Immunoglobulin levels in systemic lupus erythematosus: A narrative review.

Immunoglobulins play a fundamental role in the protection of the human body against internal and external threats. They also contribute to the immune system homeostasis and maintenance of self-tolerance. Hypogammaglobulinemia is occasionally encountered in routine clinical practice by rheumatologists. Low levels of immunoglobulins can occur as primary or secondary issues and may predispose patients to various forms of infection. However, the impact of the low immunoglobulin level abnormality varies with the underlying condition. In this narrative review, we shed light on the overall types and functions of immunoglobulins for clinicians. We discuss important principles of immunoglobulin measurements. We then consider the primary and secondary causes of low immunoglobulins with a special focus on hypogammaglobulinemia in patients with systemic lupus erythematosus (SLE).

A Mouse Model of Oral Sensitization to Hen's Egg White.

Egg allergy is one of the most common food allergies in children, being the most important allergenic proteins found in the egg white (EW). Allergy to EW shows a complex phenotype that involves a multifaceted reaction that can only be assessed in vivo. Although other routes of sensitization have been described, oral exposure to food antigens is one of the most suitable in humans. In mice, oral administration of allergenic proteins results in the development of tolerance, and the use of adjuvants, such as cholera toxin (CT), is required to promote Th2-biased immune responses over tolerogenic responses. In this regard, among the mouse strains that readily display Th2 responses, Balb/c has been widely used. Here, we describe a frequently used protocol of oral EW sensitization by using CT as an adjuvant and we explain in detail the methods that we have developed to analyze the sensitizing and eliciting capacity of EW proteins including evaluation of signs, measurement of serum levels of specific immunoglobulins, mast cell degranulation, cytokine secretion profile of allergen-reactive T cells, phenotyping of mesenteric lymph node- and spleen-derived dendritic and T cells by flow cytometry, and quantification of intestinal gene expression.

Muscarinic Acetylcholine Receptors Modulate Interleukin-6 Production and Immunoglobulin Class Switching in Daudi Cells.

B cells express muscarinic and nicotinic acetylcholine receptors (mAChRs and nAChRs, respectively). Following immunization with ovalbumin, serum immunoglobulin G (IgG) and interleukin (IL)-6 levels were lower in M1 and M5 mAChR double-deficient mice and higher in α7 nAChR-deficient mice than in wild-type mice. This suggests mAChRs participate in the cytokine production involved in B cell differentiation into plasma cells, which induces immunoglobulin class switching from IgM to IgG. However, because these results were obtained with conventional knockout mice, in which all cells in the body were affected, the specific roles of these receptors expressed in B cells remains unclear. In the present study, Daudi B lymphoblast cells were used to investigate the specific roles of mAChRs and nAChR in B cells. Stimulating Daudi cells using Pansorbin cells (heat-killed, formalin-fixed Staphylococcus aureus coated with protein A) upregulated expression of M1-M4 mAChRs and the α4 nAChR subunit. Under these conditions, mAChRs, but not nAChRs, mediated immunoglobulin class switching to IgG. This effect was blocked by scopolamine, a non-selective mAChR antagonist, and 4-diphenylacetoxy-N-methyl-piperidine methiodide (4-DAMP), a Gq/11-coupled M1, M3, M5 antagonist. In addition, IL-6 secretion was further enhanced following mAChR activation. Thus, Gq/11-coupled mAChRs expressed in B cells thus appear to contribute to IL-6 production and B cell maturation into IgG-producing plasma cells.

AncesTree: An interactive immunoglobulin lineage tree visualizer.

High-throughput sequencing of human immunoglobulin genes allows analysis of antibody repertoires and the reconstruction of clonal lineage evolution. The study of antibodies (Abs) affinity maturation is of specific interest to understand the generation of Abs with high affinity or broadly neutralizing activities. Moreover, phylogenic analysis enables the identification of the key somatic mutations required to achieve optimal antigen binding. The Immcantation framework provides a start-to-finish set of analytical methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) data. Furthermore, Immcantation's Change-O package has developed IgPhyML, an algorithm designed to build specifically immunoglobulin (Ig) phylogenic trees. Meanwhile Phylip, an algorithm that has been originally developed for applications in ecology and macroevolution, can also be used for the phylogenic reconstruction of antibodies maturation pathway. To complement Ig lineages made by IgPhyML or Dnaml (Phylip), we developed AncesTree, a graphic user interface (GUI) that aims to give researchers the opportunity to interactively explore antibodies clonal evolution. AncesTree displays interactive immunoglobulins phylogenic tree, Ig related mutations and sequence alignments using additional information coming from specialized antibody tools. The GUI is a Java standalone application allowing interaction with Ig tree that can run under Windows, Linux and Mac OS.

Beyond Macrophages and T Cells: B Cells and Immunoglobulins Determine the Fate of the Atherosclerotic Plaque.

Atherosclerosis (AS) leading to myocardial infarction and stroke remains worldwide the main cause for mortality. Vulnerable atherosclerotic plaques are responsible for these life-threatening clinical endpoints. Atherosclerosis is a chronic, complex, inflammatory disease with interactions between metabolic dysfunction, dyslipidemia, disturbed microbiome, infectious triggers, vascular, and immune cells. Undoubtedly, the immune response is a most important piece of the pathological puzzle in AS. Although macrophages and T cells have been the focus of research in recent years, B cells producing antibodies and regulating T and natural killer (NKT) cell activation are more important than formerly thought. New results show that the B cells exert a prominent role with atherogenic and protective facets mediated by distinct B cell subsets and different immunoglobulin effects. These new insights come, amongst others, from observations of the effects of innovative B cell targeted therapies in autoimmune diseases like systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). These diseases associate with AS, and the beneficial side effects of B cell subset depleting (modifying) therapies on atherosclerotic concomitant disease, have been observed. Moreover, the CANTOS study (NCT01327846) showed impressive results of immune-mediated inflammation as a new promising target of action for the fight against atherosclerotic endpoints. This review will reflect the putative role of B cells in AS in an attempt to connect observations from animal models with the small spectrum of the thus far available human data. We will also discuss the clinical therapeutic potency of B cell modulations on the process of AS.

[Immunoglobulin concentration in equine colostrum and blood of newborn foals as well as clinically relevant IgG evaluation methods - An overview]. / Immunglobulinkonzentration im equinen Kolostrum und im Blut neugeborener Fohlen sowie klinisch relevante IgG-Bestimmungsmethoden.

Due to the special structure of the equine placenta, foals depend on an adequate intake of high-quality colostrum post natum in order to ensure the development of passive immunity. The quality of the colostrum is determined, among other things, by the IgG content. This may be evaluated in the colostrum by direct and indirect methods (density and refractive index). The density of the colostrum is measured by a colostrometer and should amount to at least 1060 g/l. Refractometry is suitable for assessing the relative density or refractive index. Good equine colostrum has a Brix value of at least 23 %. The IgG concentration in the blood of the foal may also be determined by direct and indirect methods. The SNAP®-Test is regarded as a direct semi-quantitative measurement method, with values > 800 mg/dl indicating an adequate IgG concentration. Furthermore, the radial immuno-diffusion test, the latex agglutination test, and the immunoturbimetry are direct methods that may be applied. Indirect methods include the zinc sulphate turbidity test, the glutaraldehyde coagulation test, as well as the measurement of total protein, globulin concentration and γ-glutamyl transferase activity.

Peripheral blood immunological parameters of children with adenoid hypertrophy with otitis media with effusion: propensity score matching.

PURPOSE: To evaluate peripheral blood immunological parameters and the possible correlation with age, gender and adenoid size in children with adenoid hypertrophy with OME. METHODS: A total of 664 children with adenoid hypertrophy were initially enrolled in our study, of which 83 had concomitant OME. To minimize selection bias, we performed one to two propensity score matching (PSM) between children with and without OME. After PSM, 80 children with OME (OME group) and 157 children without OME (adenoid hypertrophy [AH] group) were selected. The patients' peripheral blood samples were prepared prior to surgery and their immunological parameters were compared between groups. RESULTS: Compared to the AH group, the serum level of C3 was significantly higher in the OME group (0.88 ± 0.01 g/L vs. 0.94 ± 0.02 g/L; p = 0.014), which was the only independent risk factor for OME (odds ratio 13.58, 95% confidence interval 1.25-147.99; p = 0.032). However, no such difference was seen for serum immunoglobulin (IgG, IgA, IgM, IgE), T cell subsets (CD3+, CD4+ and CD8+ T cells), or lymphocytes and monocytes. Further subgroup analyses showed that in children ≤ 5 years old, the C3 level was significantly higher in OME patients (p = 0.023). A subgroup analysis based on sex indicated that there was a significantly higher level of serum C3 (p = 0.009) and lower CD3+ and CD4+ T cells (p = 0.010 and p = 0.021, respectively) in girls with OME compared to those without OME. No association between immunological parameters and adenoid size was found. CONCLUSIONS: There were no significant differences in cellular immunology and humoral immune indicators in children with adenoid hypertrophy with or without OME. In children ≤ 5 years old, significantly higher serum C3 levels in patients with OME demonstrate excessively activated C3 in comparison to patients without OME. For girls, a higher serum level of C3 with a lower amount of CD3+ and CD4+ T cells may be associated with OME.

Proteomic Characterization of Immunoglobulin Content in Dermal Interstitial Fluid.

Microneedles have been demonstrated to be a minimally invasive technique for sampling dermal interstitial fluid (ISF). Shotgun quantitative proteomics has already identified hundreds of proteins in ISF and quantitatively compared the proteome to matching serum and plasma. Interstitial fluid was determined to be a viable minimally invasive alternative to blood-derived fluids. In this communication, we re-examined the proteomic data from previous work to determine the diversity of immunoglobulins present compared with serum and plasma. Similar to our previous findings regarding the proteomic content across fluid types, ISF had a similar composition of IgG, IgA, IgD, and IgE antibodies as plasma or serum and lower quantities of IgM, which reflects the relative concentrations of dermal tissue T-cell and B-cell populations, indicating that the Ig's were likely locally derived. This work has significant implications for the utility of measuring Ig's in ISF for the clinical diagnosis of immunological diseases and skin infections. Data are available via ProteomeXchange with identifier PXD012658.

Comparison of reference systems in the assessment of age-related serum immunoglobulin levels in pediatric patients

Background/aim: Ig level assessment is frequently used in the diagnosis and follow-up of immunodeficiency, as well as in studies investigating the prevalence of low serum Ig level in specific diseases. Materials and methods: Patients who underwent Ig testing in the inpatient and outpatient clinics of our hospital in the years 2010­2016 were included. The Ig levels of the patients were assessed separately according to two reference systems commonly used in Turkey and another reference system used in the USA. Results: A total of 20,138 patients (57.6% male) were included in the study. The median age of the patients was 55.7 months (interquartile range: 23.1­96.7). According to the reference intervals determined by Tezcan et al., 30.6% of the patients were deficient in one or more Ig values. This rate was 4 times higher than those based on the reference intervals determined by Aksu et al. (7.7%) and those in the Nelson Textbook of Pediatrics (6.8%). We also determined that the frequency of low Ig levels with three reference systems Conclusion: In this study, we found that the rates of low Ig level in a group of pediatric patients differed significantly when evaluated using three different reference systems for age-related serum Ig levels

Immunoglobulin-Like Receptors and Their Impact on Wiring of Brain Synapses.

Synapse formation is mediated by a surprisingly large number and wide variety of genes encoding many different protein classes. One of the families increasingly implicated in synapse wiring is the immunoglobulin superfamily (IgSF). IgSF molecules are by definition any protein containing at least one Ig-like domain, making this family one of the most common protein classes encoded by the genome. Here, we review the emerging roles for IgSF molecules in synapse formation specifically in the vertebrate brain, focusing on examples from three classes of IgSF members: ( a) cell adhesion molecules, ( b) signaling molecules, and ( c) immune molecules expressed in the brain. The critical roles for IgSF members in regulating synapse formation may explain their extensive involvement in neuropsychiatric and neurodevelopmental disorders. Solving the IgSF code for synapse formation may reveal multiple new targets for rescuing IgSF-mediated deficits in synapse formation and, eventually, new treatments for psychiatric disorders caused by altered IgSF-induced synapse wiring.

Large abnormal peak on capillary zone electrophoresis due to contrast agent.

Background Some iodinated radio-contrast media absorb ultraviolet light and can therefore be detected by capillary zone electrophoresis. If seen, these peaks are typically small with 'quantifications' of below 5 g/L. Here, we describe the detection of a large peak on capillary zone electrophoresis that was due to the radio-contrast agent, Omnipaque™. Methods Serum from a patient was analysed by capillary zone electrophoresis, and the IgG, IgA, IgM and total protein concentrations were measured. The serum sample was further analysed by gel electrophoresis and immunofixation. Results Capillary zone electrophoresis results for the serum sample showed a large peak with a concentration high enough to warrant urgent investigation. However, careful interpretation alongside the serum immunoglobulin concentrations and total protein concentration showed that the abnormal peak was a pseudoparaprotein rather than a monoclonal immunoglobulin. This was confirmed by analysis with gel electrophoresis and also serum immunofixation. The patient had had a CT angiogram with the radio-contrast agent Omnipaque™; addition of Omnipaque™ to a normal serum sample gave a peak with comparable mobility to the pseudoparaprotein in the patient's serum. Conclusions Pseudoparaproteins can appear as a large band on capillary zone electrophoresis. This case highlights the importance of a laboratory process that detects significant electrophoretic abnormalities promptly and interprets them in the context of the immunoglobulin concentrations. This should avoid incorrect reporting of pseudoparaproteins which could result in the patient having unnecessary investigations.

Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci.

Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. This annotation was used to query 107 whole genome sequences from 19 breeds and identified over 5500 alleles across the 550 genes of the seven AR loci: the IG heavy, kappa, and lambda loci; and the TR alpha, beta, gamma, and delta loci. Of note was the discovery that half of the IGK variable (V) genes were located downstream of, and inverted with respect to, the rest of the locus. Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. This work brings our understanding of the genetic diversity and expression of AR in dogs to the same completeness as that of mice and men, making it the third species to have all AR loci comprehensively and accurately annotated. The large number of germline sequences serves as a reference for future studies, and has allowed statistically powerful conclusions to be drawn on the pressures that have shaped these loci.

Desenvolvimento de novos vetores para a produção de bibliotecas de anticorpos pelo sistema do phage display / Development of a antibody display library system targeted against vascular growth factor

Anticorpos são moléculas de grande interesse científico e farmacêutico, principalmente, devido a sua alta especificidade contra antígenos determinados. Atualmente, anticorpos monoclonais estão entre os medicamentos (biofármacos) mais vendidos do mundo. São utilizados para o tratamento das mais diversas doenças, como câncer, retinopatias, doenças inflamatórias e do sistema imune, entre outras. Nos últimos 30 anos, as tecnologias para a obtenção de anticorpos monoclonais evoluíram muito, desde a tecnologia do hibridoma, até os processos de humanização de anticorpos murinos. Entre os métodos mais utilizados para a produção de anticorpos humanos, destaca-se a tecnologia do Phage Display. Nesta técnica, os genes que codificam as regiões variáveis de imunoglobulinas são inseridos no genoma de um bacteriófago, resultando na produção de partículas virais híbridas que contém fragmentos de anticorpos em fusão com uma das proteínas do capsídeo viral. Neste trabalho, desenvolvemos novos vetores para a apresentação de fragmentos ScFv em fusão com duas proteínas das proteínas do capsídeo viral, a pIII e pVIII. Os oligonucleotídeos utilizados para amplificar os genes de imunoglobulinas foram redesenhados e para minimizar a perda do repertório durante a produção da biblioteca, avaliamos em bancos de dados enzimas de restrição que não apresentam sítios de restrição nas sequencias gênicas. Esses sítios de restrição foram utilizados para construir as regiões de clonagem do vetor Phagemid. Outra etapa crítica na produção de bibliotecas de anticorpos é a reação do PCR de overlap, que pode restringir a diversidade de anticorpos e resultar na produção de amplicons codificando anticorpos truncados. Por isso, nossos vetores foram desenhados para permitir a clonagem direta das regiões variáveis das imunoglobulinas humanas ou murinas, sem a necessidade do PCR de overlap. Nossa expectativa, é que estes novos reagentes serão mais efetivos para a produção de novas bibliotecas de anticorpos pelo sistema do Phage Display

Antibodies are molecules of great scientific and pharmaceutical interest, mainly because of their high specificity against certain antigens. Currently, monoclonal antibodies are among the best selling drugs (biopharmaceuticals) in the world. They are used for the treatment of the most diverse disorders, such as cancer, retinopathies, inflammatory and immune system diseases, among others. In the past 30 years, technologies for obtaining monoclonal antibodies has greatly evolved from hybridoma technology to the humanization processes of murine antibodies. Among the methods used for the production of human antibodies, the technology of Phage Display stands out. In this technique, the genes encoding the immunoglobulin variable regions are inserted into the genome of a bacteriophage, resulting in the production of hybrid virus particles which contain fragments of antibodies in fusion with one of the viral capsid proteins. In this work, we developed new vectors for the presentation of ScFv fragments in fusion with two proteins of viral capsid proteins, pIII and pVIII. The oligonucleotides used to amplify the immunoglobulin genes were redesigned and to minimize repertory loss during library production, we evaluated restriction enzymes in databases that lack restriction sites in the gene sequences. These restriction sites were used to construct the cloning regions of the Phagemid vector. Another critical step in the production of antibody libraries is the overlap PCR reaction, which may restrict the diversity of antibodies and result in the production of amplicons encoding truncated antibodies. Therefore, our vectors were designed to allow the direct cloning of human or murine Immunoglobulins variable regions without the need for overlap PCR. Our expectation is that these new reagents will be more effective for the production of new antibody libraries by the Phage Display system

Perfil de imunoglobulinas, cura clínica e bacteriológica após diferentes tratamentos para a mastite clínica bovina / Profile of immunoglobulins, clinical and bacteriological cure after different treatment routes of clinical bovine mastitis

O presente estudo objetivou avaliar o perfil das Ig durante os diferentes tratamentos de vacas com mastite clínica. Para isso, 30 vacas com mastite clínica em um quarto mamário foram utilizadas e divididas em três grupos. O primeiro grupo foi composto por 10 animais submetidos ao tratamento combinado com infusão intramamária de 8,5mg de sulfato de cefquinoma após cada ordenha, totalizando três aplicações e administração intramuscular de 2,5mg/kg de enrofloxacina por três dias. O segundo grupo foi composto por 10 animais submetidos ao tratamento intramamário, com infusão intramamária de 8,5mg de sulfato de cefquinoma, após cada ordenha, totalizando três aplicações. O terceiro grupo foi composto por 10 animais submetidos ao tratamento sistêmico, com 2,5mg/kg de enrofloxacina, durante três dias. As amostras de leite foram coletadas de todos os animais antes dos tratamentos (momento 0), no segundo (momento 1), no quinto (momento 2) e no 12º dia (momento 3) após o término dos tratamentos. Estas foram submetidas à contagem de células somáticas, ao California Mastitis Test (CMT), ao exame bacteriológico e à quantificação das IgG1, IgG2, IgA e IgM. O tratamento combinado foi mais eficaz e precoce na taxa de cura clínica, na redução dos escores de CMT e da contagem de células somáticas. Além disso, os resultados do presente estudo demonstraram que as concentrações lácteas das diferentes classes de Ig, apesar de sua importância biológica, não estão relacionadas ao prognóstico da mastite clínica bovina, ou seja, não podem ser consideradas marcadores robustos associados à cura clínica e/ou bacteriológica da infecção intramamária.(AU)

The present study aimed to evaluate the profile of immunoglobins profile, clinical and bacteriological cure after different treatment routes of clinical bovine mastitis. Here, 30 Holstein cows with clinical mastitis in one quarter were uniformly divided into: 10 dairy cows that received 8.5mg of cefquinome sulphate administrated intramammarily during three consecutive milkings and 2.5mg/kg of enrofloxacin administrated parenterally during three consecutive days (Group 1); 10 dairy cows that received 8.5mg of cefquinome sulphate administrated intramammarily during three consecutive milkings (Group 2); and 10 dairy cows that received 2.5mg/kg of enrofloxacin administrated parenterally during three consecutive days (Group 3). Milk samples for somatic cell count, California Mastitis Test (CMT), bacteriological culture and quantification of IgG1, IgG2, IgM and IgA were collected before antimicrobial treatment, and after two, five and 12 days after the antimicrobial treatment. The combined treatment was more effective in the clinical cure rate, reduction of somatic cell count and CMT scores. Furthermore, the results demonstrated that milk concentration of different Igs classes were not related to prognosis of bovine clinical mastitis, and then cannot be considered as robust markers associated with clinical and bacteriological cures.(AU)

Humoral response of mice infected with Toxocara canis following different infection schemes.

The study was focused on the dynamics of humoral response to Toxocara canis excretory-secretory antigens (TES antigens) in mice experimentally infected by T. canis L3 larvae in different ways. In particular, we compared the effect of infection with two doses of 1000 larvae vs. repeated infections with a low number of larvae (daily infection with 10 larvae and weekly infection with 100 larvae in the course of 22 weeks). In ELISA, all infections, including both schemes with lower larval doses, elicited significant antibody response. Elevated levels of total IgE and TES-antigen-specific IgM were detected on day 12 after the first infection, followed by IgG and IgG1, and later by IgG3, IgG2a and IgG2b; specific IgE response was not detected. It seems that the high levels of IgM and IgG1 represent the best markers of infection. In addition, gradual increase of IgG2a and IgG2b could help in determination of the infection course. As a byproduct of our work, a new method of infection by repeated drinking of larvae was introduced; it minimizes the pain and discomfort for the experimental mice.

Immunoglobulin Tau Heavy Chain (IgT) in Flounder, Paralichthys olivaceus: Molecular Cloning, Characterization, and Expression Analyses.

Immunoglobulin tau (IgT) is a new teleost immunoglobulin isotype, and its potential function in adaptive immunity is not very clear. In the present study, the membrane-bound and secreted IgT (mIgT and sIgT) heavy chain genes were cloned for the first time and characterized in flounder (Paralichthys olivaceus), and found the nucleic acid sequence were exactly same in the Cτ1-Cτ4 constant domains of mIgT and sIgT, but different in variable regions and the C-terminus. The amino acid sequence of mIgT shared higher similarity with Bovichtus diacanthus (51.2%) and Dicentrarchus labrax (45.0%). Amino acid of flounder IgT, IgM, and IgD heavy chain was compared and the highest similarity was found between IgT Cτ1 and IgM Cµ1 (38%). In healthy flounder, the transcript levels of IgT mRNA were the highest in gill, spleen, and liver, and higher in peripheral blood leucocytes, skin, and hindgut. After infection and vaccination with Edwardsiella tarda via intraperitoneal injection and immersion, the qRT-PCR analysis demonstrated that the IgT mRNA level was significantly upregulated in all tested tissues, with similar dynamic tendency that increased firstly and then decreased, and higher in gill, skin, hindgut, liver, and stomach in immersion than in the injection group, but no significant difference existed in spleen and head kidney between immersion and injection groups. These results revealed that IgT responses could be simultaneously induced in both mucosal and systemic tissues after infection/vaccination via injection and immersion route, but IgT might play a more important role in mucosal immunity than in systemic immunity.

Envelope-specific B-cell populations in African green monkeys chronically infected with simian immunodeficiency virus.

African green monkeys (AGMs) are natural primate hosts of simian immunodeficiency virus (SIV). Interestingly, features of the envelope-specific antibody responses in SIV-infected AGMs are distinct from that of HIV-infected humans and SIV-infected rhesus monkeys, including gp120-focused responses and rapid development of autologous neutralization. Yet, the lack of genetic tools to evaluate B-cell lineages hinders potential use of this unique non-human primate model for HIV vaccine development. Here we define features of the AGM Ig loci and compare the proportion of Env-specific memory B-cell populations to that of HIV-infected humans and SIV-infected rhesus monkeys. AGMs appear to have a higher proportion of Env-specific memory B cells that are mainly gp120 directed. Furthermore, AGM gp120-specific monoclonal antibodies display robust antibody-dependent cellular cytotoxicity and CD4-dependent virion capture activity. Our results support the use of AGMs to model induction of functional gp120-specific antibodies by HIV vaccine strategies.

Immunoglobulin Classification Using the Colored Antibody Graph.

The somatic recombination of V, D, and J gene segments in B-cells introduces a great deal of diversity, and divergence from reference segments. Many recent studies of antibodies focus on the population of antibody transcripts that show which V, D, and J gene segments have been favored for a particular antigen, a repertoire. To properly describe the antibody repertoire, each antibody must be labeled by its constituting V, D, and J gene segment, a task made difficult by somatic recombination and hypermutation events. While previous approaches to repertoire analysis were based on sequential alignments, we describe a new de Bruijn graph-based algorithm to perform VDJ labeling and benchmark its performance.

Multiple IgH Isotypes Including IgD, Subclasses of IgM, and IgY Are Expressed in the Common Ancestors of Modern Birds.

Although evolutionarily just as ancient as IgM, it has been thought for many years that IgD is not present in birds. Based on the recently sequenced genomes of 48 bird species as well as high-throughput transcriptome sequencing of immune-related tissues, we demonstrate in this work that the ostrich (Struthio camelus) possesses a functional δ gene that encodes a membrane-bound IgD H chain with seven CH domains. Furthermore, δ sequences were clearly identified in many other bird species, demonstrating that the δ gene is widely distributed among birds and is only absent in certain bird species. We also show that the ostrich possesses two µ genes (µ1, µ2) and two υ genes (υ1, υ2), in addition to the δ and α genes. Phylogenetic analyses suggest that subclass diversification of both the µ and υ genes occurred during the early stages of bird evolution, after their divergence from nonavian reptiles. Although the positions of the two υ genes are unknown, physical mapping showed that the remaining genes are organized in the order µ1-δ-α-µ2, with the α gene being inverted relative to the others. Together with previous studies, our data suggest that birds and nonavian reptile species most likely shared a common ancestral IgH gene locus containing a δ gene and an inverted α gene. The δ gene was then evolutionarily lost in selected birds, whereas the α gene lost in selected nonavian reptiles. The data obtained in this study provide significant insights into the understanding of IgH gene evolution in tetrapods.