163 research outputs found
Assessing the eligibility of kidney transplant donors
Organ transplantation is a highly complex decision processthat requires expert decisions. The major problem in a transplantationprocedure is the possibility of the receiver's immune system attack anddestroy the transplanted tissue. It is therefore of capital importance tond a donor with the highest possible compatibility with the receiver, andthus reduce rejection. Finding a good donor is not a straightforward taskbecause a complex network of relations exists between the immunologicaland the clinical variables that inuence the receiver's acceptance of thetransplanted organ. Currently the process of analyzing these variablesinvolves a careful study by the clinical transplant team. The number andcomplexity of the relations between variables make the manual processvery slow. In this paper we propose and compare two Machine Learningalgorithms that might help the transplant team in improving and speedingup their decisions. We achieve that objective by analyzing past real casesand constructing models as set of rules. Such models are accurate andunderstandable by experts
Rhesus TRIM5Ξ± disrupts the HIV-1 capsid at the inter-hexamer interfaces
TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5Ξ± (TRIM5Ξ±rh) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5Ξ± to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully understood. In this study, we investigated, by cryoEM combined with mutagenesis and chemical cross-linking, the direct interactions between HIV-1 capsid protein (CA) assemblies and purified TRIM5Ξ±rh containing coiled-coil and SPRY domains (CC-SPRYrh). Concentration-dependent binding of CC-SPRYrh to CA assemblies was observed, while under equivalent conditions the human protein did not bind. Importantly, CC-SPRYrh, but not its human counterpart, disrupted CA tubes in a non-random fashion, releasing fragments of protofilaments consisting of CA hexamers without dissociation into monomers. Furthermore, such structural destruction was prevented by inter-hexamer crosslinking using P207C/T216C mutant CA with disulfide bonds at the CTD-CTD trimer interface of capsid assemblies, but not by intra-hexamer crosslinking via A14C/E45C at the NTD-NTD interface. The same disruption effect by TRIM5Ξ±rh on the inter-hexamer interfaces also occurred with purified intact HIV-1 cores. These results provide insights concerning how TRIM5Ξ± disrupts the virion core and demonstrate that structural damage of the viral capsid by TRIM5Ξ± is likely one of the important components of the mechanism of TRIM5Ξ±-mediated HIV-1 restriction. Β© 2011 Zhao et al
Cyclophilin A interacts with diverse lentiviral capsids
BACKGROUND: The capsid (CA) protein of HIV-1 binds with high affinity to the host protein cyclophilin A (CypA). This binding positively affects some early stage of the viral life-cycle because prevention of binding either by drugs that occupy that active site of cyclophilin A, by mutation in HIV-1 CA, or RNAi that knocks down intracellular CypA level diminishes viral infectivity. The closely related lentivirus, SIVcpz also binds CypA, but it was thought that this interaction was limited to the HIV-1/SIVcpz lineage because other retroviruses failed to interact with CypA in a yeast two-hybrid assay. RESULTS: We find that diverse lentiviruses, FIV and SIVagmTAN also bind to CypA. Mutagenesis of FIV CA showed that an amino acid that is in a homologous position to the proline at amino acid 90 of HIV-1 CA is essential for FIV interactions with CypA. CONCLUSION: These results demonstrate that CypA binding to lentiviruses is more widespread than previously thought and suggest that this interaction is evolutionarily important for lentiviral infection
Predicting Progression of IgA Nephropathy: New Clinical Progression Risk Score
IgA nephropathy (IgAN) is a common cause of end-stage renal disease (ESRD) in Asia. In this study, based on a large cohort of Chinese patients with IgAN, we aim to identify independent predictive factors associated with disease progression to ESRD. We collected retrospective clinical data and renal outcomes on 619 biopsy-diagnosed IgAN patients with a mean follow-up time of 41.3 months. In total, 67 individuals reached the study endpoint defined by occurrence of ESRD necessitating renal replacement therapy. In the fully adjusted Cox proportional hazards model, there were four baseline variables with a significant independent effect on the risk of ESRD. These included: eGFR [HRβ=β0.96(0.95β0.97)], serum albumin [HRβ=β0.47(0.32β0.68)], hemoglobin [HRβ=β0.79(0.72β0.88)], and SBP [HRβ=β1.02(1.00β1.03)]. Based on these observations, we developed a 4-variable equation of a clinical risk score for disease progression. Our risk score explained nearly 22% of the total variance in the primary outcome. Survival ROC curves revealed that the risk score provided improved prediction of ESRD at 24th, 60th and 120th month of follow-up compared to the three previously proposed risk scores. In summary, our data indicate that IgAN patients with higher systolic blood pressure, lower eGFR, hemoglobin, and albumin levels at baseline are at a greatest risk of progression to ESRD. The new progression risk score calculated based on these four baseline variables offers a simple clinical tool for risk stratification
Structural Basis for Functional Tetramerization of Lentiviral Integrase
Experimental evidence suggests that a tetramer of integrase (IN) is the protagonist of the concerted strand transfer reaction, whereby both ends of retroviral DNA are inserted into a host cell chromosome. Herein we present two crystal structures containing the N-terminal and the catalytic core domains of maedi-visna virus IN in complex with the IN binding domain of the common lentiviral integration co-factor LEDGF. The structures reveal that the dimer-of-dimers architecture of the IN tetramer is stabilized by swapping N-terminal domains between the inner pair of monomers poised to execute catalytic function. Comparison of four independent IN tetramers in our crystal structures elucidate the basis for the closure of the highly flexible dimer-dimer interface, allowing us to model how a pair of active sites become situated for concerted integration. Using a range of complementary approaches, we demonstrate that the dimer-dimer interface is essential for HIV-1 IN tetramerization, concerted integration in vitro, and virus infectivity. Our structures moreover highlight adaptable changes at the interfaces of individual IN dimers that allow divergent lentiviruses to utilize a highly-conserved, common integration co-factor
Relief of Preintegration Inhibition and Characterization of Additional Blocks for HIV Replication in Primary Mouse T Cells
Development of a small animal model to study HIV replication and pathogenesis has been hampered by the failure of the virus to replicate in non-primate cells. Most studies aimed at achieving replication in murine cells have been limited to fibroblast cell lines, but generating an appropriate model requires overcoming blocks to viral replication in primary T cells.Β We have studied HIV-1 replication in CD4+ T cells from human CD4/ CCR5/Cyclin T1 transgenic mice. Expression of hCD4 and hCCR5 in mouse CD4+ T cells enabled efficient entry of R5 strain HIV-1. In mouse T cells, HIV-1 underwent reverse transcription and nuclear import as efficiently as in human T cells. In contrast, chromosomal integration of HIV-1 proviral DNA was inefficient in activated mouse T cells. This process was greatly enhanced by providing a secondary T cell receptor (TCR) signal after HIV-1 infection, especially between 12 to 24 h post infection. This effect was specific for primary mouse T cells. The pathways involved in HIV replication appear to be PKCΞΈβ, CARMA1-, and WASp-independent. Treatment with Cyclosporin A (CsA) further relieved the pre-integration block. However, transcription of HIV-1 RNA was still reduced in mouse CD4+ T cells despite expression of the hCyclin T1 transgene. Additional post-transcriptional defects were observed at the levels of Gag expression, Gag processing, Gag release and virus infectivity. Together, these post-integration defects resulted in a dramatically reduced yield of infectious virus (300β500 fold) after a single cycle of HIV-1 replication. This study implies the existence of host factors, in addition to those already identified, that are critical for HIV-1 replication in mouse cells. This study also highlights the differences between primary T cells and cell lines regarding pre-integration steps in the HIV-1 replication cycle
SUMO-Interacting Motifs of Human TRIM5Ξ± are Important for Antiviral Activity
Human TRIM5Ξ± potently restricts particular strains of murine leukemia viruses
(the so-called N-tropic strains) but not others (the B- or NB-tropic strains)
during early stages of infection. We show that overexpression of SUMO-1 in human
293T cells, but not in mouse MDTF cells, profoundly blocks N-MLV infection. This
block is dependent on the tropism of the incoming virus, as neither B-, NB-, nor
the mutant R110E of N-MLV CA (a B-tropic switch) are affected by SUMO-1
overexpression. The block occurred prior to reverse transcription and could be
abrogated by large amounts of restricted virus. Knockdown of TRIM5Ξ± in 293T
SUMO-1-overexpressing cells resulted in ablation of the SUMO-1 antiviral
effects, and this loss of restriction could be restored by expression of a human
TRIM5Ξ± shRNA-resistant plasmid. Amino acid sequence analysis of human
TRIM5Ξ± revealed a consensus SUMO conjugation site at the N-terminus and
three putative SUMO interacting motifs (SIMs) in the B30.2 domain. Mutations of
the TRIM5Ξ± consensus SUMO conjugation site did not affect the antiviral
activity of TRIM5Ξ± in any of the cell types tested. Mutation of the SIM
consensus sequences, however, abolished TRIM5Ξ± antiviral activity against
N-MLV. Mutation of lysines at a potential site of SUMOylation in the CA region
of the Gag gene reduced the SUMO-1 block and the TRIM5Ξ± restriction of
N-MLV. Our data suggest a novel aspect of TRIM5Ξ±-mediated restriction, in
which the presence of intact SIMs in TRIM5Ξ±, and also the SUMO conjugation
of CA, are required for restriction. We propose that at least a portion of the
antiviral activity of TRIM5Ξ± is mediated through the binding of its SIMs to
SUMO-conjugated CA
Human cellular restriction factors that target HIV-1 replication
Recent findings have highlighted roles played by innate cellular factors in restricting intracellular viral replication. In this review, we discuss in brief the activities of apolipoprotein B mRNA-editing enzyme 3G (APOBEC3G), bone marrow stromal cell antigen 2 (BST-2), cyclophilin A, tripartite motif protein 5 alpha (Trim5Ξ±), and cellular microRNAs as examples of host restriction factors that target HIV-1. We point to countermeasures encoded by HIV-1 for moderating the potency of these cellular restriction functions
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