identified four of the 42 strains as mixed growth, compared with RAPD-PCR which did not reveal any co-colonisation. Diversity among H. pylori clinical isolates was demonstrated distinctly by both methods; however, RAPD-PCR showed greater discriminatory power in distinguishing between isolates.

Bacterial Typing Techniques↗
PubMed1998

Human immunodeficiency virus type 1 long terminal repeat quasispecies differ in basal transcription and nuclear factor recruitment in human glial cells and lymphocytes.

The generation of genomic diversity during the course of infection has the potential to affect all aspects of HIV-1 replication, including expression of the proviral genome. To gain a better understanding of the impact of long terminal repeat (LTR) sequence diversity on LTR-directed gene expression in cells of the central nervous system (CNS) and immune system, we amplified and cloned LTRs from proviral DNA in HIV-1-infected peripheral blood. Sequence analysis of nineteen LTRs cloned from 2 adult and 3 pediatric patients revealed an average of 33 nucleotide changes (with respect to the sequence of the LAI LTR) within the 455-bp U3 region. Transient expression analyses in cells of neuroglial and lymphocytic origin demonstrated that some of these LTRs had activities which varied significantly from the LAI LTR in U-373 MG cells (an astrocytoma cell line) as well as in Jurkat cells (a CD4-positive lymphocyte cell line). While LTRs which demonstrated the highest activities in U-373 MG cells also yielded high activities in Jurkat cells, the LTRs were generally more active in Jurkat cells when compared to the LAI LTR. Differences in LTR sequence also resulted in differences in transcription factor recruitment to cis-acting sites within the U3 region of the LTR, as demonstrated by electrophoretic mobility shift assays. In particular, naturally occurring sequence variation impacted transcription factor binding to an activating transcription factor/cAMP response element binding (ATF/CREB) binding site (located between the LEF-1 and distal NF-kappaB transcription factor binding sites) that we identified in previous studies of the HIV-1 LTR. These findings suggest that LTR sequence changes can significantly affect basal LTR function and transcription factor recruitment, which may, in turn, alter the course of viral replication in cells of CNS and immune system origin.

Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

Genetic diversity present within the near-complete mtDNA genome of 17 breeds of indigenous Chinese pigs.

The genetic diversity present within the near-complete mitochondrial genome (15,982 bp) was determined from 17 indigenous Chinese pig breeds and 3 European breeds. Animals were selected from 17 Chinese breeds that reflect the large phenotypic diversity of Chinese pigs and represent each of the six breed types, which are grouped based on morphological characteristics. Analysis of nucleotide diversity confirmed a high level of divergence between animals of European versus Asian origin; however, much more limited variation was observed between the 17 indigenous Chinese breeds. Each had a unique haplotype, but the lowest pairwise sequence divergence was only 0.01 +/- 0.01%, observed between the Tongcheng and Yushan Black. Comparison of control region sequence diversity revealed the 17 Chinese breeds contain a lower average pairwise distance (0.61 +/- 0.19%) than a group of European commercial breeds (0.91 +/- 0.21%). The dendrogram constructed from the near-complete mtDNA sequences showed the Chinese sequences loosely clustering into two groups. Although some correspondence with geographic origin was present, notable differences between the dendrogram and the traditional pig breed grouping system were observed.

Animals↗
PubMed2003

SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence.

Prediction of protein function is of significance in studying biological processes. One approach for function prediction is to classify a protein into functional family. Support vector machine (SVM) is a useful method for such classification, which may involve proteins with diverse sequence distribution. We have developed a web-based software, SVMProt, for SVM classification of a protein into functional family from its primary sequence. SVMProt classification system is trained from representative proteins of a number of functional families and seed proteins of Pfam curated protein families. It currently covers 54 functional families and additional families will be added in the near future. The computed accuracy for protein family classification is found to be in the range of 69.1-99.6%. SVMProt shows a certain degree of capability for the classification of distantly related proteins and homologous proteins of different function and thus may be used as a protein function prediction tool that complements sequence alignment methods. SVMProt can be accessed at http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.

Amino Acid Sequence↗
PubMed2001

Great ape DNA sequences reveal a reduced diversity and an expansion in humans.

The extent of DNA sequence variation of chimpanzees is several-fold greater than that of humans. It is unclear, however, if humans or chimpanzees are exceptional among primates in having low and high amounts of DNA sequence diversity, respectively. To address this, we have determined approximately 10,000 bp of noncoding DNA sequences at Xq13.3 (which has been extensively studied in both humans and chimpanzees) from 10 western lowland gorillas (Gorilla gorilla gorilla) and 1 mountain gorilla (Gorilla gorilla beringei; that is, from 2 of the 3 currently recognized gorilla subspecies), as well as 8 Bornean (Pongo pygmaeus pygmaeus) and 6 Sumatran (Pongo pygmaeus abelii) orang-utans, representing both currently recognized orang-utan subspecies. We show that humans differ from the great apes in having a low level of genetic variation and a signal of population expansion.

Animals↗
PubMed1998

Molecular basis for evasion of host immunity and pathogenesis in malaria.

The article relates the ability of the malaria parasite Plasmodium falciparum to avoid a protective immune response, and to induce pathological changes, to the properties of specific parasite molecules. Cytoadherence and rosetting are important features of cerebral malaria and involve proteins located on the surface of the infected red blood cell. Proinflammatory cytokines, particularly tumour necrosis factor (TNF), play a role in protective immunity and in inducing pathology. Glycophosphatidyl inositol membrane anchors of parasite proteins possess insulin like activity and induce TNF synthesis. People subject to repeated infections in malaria endemic areas rarely develop complete or sterile immunity to malaria. They frequently carry small numbers of parasites in the blood, with little symptoms of the disease, illustrating a phenomenon termed semi-immunity. The basis for semi-immunity is incompletely understood. Malaria parasites are susceptible to several immunological effector mechanisms. The presence of extensive repetitive regions is a feature of many P. falciparum proteins. Available evidence suggests that the structural characteristics of the repeats and their location on the surface of parasite proteins promote immunogenicity. The repeats may help the parasite evade host immunity by (i) exhibiting sequence polymorphism, (ii) preventing the normal affinity and isotype maturation of an immune response, (iii) functioning possibly as B cell superantigens, (iv) generating predominantly thymus independent antibody responses, and (v) acting as a sink for binding protective antibodies. Sequence diversity in non-repetitive regions and antigenic variation in parasite molecules located on the surface of infected red blood cells also play a role in immune evasion. Some sequence homologies between parasite and human proteins may be due to molecular mimicry. Homologies in other instances can cause autoimmune responses. The immune evasion mechanisms of the parasite need to be considered in developing vaccines. Protective immunity and pathology may be delicately balanced in malaria.

Animals↗
PubMed1992

Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution.

Sequencing of multiple recombinant clones generated from polymerase chain reaction-amplified products demonstrated that the degree of heterogeneity of two well-conserved regions of the hepatitis C virus (HCV) genome within individual plasma samples from a single patient was consistent with a quasispecies structure of HCV genomic RNA. About half of circulating RNA molecules were identical, while the remaining consisted of a spectrum of mutants differing from each other in one to four nucleotides. Mutant sequence diversity ranged from silent mutations to appearance of in-frame stop codons and included both conservative and nonconservative amino acid substitutions. From the relative proportion of essentially defective sequences, we estimated that most circulating particles should contain defective genomes. These observations might have important implications in the physiopathology of HCV infection and underline the need for a population-based approach when one is analyzing HCV genomes.

Amino Acid Sequence↗
PubMed2003

[Preliminary study on hepatitis B virus quasispecies in a patient with chronic hepatitis B].

OBJECTIVE: To investigate whether the hepatitis B virus (HBV) has quasispecies character by studying nucleotide sequence polymorphism and mutation features of HBV PreC/C gene region, and preliminaryly explore the heterogeneity of HBV quasispecies. METHODS: The serum sample was obtained from a patient with chronic hepatitis B, and the whole HBV PreC/C gene region was amplified by PCR and cloned. Thirty-four clones that contained HBV PreC/C gene fragments were sequenced. RESULTS: There were 28 kinds of different nucleotide sequences in 34 clones, and the nucleotide sequences diversity ranged from 0.2% to 2.1%. The mutation points were almost distributed in the whole region, but there wasn't mutation at PreC region nt.1 896 point in all sequences. CONCLUSION: Hepatitis B virus has complex quasispecies character in the patients with chronic hepatitis B.

Adult↗
PubMed1992

Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient.

In an investigation of the evolution of the third hypervariable loop of gp120 (V3), the principal neutralization determinant of human immunodeficiency virus type 1, we have analyzed 89 V3 sequences of plasma viral RNA purified from peripheral blood samples donated over 7 years by an infected hemophiliac. Considerable sequence diversity in the V3 region was found at all time points after seroconversion. Phylogenetic analysis revealed that an important diversification had occurred by 3 years postinfection and that, subsequently, most sequences could be allocated to either one of two major lineages that persisted throughout the remainder of the infection. Rapid changes in frequency of the most common sequences and the observation that the same hexapeptide motif (GPGSAV) at the crown of the V3 loop has evolved convergently provide strong evidence that selective processes determine the evolutionary fate of sequence variants in this region.

Amino Acid Sequence↗
PubMed2000

Cloning and sequence analysis of a highly polymorphic Cryptosporidium parvum gene encoding a 60-kilodalton glycoprotein and characterization of its 15- and 45-kilodalton zoite surface antigen products.

The apicomplexan parasite Cryptosporidium parvum is a major cause of serious diarrheal disease in both humans and animals. No efficacious chemo- or immunotherapies have been identified for cryptosporidiosis, but certain antibodies directed against zoite surface antigens and/or proteins shed by gliding zoites have been shown to neutralize infectivity in vitro and/or to passively protect against, or ameliorate, disease in vivo. We previously used monoclonal antibody 11A5 to identify a 15-kDa surface glycoprotein that was shed behind motile sporozoites and was recognized by several lectins that neutralized parasite infectivity for cultured epithelial cells. Here we report the cloning and sequence analysis of the gene encoding this 11A5 antigen. Surprisingly, the gene encoded a 330-amino-acid, mucin-like glycoprotein that was predicted to contain an N-terminal signal peptide, a homopolymeric tract of serine residues, 36 sites of O-linked glycosylation, and a hydrophobic C-terminal peptide specifying attachment of a glycosylphosphatidylinositol anchor. The single-copy gene lacked introns and was expressed during merogony to produce a 60-kDa precursor which was proteolytically cleaved to 15- and 45-kDa glycoprotein products that both localized to the surface of sporozoites and merozoites. The gp15/45/60 gene displayed a very high degree of sequence diversity among C. parvum isolates, and the numerous single-nucleotide and single-amino-acid polymorphisms defined five to six allelic classes, each characterized by additional intra-allelic sequence variation. The gp15/45/60 single-nucleotide polymorphisms will prove useful for haplotyping and fingerprinting isolates and for establishing meaningful relationships between C. parvum genotype and phenotype.

Alleles↗
PubMed2001

Nucleotide sequences of the coat protein and readthrough protein genes of the Chinese GAV isolate of barley yellow dwarf virus.

The nucleotide sequences of the coat protein (CP) and readthrough protein (RTP) genes of the Chinese GAV isolate of Barley yellow dwarf virus (BYDV) were determined. The CP and RTP genes of GAV isolate comprised 600 and 1374 nucleotides, respectively. When the CP and RTP gene sequences of GAV isolate were compared with those of BYDV isolates MAV-PS1, P-PAV, NY-SGV and Cereal yellow dwarf virus RPV (CYDV-RPV), the highest similarity (97.2%) between the CP genes of GAV and MAV-PS1 isolates was observed, while the RTP genes of these two isolates shared a lower similarity (87.8%). The results of the alignment of the deduced amino acid sequences of RTP showed that the sequence diversity observed was located at the C terminus.

Amino Acid Sequence↗
PubMed1995

The centromere: kinetochore complex.

At the meta-anaphase transition the centromeres in a genome separate in non-random sequential manner. This sequential separation depends upon the timing of replication of DNA located in the pericentric and centromeric region. Cells in long term cultures as well as some newborn humans carry dicentric chromosomes. The inactive centromeres in these dicentric chromosomes do not show any sequence of separation. Whether or not a dicentric chromosome would segregate equationally depends upon if only one centromere binds to microtubules or both are functional. In man and other higher apes, a 171 base pair long DNA repeat (the alphoid sequence) is present on all centromeres. In mouse, the minor satellite fraction is said to constitute the centromere. These two DNAs also carry a 17 bp long sequence, the CENP-B 'box' to which the CENP-B antigen is bound. Other species-eg, rat, pig, fish, Chinese hamster-exhibit still different sequences at the centromere and do not carry the CENP-B 'box' even though the antigen is ubiquitously present in all species. It is not clear why so many diverse sequences constitute the centromere when all centromeres look alike and perform the same function. I propose that the primary constriction owes its property not necessarily to its DNA composition but to some stereophysical property, eg the curvature and that the region is held together till late metaphase-anaphase due to a specific proteinaceous factor. The mammalian centromeres bind a complex of several proteins dubbed as CENtromere Proteins (CENP's). This complex, however, is not what constitutes the trilamellar kinetochore structure as see under the electron microscope.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2002

Genetic diversity and selection in the maize starch pathway.

Maize is both phenotypically and genetically diverse. Sequence studies generally confirm the extensive genetic variability in modern maize is consistent with a lack of selection. For more than 6,000 years, Native Americans and modern breeders have exploited the tremendous genetic diversity of maize (Zea mays ssp. mays) to create the highest yielding grain crop in the world. Nonetheless, some loci have relatively low levels of genetic variation, particularly loci that have been the target of artificial selection, like c1 and tb1. However, there is limited information on how selection may affect an agronomically important pathway for any crop. These pathways may retain the signature of artificial selection and may lack genetic variation in contrast to the rest of the genome. To evaluate the impact of selection across an agronomically important pathway, we surveyed nucleotide diversity at six major genes involved in starch metabolism and found unusually low genetic diversity and strong evidence of selection. Low diversity in these critical genes suggests that a paradigm shift may be required for future maize breeding. Rather than relying solely on the diversity within maize or on transgenics, future maize breeding would perhaps benefit from the incorporation of alleles from maize's wild relatives.

Genetic Variation↗
PubMed2002

Diversity and function of orphan nuclear receptors in nematodes.

Nuclear receptors (NRs) have key regulatory functions in a wide range of biological processes and are one of the most abundant classes of transcriptional regulators in metazoans. NRs are particularly numerous in nematodes, in which the NR gene family has undergone extensive expansion and diversification, providing an evolutionary structure function experiment that is yielding new perspectives on the mechanisms of NR function and on nematode biology. The genome sequence of the free-living nematode Caenorhabditis elegans reveals 270 predicted NR genes, more than fivefold more than observed for any other species to date, though existing data suggest that NR genes are similarly abundant in other nematodes. Most of the currently available information regarding the functions of nematode NRs comes from ongoing studies with C. elegans, and we review here what has been learned thus far in three key areas: the relationships of C. elegans NRs to those in other species; the biochemical consequences of nematode NR sequence diversity.

Amino Acid Sequence↗
PubMed1996

Phylogeographic variability in traditional societies.

Our perception of the amount, and distribution, of human genetic diversity is becoming radically altered by the introduction of sophisticated molecular techniques into the field of evolutionary biology. Along with the exponential increase in the number of informative DNA markers, has come an increased precision in estimating the evolutionary relationships between populations. Evaluating DNA variability in terms of the phylogenetic analysis of sequence variability at the population level has been especially informative in illuminating the long-term ancestry of our species. An extension of this strategy, phylogeography, aims to evaluate the evolutionary ancestry of specific genomic regions in terms of the geographic distribution of phylogenetic lineages within and among populations. We have started to apply this approach by studying the distribution of mitochondrial DNA sequence diversity within and among a variety of Amerindian tribes. These data provide an illuminating contrast to regional data on sequence variability, especially when analysed within the theoretical framework of the coalescent. To interpret these results, we have analysed a simple model in which the rate of coalescence between subpopulations varies with respect to the rate of coalescence of individual ancestry. The model indicates that extensively isolated subpopulations will have distinct distributions of ancestry, and hence of sequence variability, compared to subpopulations which arise due to a series of rapid fissioning events. Subpopulations within tribes, such as bands, appear to correspond to the latter category, whereas tribal populations appear intermediate between the two extremes.

Animals↗