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In the previous study, antibodies against CD3 molecule have been produced and were used in labeling T cells in Japanese flounder ( Paralichthys olivaceus ). In this paper, CD4 + and CD8 + lymphocytes subpopulations in peripheral blood leucocytes (PBL), spleen and head kidney of flounder were investigated. The flounder CD4-1, CD4-2 and CD8β recombinant proteins and their antibodies (Abs) were produced, then the cross-reactivity of the Abs to CD4-1, CD4-2 and CD8β was detected by Western blotting, respectively, and the reactions of Abs to PBL were analyzed by immunofluorescence staining (IFS) and flow cytometry (FCM). CD4-1 + /CD3 + , CD4-2 + /CD3 + , and CD8β + /CD3 + lymphocytes in PBL, spleen and head kidney were observed by double IFS, then their proportions were analyzed using two-color FCM, respectively. Further, CD4-1/CD8β, CD4-2/CD8β, or CD4-1/CD4-2 lymphocytes were analyzed using double-IFS and two-color FCM. Finally, CD4-1 + , CD4-2 + , and CD8β + lymphocytes in spleen and head kidney were observed by immunohistochemistry. The results showed that the Abs were specific for CD4-1, CD4-2 and CD8β molecules, respectively. The proportions of CD4-1 + /CD3 + , CD4-2 + /CD3 + , and CD8β + /CD3 + lymphocytes were 6.7 ± 2.0%, 8.6 ± 2.8%, 2.1 ± 1.3% in PBL; 13.6 ± 3.6%, 15.6 ± 5.2%, 2.8 ± 1.4% in spleen; 20.0 ± 4.6%, 20.5 ± 4.6%, 3.2 ± 1.5% in head kidney, respectively. Most CD4 + and CD8 + cell subpopulations belonged to CD3 + cells; there were no cross-reactivity between CD4 + and CD8 + cells. CD4-1 + /CD4-2 − , CD4-1 − /CD4-2 + , and CD4-1 + /CD4-2 + cells presented different proportions in PBL, spleen and head kidney, among them, CD4-1 + /CD4-2 + cell is the majority of CD4T cell subpopulation. [ABSTRACT FROM AUTHOR]

Nucleosomes and modifications on the histones constitute the fundamental genomic structure of eukaryotes. It was reported that particular combinations of histone modifications occurring on the genome indicate specific chromatin states, which are related to a series of cell states. Although the histone code principle has been found for over a decade, the mechanism of the code is not yet known clearly. In this paper, we first conducted an extensive analysis on 38 histone modifications and 1 histone variant in human CD4+ T cells to reveal possible connections among these modifications. Then, we analyzed the different roles that histone modifications play in highly differentiated cells and undifferentiated cells, and found that the number of histone modifications on genes of differentiated cells is correlated to the expression levels of genes, while there is no direct effect of histone modification on gene expression level in undifferentiated cells. Finally, we compared the distributions of histone modifications of CD4+ T cell line and K562 cell line, and observed that they have similar distribution patterns. So we guess that there may exist certain conservative regions of histone modifications. [ABSTRACT FROM AUTHOR]

The koala ( Phascolarctos cinereus ) is an arboreal herbivorous marsupial that is an Australian icon. Koalas in many parts of Australia are under multiple threats including habitat destruction, dog attacks, vehicular accidents, and infectious diseases such as Chlamydia spp. and the koala retrovirus (KoRV), which may contribute to the incidence of lymphoma and leukaemia in this species. Due to a lack of koala-specific immune reagents and assays there is currently no way to adequately analyse the immune response in healthy, diseased or vaccinated animals. This paper reports the production and characterisation of the first anti-koala CD4 monoclonal antibody (mAb). The koala CD4 gene was identified and used to develop recombinant proteins for mAb production. Fluorochrome-conjugated anti-CD4 mAb was used to measure the levels of CD4 + lymphocytes collected from koala spleens (41.1%, range 20–45.1%) lymph nodes (36.3%, range 19–55.9%) and peripheral blood (23.8%, range 17.3–35%) by flow cytometry. Biotin-conjugated anti-CD4 mAb was used for western blot to determine an approximate size of 52 kDa for the koala CD4 molecule and used in immunohistochemistry to identify CD4 + cells in the paracortical region and germinal centres of spleen and lymph nodes. Using the anti-CD4 mab we showed that CD4 cells from vaccinated, but not control, koalas proliferated following in vitro stimulation with UV-inactivated Chlamydia pecorum and recombinant chlamydial antigens. Since CD4 + T cells have been shown to play a pivotal role in clearing chlamydial infection in both human and mouse infections, using this novel antibody will help determine the role CD4 + T cells play in protection against chlamydial infection in koalas and also enhance our knowledge of how KoRV affects the koala immune system. [ABSTRACT FROM AUTHOR]

T-cell CD4+ epitopes are important targets of immunity against infectious diseases and cancer. State-of-the-art methods for MHC class II epitope prediction rely on supervised learning methods in which an implicit or explicit model of sequence specificity is constructed using a training set of peptides with experimentally tested MHC class II binding affinity. In this paper we present a novel method for CD4+ T-cell eptitope prediction based on modeling antigen-processing constraints. Previous work indicates that dominant CD4+ T-cell epitopes tend to occur adjacent to sites of initial proteolytic cleavage. Given an antigen with known three-dimensional structure, our algorithm first aggregates four types of conformational stability data in order to construct a profile of stability that allows us to identify regions of the protein that are most accessible to proteolysis. Using this profile, we then construct a profile of epitope likelihood based on the pattern of transitions from unstable to stable regions. We validate our method using 35 datasets of experimentally measured CD4+ T cell responses of mice bearing I-Ab or HLA–DR4 alleles as well as of human subjects. Overall, our results show that antigen processing constraints provide a significant source of predictive power. For epitope prediction in single-allele systems, our approach can be combined with sequence-based methods, or used in instances where little or no training data is available. In multiple-allele systems, sequence-based methods can only be used if the allele distribution of a population is known. In contrast, our approach does not make use of MHC binding prediction, and is thus agnostic to MHC class II genotypes. [ABSTRACT FROM AUTHOR]

Background: Despite dramatic improvement in antiretroviral therapy (ART) access globally, people living with HIV who inject drugs continue to face barriers that limit their access to treatment. This paper explores barriers and facilitators to ART initiation among clients attending a methadone clinic in Dar es Salaam, Tanzania.Methods: We interviewed 12 providers and 20 clients living with HIV at the Muhimbili National Hospital methadone clinic between January and February 2015. We purposively sampled clients based on sex and ART status and providers based on job function. To analyze interview transcripts, we adopted a content analysis approach.Results: Participants identified several factors that hindered timely ART initiation for clients at the methadone clinic. These included delays in CD4 testing and receiving CD4 test results; off-site HIV clinics; stigma operating at the individual, social and institutional levels; insufficient knowledge of the benefits of early ART initiation among clients; treatment breakdown at the clinic level possibly due to limited staff; and initiating ART only once one feels physically ill. Participants perceived social support as a buffer against stigma and facilitator of HIV treatment. Some clients also reported that persistent monitoring and follow-up on their HIV care and treatment by methadone clinic providers led them to initiate ART.Conclusion: Health system factors, stigma and limited social support pose challenges for methadone clients living with HIV to initiate ART. Our findings suggest that on-site point-of-care CD4 testing, a peer support system, and trained HIV treatment specialists who are able to counsel HIV-positive clients and initiate them on ART at the methadone clinic could help reduce barriers to timely ART initiation for methadone clients. [ABSTRACT FROM AUTHOR]

The counting of CD4 + T lymphocytes is a clinical parameter used for AIDS diagnosis and follow-up. As this disease is particularly prevalent in developing countries, simple and affordable CD4 cell counting methods are urgently needed in resource-limited settings. This paper describes an electrochemical magneto-actuated biosensor for CD4 count in whole blood. The CD4 + T lymphocytes were isolated, preconcentrated and labeled from 100 μL of whole blood by immunomagnetic separation with magnetic particles modified with antiCD3 antibodies. The captured cells were labeled with a biotinylated antiCD4 antibody, followed by the reaction with the electrochemical reporter streptavidin-peroxidase conjugate. The limit of detection for the CD4 counting magneto-actuated biosensor in whole blood was as low as 44 cells μL −1 while the logistic range was found to be from 89 to 912 cells μL −1 , which spans the whole medical interest range for CD4 counts in AIDS patients. The electrochemical detection together with the immunomagnetic separation confers high sensitivity, resulting in a rapid, inexpensive, robust, user-friendly method for CD4 counting. This approach is a promising alternative for the costly standard flow cytometry and suitable as diagnostic tool at decentralized practitioner sites in low resource settings, especially in less developed countries. [ABSTRACT FROM AUTHOR]

The term immunodominance was originally defined as a restricted T cell response to a short peptide sequence derived from a given protein [ 1 ]. The question of what determines immunodominance has been a longstanding battle for the past two decades. Hundreds of papers have been written on different aspects of epitope selection during antigen processing documenting the complexity of the process. Antigen processing machinery involves several accessory molecules and chaperons coevolved with proteins of Major Histocompatibility Complex (MHC) molecules that each plays its part in epitope selection. These molecules are targeted to specialized vesicular compartments that also accommodate antigen processing enzymes called cathepsins. Within the antigen processing compartments, highly regulated pH gradient and reducing conditions and enzymes necessary for denaturation of the antigens are available and function to optimize processing of antigen and selection of the fittest for transport to the cell membrane and presentation to T cells. Despite the complexity, a cell free reductionist antigen processing system was recently reported that included only few purified proteins, but was shown to process and select physiologically relevant epitopes from full length protein antigens [ 2 •• ]. Due to its minimalist nature the system has been quite helpful in dissecting the factors that contribute to epitope selection during antigen processing. In this review, we would summarize and highlight models that may explain how the dominant epitope may be selected for presentation to CD4 + helper T cells. [ABSTRACT FROM AUTHOR]

Based on some important biological meanings, we propose a class of HIV infection models incorporating both classical cell-free virus diffusion and direct cell-to-cell transmission. According to recent studies, the direct cell-to-cell transfer of HIV is a significantly more efficient mode of retroviral dissemination. In the first part of our analysis, we show that our model possesses non-negative solutions. Then, we derive sufficient conditions for the asymptotic stability of equilibriums. The analytical solutions are verified by simulation results. At the end of the paper, some important conclusions are given. [ABSTRACT FROM AUTHOR]

This paper discusses potential avenues to abate the last bulwark to the HIV-1 eradication i.e. viral reservoirs in the body, consisting mainly of viral DNA hidden, in latent form, into long-lived memory CD4 + T-cells, resulting unaffected by either drugs or immune system. Activation of the innate immune system is necessary for the induction of adaptive immune responses against invading pathogens. In part, this is achieved by recognition of molecules associated with infection by a plethora of pattern recognition receptors comprising Toll-like receptors (TLRs) which are express on numerous cells of immune system such as, dendritic cells and B cells, and are activated by some TLR ligands. TLR-9, localized in endosomal compartment, specifically recognizes unmethylated oligonucleotide sequences containing CpG motifs which are particularly abundant in microbial genome, including HIV-1 DNA. Naïve B cells are activated following antigen binding to the B cell receptor (BCR). The complex antigen/BCR, internalises and synergises with TLR leading to hyper activation of B cells and antibodies production. Cross-link of the BCR with TLR9, followed by upregulation of TLR-9, in response to self DNA-containing antigens, on DNA-specific B lymphocytes lead to the development of DNA-specific autoantibodies. This occur in systemic autoimmune disorders, such as, systemic lupus erythematosus (SLE). Although such DNA-specific B lymphocytes, are usually present in B cell repertoire at low frequency, they normally do not produce autoantibodies, they can be activated by antigen BCR ligation, with plasmacytoid dendritic cells (pDCs) providing helper signals. The hypothesis here derives by insight that stimulation of BCR, by exogenously added HIV-1 DNA, on potentially reactive HIV-1 DNA-specific B cells, from HIV-1 and/or HIV-1/SLE patients, co-cultured with autologous viral DNA-stimulated pDCs, could lead to desirable in vitro production of antibodies direct against HIV-1 DNA by involving BCR/TLR9 pathway. These antibodies, suitably delivered into infected or uninfected CD4 + T-cells, by a carrier, such as, peptide transduction domain of Tat, could selectively recognize viral nucleic acid, rich in CpG motifs, respect to host DNA, both in productively than latently infected T cells. Because HIV-1 DNA into latently infected cells is heavily methylated and deacetylated, co-treatment with a small molecule inhibitor of DNA methylation, such as 5-aza-2′-deoxycytidine (aza-Cdr), and histone deacetylase inhibitors (HDACi), they would favor higher accessibility by antibodies to viral DNA, which is harbored into human chromosomes. The in vitro production of anti-HIV-1 DNA antibodies and their in vivo reintroduction, could find future application as interesting strategy to pave the way to an eventual cure to decrease and/or eliminate viral reservoirs from the body, and providing possible therapeutic applications not only for HIV-1/AIDS, but also for other infectious diseases. [ABSTRACT FROM AUTHOR]

[Display omitted] The HIV-1 invasion is initiated with the interaction of viral glycoprotein gp120 and cellular receptor CD4. The binding mechanism reveals two major hotspots involved in gp120-CD4 interaction. The first one is a hydrophobic cavity (Phe43 cavity) on gp120 capped with phenyl ring of phe43 CD4 and the second is the electrostatic interaction between positive charge of Arg59 CD4 and negative charge of Asp368 gp120. Targeting these hotspots, small molecules for entry inhibition and HIV-1 neutralization were designed and tested. In the process, pyrimidine derivatives were identified as potent molecules to intercept gp120-CD4 binding by targeting both the hotspots. Herein, the synthesis, characterization of 1,2,3,4-Tetrahydropyrimidine derivatives, and biological evaluation on 93IN101, a clade C virus are presented. The paper presents a novel set of entry inhibitors to target dual hotspots on gp120 to inhibit protein-protein interactions. [ABSTRACT FROM AUTHOR]

Abstract: Histone modifications play a crucial role in regulating gene expression and cell lineage determination and maintenance at the epigenetic level. To systematically investigate this phenomenon, this paper presented a statistical hybrid clustering algorithm to identify common combinatorial histone modification patterns. We applied the algorithm to 39 histone modification marks in human CD4+ T cells and detected 854 common combinatorial histone modification patterns. Our results could cover 211 (76.17%) patterns among 277 patterns identified by the tandem mass spectrometry experiments. Based on the frequency statistical analysis, it was found that the co-occurrence frequencies of 20 backbone modifications are greater than or close to 0.2 in the 854 patterns. we also found that 15 modifications (H2BK120ac, H4K91ac, H2BK20ac, etc.), three histone acetylations (H2AK9ac, H4K16ac, and H4K12ac) and five histone methylations (H3K79me1, H3K79me2, 3K79me3, H4K20me1, and H2BK5me1) were most likely prone to coexist respectively in these patterns. In addition, we found that DNA methylation tends to combine with histone acetylation rather than histone methylation. [Copyright &y& Elsevier]

Abstract: Patients living with HIV are eligible for treatment when their CD4 count is less than 350 cells/mm3. The patients receive antiretroviral treatment (ART) which they need to take every day for the rest of their life. To maintain treatment effcacy, it is necessary to avoid the event of treatment failure. In order to assist physicians monitoring HIV patients this paper propose temporal data mining to predict treatment outcome by providing visual representation of prediction results. Temporal abstraction is used to classify time series data into discrete categories, each represented typically with a symbol. Artificial neural networks are used in this study where the problem of unbalanced data size occurs during the learning process. Two under-sampling techniques are proposed. With the nearest samples to cluster center technique, accuracy is achieved at levels higher than 85% and the discovered patterns correspond with real world diagnosis where viral load is the primary feature to predict treatment outcome. [Copyright &y& Elsevier]

Background: The immunosuppressive properties of regulatory T cells have emerged as an attractive tool for the development of immunotherapies in various disease contexts, e.g. to treat transplantation induced immune reactions. This paper focuses on the process of obtaining and functionally characterizing CD4+CD25+FoxP3+ regulatory T cells and Tr1 cells from uremic patients awaiting kidney transplantation. Methods: From October 2010 to March 2011 uremic patients awaiting living donor kidney transplantation, and their corresponding kidney donors, were enrolled in the study. A total of seven pairs were included. Isolation of CD4+CD25+FoxP3+ regulatory T cells was performed by magnetic activated cell sorting of peripheral blood mononuclear cells obtained from the uremic patients. Donor specific Trl cells were differentiated by repetitive stimulation of immature CD4+ T cells with immature dendritic cells, with the T cells coming from the future kidney recipients and the dendritic cells from the corresponding kidney donors. Cells were then expanded and functionally characterized by the one-way mixed leukocyte reaction and assessment of IL-10 production. Phenotypic analysis was performed by flow cytometry. Results: The fraction of CD4+CD25+FoxP3+ regulatory T cells after expansion varied from 39.1 to 50.4% and the cells retained their ability to substantially suppress the mixed leukocyte reaction in all but one patient (3.8-19.2% of the baseline stimulated leukocyte activity, p<0.05). Trl cells were successfully differentiated from all but one patient and produced high levels of IL-10 when stimulated with immature dendritic cells (1,275-11,038% of the baseline IL-10 secretion, p<0.05). Conclusion: It is practically feasible to obtain and subsequently expand CD4+CD25+FoxP3+ regulatory T cells and Tr1 cells from uremic patients without loss of function as assessed by in vitro analyses. This forms a base for adoptive regulatory T cell therapy in the setting of living donor kidney transplantation. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, we consider an HIV pathogenesis model including cure rate and the full logistic proliferation term of CD4+ T cells in healthy and infected populations. Let be the number of virus released by each productive infected CD4+ T cell. The critical number that ensures the existence of the positive equilibrium is obtained. We further show that if , then there exists a unique uninfected equilibrium point that is locally asymptotically stable. If , then the system is persistent and the only infected steady state is globally asymptotically stable in the feasible region. Numerical simulations are presented to illustrate the obtained main results. Moreover, we find that there exist periodic solutions when the infected steady state is unstable. [Copyright &y& Elsevier]

Abstract: Contamination of water with arsenic is a problem affecting several regions of the world. Peripheral blood mononuclear cells (PBMC) from chronically exposed individuals show a lower replicating activity than non-exposed individuals when stimulated with phytohemagglutinin (PHA). We have previously reported that PBMC from healthy donors treated in vitro with 1 μM sodium arsenite (NaAsO2) and stimulated with PHA showed a reduction in proliferation by a delay in cell cycle entry and a decrease in the rounds of cell division. In this paper we tested the effect of 1–5 μM NaAsO2 on the proliferation, viability, blast transformation, expression of the CD4 and CD8 molecules, and during the activation and proliferation of both CD4+ and CD8+ T lymphocytes. We found a reduction in cell proliferation and an increase in non-dividing cells with higher concentrations of NaAsO2 (2–5 μM) when proliferation was studied by 5,6-carboxyfluorescein diacetate succinimidyl ester (CFSE) dilution. The use of 7-aminoactinomycin D (7-AAD) in CFSE-labeled cells allowed us to detect an increase in percentage of non-dividing cells, and an increase in apoptotic/dead cells mainly in non-proliferating cells. Analysis of the expression of CD4 and CD8 molecules on these cells showed that concentrations ≥2 μM NaAsO2 reduced the expression of the CD8 molecule and induced apoptosis/death in CD4+ cells. Analysis of blast transformation by flow cytometry showed an accumulation of CD8+ resting cells in the presence of NaAsO2. Analysis of CD25 and CD69 expression in kinetics experiments in both subtypes showed a delay in the expression of CD25 and a delay in the downregulation of the CD69 molecule, in both CD4+ and CD8+ cells. However, in the case of CD8+ cells, we detected an accumulation of a CD25−CD69− population in the presence of increasing concentrations of NaAsO2. Altogether, our results show that NaAsO2 alters the expression kinetics of the early activation molecules CD25 and CD69 similarly in both subtypes. In addition, activated and non-activated CD4+ cells die by apoptotic mechanisms and although a percentage of CD8+ cells also die by apoptosis, a subpopulation of these cells is unable to activate and thus accumulates as resting cells. [Copyright &y& Elsevier]

In this paper, an ab initio approach is used to study high-order harmonic generation (HHG) from methane and its deuteriated isotopomer within the framework of time-dependent density functional theory. The time-dependent Kohn-Sham equations are numerically solved in real-time and real-space evolution scheme. We showed that by adding a static electric field to the two-color chirped laser field, not only is the harmonic cutoff frequency extended remarkably, but also the quantum paths of the HHG are modified significantly. Furthermore, our results showed that due to the faster Jahn-Teller distortion of CH 4 cation relative to CD 4 cation, the high-order harmonic signals are more intense in heavier isotopomer. Additionally, it is found that by adding a static electric field, the difference in the cutoff frequency of the high-order harmonics increases. Finally, in order to obtain a deeper insight into the physical origin of the HHG enhancement, the semiclassical calculations and quantum time–frequency analysis are carried out. [ABSTRACT FROM AUTHOR]