SEARCH · Search PubMed

Results for “Lineage”

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.

SourceResearch connectionFrom yearThrough year

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

At least 523 records · Page 29Linked to original sources

PubMed2006

Viral load, E2 gene disruption status, and lineage of human papillomavirus type 16 infection in cervical neoplasia.

The clinical utility of human papillomavirus (HPV) load and integration status remains unclear. We applied refined methods to delineate the viral load, integration status, and lineage of 104 women with HPV-16 monotype infection, including 19 with normal cervices, 9 with histologically proven cervical intraepithelial neoplasia (CIN) 1, 24 with CIN 2, 27 with CIN 3, and 25 with squamous cell carcinoma (SCC). Higher crude viral load, as determined by real-time polymerase chain reaction (PCR) targeting the E7 gene, was observed for SCC but became insignificant after normalization for cell content. Integration was located and quantified by real-time PCRs targeting, respectively, the carboxyl, amino, and hinge domains of the E2 gene. Pure episomal, integrated, and mixed forms were observed in all disease groups. Most E2 gene disruptions involved the amino-terminal, but sparing the hinge region that has been frequently used as a surrogate marker of integration. Large-fragment disruption involving all 3 E2 regions was observed only in the CIN 3 and SCC groups. Altogether, 33.3% of the CIN 3 group and 28.0% of the SCC group harbored pure episomal genomes. The Asian lineage was associated with a higher risk for CIN 3/SCC than the European lineage, and 6 of the 7 large-fragment E2 disruptions were from Asian lineage. The link between viral lineage, integration pattern, and oncogenesis deserves further study.

Adolescent↗

PubMed1994

Paraffin-resistant antigens detectable by antibodies L26 and polyclonal CD3 predict the B- or T-cell lineage of 95% of diffuse aggressive non-Hodgkin's lymphomas.

The reactivity of eight preferential B-cell (L26, 4KB5, and KiB3) and T-cell (polyclonal CD3, Leu22, MT-1, UCHL-1, and OPD4) antibodies which detect paraffin-resistant antigens was examined by a three-step immunoperoxidase technique in 111 formalin-fixed, paraffin-embedded diffuse aggressive non-Hodgkin's lymphomas (NHLs) to determine the optimal panel for accurate lineage assignment. L26 (CD20) and polyclonal CD3 (CD3) were the most sensitive (> 95%) and specific (100%) antibodies. They identified the B- or T-cell lineages correctly in 106 (95%) cases. The five L26-negative, polyclonal CD3-negative cases included all three precursor B lymphoblastic NHLs and two (one B and one T) diffuse large-cell NHLs. Immunostaining with the second most sensitive preferential B-cell (4KB5) and T-cell (Leu22) antibodies correctly identified the lineage in two additional NHLs, but one false-positive result occurred. Preferential B-cell antibody KiB3 reacted with two precursor B lymphoblastic NHLs. Use of additional paraffin-reactive antibodies did not increase the number of NHLs assigned to the correct cell lineage. In conclusion, it appears that a two-tiered approach, with a first-line panel consisting of L26 and polyclonal CD3, followed by 4KB5 and Leu22 in nonlymphoblastic NHLs and by KiB3 in lymphoblastic NHLs, represents the most efficient method of correctly identifying the B- or T-cell lineage of diffuse aggressive NHLs by paraffin tissue section immunohistochemistry.

Antibodies, Monoclonal↗

PubMed1990

Kappa immunoglobulin light chain gene rearrangement in a T-lineage chronic lymphocytic leukemia.

Until recently, only B-lineage lymphoid cells were observed to rearrange kappa immunoglobulin light chain genes. The authors examine peripheral blood mononuclear cells from a patient with chronic lymphocytic leukemia. More than 90% of these cells bound T-lymphocyte specific antibodies, failed to bind B-lymphocyte specific antibodies, had rearranged T-cell receptor beta-chain genes and had retained immunoglobulin heavy chain genes in the germline configuration. Despite these T-lineage markers, the majority of these cells had rearranged kappa immunoglobulin light chain genes. This provides the first conclusive evidence for rearranged kappa genes in malignant T-lineage cells and warns that gene rearrangement studies alone cannot indicate tumor cell lineage. To detect T-lineage cells that rearrange immunoglobulin genes, multiple immunophenotypic and genotypic parameters must be evaluated. These cells may provide important models to study how normal and malignant cells rearrange lymphocyte receptor genes.

Adult↗

PubMed1999

HLS7, a hemopoietic lineage switch gene homologous to the leukemia-inducing gene MLF1.

Hemopoietic lineage switching occurs when leukemic cells, apparently committed to one lineage, change and display the phenotype of another pathway. cDNA representational difference analysis was used to identify myeloid-specific genes that may be associated with an erythroid to myeloid lineage switch involving the murine J2E erythroleukemic cell line. One of the genes isolated (HLS7) is homologous to the novel human oncogene myeloid leukemia factor 1 (MLF1) involved in the t(3;5)(q25.1;q34) translocation associated with acute myeloid leukemia. Enforced expression of HLS7 in J2E cells induced a monoblastoid phenotype, thereby recapitulating the spontaneous erythroid to myeloid lineage switch. HLS7 also inhibited erythropoietin- or chemically-induced differentiation of erythroleukemic cell lines and suppressed development of erythropoietin-responsive colonies in semi-solid culture. However, intracellular signaling activated by erythropoietin was not impeded by ectopic expression of HLS7. In contrast, HLS7 promoted maturation of M1 monoblastoid cells and increased myeloid colony formation in vitro. These data show that HLS7 can influence erythroid/myeloid lineage switching and the development of normal hemopoietic cells.

Amino Acid Sequence↗

PubMed2000

NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans.

Phylogenetic analyses of non-LTR retrotransposons suggest that all elements can be divided into 11 lineages. The 3 oldest lineages show target site specificity for unique locations in the genome and encode an endonuclease with an active site similar to certain restriction enzymes. The more "modern" non-LTR lineages possess an apurinic endonuclease-like domain and generally lack site specificity. The genome sequence of Caenorhabditis elegans reveals the presence of a non-LTR retrotransposon that resembles the older elements, in that it contains a single open reading frame with a carboxyl-terminal restriction-like endonuclease domain. Located near the N-terminal end of the ORF is a cysteine protease domain not found in any other non-LTR element. The N2 strain of C. elegans appears to contain only one full-length and several 5' truncated copies of this element. The elements specifically insert in the Spliced leader-1 genes; hence the element has been named NeSL-1 (Nematode Spliced Leader-1). Phylogenetic analysis confirms that NeSL-1 branches very early in the non-LTR lineage and that it represents a 12th lineage of non-LTR elements. The target specificity of NeSL-1 for the spliced leader exons and the similarity of its structure to that of R2 elements leads to a simple model for its expression and retrotransposition.

Amino Acid Sequence↗

PubMed2000

Archaic lineages in the history of modern humans.

An important question in the ongoing debate on the origin of Homo sapiens is whether modern human populations issued from a single lineage or whether several, independently evolving lineages contributed to their genetic makeup. We analyzed haplotypes composed of 35 polymorphisms from a segment of the dystrophin gene. We find that the bulk of a worldwide sample of 868 chromosomes represents haplotypes shared by different continental groups. The remaining chromosomes carry haplotypes specific for the continents or for local populations. The haplotypes specific for non-Africans can be derived from the most frequent ones through simple recombination or a mutation. In contrast, chromosomes specific for sub-Saharan Africans represent a distinct group, as shown by principal component analysis, maximum likelihood tree, structural comparison, and summary statistics. We propose that African chromosomes descend from at least two lineages that have been evolving separately for a period of time. One of them underwent range expansion colonizing different continents, including Africa, where it mixed with another, local lineage represented today by a large fraction of African-specific haplotypes. Genetic admixture involving archaic lineages appears therefore to have occurred within Africa rather than outside this continent, explaining greater diversity of sub-Saharan populations observed in a variety of genetic systems.

Africa↗

PubMed2004

Maternal and paternal lineages in cross-breeding bovine species. Has wisent a hybrid origin?

The tribe Bovini comprises cattle and cattle-like species. Reconstructions of their phylogeny have so far been incomplete and have yielded conflicting conclusions about the relationship of American bison and wisent (European bison). We have compared the sequences of three mitochondrial and two Y-chromosomal DNA segments. Mitochondrial DNA indicates that four distinct maternal lineages diverged after an early split-off of the buffalo species, leading to (1) taurine cattle and zebu, (2) wisent, (3) American bison and yak, and (4) banteng, gaur, and gayal, respectively. At a higher level, lineages (1) and (2) and lineages (3) and (4) are probably associated. In contrast, Y-chromosomal sequences indicate a close association of American and European bison, which is in agreement with their morphological similarity, complete fertility of hybrid offspring, and amplified fragment length polymorphism (AFLP) fingerprints of nuclear DNA. One explanation for the anomalous divergence of the mitochondrial DNA from the two bison species is lineage sorting, which implies that two distinct mitochondrial lineages coexisted in the bison-yak branch until the recent divergence of American bison and wisent. Alternatively, the wisent may have emerged by species hybridization initiated by introgression of bison bulls in another ancestral species. This "transpatric" mode of species formation would be consistent with the recent appearance of the wisent in the fossil record without clearly identifiable ancestors.

Animals↗

PubMed2004

A genetic algorithm approach to detecting lineage-specific variation in selection pressure.

The ratio of nonsynonymous (dN) to synonymous (dS) substitution rates, omega, provides a measure of selection at the protein level. Models have been developed that allow omega to vary among lineages. However, these models require the lineages in which differential selection has acted to be specified a priori. We propose a genetic algorithm approach to assign lineages in a phylogeny to a fixed number of different classes of omega, thus allowing variable selection pressure without a priori specification of particular lineages. This approach can identify models with a better fit than a single-ratio model, and with fits that are better than (in an information theoretic sense) a fully local model, in which all lineages are assumed to evolve under different values of omega, but with far fewer parameters. By averaging over models which explain the data reasonably well, we can assess the robustness of our conclusions to uncertainty in model estimation. Our approach can also be used to compare results from models in which branch classes are specified a priori with a wide range of credible models. We illustrate our methods on primate lysozyme sequences and compare them with previous methods applied to the same data sets.

Algorithms↗

PubMed2005

Lineage-specific differences in evolutionary mode in a salamander courtship pheromone.

Functionally equivalent genes may evolve heterogeneously across closely related taxa as a consequence of lineage-specific selective pressures. Such disparate evolutionary modes are especially prevalent in genes that encode postcopulatory reproductive proteins, presumably as a result of sexual selection. We might therefore expect genes that mediate reproduction prior to insemination to evolve in a similar manner. Plethodontid receptivity factor (PRF), a proteinaceous salamander pheromone produced by the male, increases female receptivity during courtship interactions. To test for lineage-specific differences in PRF's evolution, we intensively sampled PRF genes across the eastern Plethodon phylogeny (27 spp.; 34 populations) to compare gene diversification, rates of evolution, modes of selection, and types of amino acid substitution. Our analyses indicate that PRF evolutionary dynamics vary considerably from lineage to lineage. Underlying this heterogeneity, however, are two well-defined transitions in evolutionary mode. The first mode is representative of a typical protein profile, wherein neutral divergence and purifying selection are the dominant features. The second mode is characterized by incessant, cyclical evolution driven by positive selection. In this mode, the positively selected sites are bound by a limited assortment of acceptable amino acids that appear to evolve independently of other sites, resulting in a tremendous number of unique PRF alleles. Several of these selected sites are implicated in receptor binding. These sites are apparently involved in a molecular tango in which the male signal and female receptors coevolve within a confined molecular space. PRF's lineage-specific evolutionary dynamics, in combination with evidence of a molecular tango, highlight the molecular action of sexual selection on a chemical signal that is used during courtship.

Amino Acid Sequence↗

PubMed2025

Snapshot Genomic Surveillance Reveals Insights into Antimicrobial Resistance and Lineage Diversity of Uropathogens in Older Adults in Queensland.

BACKGROUND: Community-acquired urinary tract infections (UTIs) are a significant health concern in older adults. However, few studies have investigated the epidemiology of uropathogens across diverse settings where older adults reside. METHODS: In this study, we whole-genome sequenced urinary isolates of Escherichia coli, Klebsiella species, and Enterobacter cloacae complex collected from individuals aged 70 and over living in the community and residential aged care facilities (RACFs) in Queensland, Australia. We investigated the prevalence of antimicrobial resistance (AMR), pathogen population structure, and transmission dynamics across the settings. RESULTS: E. coli was most frequently identified (82.2%, 447/544), followed by K. pneumoniae (10.8%, 59/544) and E. hormaechei (2.6%, 14/544). Intraspecies lineages were diverse, and a total of 177 sequence types were identified. The three predominant lineages were E. coli ST73 (10.7%, 54/504), ST95 (8.1%, 41/504), and ST131 (5.4%, 27/504). Transmission events were minimal, being identified in 13 patients (2.5%), mainly from the community. The resistance rate to antibiotics was low, with only a small proportion (9.7%) of multidrug-resistant (MDR) isolates. The predominant MDR lineage was E. coli ST131, which carried extended-spectrum beta-lactamase bla CTX-M genes. CONCLUSIONS: Community-acquired UTIs in older adults are predominantly caused by diverse E. coli lineages, with limited evidence of transmission within aged care facilities. The low rates of AMR in the community, along with the absence of strains adapted to a particular setting, suggest that current empiric therapy guidelines remain appropriate. Our prospective genomic surveillance offers valuable insights for monitoring UTIs in this population. It demonstrates the importance of an unbiased approach to accurately capture the prevalence and diversity of uropathogen lineages.

Enterobacteriaceae↗

PubMed1996

Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans.

Relationships among and within baleen and toothed whales were examined using the complete sequence of the mitochondrial cytochrome b gene. Based on parsimony analyses of conservative nucleotide substitutions, five primary evolutionary lineages of extant cetaceans were identified, one represented by baleen whales (Mysticeti) and four represented by odontocetes (toothed whales). Based on the most comprehensive representation of taxa, both cetaceans and artiodactyls, the most parsimonious relationship among the five lineages is (Mysticeti, Odontoceti (Platanistoidea (Physeteroidea (Ziphioidea (Delphinida))))). This relationship, however, is labile and sensitive to ingroup representation and the choice of outgroup. The short nodes among the five cetacean lineages suggest that the divergence among these lineages occurred over a narrow time period, a finding consistent with the limited fossil evidence that indicates a major cetacean radiation 30-34 Mya. The level of divergence among the five cetacean lineages, and that seen between cetaceans and artiodactyls, suggests that cetaceans and artiodactyls had a common ancestor approximately 60 Mya.

Animals↗

PubMed2000

Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites.

Maximum-likelihood models of codon substitution were used to analyze sperm lysin genes of 25 abalone (HALIOTIS:) species to identify lineages and amino acid sites under diversifying selection. The models used the nonsynonymous/synonymous rate ratio (omega = d(N)/d(S)) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio tests suggested significant variation in selective pressure among lineages. The variable selective pressure provided an explanation for the previous observation that the omega ratio is >1 in comparisons of closely related species and <1 in comparisons of distantly related species. Computer simulations demonstrated that saturation of nonsynonymous substitutions and constraint on lysin structure were unlikely to account for the observed pattern. Lineages linking closely related sympatric species appeared to be under diversifying selection, while lineages separating distantly related species from different geographic locations were associated with low evolutionary rates. The selective pressure indicated by the omega ratio was found to vary greatly among amino acid sites in lysin. Sites under potential diversifying selection were identified. Ancestral lysins were inferred to trace the route of evolution at individual sites and to provide lysin sequences for future laboratory studies.

Adaptation, Biological↗

PubMed1993

Mitochondrial phylogeny of the endemic mouthbrooding lineages of cichlid fishes from Lake Tanganyika in eastern Africa.

Of the three cichlid species flocks in eastern Africa, Lake Tanganyika harbors the oldest species assemblage, which is also the most diverse morphologically and behaviorally. For 12 species (20 individuals) of 12 genera of the tribe Ectodini, 852 bp from two segments (cytochrome b and control region) of the mitochondrial genome were sequenced. In addition, orthologous sequences were obtained from eight species (11 individuals) representing other mouthbrooding lineages from Lake Tanganyika. Comparisons of sequence divergences revealed that the single Tanganyikan tribe Ectodini appears to be approximately five times older than the whole Lake Malawi cichlid species flock, suggesting that the radiation of the Tanganyikan mouthbrooding lineages took place long before the species flocks of Lakes Malawi and Victoria evolved. Seven of nine surveyed tribes of Tanganyikan cichlids appear to be approximately equally divergent, and this seems to corroborate the hypothesis of a rapid simultaneous formation of lineages at an early stage in the history of the Lake Tanganyika species flock. The close genetic relationship between the endemic Tropheus lineage and a nonendemic "Haplochromine," Astatotilapia burtoni, indicates that members of the tribe Tropheini may be the sister group of the cichlid flocks of Lakes Malawi and Victoria. The phylogenetic analyses demonstrate the monophyly of the Ectodini and identify the Cyprichromini as their sister group among the Tanganyikan cichlids. Within the tribe Ectodini the molecular data suggest both a branching pattern different than that previously proposed and a subdivision of the Ectodini into four clades, instead of the two originally described. The previously postulated model of morphological transformations believed to be responsible for the drastically different types of ecological specialization found among the Ectodini might therefore be in need of reinterpretation. Characters immediately related to foraging and nutrition seem to be particularly prone to homoplasy, even among members of a single lineage of cichlid fishes.

Africa, Eastern↗

PubMed1995

Male and female mitochondrial DNA lineages in the blue mussel (Mytilus edulis) species group.

In blue mussels of the Mytilus edulis species complex, mitochondrial DNA (mtDNA) inheritance is coupled with gender. Females receive their mother's mtDNA and pass it on to both their daughters and sons. In addition, males receive mtDNA from their father and transmit this male mtDNA to their sons. If this pattern of "doubly uniparental inheritance" is older than the M. edulis species complex, then all members of this group must have two distinct mtDNA lineages: a maternal lineage that is transmitted through females and a paternal lineage that is transmitted through males. To test this hypothesis, we scored mtDNA variation in two taxa in this complex, M. edulis and M. trossulus, by means of restriction fragment profiles of whole-mtDNA genomes and DNA sequence of a region of the cytochrome c oxidase subunit III gene (COIII). The various mitotypes present in these mussels were classified as "male" or "female" based on their gender association and as belonging to M. edulis or M. trossulus based on species-specific allozymes. Both maximum parsimony and neighbor-joining phylogenies based on the COIII sequences grouped female and male mtDNAs into two distinct lineages irrespective of specific origin in accordance with the hypothesis that the origin of these lineages predates the divergence of M. edulis and M. trossulus.

Animals↗

PubMedDate not supplied

Childhood B lineage acute lymphoblastic leukemia clonality study by the polymerase chain reaction.

PURPOSE: B cell precursors acute lymphoblastic leukemia (ALL) present rearrangements in the heavy chain immunoglobulin and T cell receptor genes, especially in the complementarity determining region 3 (CDR-3) and T cell receptor delta (TCR delta) (V delta 2 D delta 3) regions. These rearrangements may be amplified by the polymerase chain reaction (PCR) and used as clonal markers of B lineage ALL. Our purpose was to study clonality at the DNA level by PCR in B lineage ALL. PATIENTS AND METHODS: Fifty-three pediatric patients (36 with B lineage ALL, 7 with ALL-T, and 10 with nonlymphocytic disease) were investigated using consensus primers for the CDR-3 regions of IgH and TCR delta. RESULTS: Clonality was detected in 86.1% of the patients with B lineage ALL when the primers for the CDR-3 regions were used, in 41.6% when the primers for TCR delta were used, and in 91.6% when the two primers were used together. Biclonality was found in 22.5% and 6.6% of patients that have shown clonality for CDR-3 and TCR delta, respectively. Clonality was not detected in any other samples using these primers. CONCLUSIONS: PCR using CDR-3 and TCR delta primers can be used as an aid for B lineage ALL diagnosis and clonal evolution of theses disease.

Burkitt Lymphoma↗

PubMed2004

Ancient wolf lineages in India.

All previously obtained wolf (Canis lupus) and dog (Canis familiaris) mitochondrial (mt) DNA sequences fall within an intertwined and shallow clade (the 'wolf-dog' clade). We sequenced mtDNA of recent and historical samples from 45 wolves from throughout lowland peninsular India and 23 wolves from the Himalayas and Tibetan Plateau and compared these sequences with all available wolf and dog sequences. All 45 lowland Indian wolves have one of four closely related haplotypes that form a well-supported, divergent sister lineage to the wolf-dog clade. This unique lineage may have been independent for more than 400,000 years. Although seven Himalayan wolves from western and central Kashmir fall within the widespread wolf-dog clade, one from Ladakh in eastern Kashmir, nine from Himachal Pradesh, four from Nepal and two from Tibet form a very different basal clade. This lineage contains five related haplotypes that probably diverged from other canids more than 800,000 years ago, but we find no evidence of current barriers to admixture. Thus, the Indian subcontinent has three divergent, ancient and apparently parapatric mtDNA lineages within the morphologically delineated wolf. No haplotypes of either novel lineage are found within a sample of 37 Indian (or other) dogs. Thus, we find no evidence that these two taxa played a part in the domestication of canids.

Animals↗

PubMed2007

Emergence of recent echovirus 30 lineages is marked by serial genetic recombination events.

In an earlier report, different variants of echovirus 30 (E-30), an enterovirus serotype, were identified during two outbreaks in 1997 and 2000. Here, the diversity of E-30 was investigated over a longer period (1991-2005) and the variations in four genomic segments were determined in 52 isolates involved in meningitis cases, to characterize the evolutionary processes underlying the emergence of lineages. Phylogenetic analysis of the VP1 sequences showed that five phylogenetic variants succeeded one another. When a partial 3CD segment was examined, the five variants split further into 10 lineages. Phylogenetic groupings observed with both the VP1 and 3CD sequences were clearly related to the calendar time of virus isolation. The rapid turnover of lineages during the study period was not associated with variations in amino acid residues in either the VP1 or the 3CD sequences, indicating major evolutionary contraints in E-30. The variation patterns were examined further along a subgenomic segment of 4878 nt in 13 virus isolates, representative of the 10 lineages. Breakpoints detected in the similarity profiles were investigated by bootscanning and maximum-likelihood phylogenetic analysis of virus genes. Evidence of several past recombination events was observed in the middle of the genome and predicted recombination crossover sites were mapped with precision. The contribution of recombination to the evolution of E-30 is substantial. It is associated tightly with the emergence of new genetic lineages and certain recombinants have undergone epidemic spread.

Enterovirus B, Human↗

PubMed2025

Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.

Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational framework that jointly models gene expression and clonotype information to infer cell state transitions and fate biases with higher fidelity. While motivated by challenges in analyzing T cell populations, especially in the tumor microenvironment and immunotherapy settings, Clonotrace is broadly applicable to any lineage-barcoded single-cell dataset. Across diverse systems including T cells, hematopoietic differentiation, and cancer therapy resistance models, Clonotrace reveals differentiation hierarchies, distinguishes unipotent from multipotent states, and identifies candidate fate-determining genes driving lineage commitment.

Journal Article↗