The Unique Binding Mode of Laulimalide to Two Tubulin Protofilaments

Laulimalide, a cancer chemotherapeutic in preclinical development, has a unique binding site located on two adjacent β‐tubulin units between tubulin protofilaments of a microtubule. Our extended protein model more accurately mimics the microtubule environment, and together with a 135 ns molecular dynamics simulation, identifies a new binding mode for laulimalide, which differs from the modes presented in work using smaller protein models. The new laulimalide–residue interactions that are computationally revealed explain the contacts observed via independent mass shift perturbation experiments. The inclusion of explicit solvent shows that many laulimalide–tubulin interactions are water mediated. The new contacts between the drug and the microtubule structure not only improve our understanding of laulimalide binding but also will be essential for efficient derivatization and optimization of this prospective cancer chemotherapy agent. Observed changes in secondary protein structure implicate the S7–H9 loop (M–loop) and H1′–S2 loop in the mechanism by which laulimalide stabilizes microtubules to exert its cytotoxic effects.     

Comparing within‐subject classification and regularization methods in fMRI for large and small sample sizes

In recent years, a variety of multivariate classifier models have been applied to fMRI, with different modeling assumptions. When classifying high‐dimensional fMRI data, we must also regularize to improve model stability, and the interactions between classifier and regularization techniques are still being investigated. Classifiers are usually compared on large, multisubject fMRI datasets. However, it is unclear how classifier/regularizer models perform for within‐subject analyses, as a function of signal strength and sample size. We compare four standard classifiers: Linear and Quadratic Discriminants, Logistic Regression and Support Vector Machines. Classification was performed on data in the linear kernel (covariance) feature space, and classifiers are tuned with four commonly‐used regularizers: Principal Component and Independent Component Analysis, and penalization of kernel features using L₁ and L₂ norms. We evaluated prediction accuracy (P) and spatial reproducibility (R) of all classifier/regularizer combinations on single‐subject analyses, over a range of three different block task contrasts and sample sizes for a BOLD fMRI experiment. We show that the classifier model has a small impact on signal detection, compared to the choice of regularizer. PCA maximizes reproducibility and global SNR, whereas L_p‐norms tend to maximize prediction. ICA produces low reproducibility, and prediction accuracy is classifier‐dependent. However, trade‐offs in (P,R) depend partly on the optimization criterion, and PCA‐based models are able to explore the widest range of (P,R) values. These trends are consistent across task contrasts and data sizes (training samples range from 6 to 96 scans). In addition, the trends in classifier performance are consistent for ROI‐based classifier analyses. Hum Brain Mapp 35:4499–4517, 2014. © 2014 Wiley Periodicals, Inc .     

Mortality in children hospitalised with respiratory syncytial virus infection in Singapore

INTRODUCTIONThis study aimed to investigate the trend and seasonality of infection due to respiratory syncytial virus (RSV) at KK Women’s and Children’s Hospital (KKH) in Singapore and to examine the risk factors for mortality among children with RSV infection requiring admission to the paediatric intensive care unit (PICU).METHODSA retrospective study was conducted at KKH on children with RSV infections who were admitted to the PICU between January 2004 and December 2010. The medical records of children who died from RSV infections were reviewed. Linear regression was performed to determine the risk factors for RSV mortality.RESULTSRSV infection was documented in 5,785 children during the study period; the infection was noted to be occurring throughout the year, with a small increase in prevalence between the months of June and August every year. Among 85 (1.5%) out of 5,785 children who were admitted to the PICU for RSV infection, 74 (1.3%) survived and 11 (0.2%) died. Multivariate logistic regression analysis showed that haemodynamically significant cardiac disease (odds ratio [OR] 12.2, 95% confidence interval [CI] 0.9–16.7, p = 0.05), immunodeficiency (OR 71.4, 95% CI 8.2–500, p < 0.001) and metabolic disease (OR 71.4, 95% CI 4.3–1,000, p = 0.003) were independent risk factors for mortality in RSV infections. Prematurity increased the risk of admission to the PICU but was not significantly associated with mortality.CONCLUSIONChildren with haemodynamically significant cardiac disease, immunodeficiency and metabolic disease were at higher risk of death after hospitalisation for RSV-related illnesses. These children should be considered for palivizumab prophylaxis.     

Phagocytic efficiency of monocytes and macrophages obtained from Sydney blood bank cohort members infected with an attenuated strain of HIV-1

Defective function of monocyte-derived macrophages contributes to HIV-1 pathogenesis. We found that phagocytosis of the opportunistic pathogens Mycobacterium avium complex and Toxoplasma gondii was impaired in monocytes obtained from individuals infected with wild-type strains of HIV-1 but generally not in monocytes collected over a 6-year period from Sydney Blood Bank Cohort (SBBC) members infected with nef/long terminal repeats (LTR) region-defective strains of HIV-1. However, longitudinal analysis of phagocytosis in 1 SBBC member, C54, showed the development of defective engulfment of opportunistic pathogens at the most recent time points, coincident with the development of further molecular deletions in the nef/LTR region. Another SBBC member, C98, underwent bronchoscopy, which provided material to examine phagocytic signaling in alveolar macrophages. In contrast to normal phagocytic efficiency of C98's monocytes (over a 6-year period), defective signaling events during FcgammaR-mediated phagocytosis by C98's alveolar macrophages were observed. High basal phosphorylation within HIV-infected macrophages correlated with colocalization of tyrosine-phosphorylated proteins with HIV-1 p24 antigen rather than around the phagocytic targets as observed in uninfected cells. Thus, although phagocytic efficiency appears to be generally unimpaired in monocytes from SBBC members, evidence of impairment in recent samples from 1 SBBC member, coincident with further genetic changes within the virus, and abnormal phagocytic signaling in alveolar macrophages from another SBBC member may herald loss of attenuation of those strains.     

The evolutionary origin of the major histocompatibility complex: Polymorphism of class II α chain genes in the cartilaginous fish

T cells recognize antigen (Ag) in the form of peptides bound to the major histocompatibility complex (MHC) molecule. One of the important issues in evolutionary immunology is to identify the stage in phylogeny when this mode of Ag recognition emerged. At present, there is a considerable controversy as to whether the cartilaginous fish have the bona fide MHC. In our previous study, we showed that the nurse shark, a member of the cartilaginous fish, has (a) gene(s) capable of encoding MHC class II a chains. In the present study, we examined the polymorphism of nurse shark MHC class II a chain genes designated Gici-DAA and Gici-DBA using the polymerase chain reaction. The Gici-DAA and Gici-DBA genes had six and five alleles, respectively, and individual alleles usually differed by multiple nucleotides. In addition, most of the nucleotide substitutions were located at the putative Ag-binding sites, where non-synonymous substitutions occurred more frequently than synonymous substitutions. The fact that the Gici-DAA and Gici-DBA genes display a polymorphism pattern essentially similar to that of mammalian MHC genes playing a major role in Ag presentation suggests that the cartilaginous fish have the bona fide MHC. Thus, the MHC-peptide-based T cell recognition system appears to have arisen at or before the emergence of the cartilaginous fish.     

Diphenylhydantoin-induced pure red cell aplasia

The pathogenesis of diphenylhydantoin-induced pure red cell aplasia was investigated in the case of a 32-year-old man who developed pure red cell aplasia while he was under treatment with diphenylhydantoin. The patient's serum IgG purified from serum drawn at the time of diagnosis suppressed normal allogeneic marrow colony-forming (CFU-E) and burst- forming (BFU-E) and autologous blood BFU-E growth in vitro only in the presence of diphenylhydantoin. This IgG-diphenylhydantoin complex had no effect on CFU-GM growth in vitro. Normal IgG or patient's IgG purified from serum drawn after the remission of red cell aplasia had no effect on erythroid colony formation in vitro in the presence of diphenylhydantoin. The IgG-diphenylhydantoin complex exerted no direct cytotoxic effect on normal marrow erythroblasts, CFU-E, and BFU-E, nor did it interfere with the action of erythropoietin on marrow erythroblasts. These studies suggest that diphenylhydantoin-induced red cell aplasia is immunologically mediated through an IgG inhibitor, which requires the presence of the drug to suppress erythroid colony formation in vitro. This inhibitor seems to exert its effect on erythroid progenitors at or beyond the stage of differentiation of CFU- E, but not on erythroblasts.