Gouania willdenowi is a teleost fish without immunoglobulin genes.

Immunoglobulin (Ig) genes encode antibodies in jawed vertebrates. They are essential elements of the adaptive immune response. Ig exists in soluble form or as part of the B cell membrane antigen receptor (BCR). Studies of Ig genes in fish genomes reveal the absence of Ig genes in Gouania willdenowi by deletion of the entire Ig locus from the canonical chromosomal region. The genes coding for integral BCR proteins, CD79a and CD79b, are also absent. Genes exist for T α/ß lymphocyte receptors but not for the T γ/δ receptors. The results of the genomic analysis are independently corroborated with RNA-Seq transcriptomes from other Gobiesocidae species. From the transcriptome studies, Ig is also absent from these other Gobiesocidae species, Acyrtus sp. and Tomicodon sp. Present evidence suggests that Ig is missing from all species of the Gobiesocidae family.

Insights into the evolution of IG genes in Amphibians and reptiles.

Immunoglobulins are essential proteins of the immune system to neutralize pathogens. Gene encoding B cell receptors and antibodies (Ig genes) first appeared with the emergence of early vertebrates having a jaw, and are now present in all extant jawed vertebrates, or Gnathostomata. The genes have undergone evolutionary changes. In particular, genomic structural changes corresponding to genes of the adaptive immune system were coincident or in parallel with the adaptation of vertebrates from the sea to land. In cartilaginous fish exist IgM, IgD/W, and IgNAR and in bony fish IgM, IgT, IgD. Amphibians and reptiles witnessed significant modifications both in the structure and orientation of IG genes. In particular, for these amphibians and Amniota that adapted to land, IgM and IgD genes were retained, but other isotypes arose, including genes for IgA(X)1, IgA(X)2, and IgY. Recent progress in high throughput genome sequencing is helping to uncover the IG gene structure of all jawed vertebrates. In this work, we review the work and present knowledge of immunoglobulin genes in genomes of amphibians and reptiles.

Immunoglobulin T genes in Actinopterygii.

In teleost fishes, there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD), and T (IgT). IgT was the last to be described in teleost fishes, and it is specific to them. From recent fish genomes, we identified and studied the immunoglobulin heavy chain genes in Actinopterygii. For this analysis, a custom bioinformatics and machine learning pipeline, we call CHfinder, was developed that identifies the exons coding for the CH domains of fish immunoglobulins. Some IgT in teleost and holostean fish found from this systematic study have not been previously described. Phylogenetic analysis of the deduced amino acid sequences of the IgT CH1 exons reveals they are similar to the CH1 of IgM. This analysis also shows that the other three domains (CH2, CH3, and CH4) were not the result of recent IgM duplication processes in Actinopterygii, demonstrating that it is an immunoglobulin of earlier origin. The bioinformatics program, CHfinder, is publicly available at https://github.com/compimmuno/CHfinder.

B220 expression as an immunological marker for differentiation of Feline Leukemia Virus carrying cats / A expressão de B220 como um marcador imunológico para diferenciação de gatos portadores do vírus da Leucemia Felina

ABSTRACT: Feline leukemia virus (FeLV) causes an infection in cats that, in some cases, can also be reported with other pathologies, such as infection with feline immunodeficiency virus (FIV), feline infectious peritonitis (FIP), and lymphoma. Although, a compromised immune response is reported in these animals, little is known about the immunological state of their cells. To shed some light in this area, we studied peripheral blood samples from both infected and non-infected cats with FeLV, with or without FIV, FIP, and lymphoma. We tested a panel of monoclonal antibodies (n=11) against mouse and human antigens and we reported that cat leukocytes can be stained with anti-mouse B220 monoclonal antibody; therefore, percentages of B cells were evaluated in different cat groups. Our results showed that cats with FeLV and FIP, or with leukemia, presented a large decrease in B220+ mononuclear cells. However, FeLV+ cats without clinical signs, or with unspecific clinical signs, had the same amount of B220+ mononuclear cells as healthy cats (control cats). Since the expression of B220 is exclusively restricted to the naïve B cell population, we inferred that the absence of these B cells in FeLV+ cats is related to other conditions that affect B cell numbers, such as viral infections and leukemias. Therefore, the amount of naïve B cells in peripheral blood (i.e., B220+ cells) can be used to identify FeLV+ cats concomitantly carrying FIP or leukemia, from FeLV+ cats with lymphoma or without any clinical signs.

RESUMO: O vírus da leucemia felina (FeLV) causa de uma infecção em gatos, que também podem ter outras patologias, como a imunodeficiência felina (FIV), a peritonite infecciosa felina (FIP) e linfoma. Embora uma resposta imune comprometida seja encontrada nestes animais, pouco se sabe sobre o estado imunológico de suas células. Para ampliar o número de testes com a finalidade de avaliar o estado imunológico destes animais, estudamos amostras de sangue periférico de gatos infectados, ou não, com FeLV, e que apresentavam (concomitantemente) FIV, FIP e linfoma. Para isto, amostras de sangue foram marcadas com um painel de anticorpos monoclonais contra antígenos de camundongos e humanos (n = 11), para avaliar seu potencial para estudos imunológicos em gatos. De todo o painel de anticorpos testados, apenas o anticorpo anti-B220 de camundongo foi capaz de marcar leucócitos de gato. Nossos resultados mostraram que os gatos com FeLV e FIP, ou com leucemia, apresentaram uma grande diminuição nas células mononucleares B220+. No entanto, gatos FeLV+ sem sinais clínicos, ou com sinais clínicos inespecíficos, tiveram a mesma quantidade de células B220+ que os gatos saudáveis (gatos controle). Como a expressão de B220 é restrita à população de células B naïve, podemos inferir que a ausência dessas células B em gatos FeLV+ está relacionada a outras condições que afetam o número destas células, como infecções virais e leucemias. Portanto, a quantidade de células B naïve no sangue periférico pode ser usada para identificar gatos FeLV+ concomitantemente portadores de PIF ou leucemia, de gatos FeLV+ com linfoma ou sem sinais clínicos.

Inhale, exhale: Why particulate matter exposure in animal models are so acute? Data and facts behind the history.

We present a dataset obtained by extracting information from an extensive literature search of toxicological experiments using mice and rat animal models to study the effects of exposure to airborne particulate matter (PM). Our dataset covers results reported from 75 research articles considering paper published in 2017 and seminal papers from previous years. The compiled data and normalization were processed with an equation based on a PM dosimetry model. This equation allows the comparison of different toxicological experiments using instillation and inhalation as PM exposure protocols with respect to inhalation rates, concentrations and PM exposure doses of the toxicological experiments performed by different protocols using instillation and inhalation PM as exposure methods. This data complements the discussions and interpretations presented in the research article "Inhale, exhale: why particulate matter exposure in animal models are so acute?" Curbani et al., 2019.

Vortex revivals and Fermi-Pasta-Ulam-Tsingou recurrence.

We study the self-trapped vortex-ring eigenstates of the two-dimensional Schrödinger equation with focusing Poisson and cubic nonlinearities. For each value of the topological charge l, there is a family of solutions depending on a parameter that can be understood as the relative importance of the cubic term. We analyze the perturbative stability of the solutions and simulate the fate of the unstable ones. For l=1 and l=2, there is an interval of the family of eigenstates for which the initial profile breaks apart but subsequently reconstructs itself, a process that can be interpreted as a nontrivial nonlinear oscillation between the vortex and an azimuthon. This revival provides a compelling realization of a recurrence of the Fermi-Pasta-Ulam-Tsingou type. Outside this interval, the vortices can be stable (for small cubic terms) or unstable and nonrecurrent (for large cubic terms). We argue that there is a crossover between these regimes that resembles a strong stochasticity threshold. For l≥3, all solutions are unstable and nonrecurrent. Finally, we comment on the possible experimental implementation of this phenomenon in the context of nonlinear laser beam propagation in thermo-optical media.

Inhale, exhale: Why particulate matter exposure in animal models are so acute?

Ecotoxicological studies that try to describe the effects of particulate matter (PM) on human health are important in order to gain a deeper understanding of their effects in disease outcomes. Because exposure protocols are not easily comparable, evaluating human PM exposure is a difficult task. Thus, interpreting ambiguous or conflicting results from different experiments could lead to misleading conclusions about the true nature of PM effects. To address these issues, we compiled a collection of relevant research articles in order to compare present PM exposure methods and extract data related to concentration, inhalation rates (IR), and doses. We also compare the experimental exposure levels reported in these articles to PM levels around the world. In particular, our dataset covers reported results from 75 research articles. To allow for comparison between protocols, we used this data to fit a normalization equation that depends upon concentration, exposure time, dose, inhalability, and physiological parameters. Based on the collected research papers, instillation is the prevalent exposure method. Also, the median PM IR from these experiments is three orders of magnitude higher than the PM IR found in environmental conditions (EAP). Experiments employing inhalation of concentrated PM show IR results that are two orders of magnitude higher than EAP; these results are cause for concerns, since the PM exposure were acute, sudden, and higher than the worst-case exposure scenarios reported by the world megacities. We also found that different PM exposure protocols are sources for the observed variability in physiological response results found from animal models. We discuss these findings and make suggestions for future exposure methodologies. Such considerations should be valuable for quantifying PM exposure in disease outcomes.

Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm.

In jawed vertebrates, variable (V) genes code for antigen-binding regions of B and T lymphocyte receptors, which generate a specific response to foreign pathogens. Obtaining the detailed repertoire of these genes across the jawed vertebrate kingdom would help to understand their evolution and function. However, annotations of V-genes are known for only a few model species since their extraction is not amenable to standard gene finding algorithms. Also, the more distant evolution of a taxon is from such model species, and there is less homology between their V-gene sequences. Here, we present an iterative supervised machine learning algorithm that begins by training a small set of known and verified V-gene sequences. The algorithm successively discovers homologous unaligned V-exons from a larger set of whole genome shotgun (WGS) datasets from many taxa. Upon each iteration, newly uncovered V-genes are added to the training set for the next predictions. This iterative learning/discovery process terminates when the number of new sequences discovered is negligible. This process is akin to "online" or reinforcement learning and is proven to be useful for discovering homologous V-genes from successively more distant taxa from the original set. Results are demonstrated for 14 primate WGS datasets and validated against Ensembl annotations. This algorithm is implemented in the Python programming language and is freely available at http://vgenerepertoire.org.

Immunoglobulin genes in Primates.

Five classes of immunoglobulins are known to exist in mammals. The number of isotypes of classes G, E and A varies among species for unknown reasons. Here, a study of the presence of immunoglobulin genes in Primates was carried out from the genomes and transcriptomes deposited in the NCBI repository. For this, a machine learning application based upon neural networks was implemented that scans the genomes and identifies the exon sequences that encode the immunoglobulin CH domains. From these exons, the immunoglobulins that each species possess can be inferred. Also, the presence of sequences outside the IGHC locus was found which were produced by retrotranscription of RNA that are probably not viable. From this study, the distribution of immunoglobulin genes across primate orders is described in detail. In Prosimians, IgD genes are not found; in Platyrrhines, a gene is identified for each of the immunoglobulin classes but the IgD gene does not have the CH2 exon; in the Cercopithecidae family, a gene is detected for each class in the Colobinae family, while in Cercopithecidae the genes for IgG have been duplicated several times. In hominids, a greater number of duplications that include the genes that code for IgA and IgE are observed. These results indicate that from the appearance of the Cercopithecidae, there is an evolutionary instability in the Ig locus.

Immunoglobulin and T cell receptor genes in Chinese crocodile lizard Shinisaurus crocodilurus.

Squamata are reptiles that diverged from mammals 300 million years ago. During this period, the immunoglobulin (IG) and T lymphocyte receptor (TCR) genes evolved parallel to mammals. However, unlike mammals whose IG/TCR locus has retained a constant structure throughout evolution, Squamata have witnessed duplications, losses, and/or gains in the domains of their immunoglobulin genes. The recent genome sequencing of Shinisaurus crocodilurus, a representative species of the oldest reptiles, provides an opportunity to contrast the structure of IG and TCR genes from previously studied Squamata. This study revealed ten immunoglobulin genes: five genes for immunoglobulin M (IgM), two for immunoglobulin D (IgD), one for immunoglobulin D2 (IgD2), and two for immunoglobulin Y (IgY). As in other Squamata, there are genes for the λ light chain (IGLV) but not for the κ chain (IGKV). Here, the data shows that in some IgM genes, the cysteine needed to bind the λ chains does not exist, but we present evidence for possible non-covalent binding to the light chain. With respect to TCR, one gene is detected for the α constant chain (TRAC) and two genes for the ß constant chain (TRBC); one of which is located in the locus of the variable regions of the heavy chain. As in the rest of the Squamata, genes for the γ/δ T cell receptor were not found. The V gene repertoire is found to be consistent with all other Squamata with few V genes for beta chain of TCR.

Clinical and hematological data to group different chronic kidney disease patients: A practical approach to establish different groups of patients.

BACKGROUND: Chronic kidney disease (CKD) is the convergent point of several pathological processes, and its evolution is insidious and characterized by a progressive and irreversible loss of kidney function. This impaired function induces the accumulation of uremic toxins and individuals with terminal CKD often have altered physiological responses, including a persistent state of immuno-suppression and development of diseases. A better characterization and stratification of these patients with CKD in different immuno-compromised groups would contribute to more effective and personalized treatments. The focus of this study was to use two parameters to stratify patients with CKD into four separate groups that are representative of different immunological status. METHODS: Patients with CKD were chosen randomly and stratified into four separate groups according to the period of time receiving dialysis treatment and leukocyte blood counts. The amount of apoptotic CD4 T cells were measured in each group of patients, and clinical/hematological parameters were correlated by multivariate analysis with each group. RESULTS: Observations reveal that one of the four groups of patients with CKD (group 3) had more apoptotic CD4 T cells than the other group; this group also had an increased malnutrition inflammation score (MIS), an elevated Kt/V, and a higher incidence of smoking. CONCLUSION: A simple two-parameter-based stratification strategy could be used to design effective immunological therapies that differentiate the degrees of immuno-suppression across groups of patients with CKD.

P2X7 receptor drives Th1 cell differentiation and controls the follicular helper T cell population to protect against Plasmodium chabaudi malaria.

A complete understanding of the mechanisms underlying the acquisition of protective immunity is crucial to improve vaccine strategies to eradicate malaria. However, it is still unclear whether recognition of damage signals influences the immune response to Plasmodium infection. Adenosine triphosphate (ATP) accumulates in infected erythrocytes and is released into the extracellular milieu through ion channels in the erythrocyte membrane or upon erythrocyte rupture. The P2X7 receptor senses extracellular ATP and induces CD4 T cell activation and death. Here we show that P2X7 receptor promotes T helper 1 (Th1) cell differentiation to the detriment of follicular T helper (Tfh) cells during blood-stage Plasmodium chabaudi malaria. The P2X7 receptor was activated in CD4 T cells following the rupture of infected erythrocytes and these cells became highly responsive to ATP during acute infection. Moreover, mice lacking the P2X7 receptor had increased susceptibility to infection, which correlated with impaired Th1 cell differentiation. Accordingly, IL-2 and IFNγ secretion, as well as T-bet expression, critically depended on P2X7 signaling in CD4 T cells. Additionally, P2X7 receptor controlled the splenic Tfh cell population in infected mice by promoting apoptotic-like cell death. Finally, the P2X7 receptor was required to generate a balanced Th1/Tfh cell population with an improved ability to transfer parasite protection to CD4-deficient mice. This study provides a new insight into malaria immunology by showing the importance of P2X7 receptor in controlling the fine-tuning between Th1 and Tfh cell differentiation during P. chabaudi infection and thus in disease outcome.

Sensitive and non-invasive method for the in vivo analysis of membrane permeability in small animals.

Tissue membranes are boundaries that isolate organs or cavities in the body. These semi-permeable membranes are responsible for passive protection that acts through the regulation of nutrient absorption, secretion and filtration of small molecules. These functions could be altered as a consequence of inflammation or trauma, which in turn could lead to changes in permeability, allowing the entrance of toxins, antigens, proteins or facilitating the spread of tumors. Membrane permeability therefore plays an important role in numerous diseases. However, current experimental techniques that are available to quantify membrane permeability in small animals have limited precision and temporal specificity. Improvements in such measurements would lead to a deeper understanding of disease pathogenesis and this may accelerate the development of specific therapies. The study reported here concerns the efficacy of a novel, non-invasive imaging analysis-based measurement method that significantly improves the quantification of tissue membrane permeability in small animals, while at the same time mitigating the adverse effects experienced by the animals under study.

The role of clinical pharmacists in treatment adherence: fast impact in suppression of chronic myeloid leukemia development and symptoms.

PURPOSE: Chronic myeloid leukemia (CML) is a clonal myeloproliferative disease, accounting for 15 to 20% of leukemias, with an incidence of one to two cases/100,000 inhabitants. In Brazil, the estimated incidence of leukemia is six cases/100,000 men and 4.28 cases/100,000 women. CML is characterized by the presence of the Philadelphia chromosome. At present, three types of tyrosine kinase inhibitors (TKI) are administered to treat CML patients in the Brazilian public national health system (NHS), called the Unified Health System (in Portuguese, "Sistema Único de Saúde", SUS). Such treatments are only effective if patients adhere to strict dosage regimens; protocol improvements that increase patient adherence to treatment would have economic and health benefits for overburdened health care systems. Here, pharmacist-monitored treatment is assessed. METHODS: In our study, we applied two questionnaires, one to assess the adherence to pharmacological treatment and another to assess the quality of life. All patients studied (n = 23) were diagnosed with CML at a local hospital in "Espírito Santo" State, the "Hospital Evangélico Vila Velha" (HEVV). RESULTS: Treatment adherence was significantly higher in pharmacist-monitored patients than in nonmonitored patients (p = 0.0135). The quality of life of CML patients was also analyzed, indicating that monitored patients had a lower number of symptoms/complaints during treatment periods than nonmonitored patients. Finally, improved treatment adherence also translated into better clinical conditions, particularly during the early stage of treatment (e.g., the first 4 months). CONCLUSIONS: The intervention of a clinical pharmacist is significant to obtain positive clinical results. Therefore, it is recommended that this protocol be included in the standard NHS treatment protocol CML patient outcomes to reduce the indirect and recurring costs to the health care system caused by nonadherence.

Genomic structure and expression of immunoglobulins in Squamata.

The Squamata order represents a major evolutionary reptile lineage, yet the structure and expression of immunoglobulins in this order has been scarcely studied in detail. From the genome sequences of four Squamata species (Gekko japonicus, Ophisaurus gracilis, Pogona vitticeps and Ophiophagus hannah) and RNA-seq datasets from 18 other Squamata species, we identified the immunoglobulins present in these animals as well as the tissues in which they are found. All Squamata have at least three immunoglobulin classes; namely, the immunoglobulins M, D, and Y. Unlike mammals, however, we provide evidence that some Squamata lineages possess more than one Cµ gene which is located downstream from the Cδ gene. The existence of two evolutionary lineages of immunoglobulin Y is shown. Additionally, it is demonstrated that while all Squamata species possess the λ light chain, only Iguanidae species possess the κ light chain.

Amphibians have immunoglobulins similar to ancestral IgD and IgA from Amniotes.

We studied the immunoglobulin genes from either the genomes or RNAs of amphibians. In particular, we obtained data from one frog genome (Nanorana parkeri) and three transcriptomes of the Caudata order (Andrias davidianus, Notophthalmus viridescens and Cynops pyrrhogaster). Apart from the immunoglobulins IgM and IgY previously described, we identified several IgD related immunoglobulins. The species N. parkeri, N. viridescens and C. pyrrhogaster have two IgD genes, while Andrias davidianus has three such genes. The three Caudata species have long IgD immunoglobulins similar to IgD of reptiles, and could be an ancient relic from the common ancestor of IgD of all mammals and reptiles. We also found two IgA isotypes. The results suggest that one of the IgA may be the ancestor of IgA in crocodiles and birds, while the other could be the ancestor IgA found in mammals. These results provide information that could help understand the evolution of immunoglobulins in terrestrial vertebrates.

Stabilizing 3D in vivo intravital microscopy images with an iteratively refined soft-tissue model for immunology experiments.

We describe a set of new algorithms and a software tool, StabiTissue, for stabilizing in vivo intravital microscopy images that suffer from soft-tissue background movement. Because these images lack predetermined anchors and are dominated by noise, we use a pixel weighted image alignment together with a correction for nonlinear tissue deformations. We call this correction a poor man׳s diffeomorphic map since it ascertains the nonlinear regions of the image without resorting to a full integral equation method. To determine the quality of the image stabilization, we developed an ensemble sampling method that quantifies the coincidence between image pairs from randomly distributed image regions. We obtain global stabilization alignment through an iterative constrained simulated annealing optimization procedure. To show the accuracy of our algorithm with existing software, we measured the misalignment error rate in datasets taken from two different organs and compared the results to a similar and popular open-source solution. Present open-source stabilization software tools perform poorly because they do not treat the specific needs of the IV-2pM datasets with soft-tissue deformation, speckle noise, full 5D inter- and intra-stack motion error correction, and undefined anchors. In contrast, the results of our tests demonstrate that our method is more immune to noise and provides better performance for datasets' possessing nonlinear tissue deformations. As a practical application of our software, we show how our stabilization improves cell tracking, where the presence of background movement would degrade track information. We also provide a qualitative comparison of our software with other open-source libraries/applications. Our software is freely available at the open source repository http://sourceforge.net/projects/stabitissue/.

Evolution of V genes from the TRV loci of mammals.

Information concerning the evolution of T lymphocyte receptors (TCR) can be deciphered from that part of the molecule that recognizes antigen presented by major histocompatibility complex (MHC), namely the variable (V) regions. The genes that code for these variable regions are found within the TCR loci. Here, we describe a study of the evolutionary origin of V genes that code for the α and ß chains of the TCR loci of mammals. In particular, we demonstrate that most of the 35 TRAV and 25 TRBV conserved genes found in Primates are also found in other Eutheria, while in Marsupials, Monotremes, and Reptiles, these genes diversified in a different manner. We also show that in mammals, all TRAV genes are derived from five ancestral genes, while all TRBV genes originate from four such genes. In Reptiles, the five TRAV and three out of the four TRBV ancestral genes exist, as well as other V genes not found in mammals. We also studied the TRGV and TRDV loci from all mammals, and we show a relationship of the TRDV to the TRAV locus throughout evolutionary time.

Automatic recognition and scoring of olympic rhythmic gymnastic movements.

We describe a conceptually simple algorithm for assigning judgement scores to rhythmic gymnastic movements, which could improve scoring objectivity and reduce judgemental bias during competitions. Our method, implemented as a real-time computer vision software, takes a video shot or a live performance video stream as input and extracts detailed velocity field information from body movements, transforming them into specialized spatio-temporal image templates. The collection of such images over time, when projected into a velocity covariance eigenspace, trace out unique but similar trajectories for a particular gymnastic movement type. By comparing separate executions of the same atomic gymnastic routine, our method assigns a quality judgement score that is related to the distance between the respective spatio-temporal trajectories. For several standard gymnastic movements, the method accurately assigns scores that are comparable to those assigned by expert judges. We also describe our rhythmic gymnastic video shot database, which we have made freely available to the human movement research community. The database can be obtained at http://www.milegroup.net/apps/gymdb/.