Individual Repertoires Research Articles

Extraordinary variation in a simple song: No geographical patterns in initial phrase variation of the Yellowhammer, a passerine with pronounced dialects

AbstractGeographical variation of birdsong is used to study various topics from cultural evolution to mechanisms responsible for reproductive barriers or song acquisition. In species with pronounced dialects, however, patterns of variation in non-dialect parts of the song are usually overlooked. We focused on the individually variable initial phrase of the song of the Yellowhammer (Emberiza citrinella), a common Palearctic passerine which became a model species for dialect research. We used a quantitative method to compare the similarity of initial phrases from the repertoires of 237 males recorded at different spatial scales in a central European country covering all main dialect types. We hypothesized that patterns of initial phrase sharing and/or phrase similarity are affected by dialect boundaries and geographical proximity (i.e. that birds from the same dialect regions use more similar phrases or share them more often). Contrary to our expectations, initial phrase variation seems unrelated to dialects, as we did not find higher similarity either among recordings from the same dialect areas or among those from the same locality. Interestingly, despite the immense variability of phrase types detected (only 16% of 368 detected initial phrase types were shared between at least 2 males), a relatively high proportion of males (45%) was involved in sharing, and males using the same initial phrase were located anywhere from tens of meters to hundreds of kilometers apart. The patterns of variation suggest that precise copying during song learning as well as improvisation play important roles in forming individual repertoires in the Yellowhammer. Our data also confirm previous indications that the repertoires of Yellowhammer males (i.e. the composition of initial phrases) are individually unique and temporally stable. This makes the species a good candidate for individual acoustic monitoring, useful for detailed population or behavioral studies without the need for physical capture and marking of males.

The Evolutionary Arms Race between Virus and NK Cells: Diversity Enables Population-Level Virus Control.

Viruses and natural killer (NK) cells have a long co-evolutionary history, evidenced by patterns of specific NK gene frequencies in those susceptible or resistant to infections. The killer immunoglobulin-like receptors (KIR) and their human leukocyte antigen (HLA) ligands together form the most polymorphic receptor-ligand partnership in the human genome and govern the process of NK cell education. The KIR and HLA genes segregate independently, thus creating an array of reactive potentials within and between the NK cell repertoires of individuals. In this review, we discuss the interplay between NK cell education and adaptation with virus infection, with a special focus on three viruses for which the NK cell response is often studied: human immunodeficiency virus (HIV), hepatitis C virus (HCV) and human cytomegalovirus (HCMV). Through this lens, we highlight the complex co-evolution of viruses and NK cells, and their impact on viral control.

Variation in Wolbachia cidB gene, but not cidA, is associated with cytoplasmic incompatibility mod phenotype diversity in Culex pipiens.

Endosymbiotic Wolbachia bacteria are, to date, considered the most widespread symbionts in arthropods and are the cornerstone of major biological control strategies. Such a high prevalence is based on the ability of Wolbachia to manipulate their hosts' reproduction. One manipulation called cytoplasmic incompatibility (CI) is based on the death of the embryos generated by crosses between infected males and uninfected females or between individuals infected with incompatible Wolbachia strains. CI can be seen as a modification‐rescue system (or mod‐resc) in which paternal Wolbachia produce mod factors, inducing embryonic defects, unless the maternal Wolbachia produce compatible resc factors. Transgenic experiments in Drosophila melanogaster and Saccharomyces cerevisiae converged towards a model where the cidB Wolbachia gene is involved in the mod function while cidA is involved in the resc function. However, as cidA expression in Drosophila males was required to observe CI, it has been proposed that cidA could be involved in both resc and mod functions. A recent correlative study in natural Culex pipiens mosquito populations has revealed an association between specific cidA and cidB variations and changes in mod phenotype, also suggesting a role for both these genes in mod diversity. Here, by studying cidA and cidB genomic repertoires of individuals from newly sampled natural C. pipiens populations harbouring wPipIV strains from North Italy, we reinforce the link between cidB variation and mod phenotype variation fostering the involvement of cidB in the mod phenotype diversity. However, no association between any cidA variants or combination of cidA variants and mod phenotype variation was observed. Taken together our results in natural C. pipiens populations do not support the involvement of cidA in mod phenotype variation.

Exploring syntactic variation by means of “Language Production Experiments”: Methods from and analyses on German in Austria

AbstractThis article presents computer supported “language production experiments” (LPEs) as a method for the investigation of syntactic variation. It describes the setup for the investigation of numerous syntactic phenomena and provides a sample study of the German GET passive across Austria. It also suggests that LPEs offer possibilities for the targeted investigation of linguistic variation in various ways. They may be used to explore speakers’ individual linguistic repertoires and an according corpus setup can be used to examine e.g., interspeaker patterns of variation. LPEs also enable researchers to investigate which linguistic factors control or influence syntactic variation.

Exploring the Betsy Rymes' Three-Dimensional Approach: A Review of Classroom Discourse Analysis: A Tool for Critical Reflection

This book review examines the 2nd edition of Betsy Rymes' Classroom Discourse Analysis: A Tool for Critical Reflection. It includes an outline of each chapter's content, discusses the several distinctive features of the book, and its possible contribution to educational research from a practitioner's point of view. The book has nine chapters. The first four chapters first introduce the readers to basic concepts of discourse analysis within a three-dimensional approach, and then provides techniques and strategies for recording, viewing, transcribing and analyzing classroom talk through examples, activities, and questions. From Chapter V to VIII, Rymes focuses on particular resources utilized in classroom discourse such as turn taking, contextualization, storytelling and framing. Chapter IX revisits the three dimensions of classroom discourse and discusses how such a perspective may be integrated in teaching practice with an understanding of individual communicative repertoire. Overall, the book is a how-to-book for in-service teachers who would like to resolve issues of communication in their classrooms, and develop their interaction with their students.

A Framework for Annotation of Antigen Specificities in High-Throughput T-Cell Repertoire Sequencing Studies.

Recently developed molecular methods allow large-scale profiling of T-cell receptor (TCR) sequences that encode for antigen specificity and immunological memory of these cells. However, it is well-known that the even unperturbed TCR repertoire structure is extremely complex due to the high diversity of TCR rearrangements and multiple biases imprinted by VDJ rearrangement process. The latter gives rise to the phenomenon of “public” TCR clonotypes that can be shared across multiple individuals and non-trivial structure of the TCR similarity network. Here, we outline a framework for TCR sequencing data analysis that can control for these biases in order to infer TCRs that are involved in response to antigens of interest. We apply two previously published methods, ALICE and TCRNET, to detect groups of homologous TCRs that are enriched in samples of interest. Using an example dataset of donors with known HLA haplotype and CMV status, we demonstrate that by applying HLA restriction rules and matching against a database of TCRs with known antigen specificity, it is possible to robustly detect motifs of epitope-specific responses in individual repertoires. We also highlight potential shortcomings of TCR clustering methods and demonstrate that highly expanded TCRs should be individually assessed to get the full picture of antigen-specific response.

Working with mediagrams: a methodology for collaborative research on mediational repertoires in multilingual families

ABSTRACT This paper contributes to current sociolinguistic research on the rapidly-changing landscape of digitally mediated communication (Androutsopoulos and Stæhr 2018) by presenting mediagrams, a new method for research on transnational mediated interaction. Based on an ethnographic study of mediated multilingual communication in four families with Senegalese-background living in Norway, we develop a visualisation scheme for the documentation and analysis of individual mediational repertoires. Starting with a review of visualisations used in relevant research and an outline of the context of our study, we present the production of mediagrams as a collaborative research process and their subsequent use in further data collection and analysis. Based on participants’ language portraits, media maps, and self-selected excerpts of digital conversations, the collected data is coded and visualised in graphs that represent individual networks of interlocutors, language choices, language modalities, and media channels. Follow-up interviews lead to amended versions of mediagrams, which eventually form the basis for the analysis of individual mediational repertoires. In concluding we assess mediagram research as a contribution to citizen sociolinguistics (Svendsen 2018) and discuss blind spots of the method and its potential for wider application.

An integrated hierarchical model of 5th grade students’ computational estimation strategies

ABSTRACT In this study, we propose an integrated hierarchical model of computational estimation strategies (IHMCES), which can be used to organize a set of computational estimation strategies, used by a group of individuals, in strategy ranges. IHMCES can be used for the description of the repertoire, profile and flexibility of individuals regarding the strategies used. We investigated the computational estimation strategies used by sixty-two 5th grade Greek students. One group of students, were taught with traditional teaching methods while another group, with instructional intervention in computational estimation strategies. Both groups were examined and their computational estimation strategies were analysed. The students’ strategy analysis enabled us to identify the strategy ranges used by every student and also describe the changes in every student’s strategy range.

Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets.

The strength and breadth of an individual’s antibody repertoire is an important predictor of their response to influenza infection or vaccination. Although progress has been made in understanding qualitatively how repeated exposures shape the antibody mediated immune response, quantitative understanding remains limited. We developed a set of mathematical models describing short-term antibody kinetics following influenza infection or vaccination and fit them to haemagglutination inhibition (HI) titres from 5 groups of ferrets which were exposed to different combinations of trivalent inactivated influenza vaccine (TIV with or without adjuvant), A/H3N2 priming inoculation and post-vaccination A/H1N1 inoculation. We fit models with various immunological mechanisms that have been empirically observed but have not previously been included in mathematical models of antibody landscapes, including: titre ceiling effects, antigenic seniority and exposure-type specific cross reactivity. Based on the parameter estimates of the best supported models, we describe a number of key immunological features. We found quantifiable differences in the degree of homologous and cross-reactive antibody boosting elicited by different exposure types. Infection and adjuvanted vaccination generally resulted in strong, broadly reactive responses whereas unadjuvanted vaccination resulted in a weak, narrow response. We found that the order of exposure mattered: priming with A/H3N2 improved subsequent vaccine response, and the second dose of adjuvanted vaccination resulted in substantially greater antibody boosting than the first. Either antigenic seniority or a titre ceiling effect were included in the two best fitting models, suggesting a role for a mechanism describing diminishing antibody boosting with repeated exposures. Although there was considerable uncertainty in our estimates of antibody waning parameters, our results suggest that both short and long term waning were present and would be identifiable with a larger set of experiments. These results highlight the potential use of repeat exposure animal models in revealing short-term, strain-specific immune dynamics of influenza.

Songbird presumed to be age‐limited learner may change repertoire size and composition throughout their life

AbstractSongbirds learn to sing by imitating their conspecific songs through social learning. It is commonly thought that in species with small repertoires, so‐called crystallization of the song repertoire takes place before the first breeding attempt and afterwards their repertoires remain unchanged. However, the number of studies in which individual song repertoires have been tracked longitudinally under natural conditions is still small. The ortolan bunting (Emberiza hortulana) is a small Eurasian passerine species. Studies on this species have shown that males have small song repertoires (usually 2–3), share the same final phrase within a local dialect area, and their repertoires remain unchanged during their lifetimes. We studied the whole, isolated Norwegian population of this species with 100–150 individually marked males. We compared repertoire sizes and contents using cross‐sectional and longitudinal approaches. We focused on marked males aged 2–10 years and recorded in up to five breeding seasons between 2001 and 2006. There was no local dialect because songs with different final phrases occurred both within and between males. Repertoire size varied between 1 and 24 (4.7 ± 3.4) song types per male. Longitudinal analysis showed an increase in repertoire size in 29% and a decrease in 21% of males. Males whose repertoires remained the same in size between years often substantially changed in contents. New song types appeared in almost 70% of males, and over 30% of males started singing new syllable types after the second calendar year. In almost 50% of males, new song types appeared that were built as new combinations of syllables shown in previous years. In 30% of males, the song complexity increased with age. Simultaneously, over 60% of males selectively ceased singing some song types. We suggest that these repertoire alterations are linked to the isolation and fragmentation of this population, which may affect song learning patterns through increased breeding dispersal and a strongly male‐biased sex ratio. Similar studies from abundant and continuous populations of the species are needed to test this idea.

Peripheral IgE Repertoires of Healthy Donors Carry Moderate Mutation Loads and Do Not Overlap With Other Isotypes.

IgE-mediated allergic disease represents an increasing health problem. Although numerous studies have investigated IgE sequences in allergic patients, little information is available on the healthy IgE repertoire. IgM, IgG, IgA, and IgE transcripts from peripheral blood B cells of five healthy, non-atopic individuals were amplified by unbiased, template-switching, isotype-specific PCR. Complete VDJ regions were sequenced to near-exhaustion on the PacBio platform. Sequences were analyzed for clonal relationships, degree of somatic hypermutation, IGHV gene usage, evidence of antigenic selection, and N-linked glycosylation motifs. IgE repertoires appeared to be highly oligoclonal with preferential usage of certain IGHV genes compared to the other isotypes. IgE sequences carried more somatic mutations than IgM, yet fewer than IgG and IgA. Many IgE sequences contained N-linked glycosylation motifs. IgE sequences had no clonal relationship with the other isotypes. The IgE repertoire in healthy individuals is derived from relatively few clonal expansions without apparent relations to immune reactions that give rise to IgG or IgA. The mutational burden of normal IgE suggests an origin through direct class-switching from the IgM repertoire with little evidence of antigenic drive, and hence presumably low affinity for specific antigens. These findings are compatible with a primary function of the healthy IgE repertoire to occupy Fcε receptors for competitive protection against mast cell degranulation induced by allergen-specific, high-affinity IgE. This background knowledge may help to elucidate pathogenic mechanisms in allergic disease and to design improved desensitization strategies.

Species-level repertoire size predicts a correlation between individual song elaboration and reproductive success.

Birdsong has long been considered a sexually selected trait that relays honest information about male quality, and laboratory studies generally suggest that female songbirds prefer larger repertoires. However, analysis of field studies across species surprisingly revealed a weak correlation between song elaboration and reproductive success, and it remains unknown why only certain species show this correlation in nature. Taken together, these studies suggest that females in numerous species can detect and prefer larger repertoires in a laboratory setting, but larger individual repertoires correlate with reproductive success only in a subset of these species. This prompts the question: Do the species that show a stronger correlation between reproductive success and larger individual repertoires in nature have anything in common? In this study, we test whether between‐species differences in two song‐related variables—species average syllable repertoire size and adult song stability over time—can be used to predict the importance of individual song elaboration in reproductive success within a species. Our cross‐species meta‐analysis of field studies revealed that species with larger average syllable repertoire sizes exhibited a stronger correlation between individual elaboration and reproductive success than species with smaller syllable repertoires. Song stability versus plasticity in adulthood provided little predictive power on its own, suggesting that the putative correlation between repertoire size and age in open‐ended learners does not explain the association between song elaboration and reproductive success.

Board Certified Behavior Analysts' Supervisory Practices of Trainees: Survey Results and Recommendations.

The field of behavior analysis relies on supervised fieldwork to shape the repertoires of individuals aspiring to sit for the Behavior Analyst Certification Board® (BACB®) exam. Board Certified Behavior Analysts® (BCBAs®) who are providing supervision to those seeking certification must follow the supervision and ethics requirements as directed by the BACB. We conducted a survey of BCBAs currently providing supervision to gather information about current practices and barriers. The top areas of success and need are presented based on the responses of 284 participants who completed the entire survey, along with recommendations.

Fragmentation in high-choice media environments from a micro-perspective: Effects of selective exposure on issue diversity in individual repertoires

AbstractOnline communication is often seen to promote audience fragmentation because it facilitates selective exposure and therefore is likely to divide audiences into sub-publics that hardly share common issues with other sub-publics. This study takes a micro-perspective on fragmentation by focusing on issue diversity in media items users have encountered in a particular week. Diversity was assessed via content analyses based on online diaries of 645 participants who recorded their media use concerning the German debates on climate change and federal elections. Findings show lower degrees of diversity for users of non-journalistic online media than for users of journalistic mass media.

PF444 IDENTIFICATION OF T‐CELL RECEPTORS FROM THE ALLOGENEIC‐HLA REPERTOIRE SPECIFIC FOR MELANOMA‐ASSOCIATED ANTIGENS

Background:Melanoma‐associated antigens (MAGE) are highly expressed in multiple myelomas as well as solid tumors, but silent in normal cells except for male germ line cells. This tumor‐restricted expression makes it an excellent target for adoptive T cell therapy. However, due to thymic selection high‐affinity T cells against self‐antigens presented in the context of self‐HLA are deleted from the T‐cell repertoire of a patient. To overcome this problem, we identify T‐cell receptors (TCRs) from the allogeneic‐HLA repertoire instead of the autologous‐HLA repertoire.Aims:To identify high‐affinity T‐cell receptors from the allogeneic‐HLA repertoire specific for melanoma‐associated antigens.Methods:In this study we selected MAGE peptides by peptide elution experiments from HLA class I and subsequent mass spectrometric analysis of tumor cells. Only peptides binding in the most frequently occurring HLA‐alleles were selected. From the identified peptides, HLA‐tetramers were formed to isolate peptide specific CD8+ T cells from healthy allogeneic donors. Avidity of the selected T‐cell clones was determined by stimulation assays including a broad range of MAGE expressing tumor cell lines. To examine off‐target recognition, T‐cell clones were stimulated with MAGE negative cell lines and EBV‐transformed B lymphoblastic cells expressing all prevalent HLA molecules.Results:MAGE peptides were eluted from multiple myelomas, EBV‐transformed lymphoblastic cells, acute myeloid leukemia and ovarium carcinomas. For MAGE‐A1, T‐cell clones specific for four different epitopes presented in the context of HLA‐A∗01:01, HLA‐A∗03:01, HLA‐B∗07:02 and HLA‐C∗07:02 were selected. For MAGE‐A3, T‐cell clones specific for one epitope presented in the context of HLA‐A∗01:01 and HLA‐B∗35:01 were identified. The selected T‐cell clones demonstrated efficient recognition of MAGE‐A1 or MAGE‐A3 positive multiple myeloma and solid tumor cell lines without detectable cross‐reactivity.Summary/Conclusion:MAGE‐A1 and MAGE‐A3 specific T‐cell clones were isolated from the allogeneic‐HLA repertoire of healthy individuals. The identified clones were activated upon exposure to MAGE‐A1 or MAGE‐A3 positive tumor cell lines and showed limited off‐target recognition. These newly identified TCRs could potentially be used for TCR‐gene therapy strategies targeting MAGE‐A1 or MAGE‐A3 positive tumors.

Trilingual repertoires, multifaceted experiences: multilingualism among Poles in Norway

ABSTRACTThis article examines the multilingual repertoires of adult and adolescent Poles living in Norway. The study draws on language portraits and interviews conducted with 14 adults and 12 adolescents living in and around Oslo. The article first discusses multilingualism of the research participants through an analysis of the 26 portraits and then zooms in on the drawings and interview data provided by one family in order to shed light on the ways the participants experience and construct the roles of their different linguistic resources. The study demonstrates that, in general, the research participants are multilingual and that three languages in particular – Polish, English and Norwegian – form an important part of their repertoires. The findings suggest that these linguistic resources and the roles they take on in the individual repertoires, however, might be experienced very differently by the participants. Furthermore, the analysis points to the existence of competing language ideologies among the researched cohort.

Detection of a Low Level and Heterogeneous B Cell Immune Response in Peripheral Blood of Acute Borreliosis Patients With High Throughput Sequencing.

The molecular diagnosis of acute Borreliosis is complicated and better strategies to improve the diagnostic processes are warranted. High Throughput Sequencing (HTS) of human B cell repertoires after e.g., Dengue virus infection or influenza vaccination revealed antigen-associated “CDR3 signatures” which may have the potential to support diagnosis in infectious diseases. The human B cell immune response to Borrelia burgdorferi sensu lato—the causative agent of Borreliosis—has mainly been studied at the antibody level, while less attention has been given to the cellular part of the humoral immune response. There are indications that Borrelia actively influence the B cell immune response and that it is therefore not directly comparable to responses induced by other infections. The main goal of this study was to identify B cell features that could be used to support diagnosis of Borreliosis. Therefore, we characterized the B cell immune response in these patients by combining multicolor flow cytometry, single Borrelia-reactive B cell receptor (BCR) sequencing, and B cell repertoire deep sequencing. Our phenotyping experiments showed, that there is no significant difference between B cell subpopulations of acute Borreliosis patients and controls. BCR sequences from individual epitope-reactive B cells had little in common between each other. HTS showed, however, a higher complementarity determining region 3 (CDR3) amino acid (aa) sequence overlap between samples from different timepoints in patients as compared to controls. This indicates, that HTS is sensitive enough to detect ongoing B cell immune responses in these patients. Although each individual's repertoire was dominated by rather unique clones, clustering of bulk BCR repertoire sequences revealed a higher overlap of IgG BCR repertoire sequences between acute patients than controls. Even if we have identified a few Borrelia-associated CDR3aa sequences, they seem to be rather unique for each patient and therefore not suitable as biomarkers.

Yemeni EFL Learners’ Identity Conflicts: An Exploratory Case Study

The importance of the concept of “identity” in the context of language learning is unassailable. Stemming from this premise, the current study is intended to explore the identity conflicts of a group of Yemeni learners who were studying English, as well as the techniques and strategies used to mitigate and/or lessen the conflicts between their actual identity and the identity associated with the target language, i.e., English. This research project used a qualitative exploratory case study research design with a sample of 20 students who were requested to write their journal diaries. Following that, semi-structured interviews were conducted using the double-sampling technique to select 10 of the previously sampled students who were proven to have written the most stimulating and intriguing journal entries. From the results of the study, tangible identity conflicts between the Yemeni culture and society at large and the implied behaviors and conventions accompanying the intensive study of the English language became apparent. The students exhibit a high level of motivation and they also exert their efforts using different techniques and strategies to excel at the learning and/or acquisition of the speaking skill of the English language. These conflicts may be consciously or subconsciously realized by the language learners, but what has been proven is that their attitudes, motivation and general inclinations towards the goal of speaking with a native or a native-like accent are unquestionably genuine. Lastly, the study suggested or recommended a revamp of the current textbooks giving teachers more training sessions in order to improve their individual repertoire, as well as a higher degree of awareness upon the part of the Yemeni society at large that these conflicts can interfere with the strong motivations, both aspirational and actual, to achieve the learning outcomes of the nation’s most promising future leaders and pioneers.

Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing

Studying immune repertoire in the context of organ transplant provides important information on how adaptive immunity may contribute and modulate graft rejection. Here we characterize the peripheral blood immune repertoire of individuals before and after kidney transplant using B cell receptor sequencing in a longitudinal clinical study. Individuals who develop rejection after transplantation have a more diverse immune repertoire before transplant, suggesting a predisposition for post-transplant rejection risk. Additionally, over 2 years of follow-up, patients who develop rejection demonstrate a specific set of expanded clones that persist after the rejection. While there is an overall reduction of peripheral B cell diversity, likely due to increased general immunosuppression exposure in this cohort, the detection of specific IGHV gene usage across all rejecting patients supports that a common pool of immunogenic antigens may drive post-transplant rejection. Our findings may have clinical implications for the prediction and clinical management of kidney transplant rejection.

Differential Recognition of Diet-Derived Neu5Gc-Neoantigens on Glycan Microarrays by Carbohydrate-Specific Pooled Human IgG and IgA Antibodies.

Sialic acids (Sias) cover vertebrate cell surface glycans. N-Acetylneuraminic acid (Neu5Ac) and its hydroxylated form N-glycolylneuraminic acid (Neu5Gc) are common Sia in mammals. Humans cannot synthesize Neu5Gc but accumulate it on cells through red-meat rich diets, generating numerous immunogenic Neu5Gc-neoantigens. Consequently, humans have diverse anti-Neu5Gc antibodies affecting xenotransplantation, cancer, atherosclerosis, and infertility. Anti-Neu5Gc antibodies circulate as IgG, IgM, and IgA isotypes; however, repertoires of the different isotypes in a large population have not been studied yet. Here, we used glycan microarrays to investigate anti-Neu5Gc IgGs and IgAs in intravenous immunoglobulin (IVIG) or pooled human IgA, respectively. Binding patterns on microarrays fabricated with Neu5Gc- and Neu5Ac-glycans, together with inhibition assays, revealed that different IVIG preparations have highly specific anti-Neu5Gc IgG reactivity with closely related repertoires, while IgAs show cross-reactivity against several Neu5Ac-glycans. Such different anti-Neu5Gc IgG/IgA repertoires in individuals could possibly mediate distinctive effects on human diseases.