Search PubMed⌕ Search

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.

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

At least 163 records · Page 9Linked to original sources

Postglacial colonization of Northern Europe by distinct phylogeographic lineages of the bullhead, Cottus gobio.

Three major phylogeographic lineages of the cottid fish Cottus gobio (bullhead) were identified in northern Europe from mitochondrial DNA sequences and allozyme data. The largely separate freshwater distributions of the lineages demonstrate distinct postglacial colonization histories. West of the Baltic Sea, Swedish lakes were invaded from the southwest (Germany). Another, eastern lineage has colonized the inland waters northeast and east of the Baltic, from refugia in northwest Russia; this lineage comprises a distinct subgroup found only from Estonia. The third lineage, found south and southeast of the Baltic, probably descended from rivers draining to the Black Sea from the north (e.g. Dnepr). In coastal waters of the Baltic Sea, and in near-coast inland waters, the lineages are now found intermixed in various combinations. The alternating fresh- and saltwater phases of the Baltic basin have variously enabled and disabled the use of coastal waters as colonization routes. Hypotheses on the chronology of dispersal and lineage mixing can be based on the distribution of the marker genes and the paleohydrographical record. The diversity of the Fennoscandian bullhead thus comprises anciently diverged (probably mid-Pleistocene) refugial lineages that in their freshwater range constitute distinct evolutionarily significant units. The thorough mixing of the various genomic origins in and around the Baltic, however, refutes the controversial view of distinct species status for the western and eastern ('Cottus koshewnikowi') bullheads. The postglacial contact of the lineages has created new diversity that cannot be interpreted in a conventional hierarchical framework of taxonomic or conservation units.

Animals↗

Clonal chromosomal abnormalities showing multiple-cell-lineage involvement in acute myeloid leukemia.

To determine whether one or more hematopoietic-cell lineages are involved in acute myeloid leukemia (AML), we designed a technique that simultaneously identifies a cell as malignant and determines its lineage. We used numerical clonal chromosomal abnormalities, which are readily detected, to indicate neoplasia, and monoclonal antibodies in an alkaline phosphatase-antialkaline phosphatase detection procedure to identify lineages as granulocytic-monocytic, erythrocytic, or megakaryocytic. Examination of bone marrow from 12 patients with AML showed metaphases of granulocytic-monocytic lineage with abnormal karyotypes in all patients. In seven patients, we also detected abnormal karyotypes in the erythrocytic or megakaryocytic lineage. In all four patients with monosomy 7, both granulocytic-monocytic and erythrocytic cells were affected. Two of four patients with trisomy 8 also had evidence of multiple-lineage involvement, but in two the erythrocytic lineage had normal karyotypes, suggesting an origin at a progenitor-cell stage committed to granulocytic-monocytic development. Multiple-lineage involvement was found in AML both arising de novo (four of five analyzable cases) and following another cancer (three of four analyzable cases). These data demonstrate multiple-lineage involvement in a high proportion of cases of AML and suggest that many cases originate from the multipotent hematopoietic cell or from an earlier progenitor cell.

Adult↗

Degree of selective constraint as an explanation of the different rates of evolution of gender-specific mitochondrial DNA lineages in the mussel mytilus.

Mussels of the genus Mytilus segregate for a maternally transmitted F lineage and a paternally transmitted M lineage of mitochondrial DNA. Previous studies demonstrated that these lineages are older than the species of the M. edulis complex and that the M lineage evolves faster than the F lineage. Here we show that the latter observation also applies to a region of the molecule with no assigned function. Sequence data for the mitochondrial COIII gene and the "unassigned" region of the F and M lineages of M. edulis and M. trossulus are used to evaluate various hypotheses that may account for the faster rate of evolution of the M lineage. Tests based on the proportion of synonymous and nonsynonymous substitutions suggest that the M lineage experiences relatively relaxed selection. Further support for this hypothesis comes from an examination of COIII amino acid substitutions at sites defined as either conserved or variable based on the pattern of variation in other mollusks and Drosophila. Most substitutions in the M lineage occur in regions that are also variable among non-Mytilus taxa. We suggest that these differences in selection pressure are a consequence of doubly uniparental mitochondrial DNA transmission in Mytilus.

Amino Acid Sequence↗

Virulence and cord blood mononuclear cells cytokine production induced by perinatal listeria monocytogenes strains from different phylogenetic lineages.

Some of the phylogenetic lineages of Listeria monocytogenes are more likely to cause invasive disease in humans than are strains from other phylogenetic lineages. This suggests that strains belonging to these lineages display different levels of pathogenicity. To investigate this, we carried out a plaque-forming assay with HT-29 cells to evaluate the virulence of six perinatal strains from the three lineages that compose the species. All of the strains were largely over the 3.34 cutoff (between 4.29 and 5.97 mean log) with the HT-29 model and can therefore be considered to be equally virulent. We also explored part of the immune response of cord blood mononuclear cells by measuring cytokine production. All strains induced the production of similar amounts of TNF-alpha and IL-1beta. High concentrations of IL-6 and IL-8 were produced (between 6,000 and 17,000 pg/ml), whereas little or no IFN-gamma or IL-12 was produced. Thus, there is no difference between the strains from the three genetic lineages in terms of virulence or cytokine response. Given the epidemiological distribution of the serotypes responsible for human listeriosis and the genetic structure of the L. monocytogenes species, our results suggest: (i) that all strains from lineage I (serotypes 1/2b and 4b), a genetically homogeneous subpopulation, have a similar level of pathogenicity, and (ii) that lineage II (serotypes 1/2a and 1/2c), which is genetically more heterogeneous, is composed of strains with different levels of pathogenicity. The ones responsible for invasive diseases, particularly perinatal infections, display a similar level of pathogenicity to lineage-I strains and are not virulence-attenuated strains that can only infect the most immunocompromised hosts, whereas the other lineage-II strains are probably less pathogenic for humans.

Cytokines↗

Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data.

Beginning in early 2021, unique and highly divergent lineages of SARS-CoV-2 were sporadically found in wastewater sewersheds using a sequencing strategy focused on amplifying the most rapidly evolving region of SARS-CoV-2, the receptor binding domain (RBD). Because these RBD sequences did not match known circulating strains and their source was not known, we termed them "cryptic lineages". To date, more than 20 cryptic lineages have been identified using the RBD-focused sequencing strategy. Here, we identified and characterized additional cryptic lineages from SARS-CoV-2 wastewater sequences submitted to NCBI's Sequence Read Archives (SRA). Wastewater sequence datasets were screened for individual sequence reads that contained combinations of mutations frequently found in cryptic lineages but not contemporary circulating lineages. Using this method, we identified 18 cryptic lineages that appeared in multiple (2-81) samples from the same sewershed, including 12 that were not previously reported. Partial consensus sequences were generated for each cryptic lineage by extracting and mapping sequences containing cryptic-specific mutations. Surprisingly, seven of the mutations that appeared convergently in cryptic lineages were reversions to sequences that were highly conserved in SARS-CoV-2-related enteric bat Sarbecoviruses. The apparent reversion to bat Sarbecovirus sequences is consistent with the notion that SARS-CoV-2 adaptation to replicate efficiently in respiratory tissues preceded the COVID-19 pandemic.

SARS-CoV-2↗

High lineage diversity and host sharing of malarial parasites in a local avian assemblage.

Bird populations often have high prevalences of the haemosporidians Haemoproteus spp. and Plasmodium spp., but the extent of host sharing and host switching among these parasite lineages and their avian hosts is not well known. While sampling within a small geographic region in which host individuals are likely to have been exposed to the same potential parasite lineages, we surveyed highly variable mitochondrial DNA from haemosporidians isolated from 14 host taxa representing 4 avian families (Hirundinidae, Parulidae, Emberizidae, and Fringillidae). Analyses of cytochrome b sequences from 83 independent infections identified 29 unique haplotypes, representing 2 well-differentiated Haemoproteus spp. lineages and 6 differentiated Plasmodium spp. lineages. A phylogenetic reconstruction of relationships among these lineages provided evidence against host specificity at the species and family levels, as all haemosporidian lineages recovered from 2 or more host individuals (2 Haemoproteus and 3 Plasmodium lineages) were found in at least 2 host families. We detected a similar high level of host sharing; the 3 most intensively sampled host species each harbored 4 highly differentiated haemosporidian lineages. These results indicate that some Haemoproteus spp. and Plasmodium spp. lineages exhibit a low degree of host specificity, a phenomenon with implications for ecological and evolutionary interactions among these parasites and their hosts.

Animals↗

Brood production and lineage discrimination in the red harvester ant (Pogonomyrmex barbatus).

In contrast to the system of caste determination in most social insects, reproductive caste determination in some populations of Pogonomyrmex barbatus has a genetic basis. Populations that exhibit genetic caste determination are segregated into two distinct, genetic lineages. Same-lineage matings result in female reproductives, while inter-lineage matings result in workers. To investigate whether founding P. barbatus queens lay eggs of reproductive genotype, and to determine the fate of those eggs, we genotyped eggs, larvae, and pupae produced by naturally inseminated, laboratory-raised queens. We show that founding dependent lineage queens do lay eggs of reproductive genotype, and that the proportion of reproductive genotypes decreases over the course of development from eggs to larvae to pupae. Because queens must mate with a male of each lineage to produce both workers and female reproductives, it would benefit queens to be able to distinguish males of the two lineages. Here we show that P. barbatus males from the two genetic lineages differ in their cuticular hydrocarbon profiles. Queens could use male cuticular hydrocarbons as cues to assess the lineage of males at the mating aggregation, and possibly keep mating until they have mated with males of both lineages.

Animal Communication↗

Improved clinical outcome for children with T-lineage acute lymphoblastic leukemia after contemporary chemotherapy: a Children's Cancer Group Study.

The prognostic importance of T-lineage acute lymphoblastic leukemia (ALL) in contemporary programs of intensive chemotherapy has been controversial. We therefore assessed the impact of this biological feature in risk-adjusted frontline chemotherapy studies of the Children's Cancer Group (CCG), conducted from 1983 to 1994. A substantially greater proportion of T-lineage patients (N = 730) presented with poor-risk features as compared to B-lineage patients (N = 3668) treated in the same studies (71.1% vs. 39.7%, P < 0.0001). Consequently, in the CCG-100 series of clinical trials (1983-1989), which tested regimens that were largely of moderate intensity, T-lineage ALL patients had an excess of adverse early events compared to patients in the B-lineage group: 3-year event-free survival (EFS) estimate, 65.8% vs 78.2% (P < 0.0001). With the introduction of more intensive chemotherapy in studies from 1989 to 1994 (CCG-1800 series). We observed a progressive and significant improvement in the clinical outcome of patients with T-lineage immunophenotype. Three- and 5-year EFS probabilities increased from 65.8% to 78.1% and from 61.0% to 75.2%, respectively, becoming comparable to or slightly better than results for B-lineage ALL patients. When adjusted for the competing effects of leukocyte count, age, organomegaly and other poor-risk features, T-lineage immunophenotype showed no important impact on the overall EFS pattern. These findings demonstrate the loss of adverse prognostic by T-lineage ALL in a large program of intensive chemotherapy developed over the past decade.

Adolescent↗

The importance of maternal lineage on milk yield traits of dairy cattle.

Maternal lineage effects on milk yield traits, considered indicative of cytoplasmic inheritance, were evaluated with animal models. Cattle were from a selection experiment begun in 1968. Maternal pedigrees were traced to the first female member in the Holstein-Friesian Herdbook; purchased cows entering the herd, considered foundation females, were assigned to maternal lineage groups. All models accounted for year-season of calving, parity, and selection lines. Maternal lineage effects were included in a repeated records model with cow effects and preadjustment for sire and maternal grandsire transmitting abilities. Maternal lineage accounted for 5.2, 4.1, and 10.5% of phenotypic variation of preadjusted records of milk yield, fat yield, and fat percentage, respectively. Maternal lineage was evaluated as a fixed effect in an animal model including random animal and permanent environmental effects. Maternal lineage significantly affected fat percentage but not milk yield. Maternal genetic (nuclear) effects and their covariance with additive animal effects did not significantly account for additional variation nor did they influence maternal lineage estimates. Maternal lineage affected calculated net energy of milk but was not important for SNF yield or concentration. Maternal lineage influenced fat percentage, energy concentration, and, to a lesser extent, fat yield in milk of dairy cattle.

Animals↗

[Relationship between genetic lineage and pathotype of Pyricularia grisea in Yunnan Plateau].

Rice blast caused by Pyricularia grisea is the most destructive disease in Yunnan Plateau, China. In order to elucidate the relationship between genetic lineage and pathotype of P. grisea of Yunnan Plateau as well as the variability of the fungus at DNA level,the repetitive element-based PCR (rep-PCR) of Pot2, an element found in approximately 100 copies in the fungus genome,was exploited. Two hundred and thirty-six isolates of P. grisea collected from 15 main rice-growing counties of Yunnan Plateau were fingerprinted by using rep-PCR. A linkage graph of the rep-PCR fingerprints from 134 representative isolates was generated using an unweighted pair-grouped average program (UPGMA) of the STATISTICAL 5.0 software. The isolates were classified into 8 genetic lineages (G1 approximately G8) at the level of 1.75 genetic linkage distance, of which the G1, G2 and G4 were the dominant lineages. The isolates in a certain area generally belonged to one correspondent genetic lineage and the isolates from the same plot and host rice variety mostly shared one linkage group though different genetic lineages within one lesion. Furthermore, 29 isolates representing the eight genetic lineages were inoculated on 33 rice cultivars of Yunnan at the stage of 3 approximately 4 leaves in greenhouse. The isolates were divided into 6 pathotype groups (P1 approximately P6) according to its compatibility, which demonstrated that some isolates of one genetic lineage sharing two or three pathotype groups, alternatively, one or four pathotype groups. The isolates from each genetic lineage, however, may share one pathotype group such as P2. The preliminary results implicated that the relationship between genetic lineages and pathotype groups of P. grisea in Yunnan Plateau was complicated rather than simple. On the other hand,2 rice cultivars including HeXi 16 and JingGuo 92 were resistant to the 29 isolates but YunJing 20 and HeXi 30 both susceptible to all of them, which was helpful for deploying the blast-resistant genes in rice production of Yunnan Plateau. Therefore, the rice blast-resistance spectrum of the tentative new rice cultivars should be evaluated before its release considering the blast-resistant rice breeding and the practice of rice production in Yunnan Plateau.

Ascomycota↗

Geographic ranges, population structure, and ages of sexual and parthenogenetic snail lineages.

Asexual reproduction is thought to doom organisms to extinction due to mutation accumulation and parasite exploitation. Theoretical models suggest that parthenogens may escape the negative effects of conspecifics and biological enemies through escape in space. Through intensive sequencing of a mitochondrial DNA (mtDNA) and a nuclear intron locus in sexual and parthenogenetic freshwater snails (Campeloma), I examine three questions: (1) Are sexual mtDNA lineages more restricted geographically than parthenogenetic mtDNA lineages? (2) Are independent parthenogenetic lineages shorter lived than sexual lineages? and (3) Do parthenogens have higher intraindividual nuclear sequence diversity and form well-differentiated monophyletic groups as expected under the Meselson effect? Geographic ranges of parthenogenetic lineages are significantly larger than geographic ranges of sexual lineages. Based on coalescence times under different demographic assumptions, asexual lineages are short lived, but there is variation in clonal ages. Although alternative explanations exist, these results suggest that asexual lineages may persist in the short term through dispersal, and that various constraints may cause geographic restriction of sexual lineages. Both allotriploid and diploid Campeloma parthenogens have significantly higher allelic divergence within individuals, but show limited nuclear sequence divergence from sexual ancestors. In contrast to previous allozyme evidence for nonhybrid origins of diploid Campeloma parthenogens, cryptic hybridization may account for elevated heterozygosity.

Aging↗

mtDNA variation in the Yanomami: evidence for additional New World founding lineages.

Native Americans have been classified into four founding haplogroups with as many as seven founding lineages based on mtDNA RFLPs and DNA sequence data. mtDNA analysis was completed for 83 Yanomami from eight villages in the Surucucu and Catrimani Plateau regions of Roraima in northwestern Brazil. Samples were typed for 15 polymorphic mtDNA sites (14 RFLP sites and 1 deletion site), and a subset was sequenced for both hypervariable regions of the mitochondrial D-loop. Substantial mitochondrial diversity was detected among the Yanomami, five of seven accepted founding haplotypes and three others were observed. Of the 83 samples, 4 (4.8%) were lineage B1, 1 (1.2%) was lineage B2, 31 (37.4%) were lineage C1, 29 (34.9%) were lineage C2, 2 (2.4%) were lineage D1, 6 (7.2%) were lineage D2, 7 (8.4%) were a haplotype we designated "X6," and 3 (3.6%) were a haplotype we designated "X7." Sequence analysis found 43 haplotypes in 50 samples. B2, X6, and X7 are previously unrecognized mitochondrial founding lineage types of Native Americans. The widespread distribution of these haplotypes in the New World and Asia provides support for declaring these lineages to be New World founding types.

Adult↗

Asymmetrical lymphoid and myeloid lineage commitment in multipotent hematopoietic progenitors.

The mechanism of lineage commitment from hematopoietic stem cells (HSCs) is not well understood. Although commitment to either the lymphoid or the myeloid lineage is popularly viewed as the first step of lineage restriction from HSCs, this model of hematopoietic differentiation has recently been challenged. The previous identification of multipotent progenitors (MPPs) that can produce lymphocytes and granulocyte/macrophages (GMs) but lacks erythroid differentiation ability suggests the existence of an alternative HSC differentiation program. Contribution to different hematopoietic lineages by these MPPs under physiological conditions, however, has not been carefully examined. In this study, we performed a refined characterization of MPPs by subfractionating three distinct subsets based on Flt3 and vascular cell adhesion molecule 1 expression. These MPP subsets differ in their ability to give rise to erythroid and GM lineage cells but are equally potent in lymphoid lineage differentiation in vivo. The developmental hierarchy of these MPP subsets demonstrates the sequential loss of erythroid and then GM differentiation potential during early hematopoiesis. Our results suggest that the first step of lineage commitment from HSCs is not simply a selection between the lymphoid and the myeloid lineage.

Animals↗

The order of expression of transcription factors directs hierarchical specification of hematopoietic lineages.

The mechanism of lineage specification in multipotent stem cells has not been fully understood. We recently isolated progenitors with the eosinophil, basophil, or mast cell lineage potential, all of which originate from granulocyte/monocyte progenitors (GMPs). By using these prospectively purified progenitors, we show here that the expression timing of GATA-2 and CCAAT enhancer-binding protein alpha (C/EBPalpha) can differentially control their lineage commitment. The expression of GATA-2 instructed C/EBPalpha-expressing GMPs to commit exclusively into the eosinophil lineage, while it induced basophil and/or mast cell lineage commitment if C/EBPalpha was suppressed at the GMP stage. Furthermore, simply by switching the order of C/EBPalpha and GATA-2 transduction, even lymphoid-committed progenitors recaptured these developmental processes to be reprogrammed into each of these lineages. We propose that the order of expression of key transcription factors is critical for their interplay to selectively drive lineage specification programs, by which stem cells could generate multiple lineage cells in a hierarchical manner.

Animals↗

The role of the T-cell receptor (TCR) in alpha beta/gamma delta lineage commitment: clues from intracellular TCR staining.

T cells belong to two mutually exclusive lineages expressing either alpha beta or gamma delta T-cell receptors (TCR). Although alpha beta and gamma delta cells are known to share a common precursor the role of TCR rearrangement and specificity in the lineage commitment process is controversial. Instructive lineage commitment models endow the alpha beta or gamma delta TCR with a deterministic role in lineage choice, whereas separate lineage models invoke TCR-independent lineage commitment followed by TCR-dependent selection and maturation of alpha beta and gamma delta cells. Here we review the published data pertaining to the role of the TCR in alpha beta/gamma delta lineage commitment and provide some additional information obtained from recent intracellular TCR staining studies. We conclude that a variant of the separate lineage model is best able to accommodate all of the available experimental results.

Animals↗

Genomic variability within an organism exposes its cell lineage tree.

What is the lineage relation among the cells of an organism? The answer is sought by developmental biology, immunology, stem cell research, brain research, and cancer research, yet complete cell lineage trees have been reconstructed only for simple organisms such as Caenorhabditis elegans. We discovered that somatic mutations accumulated during normal development of a higher organism implicitly encode its entire cell lineage tree with very high precision. Our mathematical analysis of known mutation rates in microsatellites (MSs) shows that the entire cell lineage tree of a human embryo, or a mouse, in which no cell is a descendent of more than 40 divisions, can be reconstructed from information on somatic MS mutations alone with no errors, with probability greater than 99.95%. Analyzing all approximately 1.5 million MSs of each cell of an organism may not be practical at present, but we also show that in a genetically unstable organism, analyzing only a few hundred MSs may suffice to reconstruct portions of its cell lineage tree. We demonstrate the utility of the approach by reconstructing cell lineage trees from DNA samples of a human cell line displaying MS instability. Our discovery and its associated procedure, which we have automated, may point the way to a future "Human Cell Lineage Project" that would aim to resolve fundamental open questions in biology and medicine by reconstructing ever larger portions of the human cell lineage tree.

Animals↗

Transcriptional profiling of human hematopoiesis during in vitro lineage-specific differentiation.

To better understand the transcriptional program that a ccompanies orderly lineage-specific hematopoietic differentiation, we performed serial oligonucleotide microarray analysis of human normal CD34+ bone marrow cells during lineage-specific differentiation. CD34+ bone marrow cells isolated from healthy individuals were selectively stimulated in vitro with the cytokines erythropoietin (EPO), thrombopoietin (TPO), granulocyte colony-stimulating factor (G-CSF), and granulocyte macrophage colony-stimulating factor (GM-CSF). Cells from each of the lineages were harvested after 4, 7, and 11 days of culture for expression profiling. Gene expression was analyzed by oligonucleotide microarrays (HG-U133A; Affymetrix, Santa Clara, CA). Experiments were done in triplicates. We identified 258 genes that are consistently upregulated or downregulated during the course of lineage-specific differentiation within each specific lineage (horizontal change). In addition, we identified 52 genes that contributed to a specific expression profile, yielding a genetic signature specific for successive stages of differentiation within each of the three lineages. Analysis of horizontal changes selected 21 continuously upregulated genes for EPO-induced differentiation (including GTPase activator proteins RAP1GA1 and ARHGAP8, which regulate small Rho GTPases), 21 for G-CSF-induced/GM-CSF-induced differentiation, and 91 for TPO-induced differentiation (including DLK1, of which the role in normal hematopoiesis is not defined). During the lineage-specific differentiation, 58 (erythropoiesis), 30 (granulopoiesis), and 37 (thrombopoiesis) genes were significantly downregulated, respectively. The expression of selected genes was confirmed by real-time polymerase chain reaction. Our data encompass the first extensive transcriptional profile of human hematopoiesis during in vitro lineage-specific differentiation.

Antigens, CD34↗

Role for transcription Pax5A factor in maintaining commitment to the B cell lineage by selective inhibition of granulocyte-macrophage colony-stimulating factor receptor expression.

During early B lymphopoiesis, developing B cells maintain lineage commitment despite the local presence of myeloid lineage-promoting cytokines such as GM-CSF and IL-3. Previous observations suggest that the B cell-specific transcription factor Pax5A (paired box 5A transcription factor) plays a role in maintaining B cell lineage commitment by limiting expansion and survival of early IL-3/GM-CSF-dependent myeloid lineage cells. To define a mechanism by which Pax5A can exert these inhibitory effects on myeloid lineage differentiation, an inducible form of the Pax5A protein was expressed in the myeloid cell line FDC-P1. This cell line models myeloid progenitors in that it responds to the survival and growth-potentiating effects of IL-3 and GM-CSF. We observed that enforced expression of Pax5A selectively suppressed proliferation in response to GM-CSF, but not IL-3. This effect was associated with specific down-regulation of GM-CSFR alpha-chain, but not beta-chain expression. These data provide a molecular mechanism to enforce commitment to the B cell lineage despite the presence of GM-CSF, a factor that has been shown to convert early developing B cells to the myeloid lineage. Furthermore, they indicate a role for B cell Pax5A expression in maintaining rather than directing commitment to the B cell lineage.

Animals↗