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Alpha beta lineage-specific expression of the alpha T cell receptor gene by nearby silencers.

T cells expressing either the alpha beta or gamma delta antigen receptor (TCR) are distinct cell lineages. The single locus encoding the TCR alpha and delta genes requires special regulation to avoid alpha gene expression in gamma delta T cells. We show here that the minimal alpha enhancer is active in the gamma delta T cell lineage but gains alpha beta lineage specificity through negative cis-acting elements 3' of the C alpha gene that silence the enhancer in gamma delta T cells. The negative elements at the C alpha locus consist of several silencers that work in an orientation- and distance-independent fashion. These silencers also act on a retroviral enhancer that is normally ubiquitously expressed, restricting its activity to alpha beta cells. The alpha silencers are active in non-T cell lines, suggesting that the decision of a cell to differentiate into the alpha beta T cell lineage may involve specific relief from these silencers. Silencers are likely to be as important as enhancers in establishing lineage-specific gene expression in many systems.

Animals↗

Cell lineage involvement in four patients with myelodysplastic syndrome and t(1;7) or trisomy 8 studied by simultaneous immunophenotyping and fluorescence in situ hybridization.

Four patients with myelodysplastic syndrome (MDS), one with t(1;7) and three with trisomy 8, were studied by immunophenotyping and fluorescence in situ hybridization (FISH) to assess cell lineage involvement. The t(1;7) was detected using a biotin-labeled chromosome 1 centromere-specific DNA probe. This aberration was present in CD34-positive stem cells, the erythroid cell lineage (GPA+), and the granulocytic/monocytic (CD13+ and CD64+) cell lineages. We were not able to demonstrate the abnormality in the lymphoid cell lineages. In the patients with trisomy 8, the aberration was detected with chromosome 8 centromere-specific DNA probe or by chromosome in situ suppression hybridization (CISS) with a chromosome 8-specific library probe. The trisomy was detected in stem cells, erythroid precursor cells, megakaryocytes, and granulocytes/monocytes. In these MDS patients, the chromosome aberrations appear to occur only in cells of myeloid lineage.

Aged↗

Thermal sensitivity and thermal tolerance of human B-lineage acute lymphoblastic leukemia (ALL) cells.

The thermal sensitivities of four B-cell precursor acute lymphoblastic (ALL) cell lines (REH and KM-3 = pre pre B-ALL; NALM-6 and HPB-NULL = pre B-ALL), and 1 B-cell ALL (NAMALWA) cell line were studied and compared to the thermal sensitivity of the T-lineage ALL cell line MOLT-3 using an in vitro clonogenic assay system by limiting dilution. B-lineage ALL cells were as sensitive to hyperthermia as were T-lineage ALL cells. D0 values at 42 degrees C ranged from 44.9 min (NALM-6) to 85.6 min (NAMALWA), D0 values at 43 degrees C ranged from 15.3 min (NALM-6) to 35.7 min (KM-3), and D0 values at 44 degrees C ranged from 11.1 min (NALM-6) to 23.8 min (HPB-NULL). By comparison, the D0 values of MOLT-3 cells were 95.1 min at 42 degrees C, 23.8 min at 43 degrees C, and 14.7 min at 44 degrees C. The maximum log kill values which were observed ranged from 0.8 log (KM-3 and HPB-NULL) to 1.3 logs (NALM-6) at 42 degrees C, from 1.4 logs (KM-3) to 4.2 logs (NALM-6) at 43 degrees C, and from 3.8 logs (HPB-NULL) to 4.8 logs (NALM-6) at 44 degrees C. A thermal tolerant plateau was observed in the hyperthermia survival curves of REH, NALM-6, and HPB-NULL cells, providing circumstantial evidence that thermal tolerance may develop in some B-cell precursor ALL cells after 90-120 min of continuous heating. In contrast, no thermal tolerant plateau was observed in the hyperthermia survival curves of pre-pre-B-ALL/KM-3 B-cell ALL/NAMALWA or T-lineage ALL/MOLT-3 cells. The kinetics of development and decay of thermotolerance was studied for NALM-6 cells. Thermotolerance after a priming heat exposure to 42 degrees C for 30 min was maximum at 8 hr with a maximum thermotolerance ratio of 2.0, and it decayed by 24 hr. These findings extend previous studies on the thermal sensitivity of human leukemia cells and provide new information on the thermal sensitivity and thermotolerance of B-lineage ALL cells.

B-Lymphocytes↗

huckebein is required for glial development and axon pathfinding in the neuroblast 1-1 and neuroblast 2-2 lineages in the Drosophila central nervous system.

huckebein encodes a predicted zinc finger transcription factor which is transiently expressed in a subset of Drosophila central nervous system precursors (neuroblasts (NBs)). We used DiI cell lineage tracing and cell fate markers to investigate the role of huckebein in the NB 1-1 and NB 2-2 cell lineages. Loss of huckebein does not switch these NBs into different NB fates, nor does it change the number of cells in their lineages; rather, it is required for glial development in the NB 1-1 lineage, and for axon pathfinding of a subset of interneurons and motoneurons in both lineages.

Animals↗

In-vitro models of B-lineage commitment.

The development of mature B lymphocytes from multipotent progenitors follows a pathway of differentiation marked by a progressive restriction in lineage options. The requirements for progression through the B lineage developmental pathway have been investigated intensively and a number of critical components of the differentiation process have been identified. However, the genetic basis for lineage determination remains unresolved. Recently, a number of in-vitro assays have been established which support the development of committed B cell progenitors from multipotent cells. These assays have provided a novel system in which the process of B lineage commitment can be followed and manipulated. In this review we present a model of B-lineage progression from multipotent progenitors to committed B-cell progenitors and discuss potential mediators of the commitment process.

Animals↗

High variability of Colombian Trypanosoma cruzi lineage I stocks as revealed by low-stringency single primer-PCR minicircle signatures.

In Colombia, high genetic variability has been found among Trypanosoma cruzi stocks isolated from different vector and host species, using isoenzyme analysis and RFLP of total kinetoplastid DNA (kDNA), suggesting that several genetically related T. cruzi populations might be present within a single geographical area or adjacent ones. The objective of this study was to use the low-stringency single primer (LSSP)-PCR technique on variable regions of kDNA minicircles of T. cruzi to determine possible genetic relationships among stocks from distinct geographical regions of Colombia and different vector species and hosts. Although LSSP-PCR analysis showed a high genetic variability among 30 Colombian T. cruzi stocks, 29 of them belonged to T. cruzi lineage I, confirming that this lineage is predominant in different vector and host species from Colombia. Interestingly, one stock isolated from a Pastrongylus geniculatus bug was identified as T. cruzi lineage IIb, using PCR strategies targeted to the intergenic region of miniexon genes, a sequence encoding the D7 domain of the 24salpha ribosomal genes and the A10 fragment, being this finding, the first description of this lineage in Colombia. The LSSP-PCR signatures allowed correlation of most isolates with their respective geographical origins, and in one case from host and vector specimens at a same region, suggesting a transmission event. Moreover, variations in LSSP-PCR profiles among T. cruzi I stocks from a same region suggest that they may have a multiclonal character. Our results show that LSSP-PCR is a fast, valuable technique for characterization of intra-lineage polymorphism among T. cruzi stocks.

Animals↗

Regional genomic analysis of lineage distribution and transferable multidrug resistance among chicken-associated Salmonella Kentucky isolates in China.

Salmonella enterica serovar Kentucky is an important multidrug-resistant foodborne pathogen in the poultry meat supply chain. Although recent broader genomic studies have elucidated the population structure and epidemiological significance of major lineages in China (e.g., ST198 and ST314), the regional dynamics within local poultry supply chains remain insufficiently characterized. In this study, 31 chicken meat-derived isolates from Shanghai and 39 publicly available genomes from China were analyzed using antimicrobial susceptibility testing, whole-genome sequencing, phylogenetic analysis, conjugation experiments, and complete sequencing of representative plasmids. This enabled a systematic characterization of the molecular epidemiological features of the population and the mechanisms underlying resistance dissemination. Population genomic analysis revealed a lineage composition markedly different from the global epidemiological pattern: ST314 was the predominant sequence type among the Shanghai chicken-derived isolates (74.2%), whereas the internationally recognized high-risk clone ST198 accounted for only 25.8% of the local isolates. However, risk stratification analysis indicated that although ST198 was detected less frequently, it carried a significantly greater burden of acquired resistance genes and therefore represented a higher-risk resistant lineage. Functional and structural validation further elucidated the molecular basis of resistance dissemination within this high-risk lineage. Conjugation experiments confirmed the co-transfer of a multidrug resistance module carrying blaTEM-1 and blaCTX-M-267 to the recipient strain Escherichia coli J53. Complete plasmid analysis revealed that these two β-lactam resistance genes were co-localized on a 242-kb transferable plasmid flanked by Tn1331, Tn3, and multiple transposase-associated elements, thereby providing a structural basis for their horizontal transfer. This study provides important molecular epidemiological evidence for lineage-specific surveillance and risk-stratified control of resistant Salmonella in the poultry meat supply chain and further underscores the need for continuous monitoring of mobile genetic elements within a One Health framework.

Animals↗

Characterisation of grass carp (Ctenopharyngodon idellus) MHC class I domain lineages.

In order to characterise grass carp MHC class I (Ctid-MHC I) sequences, 26 Ctid-MHC I genes were cloned from 12 individuals and their alpha domain lineages were analysed. Simultaneously, a quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR) assay was developed to detect Ctid-MHC I tissue-specific expression. The results suggested that Ctid-MHC I could be divided into eight lineages (Ctid-NA-Ctid-NH). Based on whether they contained the motif of eight key amino acids (YYRTKWYY), Ctid-MHC I lineages were divided into two groups [Ctid-MHC I (8(+)) and Ctid-MHC I (8(-))]. The expression analysis showed that the Ctid-MHC I locus/loci appeared in the kidney, gill, intestine, heart, spleen, liver, and brain. A GenBank homology BLAST was performed independently with each alpha domain, and Ctid-MHC I alpha1, alpha2, and alpha3 were categorised into two (V and IX), five (II, IV-VII), and four (IV-VII) domain lineages, respectively. Based on the alphabetic labelling system created in our earlier studies, one alpha1 (IX), four alpha2 (IV-VII), and unique alpha3 (V-VII) domain lineages were observed in grass carp and across the teleostean species.

Amino Acid Sequence↗

Population structure within lineages of Wheat streak mosaic virus derived from a common founding event exhibits stochastic variation inconsistent with the deterministic quasi-species model.

Structure of Wheat streak mosaic virus (WSMV) populations derived from a common founding event and subjected to serial passage at high multiplicity of infection (MOI) was evaluated. The founding population was generated by limiting dilution inoculation. Lineages of known pedigree were sampled at passage 9 (two populations) and at passage 15, with (three populations) or without mixing (four populations) of lineages at passage 10. Polymorphism within each population was assessed by sequencing 17-21 clones containing a 1371 nt region (WSMV-Sidney 81 nts 8001-9371) encompassing the entire coat protein cistron and flanking regions. Mutation frequency averaged approximately 5.0 x 10(-4)/nt across all populations and ranged from 2.4 to 11.6 x 10(-4)/nt within populations, but did not consistently increase or decrease with the number of passages removed from the founding population. Shared substitutions (19 nonsynonymous, 10 synonymous, and 3 noncoding) occurred at 32 sites among 44 haplotypes. Only four substitutions became fixed (frequency = 100%) within a population and nearly one third (10/32) never achieved a frequency of 10% or greater in any sampled population. Shared substitutions were randomly distributed with respect to genome position, with transitions outnumbering transversions 5.4:1 and a clear bias for A to G and U to C substitutions. Haplotype composition of each population was unique with complexity of each population varying unpredictably, in that the number and frequency of haplotypes within a lineage were not correlated with number of passages removed from the founding population or whether the population was derived from a single or mixed lineage. The simplest explanation is that plant virus lineages, even those propagated at high MOI, are subject to frequent, narrow genetic bottlenecks during systemic movement that result in low effective population size and stochastic changes in population structure upon serial passage.

Base Sequence↗

Molecular characterization of a novel simian immunodeficiency virus lineage (SIVtal) from northern talapoins (Miopithecus ogouensis).

Simian immunodeficiency viruses (SIVs) are found in an extensive number of African primates, and humans continue to be exposed to these viruses by hunting and handling of primate bushmeat and following occupational exposures to captive nonhuman primates. Here, we report the molecular characterization of a new SIV lineage, SIVtal, from wild-caught and captive talapoin monkeys (Miopithecus ogouensis) from Cameroon and U.S. zoos, respectively. Phylogenetic tree analyses of a small fragment in the pol gene indicated that all SIVtal strains clustered together forming a single species-specific lineage. Full-length sequence analysis for two strains, SIVtal-00CM266 and SIVtal-01CM8023, from wild-caught animals in Cameroon confirmed that SIVtal was distinct from all primate lentiviruses isolated so far and represents a new SIV lineage. Phylogenetic analyses in different viral genes showed a significant clustering of the SIVtal lineage with the Cercopithecus-specific SIVs. In addition, SIVtal and Cercopithecus-specific SIVs share functional motifs in Gag and Env that distinguish them from other primate lentiviruses. Like SIVsyk and SIVdeb, a vpu gene homologue was also absent in SIVtal. Although northern talapoins belong to the Miopithecus genus, their SIVs belong to the Cercopithecus SIV lineage, suggesting evolution from a common ancestor or cross-species transmission between both primate genera.

Amino Acid Motifs↗

Discordant temporal and geographic patterns in maternal lineages of eastern North American frogs, Rana catesbeiana (Ranidae) and Pseudacris crucifer (Hylidae).

Whether the Pleistocene has had a disproportionate impact on the recent diversification of temperate species, or played a lesser role in a more protracted process, has been a prominent evolutionary debate for the past decade. We used cytochrome b sequences to reconstruct the evolutionary histories of two widely co-distributed, and ecologically divergent frogs (Rana catesbeiana and Pseudacris crucifer) to examine the role of the Pleistocene in structuring these species. Results for R. catesbeiana reflect a pattern of allopatric fragmentation, likely in Coastal Plain refugia on either side of the Mississippi River dating to the mid to early Pleistocene. In contrast, P. crucifer contains numerous divergent lineages, including one west of the Mississippi River in the Interior Highlands, and in the east, multiple lineages that likely expanded from a number of southern Appalachian refugia with lineage sundering originating in the late Pliocene. Large-scale phylogeographic comparisons between these and other eastern North American species reflect both congruent and independent patterns of diversification, possibly reflecting the relative importance of dispersal ability and habitat associations. Although intra-lineage diversification has been structured by repeated Pleistocene glaciations, lineage sundering likely dates at least to the Pliocene in most (but not all) northern temperate amphibian and reptile species studied to date.

Animals↗

Incongruous nuclear and mitochondrial phylogeographic patterns in two sympatric lineages of the wolf spider Pardosa astrigera (Araneae: Lycosidae) from China.

We investigated the genetic structure of mitochondrial DNA (COI and 16S rRNA-tRNA(Leu(CUN))-ND1) and nuclear DNA (ITS2) variations among and within populations of Pardosa astrigera in China. Two phenotypes of males were recognized. They differed genetically also in the presence (type A) or absence (type B) of common insertions and deletions in ITS2. The concordance between mtDNA based phylogeny and the phenotypic variations of P. astrigera was weak. Haplotypes of type A did not form a monophyletic group. Instead they were found in three clades, in one of them mixed with type B haplotypes, most likely as a result of long-term and ongoing gene flow of mtDNA between the two phenotypic groups (M = 0.69). Pairwise sequence divergences of all data sets indicated that the genetic divergences between the two phenotypes fall within intraspecific range. Our results indicated that the P. astrigera populations in China consist of two sympatric lineages with male phenotypic variations. Patterns of mismatch distribution within lineages suggested long-term demographic stability in the lineage A, and growth in lineage B that expanded rapidly and recolonized from a southern refuge to the northern parts of China during the late-Pleistocene. On the basis of the estimated divergence time between the two lineages (0.18-0.41 Ma), we suggest that the dry-cold climate and the uplift of the Tibetan plateau during the mid-Pleistocene appear to have a determinating impact on the evolutionary history of P. astrigera in China.

Animals↗

Restricted killer cell immunoglobulin-like receptor repertoire without T-cell receptor gamma rearrangement supports a true natural killer-cell lineage in a subset of sinonasal lymphomas.

The cellular lineage of sinonasal T/NK (natural killer) cell lymphoma remains controversial. Lineage assignment is difficult because T cells and NK cells have a similar morphology and surface markers. Consequently, the assignment must depend heavily on the status of T-cell receptor (TCR) rearrangement. A monoclonal TCR rearrangement supports a T lineage; however, a corresponding monoclonality test for NK cells has not yet been established. Each NK cell bears a distinct set of killer cell immunoglobulin (Ig)-like receptors (KIRs) that are randomly distributed over three groups. In principle, restriction of the KIR repertoire signifies a monoclonal or possibly oligoclonal NK-cell proliferation, just as Ig light-chain restriction usually indicates a monoclonal B-cell neoplasm. Using a novel group-specific reverse transcriptase-polymerase chain reaction, we found a restricted KIR repertoire in most sinonasal lymphomas (9 of 10), but only rarely in T-cell lymphomas (2 of 10) or reactive conditions involving T/NK cells (1 of 10). KIR+ sinonasal lymphomas usually lacked a monoclonal TCR-gamma rearrangement pattern, expressed another NK cell receptor, NKG2a, and were usually CD56-positve, cyclin-dependent kinase-6 (CDK6)-positive, CD44-negative, a phenotype already reported to indicate a true NK cell lineage. We conclude that, although sinonasal lymphomas have heterogeneous genotypes and phenotypes, a restricted KIR repertoire without TCR-gamma rearrangement provides preliminary support for the monoclonality hypothesis and can be used for defining a true NK-cell lineage in a subset of sinonasal lymphomas.

Adult↗

Normal fate and altered function of the cardiac neural crest cell lineage in retinoic acid receptor mutant embryos.

Mouse embryos lacking the retinoic acid (RA) receptors RARalpha1 and RARbeta suffer from a failure to properly septate (divide) the early outflow tract of the heart into distinct aortic and pulmonary channels, a phenotype termed persistent truncus arteriosus. This phenotype is associated with a failure in the development of the cardiac neural crest cell lineage, which normally forms the aorticopulmonary septum. In this study, we examined the fate of the neural crest lineage in RARalpha1/RARbeta mutant embryos by crossing with the Wnt1-cre and conditional R26R alleles, which together constitute a genetic lineage marker for the neural crest. We find that the number, migration, and terminal fate of the cardiac neural crest is normal in mutant embryos; however, the specific function of these cells in forming the aorticopulmonary septum is impaired. We furthermore show that the neural crest cells themselves do not utilize retinoid receptors and do not respond to RA during this process, but rather that the phenotype is cell non-autonomous for the neural crest cell lineage. This suggests that an alternative tissue in the vicinity of the outflow tract of the heart responds directly to RA, and thereby induces or permits the neural crest cell lineage to initiate aorticopulmonary septation.

Animals↗

MHC class II-specific T cells can develop in the CD8 lineage when CD4 is absent.

The generation of mature CD4 T cells from CD4+CD8+ precursor thymocytes usually requires corecognition of class II MHC by a TCR and CD4, while the production of mature CD8 T cells requires corecognition of class I MHC by a TCR and CD8. To assess the role of the CD4 coreceptor in development and lineage commitment, we generated CD4-deficient mice expressing a transgenic class II-specific TCR. Surprisingly, in the absence of CD4 a large number of T cells mature, but these cells appear in the CD8 lineage. Thus, when CD4 is present, the majority of immature T cells with this class II-specific TCR choose the CD4 lineage but develop in the CD8 pathway when CD4 is absent. The results indicate that even for TCRs that are not dependent on coreceptor for MHC recognition, the coreceptor can influence the lineage choice. These findings are considered in terms of a quantitative signaling model for CD4/CD8 lineage commitment.

Animals↗

Identification of two antigenically and genetically distinct lineages of H3N8 equine influenza virus in Sweden.

Four Swedish strains of equine H3N8 influenza virus isolated from outbreaks during the last 4 years were characterized. Antigenic typing using monoclonal antibodies raised against a variety of H3N8 strains showed that the viruses are heterogeneous, the 1993 isolate being closely related to the 1991 Swedish isolate TAB/91 and the other three isolates from 1994 and 1996 being more closely related to each other. This pattern is reflected in the phylogenetic data calculated from nucleotide sequencing of the haemagglutinin genes. H3N8 equine influenza can be seen to be evolving in two distinct lineages, one European and one American. The 1993 isolate is closely related to the European lineage and is the most recent Swedish strain of this lineage to be isolated. The 1994 and 1996 isolates fit into the American lineage, which contains recent isolates from the United States and also Britain. These results indicate that American-type H3N8 viruses have become endemic in Sweden and, in light of the antigenic differences which can be observed between viruses belonging to the two lineages, we believe that equine influenza virus vaccines should be updated with an American-type virus strain.

Animals↗

A framework for automated scalable designation of viral pathogen lineages from genomic data.

Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.

Animals↗

Mitochondrial simple sequence repeats and 12S-rRNA gene reveal two distinct lineages of Crocidura russula (Mammalia, Soricidae).

A short segment (135 bp) of the control region and a partial sequence (394 bp) of the 12S-rRNA gene in the mitochondrial DNA of Crocidura russula were analyzed in order to test a previous hypothesis regarding the presence of a gene flow disruption in northern Africa. This breakpoint would have separated northeast-African C. russula populations from the European (plus the northwest-African) populations. The analysis was carried out on specimens from Tunisia (C. r. cf agilis), Sardinia (C. r. ichnusae), and Pantelleria (C. r. cossyrensis), and on C. r. russula from Spain and Belgium. Two C. russula lineages were identified; they both shared R2 tandem repeated motifs of the same length (12 bp), but not the same primary structure. These simple sequence repeats were present in 12-23 copies in the right domain of the control region. Within the northeast-African populations, a polymorphism of repeat variants, not yet found in Europe, was recorded. A neighbor-join tree, which was built by sequences of the conserved 12S-rRNA gene, separated the two sister groups; it permitted us to date a divergence time of 0.5 Myr. Our data discriminated two different mitochondrial lineages in accordance with the previous morphological and karyological data. Ecoclimatic barriers formed during the Middle Pleistocene broke the range of ancestral species in the Eastern Algeria (Kabile Mountains), leading to two genetically separate and modern lineages. The northeast-African lineage can today be located in Tunisia, Pantelleria, and Sardinia. The northwest-African lineage (Morocco and West Algeria), reaching Spain by anthropogenic introduction, spread over north Europe in modern times. The Palaearctic C. russula species is monophyletic, but a taxonomical revision (ie, to provide a full species rank for the northeast taxa and to put in synonymy some insular taxa) is required.

Africa, Northern↗