Distinct Repertoires Research Articles

Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain.

Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a ubiquitous mechanism that generates transcriptomic diversity. This process is particularly important for proper neuronal function; however, little is known about how RNA editing is dynamically regulated between the many functionally distinct neuronal populations of the brain. Here, we present a spatial RNA editing map in the Drosophila brain and show that different neuronal populations possess distinct RNA editing signatures. After purifying and sequencing RNA from genetically marked groups of neuronal nuclei, we identified a large number of editing sites and compared editing levels in hundreds of transcripts across nine functionally different neuronal populations. We found distinct editing repertoires for each population, including sites in repeat regions of the transcriptome and differential editing in highly conserved and likely functional regions of transcripts that encode essential neuronal genes. These changes are site-specific and not driven by changes in Adar expression, suggesting a complex, targeted regulation of editing levels in key transcripts. This fine-tuning of the transcriptome between different neurons by RNA editing may account for functional differences between distinct populations in the brain.

The Multifaceted B Cell Response to Influenza Virus.

Protection from yearly recurring, highly acute infections with a pathogen that rapidly and continuously evades previously induced protective neutralizing Abs, as seen during seasonal influenza virus infections, can be expected to require a B cell response that is too highly variable, able to adapt rapidly, and able to reduce morbidity and death when sterile immunity cannot be garnered quickly enough. As we outline in this Brief Review, the influenza-specific B cell response is exactly that: it is multifaceted, involves both innate-like and conventional B cells, provides early and later immune protection, employs B cells with distinct BCR repertoires and distinct modes of activation, and continuously adapts to the ever-changing virus while enhancing overall protection. A formidable response to a formidable pathogen.

Characteristics of T cell receptor repertoires of patients with acute myocardial infarction through high-throughput sequencing

BackgroundT cells are key regulators of immunity and one of the cells recruited in atherosclerosis and participated in various stages of the development of atherosclerosis. Characterizing T-cell receptor (TCR) repertoires is a priority of great scientific interest and potential clinical utility for the early diagnosis, risk stratification and prognostic evaluation of acute myocardial infarction (AMI).MethodsThe TCR repertoires in 21 subjects including 7 patients with non-ST-segment elevation myocardial infarction (NSTEMI), 6 patients with ST-segment elevation myocardial infarction (STEMI) and 8 subjects with normal coronary artery (NCA) as control were characterized by using high-throughput sequencing. Bioinformatics analysis were performed.ResultsPatients with NSTEMI displayed more diverse TCR sequences than NCA controls, but they had lower percentage of top 200 TCR sequences. However, no significant differences were observed between the patients with STEMI and NCA controls, but STEMI group had lower percentage of top 200 TCR sequences. T cells from patients with AMI and NCA controls showed a differential V and J gene usage, especially, significant difference was observed in frequencies of V gene (TRBV2, TRBV29-1, TRBV30 and TRBV12-3) and J gene (TRBJ2-1) usage. Furthermore, significantly differences in average overlap was observed in groups of AMI and NCA control. The results showed that patients with AMI had distinct TCR repertoires which revealed the association between cardiovascular condition and T-cell clonotypes.ConclusionsOur findings revealed the differences of TCR repertoires between patients with AMI and NCA controls, which might be potential biomarkers for evaluating risk stratification or diagnosis of acute coronary syndrome.

Tumor-infiltrating human CD4+ regulatory T cells display a distinct TCR repertoire and exhibit tumor and neoantigen reactivity.

CD4+ regulatory T (Treg) cells have an essential function in maintaining self-tolerance; however, they may also play a detrimental role in antitumor immune responses. The presence of elevated frequencies of Treg cells in tumors correlates with disease progression and poor survival in patients with cancer. The antigen specificity of Treg cells that have expanded in the tumor microenvironment is poorly understood; answering this question may provide important insights for immunotherapeutic approaches. To address this, we used a novel combinatorial approach to characterizing the T cell receptor (TCR) profiles of intratumoral Treg cells from patients with metastatic melanoma, gastrointestinal, and ovarian cancers and elucidated their antigen specificities. The TCR repertoires of tumor-resident Treg cells were diverse yet displayed significant overlap with circulating Treg cells but not with conventional T cells in tumor or blood. TCRs isolated from Treg cells displayed specific reactivity against autologous tumors and mutated neoantigens, suggesting that intratumoral Treg cells act in a tumor antigen-selective manner leading to their activation and clonal expansion in the tumor microenvironment. Tumor antigen-specific Treg-derived TCRs resided in the tumor and in the circulation, suggesting that both Treg cell compartments may serve as a source for tumor-specific TCRs. These findings provide insights into the TCR specificity of tumor-infiltrating human Treg cells that may have potential implications for cancer immunotherapy.

Initial Characterization of the Two ClpP Paralogs of Chlamydia trachomatis Suggests Unique Functionality for Each.

Members of Chlamydia are obligate intracellular bacteria that differentiate between two distinct functional and morphological forms during their developmental cycle, elementary bodies (EBs) and reticulate bodies (RBs). EBs are nondividing small electron-dense forms that infect host cells. RBs are larger noninfectious replicative forms that develop within a membrane-bound vesicle, termed an inclusion. Given the unique properties of each developmental form of this bacterium, we hypothesized that the Clp protease system plays an integral role in proteomic turnover by degrading specific proteins from one developmental form or the other. Chlamydia spp. have five uncharacterized clp genes, clpX, clpC, two clpP paralogs, and clpB In other bacteria, ClpC and ClpX are ATPases that unfold and feed proteins into the ClpP protease to be degraded, and ClpB is a deaggregase. Here, we focused on characterizing the ClpP paralogs. Transcriptional analyses and immunoblotting determined that these genes are expressed midcycle. Bioinformatic analyses of these proteins identified key residues important for activity. Overexpression of inactive clpP mutants in Chlamydia spp. suggested independent function of each ClpP paralog. To further probe these differences, we determined interactions between the ClpP proteins using bacterial two-hybrid assays and native gel analysis of recombinant proteins. Homotypic interactions of the ClpP proteins, but not heterotypic interactions between the ClpP paralogs, were detected. Interestingly, protease activity of ClpP2, but not ClpP1, was detected in vitro This activity was stimulated by antibiotics known to activate ClpP, which also blocked chlamydial growth. Our data suggest the chlamydial ClpP paralogs likely serve distinct and critical roles in this important pathogen.IMPORTANCEChlamydia trachomatis is the leading cause of preventable infectious blindness and of bacterial sexually transmitted infections worldwide. Chlamydiae are developmentally regulated obligate intracellular pathogens that alternate between two functional and morphologic forms, with distinct repertoires of proteins. We hypothesize that protein degradation is a critical aspect to the developmental cycle. A key system involved in protein turnover in bacteria is the Clp protease system. Here, we characterized the two chlamydial ClpP paralogs by examining their expression in Chlamydia spp., their ability to oligomerize, and their proteolytic activity. This work will help understand the evolutionarily diverse Clp proteases in the context of intracellular organisms, which may aid in the study of other clinically relevant intracellular bacteria.

Strain-Level Diversity Analysis of Pseudomonas fragi after In Situ Pangenome Reconstruction Shows Distinctive Spoilage-Associated Metabolic Traits Clearly Selected by Different Storage Conditions.

Microbial spoilage of raw meat causes huge economic losses every year. An understanding of the microbial ecology associated with the spoilage and its dynamics during the refrigerated storage of meat can help in preventing and delaying the spoilage-related activities. The raw meat microbiota is usually complex, but only a few members will develop during storage and cause spoilage upon the pressure from several external factors, such as temperature and oxygen availability. We characterized the metagenome of beef packed aerobically or under vacuum during refrigerated storage to explore how different packaging conditions may influence the microbial composition and potential spoilage-associated activities. Different population dynamics and spoilage-associated genomic repertoires occurred in beef stored aerobically or in vacuum packaging. Moreover, the pangenomes of Pseudomonas fragi strains were extracted from metagenomes. We demonstrated the presence of specific, storage-driven strain-level profiles of Pseudomonas fragi, characterized by different gene repertoires and thus potentially able to act differently during meat spoilage. The results provide new knowledge on strain-level microbial ecology associated with meat spoilage and may be of value for future strategies of spoilage prevention and food waste reduction.IMPORTANCE This work provides insights on the mechanisms involved in raw beef spoilage during refrigerated storage and on the selective pressure exerted by the packaging conditions. We highlighted the presence of different microbial metagenomes during the spoilage of beef packaged aerobically or under vacuum. The packaging condition was able to select specific Pseudomonas fragi strains with distinctive genomic repertoires. This study may help in deciphering the behavior of different biomes directly in situ in food and in understanding the specific contribution of different strains to food spoilage.

Immunoglobulin Lambda Translocations Identify Poor Outcome and IMiD Resistance in Multiple Myeloma and Co-Occur with Hyperdiploidy

▪Patients with the plasma cell malignancy multiple myeloma now benefit from treatments such as proteasome inhibitors, immunomodulatory imide drugs (IMiDs), autologous stem cell transplant, and monoclonal antibodies. However, 20% of patients still relapse or die within two years and are deemed ‘high risk’. Current markers fail to identify all high-risk patients resulting in misdiagnoses, therefore additional markers for this deadly form of the disease are required.To better understand and identify high-risk myeloma, we analyzed the structural variant landscape of 826 myelomas from newly-diagnosed patients using whole genome sequencing as part of the CoMMpass trial (NCT01454297). High-confidence somatic structural variants were determined using DELLY and quality control metrics to exclude regions with sequencing anomalies.Myeloma from newly diagnosed patients had a median of 21 somatic structural variants including 7 duplications, 2 deletions, 7 inversions, and 3 translocations. The number of deletions, duplications, and translocations corresponded to poor progression-free (PFS) and overall survival (OS), with translocations being the most significant (P <6.1x10-7). The two most common translocations occurred at the IgH (41%) and MYC (23%) loci, but did not correspond with differential outcome. However, the third most commonly translocated region (10%) occurred at the IgL locus and was indicative of poor PFS and OS with hazard ratios (HR) of 1.71 and 1.81, respectively (Figure 1). IgL-translocated myeloma did not correspond with distinct clinical features such as age, stage, gender, or b2M levels; and IgL-translocated patients were treated with similar therapeutic regimens as others. Additionally, IgL-translocated myeloma did not have a distinct mutational repertoire, gene expression subtype, and did not have many unique structural genetic elements. The notable exception is that 70% of IgL-translocated myeloma co-occurred with hyperdiploidy, a marker normally associated with better prognosis. However, patients with IgL-translocated and hyperdiploid myeloma experienced poor outcome with a median PFS of 23 months compared to 42.8 months for non-t(IgL) hyperdiploid myeloma (PFS HR=2.35; OS HR=2.41). This poor outcome is partially explained by the failure of patients with IgL-translocated myeloma to benefit from IMiDs. In fact, IMiDs provided no survival benefit to patients with IgL-translocated myeloma who experienced poor outcomes commensurate with patients that did not receive IMiDs (PFS HR=1.56; OS HR=1.49). This is in contrast to patients with myeloma that harbor other translocations, such as IgH translocation, who benefited from IMiDs (PFS HR=0.83, OS HR=0.61).These data identify IgL translocation as an independent marker of poor prognosis regardless of translocation partner, and suggest this may be due to the failure of this myeloma subtype to benefit from IMiDs. One potential mechanistic explanation is that the IgL enhancer is one of the most robust enhancers of gene expression and is therefore uniquely resistant to therapeutic inhibition. Indeed, the IgL enhancer is bound by several transcription factors at some of the highest levels in the B cell / myeloma epigenome, including BRD4, MED1, and IKZF1. This last factor is particularly interesting as IKZF1 is the target of IMiDs, and thus high-levels of IKZF1 occupancy at the IgL enhancer may be more difficult to fully deplete therapeutically than other loci. This may explain why patients with IgL-translocated myeloma do not benefit from IMiDs whereas patients with IgH- or IgK-translocated myeloma do. Finally, the co-occurrence of myeloma with IgL-translocation and hyperdiploidy is particularly unfortunate, as hyperdiploidy is routinely tested for clinically, whereas IgL-translocations are rarely diagnosed, likely resulting in their misclassification as standard risk.Figure: IgL translocations portend poor prognosis. a Circos plot showing the repertoire of IgL translocations in newly diagnosed myeloma where line thickness denotes frequency (key bottom left). b Kaplan-Meier analysis of IgL translocated [t(IgL)] patients (N=81) as compared to non-t(IgL) (N=745) for progression-free (PFS; top) and overall survival (OS; bottom). P-values were calculated using a Cox proportional hazards Wald's test or permutation based P-value with 1,000 permutations based on the hazard ratio. [Display omitted] DisclosuresNeri:Celgene: Consultancy, Honoraria; Janssen: Consultancy, Honoraria. Bahlis:Amgen: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding. Nooka:Adaptive technologies: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Membership on an entity's Board of Directors or advisory committees; GSK: Consultancy, Membership on an entity's Board of Directors or advisory committees; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; BMS: Consultancy, Membership on an entity's Board of Directors or advisory committees; Janssen pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Spectrum Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees. Kaufman:Janssen: Consultancy; Roche: Consultancy; Karyopharm: Other: data monitoring committee; Abbvie: Consultancy; BMS: Consultancy. Lonial:Amgen: Research Funding. Boise:Abbvie: Consultancy; AstraZeneca: Honoraria.

Evidence for Epitope-Specific T Cell Responses in HIV-Associated Non Neoplastic Lymphadenopathy: High-Throughput Immunogenetic Evidence

Non-neoplastic lymphadenopathy (NNL) associated with the human immunodeficiency virus (HIV) infection may develop concurrently with the onset of HIV viremia (acute retroviral syndrome) that can persist beyond the acute phase. Histopathological findings at this early phase mainly pertain to hyperplastic changes with large lymphoid follicles; with time, the number of lymphoid follicles diminishes, while plasma cells increase; at the extreme is a pattern characterized by sclerosis of the germinal centers in the residual follicles. HIV-specific CD8+ T cell responses have been reported and certain viral protein epitopes have been identified e.g. the p24 protein, a component of the HIV particle capsid. Overall, these findings reflect an ongoing immune response that is still incompletely characterized at the molecular level, particularly as it concerns the composition of the T cell receptor (TR) gene repertoire. In order to obtain a comprehensive view into the role of antigen selection in shaping T cell responses in HIV-associated NNL [HIV(+) NNL], we studied in-depth the TR repertoire in: (i) lymph node biopsy samples from 12 patients with HIV(+) NNL, (ii) lymph node samples from 5 non-HIV patients with reactive lymphadenopathy [HIV(-) RL]; and, (iii) peripheral blood samples from 4 healthy, HIV-seronegative individuals without lymphadenopathy [healthy controls, HIV(-) HC]. Genomic DNA was isolated from either paraffin-embedded lymph nodes (for patients with lymphadenopathy) or blood mononuclear cells (for healthy individuals). TRBV-TRBD-TRBJ gene rearrangements were amplified according to the BIOMED2 protocol. PCR products were subjected to next generation sequencing (NGS) on the MiSeq Illumina Platform. NGS data analysis, interpretation and visualization was performed by a validated, in-house bioinformatics pipeline. Overall, we obtained: (i) 1,440,305 (mean: 120,025) productive rearrangement sequences in the HIV(+) NNL group; (ii) 702,533 (mean: 140,506) productive sequences in the HIV(-) RL group; and, (iii) 539,981 (mean: 134,995) productive sequences in HIV(-) HC cases. Rearrangements with identical TRBV gene usage and CDR3 sequence were defined as clonotypes. In total, we identified 15,553 unique clonotypes in patients with HIV(+) NNL (mean: 1,296, range: 337-6,212), 53,874 in HIV(-) RL (mean: 10,774, range: 3,336-16,304) and 220,069 clonotypes in HIV(-) HC cases (mean; 55,017, range: 35,430-68,916), indicating significant repertoire restriction in the former group. Indeed, this group was characterized by an increased level of oligoclonality compared to the other two groups: the mean values of the sum of relative frequencies for the 10 most frequent clonotypes were 80%, 19.6% and 16.5%, respectively. Seven of 12 HIV(+) NNL cases carried the same dominant clonotype (TRBV29-1, SVDPSGTGGEGYT) that was also found in the remaining 5 patients of this group, albeit at lower frequencies; in contrast, it was completely absent in the HIV(-) RL and HIV(-) HC groups. Regarding the TRBV gene repertoire, the TRBV29-1 gene was overrepresented (p<0.005) in the HIV(+) NNL group, whereas the TRBV6-5 and TRBV19 genes were frequent in both groups of patients with lymphadenopathy (HIV-associated or not); finally, the TRBV5-1 was underrepresented (p<0.005) in patients with lymphadenopathy (HIV-associated or not) compared to HIV(-) HC cases. Comparison of the present TR gene sequence dataset against public databases identified 2 clonotypes with an established reactivity against the p24 protein that were present in 2 different patients with HIV(+) NNL of the present cohort. In conclusion, the TR gene repertoire of patients with HIV(+) NNL displays increased level of clonality, distinct TRBV gene repertoire as well as a widely shared, specific dominant clonotype compared to HIV(-) RL cases or HIV(-) healthy controls. These findings allude to an antigen-driven, HIV-specific immune process, a claim also supported by the detection of clonotypes with established anti-HIVp24 reactivity in at least a fraction of the analyzed patients. DisclosuresGemenetzi:Gilead: Research Funding. Agathangelidis:Gilead: Research Funding. Stamatopoulos:Janssen: Honoraria, Research Funding; Gilead: Honoraria, Research Funding; Abbvie: Honoraria, Research Funding. Hadzidimitriou:Gilead: Research Funding; Janssen: Honoraria, Research Funding; Abbvie: Research Funding.

Inherent DNA‐binding specificities of the HIF‐1α and HIF‐2α transcription factors in chromatin

Hypoxia‐inducible factor (HIF) is the major transcriptional regulator of cellular responses to hypoxia. The two principal HIF‐α isoforms, HIF‐1α and HIF‐2α, are progressively stabilized in response to hypoxia and form heterodimers with HIF‐1β to activate a broad range of transcriptional responses. Here, we report on the pan‐genomic distribution of isoform‐specific HIF binding in response to hypoxia of varying severity and duration, and in response to genetic ablation of each HIF‐α isoform. Our findings reveal that, despite an identical consensus recognition sequence in DNA, each HIF heterodimer loads progressively at a distinct repertoire of cell‐type‐specific sites across the genome, with little evidence of redistribution under any of the conditions examined. Marked biases towards promoter‐proximal binding of HIF‐1 and promoter‐distant binding of HIF‐2 were observed under all conditions and were consistent in multiple cell type. The findings imply that each HIF isoform has an inherent property that determines its binding distribution across the genome, which might be exploited to therapeutically target the specific transcriptional output of each isoform independently.

Distinct transcriptional repertoire of the androgen receptor in ETS fusion-negative prostate cancer

BackgroundProstate cancer (PCa) tumors harboring translocations of ETS family genes with the androgen responsive TMPRSS2 gene (ETS+ tumors) provide a robust biomarker for detecting PCa in approximately 70% of patients. ETS+ PCa express high levels of the androgen receptor (AR), yet PCa tumors lacking ETS fusions (ETS−) also express AR and demonstrate androgen-regulated growth. In this study, we evaluate the differences in the AR-regulated transcriptomes between ETS+ and ETS− PCa tumors.Methods10,608 patient tumors from three independent PCa datasets classified as ETS+ (samples overexpressing ERG or other ETS family members) or ETS− (all other PCa) were analyzed for differential gene expression using false-discovery-rate adjusted methods and gene-set enrichment analysis (GSEA).ResultsBased on the expression of AR-dependent genes and an unsupervised Principal Component Analysis (PCA) model, AR-regulated gene expression alone was able to separate PCa samples into groups based on ETS status in all PCa databases. ETS status distinguished several differentially expressed genes in both TCGA (6.9%) and GRID (6.6%) databases, with 413 genes overlapping in both databases. Importantly, GSEA showed enrichment of distinct androgen-responsive genes in both ETS− and ETS+ tumors, and AR ChIP-seq data identified 131 direct AR-target genes that are regulated in an ETS-specific fashion. Notably, dysregulation of ETS-dependent AR-target genes within the metabolic and non-canonical WNT pathways was associated with clinical outcomes.ConclusionsETS status influences the transcriptional repertoire of the AR, and ETS− PCa tumors appear to rely on distinctly different AR-dependent transcriptional programs to drive and sustain tumorigenesis.

Comparative Analysis of B-Cell Receptor Repertoires Induced by Live Yellow Fever Vaccine in Young and Middle-Age Donors.

Age-related changes can significantly alter the state of adaptive immune system and often lead to attenuated response to novel pathogens and vaccination. In present study we employed 5′RACE UMI-based full length and nearly error-free immunoglobulin profiling to compare plasma cell antibody repertoires in young (19–26 years) and middle-age (45–58 years) individuals vaccinated with a live yellow fever vaccine, modeling a newly encountered pathogen. Our analysis has revealed age-related differences in the responding antibody repertoire ranging from distinct IGH CDR3 repertoire properties to differences in somatic hypermutation intensity and efficiency and antibody lineage tree structure. Overall, our findings suggest that younger individuals respond with a more diverse antibody repertoire and employ a more efficient somatic hypermutation process than elder individuals in response to a newly encountered pathogen.

An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila.

Erwinia tracheiphila is the causal agent of bacterial wilt of cucurbits, an economically important phytopathogen affecting an economically important phytopathogen affecting few cultivated Cucurbitaceae few cultivated Cucurbitaceae host plant species in temperate eastern North America. However, essentially nothing is known about E. tracheiphila population structure or genetic diversity. To address this shortcoming, a representative collection of 88 E. tracheiphila isolates was gathered from throughout its geographic range, and their genomes were sequenced. Phylogenomic analysis revealed three genetic clusters with distinct hrpT3SS virulence gene repertoires, host plant association patterns, and geographic distributions. Low genetic heterogeneity within each cluster suggests a recent population bottleneck followed by population expansion. We showed that in the field and greenhouse, cucumber (Cucumis sativus), which was introduced to North America by early Spanish conquistadors, is the most susceptible host plant species and the only species susceptible to isolates from all three lineages. The establishment of large agricultural populations of highly susceptible C. sativus in temperate eastern North America may have facilitated the original emergence of E. tracheiphila into cucurbit agroecosystems, and this introduced plant species may now be acting as a highly susceptible reservoir host. Our findings have broad implications for agricultural sustainability by drawing attention to how worldwide crop plant movement, agricultural intensification, and locally unique environments may affect the emergence, evolution, and epidemic persistence of virulent microbial pathogens.IMPORTANCEErwinia tracheiphila is a virulent phytopathogen that infects two genera of cucurbit crop plants, Cucurbita spp. (pumpkin and squash) and Cucumis spp. (muskmelon and cucumber). One of the unusual ecological traits of this pathogen is that it is limited to temperate eastern North America. Here, we complete the first large-scale sequencing of an E. tracheiphila isolate collection. From phylogenomic, comparative genomic, and empirical analyses, we find that introduced Cucumis spp. crop plants are driving the diversification of E. tracheiphila into multiple lineages. Together, the results from this study show that locally unique biotic (plant population) and abiotic (climate) conditions can drive the evolutionary trajectories of locally endemic pathogens in unexpected ways.

Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution

Subtelomeres of most eukaryotes contain fast-evolving genes usually involved in adaptive processes. In common bean (Phaseolus vulgaris), the Co-2 anthracnose resistance (R) locus corresponds to a cluster of nucleotide-binding-site leucine-rich-repeat (NL) encoding sequences, the prevalent class of plant R genes. To study the recent evolution of this R gene cluster, we used a combination of sequence, genetic and cytogenetic comparative analyses between common bean genotypes from two distinct gene pools (Andean and Mesoamerican) that diverged 0.165 million years ago. Co-2 is a large subtelomeric cluster on chromosome 11 comprising from 32 (Mesoamerican) to 52 (Andean) NL sequences embedded within khipu satellite repeats. Since the recent split between Andean and Mesoamerican gene pools, the Co-2 cluster has experienced numerous gene-pool specific NL losses, leading to distinct NL repertoires. The high proportion of solo-LTR retrotransposons indicates that the Co-2 cluster is located in a hot spot of unequal intra-strand homologous recombination. Furthermore, we observe large segmental duplications involving both Non-Homologous End Joining and Homologous Recombination double-strand break repair pathways. Finally, the identification of a Mesoamerican-specific subtelomeric sequence reveals frequent interchromosomal recombinations between common bean subtelomeres. Altogether, our results highlight that common bean subtelomeres are hot spots of recombination and favor the rapid evolution of R genes. We propose that chromosome ends could act as R gene incubators in many plant genomes.

Genetic and nongenetic factors that may predispose individuals to allergic drug reactions.

Defining predisposition to allergic drug reactions has largely focussed on HLA associations, but other genetic and nongenetic factors are also likely to be involved. Polymorphic genetic variants in cytokine genes, including IL-10, and co-signalling pathways, including CTLA4, have been associated with allergic drug reactions, but the effect size is lower than with HLA alleles and most associations have not been replicated. Although TCR specificity seems to be important for CBZ-induced SJS/TEN in South East Asian patients, a distinct repertoire may not play a role in reactions to other drugs. New mass spectrometric techniques allowing for the identification of naturally eluted peptides from drug-exposed HLA alleles will allow for the antigenic source of T-cell activation to be defined and may shed light on the influence of disease. Indeed, preliminary data highlight the propensity of drug-responsive T cells to cross-react with T cells primed to viral antigens. Furthermore, the environment can epigenetically influence regulatory gene expression, suggesting that an individual's family exposure history may alter immune thresholds and tip the balance toward activation. It is likely that predisposition to allergic drug reactions is multifaceted in most cases. This will require the study of large numbers of patients to detect genetic factors that have a lower effect size than HLA alleles. This should be accompanied by detailed clinical phenotyping of patients and the assessment of the immunological phenotype with respect to the presence and type of drug antigen-responsive T cells.

Noc4L Dependent Ribosome Biogenesis Controls Treg Activation

Tregs activation is crucial for maintaining self-tolerance, but the translational regulation of this process is still poorly understood. Although ribosome biogenesis is considered a housekeeping process, emerging evidence supports a new hypothesis that different types of cells may actually contain distinct repertoires of ribosome biogenesis factors that generate specialized ribosomes and confer the translation of selected mRNAs. Here, we focused on the ribosome biogenesis factor Noc4L, based on the observations that Noc4L is highly expressed in activated Treg cells. Conditional Noc4L knockout in Tregs resulted in a lethal autoimmune phenotype, resembling Treg deficient scurfy mice. Interestingly, the Noc4L defect did not globally affect the overall protein translation in Tregs but rather was selectively detrimental to the expression of genes related to Treg activation. These results demonstrate the critical role of Noc4L dependent ribosome biogenesis in controlling the activation of Tregs and maintaining immune tolerance.

Narratives of Those Who “Love” Violently: Identity Issues and Construction of Meaning of the Batterers

The present study aims to identify and analyze the interpretative repertoires on love and intimate relationships used by wife batterers, exploring how the repertoires may influence the development and experience of violent intimate relationships, and how this is linked to the identity issues. Twelve wife batterers participated in the study, answering to an individual interview on their lives’ love story. Through a discourse analysis of the data, five distinct interpretative repertoires were identified—romantic, companion, passionate, pragmatic and game-playing love—and their meaning construction was analyzed. It is discussed what repertoires reveal about gender roles prescribed by the model of masculinity, and how these gender roles constrain the construction of the identity, the personal growth and the self-actualization of the batterers.

Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges.

Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.

Adult Born Periglomerular Cells of Odorant Receptor Specific Glomeruli.

The OR37 subsystem is characterized by a variety of unique features. The odorant receptors (ORs) of this subfamily are selectively tuned to specific ligands which are supposed to play a role in social communication. OR37 expressing sensory neurons project their axons to a single receptor specific glomerulus per bulb which have been shown to be unusually stable in size and to possess a distinct repertoire of periglomerular cells. Since the neuronal network surrounding glomeruli is typically modified by the integration of adult born neurons, in this study it was investigated whether the number of adult born cells might be different for OR37 glomeruli compared to other OR-specific glomeruli. Towards this goal, 23 days after BrdU injection, BrdU labeled cells in the proximity of OR37A glomeruli as well as around OR18-2 and OR256-17 glomeruli were determined. It was found that the number of BrdU labeled cells in the periglomerular region of OR37A glomeruli was significantly lower compared to glomeruli of the other OR types. This finding was in line with a lower number of neuroblasts visualized by the marker protein doublecortin. Double labeling experiments for BrdU and marker proteins revealed that despite a relatively high number of calretinin expressing cells at the OR37A glomeruli, the number of cells co-stained with BrdU was quite low compared to other glomeruli, which may point to an individual turnover rate of this cell type for different glomeruli. Together, the results of the present study support the notion that the neuronal network at the OR37 glomeruli is less dynamic than that of other glomerulus types. This indicates a specific processing of social information in OR37 glomerular networks.

Erotic mirrors. Eroticism in the mirror. An iconography of love in ancient Greece (fifth to fourth century B.C.)

This text consists of an interpretive essay about the meaning(s) of the “mirror” as an object in Mainland and Aegean Greece (in contrast to Western/Colonial Greece), based on iconography. I take into consideration two distinct repertoires of images: the paintings of Attic vases (late sixth – early fourth century B.C.) and the figurative decoration on the mirrors themselves, in relief or engraved (late fifth – early third century B.C.). The central focus of the analysis is the iconography registered on mirrors produced in the four main manufacturing centers of Greece (Athens, Corinth, Chalcis, Ionia). Greeks produced three types of mirrors between Late Archaic and Early Hellenistic times: hand-mirrors with handle, table mirrors with stand, and round box mirrors, the latter being the most important to this study. Box mirrors may bear iconography on their folding cover, in relief on the external surface (repoussé) or engraved on the interior surface. In contrast to the iconography of the vases of Magna Graecia, in which the mystic component stands out from the other symbolic aspects, in the case of the iconography of Greek mirrors erotic symbolism and the relation with the goddess Aphrodite predominate. This goddess protects all categories of women (hetaerae and "citizen-women", married or brides) and all modalities of eroticism. Under the auspices of love and desire, the symbolic power of the mirror can be related to an inclusive eroticism, which unites, that which society separates.

Taxonomic validation of Encheliophis chardewalli with description of calling abilities.

Encheliophis chardewalli was described from a single cleared and stained specimen. Twelve years later, additional specimens were found in the lagoon of Moorea (French Polynesia) in association with their host, the sea cucumber Actinopyga mauritiana. These fish were used to consolidate the species diagnosis, to validate species status and to record sound production. This species is remarkable because of its ability to penetrate inside the cloaca of sea cucumbers having anal teeth and the fact this species is largely unknown despite it lives in lagoons in 1m depth. Encheliophis chardewalli produced three sound types: long regular calls made of trains of numerous pulses, short irregular calls characterized by a constant lowering of its pulse period and short regular call (or knock) made of 3 to 6 pulses. Comparison with other sympatric Carapini supports a large and distinct repertoire. Morphological characteristics could be the result of reduced body size allowing to penetrate inside a new host, thus avoiding competition and conflict with other larger sympatric Carapini species.