RAG1 Research Articles

Metabolic sensor AMPK directly phosphorylates RAG1 protein and regulates V(D)J recombination

The ability to sense metabolic stress is critical for successful cellular adaptation. In eukaryotes, the AMP-activated protein kinase (AMPK), a highly conserved serine/threonine kinase, functions as a critical metabolic sensor. AMPK is activated by the rising ADP/ATP and AMP/ATP ratios during conditions of energy depletion and also by increasing intracellular Ca(2+). In response to metabolic stress, AMPK maintains energy homeostasis by phosphorylating and regulating proteins that are involved in many physiological processes including glucose and fatty acid metabolism, transcription, cell growth, mitochondrial biogenesis, and autophagy. Evidence is mounting that AMPK also plays a role in a number of pathways unrelated to energy metabolism. Here, we identify the recombination-activating gene 1 protein (RAG1) as a substrate of AMPK. The RAG1/RAG2 complex is a lymphoid-specific endonuclease that catalyzes specific DNA cleavage during V(D)J recombination, which is required for the assembly of the Ig and T-cell receptor genes of the immune system. AMPK directly phosphorylates RAG1 at serine 528, and the phosphorylation enhances the catalytic activity of the RAG complex, resulting in increased cleavage of oligonucleotide substrates in vitro, or increased recombination of an extrachromosomal substrate in a cellular assay. Our results suggest that V(D)J recombination can be regulated by AMPK activation, providing a potential new link between metabolic stress and development of B and T lymphocytes.

Lung type 2 innate lymphoid cells express cysteinyl leukotriene receptor 1, which regulates TH2 cytokine production

Cysteinyl leukotrienes (CysLTs) contribute to asthma pathogenesis, in part through cysteinyl leukotriene receptor 1 (CysLT1R). Recently discovered lineage-negative type 2 innate lymphoid cells (ILC2s) potently produce IL-5 and IL-13. We hypothesized that lung ILC2s might be activated by leukotrienes through CysLT1R. ILC2s (Thy1.2(+) lineage-negative lymphocytes) and CysLT1R were detected in the lungs of wild-type, signal transducer and activator of transcription 6-deficient (STAT6(-/-)), and recombination-activating gene 2-deficient (RAG2(-/-)) mice by means of flow cytometry. T(H)2 cytokine levels were measured in purified lung ILC2s stimulated with leukotriene D₄ (LTD₄) in the presence or absence of the CysLT1R antagonist montelukast. Calcium influx was measured by using Fluo-4 intensity. Intranasal leukotriene C₄, D₄, and E₄ were administered to naive mice, and levels of ILC2 IL-5 production were determined. Finally, LTD₄ was coadministered with Alternaria species repetitively to RAG2(-/-) mice (with ILC2s) and IL-7 receptor-deficient mice (lack ILC2s), and total ILC2 numbers, proliferation (Ki-67(+)), and bronchoalveolar lavage fluid eosinophil numbers were measured. CysLT1R was expressed on lung ILC2s from wild-type, RAG2(-/-), and STAT6(-/-) naive and Alternaria species-challenged mice. In vitro LTD₄ induced ILC2s to rapidly generate high levels of IL-5 and IL-13 within 6 hours of stimulation. Interestingly, LTD4, but not IL-33, induced high levels of IL-4 by ILC2s. LTD₄ administered in vivo rapidly induced ILC2 IL-5 production that was significantly reduced by montelukast before treatment. Finally, LTD₄ potentiated Alternaria species-induced eosinophilia, as well as ILC2 accumulation and proliferation. We present novel data that CysLT1R is expressed on ILC2s and LTD₄ potently induces CysLT1R-dependent ILC2 production of IL-4, IL-5, and IL-13. Additionally, LTD₄ potentiates Alternaria species-induced eosinophilia and ILC2 proliferation and accumulation.

Characterization of IGH locus breakpoints in multiple myeloma indicates a subset of translocations appear to occur in pregerminal center B cells

AbstractTranslocations in myeloma are thought to occur solely in mature B cells in the germinal center through class switch recombination (CSR). We used a targeted captured technique followed by massively parallel sequencing to determine the exact breakpoints in both the immunoglobulin heavy chain (IGH) locus and the partner chromosome in 61 presentation multiple myeloma samples. The majority of samples (62%) have a breakpoint within the switch regions upstream of the IGH constant genes and are generated through CSR in a mature B cell. However, the proportion of CSR translocations is not consistent between cytogenetic subgroups. We find that 100% of t(4;14) are CSR-mediated; however, 21% of t(11;14) and 25% of t(14;20) are generated through DH-JH recombination activation gene–mediated mechanisms, indicating they occur earlier in B-cell development at the pro–B-cell stage in the bone marrow. These 2 groups also generate translocations through receptor revision, as determined by the breakpoints and mutation status of the segments used in 10% and 50% of t(11;14) and t(14;20) samples, respectively. The study indicates that in a significant number of cases the translocation-based etiological events underlying myeloma may arise at the pro–B-cell hematological progenitor cell level, much earlier in B-cell development than was previously thought.

From widespread to microendemic: molecular and acoustic analyses show that Ischnocnema guentheri (Amphibia: Brachycephalidae) is endemic to Rio de Janeiro, Brazil

Many species of tropical amphibians are restricted to very small ranges, and this microendemism coupled with ongoing habitat loss and susceptibility to emerging pathogens imperils the long-term persistence of these species. Incomplete taxonomic and distributional knowledge may obscure conservation assessment, particularly in putatively widespread species that are typically considered to be of Least Concern in Red List assessments, but that in fact may constitute complexes of partly microendemic species. Such is the case in the Steindachner’s Robber Frog, Ischnocnema guentheri which, together with the recently recognized Ischnocnema henselii, is thought to occupy most of the Brazilian Atlantic Forest. To test whether these taxa may constitute a species complex of range-restricted and thus potentially threatened species, we analyzed 160 samples of I. guentheri and/or I. henselii for two molecular markers, 16S rRNA (16S) and recombination activation gene 1 (RAG1). To verify the monophyly of the complex, closely related species were also included in the 16S analysis. Congruent evidence from the molecular data and from analyses of advertisement calls support the existence of six distinct species within the complex: I. guentheri and I. henselii as well as four candidate new species. The lineages are distributed as a mosaic in the Atlantic Forest and are sympatric at some localities without indication of admixture. Their phylogeographical pattern partially agrees with paleo-models for the Atlantic Forest, but also suggests the existence of micro-refugia in less stable areas. I. guentheri, previously considered to be widespread, was found only in its type locality, a reserve within the urban area of Rio de Janeiro city. Although none of the species studied appears highly threatened with extinction, we recommend their IUCN threat status to be re-evaluated carefully for the next comprehensive update of the Red List of Brazil’s amphibians.

Cutaneous immunosurveillance and regulation of inflammation by group 2 innate lymphoid cells

Type 2 immunity is critical for defense against cutaneous infections but also underlies the development of allergic skin diseases. We report the identification in normal mouse dermis of an abundant, phenotypically unique group 2 innate lymphoid cell (ILC2) subset that depended on interleukin 7 (IL-7) and constitutively produced IL-13. Intravital multiphoton microscopy showed that dermal ILC2 cells specifically interacted with mast cells, whose function was suppressed by IL-13. Treatment of mice deficient in recombination-activating gene 1 (Rag1(-/-)) with IL-2 resulted in the population expansion of activated, IL-5-producing dermal ILC2 cells, which led to spontaneous dermatitis characterized by eosinophil infiltrates and activated mast cells. Our data show that ILC2 cells have both pro- and anti-inflammatory properties and identify a previously unknown interactive pathway between two innate populations of cells of the immune system linked to type 2 immunity and allergic diseases.

Human T cells depend on functional calcineurin, tumour necrosis factor-α and CD80/CD86 for expansion and activation in mice

Dysregulated T cells are a hallmark of several autoimmune and inflammatory diseases; thus, models to study human T cells in vivo are advantageous, but limited by lacking insight into human T cell functionality in mice. Using non-obese diabetic (NOD), severe combined immunodeficient (SCID) or recombination activating gene-1 (RAG1)(-/-) and interleukin-2 receptor gamma-chain (IL-2Rγ)(-/-) mice reconstituted with human peripheral blood mononuclear cells (PBMCs), we have studied the mechanisms of human T cell expansion and activation in mice. Injection of human PBMCs into mice caused consistent xeno-engraftment with polyclonal expansion and activation of functional human T cells and production of human cytokines. Human T cell expansion coincided with development of a graft-versus-host disease (GVHD)-like condition observed as weight loss, multi-organ immune infiltration and liver damage. CD8(+) T cells alone were sufficient for expansion and required for disease development; in contrast, CD4(+) T cells alone expanded but did not induce acute disease and, rather, exerted regulatory capacity through CD25(+)CD4(+) T cells. Using various anti-inflammatory compounds, we demonstrated that several T cell-activation pathways controlled T cell expansion and disease development, including calcineurin-, tumour necrosis factor-α and co-stimulatory signalling via the CD80/CD86 pathway, indicating the diverse modes of action used by human T cells during expansion and activation in mice as well as the pharmacological relevance of this model. Overall, these data provide insight into the mechanisms used by human T cells during expansion and activation in mice, and we speculate that PBMC-injected mice may be useful to study intrinsic human T cell functions in vivo and to test T cell-targeting compounds.

Molecular phylogeny of thorny catfishes (Siluriformes: Doradidae)

Doradidae is a monophyletic catfish family endemic to continental South America, and composed of 93 valid species here placed in 31 genera. Existing phylogenetic hypotheses for Doradidae are derived from comprehensive analyses of morphological data, and a single molecular-based study on a limited subset of taxa. To provide a robust molecular phylogeny commensurate with those based on morphology, we gathered original and published sequence data for 86 species-level taxa (at least 70 valid species plus 16 new or questionably nominal species) and all genera of Doradidae, as well as 10 species (nine genera) of Auchenipteridae and three species and genera of Aspredinidae as outgroups. 3011 base pairs were aligned for two mitochondrial genes (cytochrome c oxidase subunit 1, and 16S ribosomal RNA) and one nuclear gene (recombination activating gene 1), and analyzed for a total of 143 specimens (130 doradids, 10 auchenipterids and three aspredinids). Tree topologies generated by Maximum Parsimony, Maximum Likelihood, and Bayesian analyses were largely congruent, and are compared to existing phylogenies based on morphology and molecules. Although many of the relationships supported by our molecular analyses corroborated those based on morphology, others are newly hypothesized or remain in conflict.The monotypic Wertheimeria, Franciscodoras and Kalyptodoras, for example, form a newly proposed clade, and the subfamily Astrodoradinae is placed at the base of the doradid tree. The monotypic Doraops and Centrochir, endemic to Caribbean drainages north and west of the Andes, are sister to Pterodoras and Platydoras, respectively, two genera that are widely distributed in Atlantic drainages. Additional biogeographic implications are discussed for hypothesized relationships among doradids. Molecular evidence strongly supports synonymization of monotypic Merodoras with Amblydoras, and transfer of Amblydoras bolivarensis to genus Scorpiodoras. Furthermore, we consider Opsodoras ternetzi to be more properly placed in the genus Nemadoras. The genus Opsodoras may warrant synonymization with Hemidoras, and the monophyly of genus Ossancora is not supported; however, we refrain from taxonomic decisions regarding those taxa until a broader spectrum of doradids can be submitted to further morphological and molecular phylogenetic analyses.

Multi-gene barcoding to discriminate sibling species within a morphologically difficult fish genus (Sillago)

Fisheries species that cannot be reliably identified based on unique morphological features pose a challenge for research, monitoring and management. DNA barcoding, which refers to a standardized procedure for genetic species identification based on the mitochondrial cytochrome oxidase 1 (CO1) gene, is an important tool to confront this problem. Here, we present a multi-gene barcoding approach to discriminate two fisheries species flagged as sibling species within the morphologically difficult fish genus Sillago: S analis and S. ciliata. CO1 revealed low interspecific variation that was insufficient for genetic distance-based species identification. Despite this, one diagnostic site did permit genetic character-based identification. However, four cases of mismatch among morphological identifications (mIDs) and CO1 barcodes required analysing additional genes and loci. A spot test approach was used to screen five other genes in the mitochondrial genome (mtDNA) and four genes in the nuclear genome (nuDNA). The nuDNA recombination activating gene 2 (RAG2) revealed most diagnostic sites, correctly clustering mIDs of all individuals using both genetic distance- and character-based analysis. Three of four cases of mID/CO1 mismatches were found to be simultaneous CO1/RAG2 (mtDNA/nuDNA) mismatches indicative of past hybridization. The fourth mID/CO1 mismatch was found to represent an initial morphological misidentification. Five spot-tested genes, containing either fully or partially diagnostic sites (mtDNA: NADH dehydrogenase 2 [ND2], ATP synthase [ATPase] and cytochrome b; nuDNA: histone protein 3a and ring finger protein 213), confirmed these findings. Based on our preliminary data, we recommend (1) that S. analis and S. ciliata retain their taxonomic status as sibling species with full corresponding recognition as separate management and conservation units, and (2) precautionary management of S. ciliata fisheries until further research into hybridization is carried out. The multi-gene spot test approach and efficient markers (RAG2 in combination with ND2, ATPase or CO1) may help identifying other problematic fish species.

Genetic mutation of recombination activating gene 1 in Dahl salt-sensitive rats attenuates hypertension and renal damage.

Hypertension and renal damage in Dahl SS rats are associated with increased infiltrating immune cells in the kidney. To examine the role of infiltrating immune cells in this disease process, a zinc finger nuclease targeting bases 672-706 of recombination-activating gene 1 (Rag1) was injected into the pronucleus of Dahl SS (SS/JrHsdMcwi) strain embryos and implanted in pseudopregnant females. This strategy yielded a rat strain with a 13-base frame-shift mutation in the target region of Rag1 and a deletion of immunoreactive Rag1 protein in the thymus. Flow cytometry demonstrated that the Rag1-null mutant rats have a significant reduction in T and B lymphocytes in the circulation and spleen. Studies were performed on SS and Rag1-null rats fed a 4.0% NaCl diet for 3 wk. The infiltration of T cells into the kidney following high-salt intake was significantly blunted in the Rag1-null rats (1.7 ± 0.6 × 10(5) cells/kidney) compared with the Dahl SS (5.6 ± 0.9 × 10(5) cells/kidney). Accompanying the reduction in infiltration of immune cells in the kidney, mean arterial blood pressure and urinary albumin excretion rate were significantly lower in Rag1-null mutants (158 ± 3 mmHg and 60 ± 16 mg/day, respectively) than in SS rats (180 ± 11 mmHg and 251 ± 37 mg/day). Finally, a histological analysis revealed that the glomerular and tubular damage in the kidneys of the SS rats fed a high-salt diet was also attenuated in the Rag1 mutants. These studies demonstrate the importance of renal infiltration of immune cells in the pathogenesis of hypertension and renal damage in Dahl SS rats.

Cooperative recruitment of HMGB1 during V(D)J recombination through interactions with RAG1 and DNA

During V(D)J recombination, recombination activating gene (RAG)1 and RAG2 bind and cleave recombination signal sequences (RSSs), aided by the ubiquitous DNA-binding/-bending proteins high-mobility group box protein (HMGB)1 or HMGB2. HMGB1/2 play a critical, although poorly understood, role in vitro in the assembly of functional RAG–RSS complexes, into which HMGB1/2 stably incorporate. The mechanism of HMGB1/2 recruitment is unknown, although an interaction with RAG1 has been suggested. Here, we report data demonstrating only a weak HMGB1–RAG1 interaction in the absence of DNA in several assays, including fluorescence anisotropy experiments using a novel Alexa488-labeled HMGB1 protein. Addition of DNA to RAG1 and HMGB1 in fluorescence anisotropy experiments, however, results in a substantial increase in complex formation, indicating a synergistic binding effect. Pulldown experiments confirmed these results, as HMGB1 was recruited to a RAG1–DNA complex in a RAG1 concentration-dependent manner and, interestingly, without strict RSS sequence specificity. Our finding that HMGB1 binds more tightly to a RAG1–DNA complex over RAG1 or DNA alone provides an explanation for the stable integration of this typically transient architectural protein in the V(D)J recombinase complex throughout recombination. These findings also have implications for the order of events during RAG–DNA complex assembly and for the stabilization of sequence-specific and non-specific RAG1–DNA interactions.

Isolation of RAG-1 and IgM transcripts from the striped trumpeter (Latris lineata), and their expression as markers for development of the adaptive immune response

A partial sequence of the recombination activating gene-1 (RAG-1) and several full length sequences of the immunoglobulin M (IgM) heavy chain mRNA were obtained from the striped trumpeter (Latris lineata). The RAG-1 fragment consisted of 205 aa and fell within the core region of the open reading frame. The complete IgM heavy chain sequences translated into peptides ranging between 581 and 591 aa. Both genes showed good homology to other vertebrate sequences. The expression of the two genes was assessed throughout the early developmental stages of striped trumpeter larvae (5–100 dph) and used as markers to follow the ontogeny of the adaptive immune response. Using RT-PCR, RAG-1 mRNA expression was detectable at 5 dph and remained so until 80 dph, before becoming undetectable at 100 dph. IgM expression was also detectable at 5 dph, and remained so throughout. These patterns of expression may suggest that the striped trumpeter possess mature B cells with surface IgM at 100 dph. However, complete immunological competence is likely not reached until some time later. The early detection of IgM mRNA at 5 dph led to the investigation of its presence in oocytes. Both RAG-1 and IgM mRNA transcripts were detected in unfertilized oocytes, suggesting that they are maternally transferred. The biological significance of such a phenomenon remains to be investigated.

A Novel Quantitative Fluorescent Reporter Assay for RAG Targets and RAG Activity

Recombination-Activating Genes (RAG) 1 and 2 form the site specific recombinase that mediates V(D)J recombination, a process of DNA editing required for lymphocyte development and responsible for their diverse repertoire of antigen receptors. Mistargeted RAG activity associates with genome alteration and is responsible for various lymphoid tumors. Moreover several non-lymphoid tumors express RAG ectopically. A practical and powerful tool to perform quantitative assessment of RAG activity and to score putative RAG-Recognition signal sequences (RSS) is required in the fields of immunology, oncology, gene therapy, and development. Here we report the detailed characterization of a novel fluorescence-based reporter of RAG activity, named GFPi, a tool that allows measuring recombination efficiency (RE) by simple flow cytometry analysis. GFPi can be produced both as a plasmid for transient transfection experiments in cell lines or as a retrovirus for stable integration in the genome, thus supporting ex vivo and in vivo studies. The GFPi assay faithfully quantified endogenous and ectopic RAG activity as tested in genetically modified fibroblasts, tumor derived cell lines, developing pre-B cells, and hematopoietic cells. The GFPi assay also successfully ranked the RE of various RSS pairs, including bona fide RSS associated with V(D)J segments, artificial consensus sequences modified or not at specific nucleotides known to affect their efficiencies, or cryptic RSS involved in RAG-dependent activation of oncogenes. Our work validates the GFPi reporter as a practical quantitative tool for the study of RAG activity and RSS efficiencies. It should turn useful for the study of RAG-mediated V(D)J and aberrant rearrangements, lineage commitment, and vertebrate evolution.

Clinical phenotype and gene diagnostic analysis of Omenn syndrome

Omenn syndrome is a rare autosomal recessive hereditary severe combined immunodeficiency. The purpose of this study was to understand clinical characteristics and genetic mutation type of Omenn syndrome and to improve the recognition of Omenn syndrome among pediatric clinicians. One suspected case of severe combined immunodeficiency was found to have pneumonia repeatedly, intractable diarrhea, poor antibiotic treatment effect, lymphadenopathy, hepatosplenomegaly and erythroderma. The patient was diagnosed as having Omenn syndrome by RT-PCR, and the expression of RAG1/RAG2 and gene analysis of RAG1/RAG2 were performed. The classification of lymphocyte was CD3(+) cells (35.3%), CD19(+) cells (0.4%), CD16(+) cells (57.6%). After stimulation with phytohemagglutinin (PHA), lymphocyte proliferation of the child was extremely low. Genetic studies showed RAG1 homozygous deletion mutation (2302 del T). He had detectable activated T-lymphocytes with low circulating B-lymphocytes and no evidence of maternal T-cell engrafment as indicated by the short tandem repeat (STR) analysis. Omenn syndrome is a severe combined immunodeficiency disease caused by mutations in the RAG1/RAG2 gene. The disease has been reported rarely in China. The clinical manifestations of the disease is early postnatal repeated infections and erythroderma. Mutation analysis of RAG1/RAG2 gene may help to confirm the diagnosis and may be useful in early immune reconstitution and genetic counseling.

RPA Accumulation during Class Switch Recombination Represents 5′–3′ DNA-End Resection during the S–G2/M Phase of the Cell Cycle

Activation-induced cytidine deaminase (AID) promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in the G1 phase. RPA is a single-stranded DNA (ssDNA)-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR), such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here, we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, recombination-activating genes (RAG), or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in the S-G2/M phase is extensive, ATM independent, and associated with Rad51 accumulation. In the S-G2/M phase, RPA increases in nonhomologous-end-joining-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during class switch recombination represents salvage of unrepaired breaks by homology-based pathways during the S-G2/M phase of the cell cycle.

The majority of T cells, including Treg cells, are developed from CD4−CD8− T progenitor cells without the involvement of the CD4+CD8+ stage in the thymus

In this study, we examined CD4−CD8− (DN) cells as precursors of T cells. We provided evidence that DN-CD25+ T cells could express the gene encoding forkhead box P3 (Foxp3) at high levels but were unable to express genes for T cell receptor (TCR) and cluster of differentiation 3 (CD3). In contrast, DN-CD25− cells could express and produce TCR and CD3 but not Foxp3. Furthermore, DN cells exhibited a higher-level expression of cell surface marker CD25, as well as Foxp3, but reduced expression of CD44, CD3, and TCR when compared to CD4+CD8− T cells. In the process of T cell development in the thymus, we noted that CD25 was down-regulated, and there occurred an up-regulation of TCR during maturation of T cells. These results suggested to us that DN cells might represent precursors of Treg cells, which contradicts the traditional view that double-positive (DP) cells constitute an intermediate cell stage. In addition, studies from other groups demonstrated that DP cells were not required for gene expression involving major histocompatability complex, Notch protein that dictates fate of a cell during development, TCR, and recombination activating (RAG) genes, which are involved in B cell development. Consequently, it is not surprising that DP cells might not be involved in the process of T cell development. One may speculate that DP cells are in a state of degeneration with down-regulated cell surface markers, which would most likely die by apoptosis.

B cell activating factor (BAFF) induces the transcription of recombination-activating genes in transitional stage 1 B cells

ENWEndNote BIBJabRef, Mendeley RISPapers, Reference Manager, RefWorks, Zotero AMA He Y, Ma N, Xiao H, et al. B cell activating factor (BAFF) induces the transcription of recombination-activating genes in transitional stage 1 B cells. Central European Journal of Immunology. 2013;38(3):336-342. doi:10.5114/ceji.2013.37758. APA He, Y., Ma, N., Xiao, H., Han, G., Chen, G., & Hou, C. et al. (2013). B cell activating factor (BAFF) induces the transcription of recombination-activating genes in transitional stage 1 B cells. Central European Journal of Immunology, 38(3), 336-342. https://doi.org/10.5114/ceji.2013.37758 Chicago He, Youdi, Ning Ma, He Xiao, Gencheng Han, Guojiang Chen, Chunmei Hou, and Beifen Shen et al. 2013. "B cell activating factor (BAFF) induces the transcription of recombination-activating genes in transitional stage 1 B cells". Central European Journal of Immunology 38 (3): 336-342. doi:10.5114/ceji.2013.37758. Harvard He, Y., Ma, N., Xiao, H., Han, G., Chen, G., Hou, C., Shen, B., Li, Y., Wang, R., and Hu, W. (2013). B cell activating factor (BAFF) induces the transcription of recombination-activating genes in transitional stage 1 B cells. Central European Journal of Immunology, 38(3), pp.336-342. https://doi.org/10.5114/ceji.2013.37758 MLA He, Youdi et al. "B cell activating factor (BAFF) induces the transcription of recombination-activating genes in transitional stage 1 B cells." Central European Journal of Immunology, vol. 38, no. 3, 2013, pp. 336-342. doi:10.5114/ceji.2013.37758. Vancouver He Y, Ma N, Xiao H, Han G, Chen G, Hou C et al. B cell activating factor (BAFF) induces the transcription of recombination-activating genes in transitional stage 1 B cells. Central European Journal of Immunology. 2013;38(3):336-342. doi:10.5114/ceji.2013.37758.

Diversification and reproductive isolation: cryptic species in the only New World high-duty cycle bat, Pteronotus parnellii

BackgroundMolecular techniques are increasingly employed to recognize the presence of cryptic species, even among commonly observed taxa. Previous studies have demonstrated that bats using high-duty cycle echolocation may be more likely to speciate quickly. Pteronotus parnellii is a widespread Neotropical bat and the only New World species to use high-duty cycle echolocation, a trait otherwise restricted to Old World taxa. Here we analyze morphological and acoustic variation and genetic divergence at the mitochondrial COI gene, the 7th intron region of the y-linked Dby gene and the nuclear recombination-activating gene 2, and provide extensive evidence that P. parnellii is actually a cryptic species complex.ResultsCentral American populations form a single species while three additional species exist in northern South America: one in Venezuela, Trinidad and western Guyana and two occupying sympatric ranges in Guyana and Suriname. Reproductive isolation appears nearly complete (only one potential hybrid individual found). The complex likely arose within the last ~6 million years with all taxa diverging quickly within the last ~1-2 million years, following a pattern consistent with the geological history of Central and northern South America. Significant variation in cranial measures and forearm length exists between three of the four groups, although no individual morphological character can discriminate these in the field. Acoustic analysis reveals small differences (5–10 kHz) in echolocation calls between allopatric cryptic taxa that are unlikely to provide access to different prey resources but are consistent with divergence by drift in allopatric species or through selection for social recognition.ConclusionsThis unique approach, considering morphological, acoustic and multi-locus genetic information inherited maternally, paternally and bi-parentally, provides strong support to conclusions about the cessation of gene flow and degree of reproductive isolation of these cryptic species.

Phylogenetic Relationships of the Genus Homatula (Cypriniformes: Nemacheilidae), with Special Reference to the Biogeographic History around the Yunnan-Guizhou Plateau

Species of the nemacheilid genus Homatula are endemic to the Yunnan-Guizhou Plateau of China. Herein we provide phy-logenetic inferences of species relationships based on complete sequences of the mitochondrial cytochrome b gene (cyt b)and partial sequences of the nuclear recombination activation gene (RAG 1). Both gene trees (and the concatenated dataset) support the recognition of five clades in the genus. These analyses also support the hypothesis that two of the lineagesresolved represent undescribed species awaiting formal description, and, further, that two previously recognized speciesare junior synonyms; both are genetically indistinguishable from other previously recognized species. Divergence timesof the major clades in Homatula are inferred to be Late Pliocene and the Early Pleistocene, and are correlated with themassive geological events associated with the uplift of the Qinghai-Tibetan Plateau occurring at these times. The recon-struction of drainage histories suggests that the fish faunas of the Nu and Lancang rivers are basal relative to other riverinefaunas in the region, and that the Nanpan and the Jinsha rivers share a more recent history than with any other river systems included in our study.

A new species of prickleback, Dictyosoma tongyeongensis (Perciformes: Stichaeidae) from the South Sea of Korea

A new prickleback is described based on six specimens collected by fish trap in southern Korea (water depth 5–12 m) in 2009 and 2010. The new prickleback is most similar to Dictyosoma burgeri and Dictyosoma rubrimaculatum in general morphology, but differs in the following combination of characters: dorsal contour of head almost a straight line; anal-fin rays 45–47; vertebrae 70–74; no blackish-brown blotches on head. In addition, mitochondrial DNA cytochrome oxidase subunit I (COI) sequences and recombination activating gene 2 (RAG2) sequences were analyzed for clarifying their genetic relationship. The neighbor-joining tree using mtDNA COI and nDNA RAG2 shows the reciprocal monophyly of the new prickleback. Accordingly, our specimens are regarded as a new species, named Dictyosoma tongyeongensis, after its type locality (Tongyeong).

Dispersal and vicariance of Hoplias malabaricus (Bloch, 1794) (Teleostei, Erythrinidae) populations of the Brazilian continental margin

AbstractAimThe aim of this study was to test the hypothesis that the Brazilian coastal populations of Hoplias malabaricus were subject to the same geomorphological and palaeohydrological factors that resulted in endemic fish regions, by characterizing the mitochondrial DNA, nuclear sequences and cytogenetic data of these populations.LocationSeventeen coastal basins in north‐eastern, eastern and south‐eastern Brazil, plus the São Francisco Basin.MethodsForty‐two specimens were analysed. Mitochondrial ATP synthase 6 (ATPase‐6) and nuclear recombination activating gene 2 (RAG2) gene sequences were used for Bayesian inference and maximum parsimony analyses. Molecular models were selected using MrModeltest.ResultsMolecular analyses indicated four haplogroups (Northeastern, Eastern A, Eastern B and Southeastern) for ATPase‐6 and three clades for RAG2. All topologies were congruent with Hoplias malabaricus diploid numbers, with most regions of proposed endemism and coastal geomorphological units.Main conclusionsDeep genetic divergence between the Northeastern and the other haplogroups was interpreted as evidence of the vicariant effect of the Abrolhos Formation, which effectively isolates 2n = 40 and 2n = 42 coastal populations. To the south, the Cabo Frio Magmatic Lineament also isolates the Eastern and Southeastern 2n = 42 populations. In the Northeastern haplogroup, stream piracy was probably involved in chronologically varied dispersal events between coastal and continental basins. All haplogroups also included haplotypes that dispersed in recent times. Results show an older vicariant pattern and recent dispersal events congruent with the occurrence of temporary connections along the coast caused by eustatic sea level variations and the occurrence of stream piracy involving either continental or coastal basins, and suggest these processes contributed to the current distribution patterns of Brazilian coastal freshwater fish.