Structural Basis for Highly Effective HIV-1 Neutralization by CD4-Mimetic Miniproteins Revealed by 1.5 Å Cocrystal Structure of gp120 and M48U1

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Application of higher order statistics for atrial arrhythmia classification

Atrial fibrillation (AF) and atrial flutter (AFL) are the two common atrial arrhythmia encountered in the clinical practice. In order to diagnose these abnormalities the electrocardiogram (ECG) is widely used. The conventional linear time and frequency domain methods cannot decipher the hidden complexity present in these signals. The ECG is inherently a non-linear, non-stationary and non-Gaussian signal. The non-linear models can provide improved results and capture minute variations present in the time series. Higher order spectra (HOS) is a non-linear dynamical method which is highly rugged to noise. In the present study, the performances of two methods are compared: (i) 3rd order HOS cumulants and (ii) HOS bispectrum. The 3rd order cumulant and bispectrum coefficients are subjected to dimensionality reduction using independent component analysis (ICA) and classified using classification and regression tree (CART), random forest (RF), artificial neural network (ANN) and k-nearest neighbor (KNN) classifiers to select the best classifier. The ICA components of cumulant coefficients have provided the average accuracy, sensitivity, specificity and positive predictive value of 99.50%, 100%, 99.22% and 99.72% respectively using KNN classifier. Similarly, the ICA components of HOS bispectrum coefficients have yielded the average accuracy, sensitivity, specificity and PPV of 97.65%, 98.16%, 98.75% and 99.53% respectively using KNN. So, the ICA performed on the 3rd order HOS cumulants coupled with KNN classifier performed better than the HOS bispectrum method. The proposed methodology is robust and can be used in mass screening of cardiac patients.     

ECG beat classification using PCA,LDA, ICA and Discrete Wavelet Transform

Electrocardiogram (ECG) is the P-QRS-T wave, representing the cardiac function. The information concealed in the ECG signal is useful in detecting the disease afflicting the heart. It is very difficult to identify the subtle changes in the ECG in time and frequency domains. The Discrete Wavelet Transform (DWT) can provide good time and frequency resolutions and is able to decipher the hidden complexities in the ECG. In this study, five types of beat classes of arrhythmia as recommended by Association for Advancement of Medical Instrumentation (AAMI) were analyzed namely: non-ectopic beats, supra-ventricular ectopic beats, ventricular ectopic beats, fusion betas and unclassifiable and paced beats. Three dimensionality reduction algorithms; Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA) and Independent Component Analysis (ICA) were independently applied on DWT sub bands for dimensionality reduction. These dimensionality reduced features were fed to the Support Vector Machine (SVM), neural network (NN) and probabilistic neural network (PNN) classifiers for automated diagnosis. ICA features in combination with PNN with spread value (σ) of 0.03 performed better than the PCA and LDA. It has yielded an average sensitivity, specificity, positive predictive value (PPV) and accuracy of 99.97%, 99.83%, 99.21% and 99.28% respectively using ten-fold cross validation scheme.     

Functional significance of active site residues in the enzymatic component of the Clostridium difficile binary toxin

Clostridium difficile binary toxin (CDT) is an ADP-ribosyltransferase which is linked to enhanced pathogenesis of C. difficile strains. CDT has dual function: domain a (CDTa) catalyses the ADP-ribosylation of actin (enzymatic component), whereas domain b (CDTb) transports CDTa into the cytosol (transport component). Understanding the molecular mechanism of CDT is necessary to assess its role in C. difficile infection. Identifying amino acids that are essential to CDTa function may aid drug inhibitor design to control the severity of C. difficile infections. Here we report mutations of key catalytic residues within CDTa and their effect on CDT cytotoxicity. Rather than an all-or-nothing response, activity of CDTa mutants vary with the type of amino acid substitution; S345A retains cytotoxicity whereas S345Y was sufficient to render CDT non-cytotoxic. Thus CDTa cytotoxicity levels are directly linked to ADP-ribosyltransferase activity.     

Revisiting cobalt chloride preconditioning to prevent hypobaric hypoxia-induced damage: identification of global proteomic alteration and key networks

Several studies have supported the hypoxia mimetic roles and cytoprotective properties of cobalt chloride in vitro and in vivo. However, a clear understanding of biological process-based mechanism that integrates the available information remains unknown. This study was aimed to explore the potential mechanism of cobalt chloride deciphering its benefits and well-known physiological challenge caused by hypobaric hypoxia that reportedly affects nearly 24 % of the global population. In order to explore the mechanism of CoCl₂, we used global proteomic and systems biology approach in rat model to provide a deeper insight into molecular mechanisms of preconditioning. Furthermore, key conclusions were drawn based on biological network analysis and their enrichment with ontological overlaps. The study was further strengthened by consistent identification of validation of proteins using immunoblotting. CoCl₂-pretreated animals exposed to hypoxia showed two significant networks, one lipid metabolism and other cell cycle associated, with a total score of 23 and eight focus molecules. In this study, we delineated two primary routes: one, by direct modulation of reactive oxygen species metabolism and, second, by regulation of lipid metabolism which was not known until now. The previously known benefits of cobalt chloride during physiological challenge by hypobaric hypoxia are convincing and could be explained by some basic set of metabolic and molecular reorganization within the hypoxia model. Interestingly, we also observed some of the completely unknown roles of cobalt chloride such as regulation of lipid that could undulate the translational roles of cobalt chloride supplementation beyond hypoxia preconditioning.     

Energy Homeostasis and Obesity: The Therapeutic Role of Anorexigenic and Orexigenic Peptide

International Journal of Peptide Research and Therapeutics - The brain detects changes in energy depots and actuates metabolic and behavioral responses planned to hold energy balance. Hunger,...     

Virulence and pathogenicity of a Candida albicans mutant with reduced filamentation

Deletion of DNA polymerase eta (Rad30/Polη) in pathogenic yeast Candida albicans is known to reduce filamentation induced by serum, ultraviolet, and cisplatin. Because nonfilamentous C. albicans is widely accepted as avirulent form, here we explored the virulence and pathogenicity of a rad30Δ strain of C. albicans in cell‐based and animal systems. Flow cytometry of cocultured fungal and differentiated macrophage cells revealed that comparatively higher percentage of macrophages was associated with the wild‐type than rad30Δ cells. In contrast, higher number of Polη‐deficient C. albicans adhered per macrophage membrane. Imaging flow cytometry showed that the wild‐type C. albicans developed hyphae after phagocytosis that caused necrotic death of macrophages to evade their clearance. Conversely, phagosomes kill the fungal cells as estimated by increased metacaspase activity in wild‐type C. albicans. Despite the morphological differences, both wild‐type and rad30? C. albicans were virulent with a varying degree of pathogenicity in mice models. Notably, mice with Th1 immunity were comparatively less susceptible to systemic fungal infection than Th2 type. Thus, our study clearly suggests that the modes of interaction of morphologically different C. albicans strains with the host immune cells are diverged, and host genetic background and several other attributing factors of the fungus could additionally determine their virulence.     

Red panda fine‐scale habitat selection along a Central Himalayan longitudinal gradient

Red panda Ailurus fulgens, an endangered habitat specialist, inhabits a narrow distribution range in bamboo abundance forests along mountain slopes in the Himalaya and Hengduan Mountains. However, their habitat use may be different in places with different longitudinal environmental gradients, climatic regimes, and microclimate. This study aimed to determine the habitat variables affecting red panda distribution across different longitudinal gradients through a multivariate analysis. We studied habitat selection patterns along the longitudinal gradient in Nepal's Himalaya which is grouped into the eastern, central, and western complexes. We collected data on red panda presence and habitat variables (e.g., tree richness, canopy cover, bamboo abundance, water availability, tree diameter, tree height) by surveys along transects throughout the species’ potential range. We used a multimodal inference approach with a generalized linear model to test the relative importance of environmental variables. Although the study showed that bamboo abundance had a major influence, habitat selection was different across longitudinal zones. Both canopy cover and species richness were unimportant in eastern Nepal, but their influence increased progressively toward the west. Conversely, tree height showed a decreasing influence on habitat selection from Eastern to Western Nepal. Red panda's habitat selection revealed in this study corresponds to the uneven distribution of vegetation assemblages and the dry climatic gradient along the eastern‐western Himalayas which could be related to a need to conserve energy and thermoregulate. This study has further highlighted the need of importance of bamboo conservation and site‐specific conservation planning to ensure long‐term red panda conservation.     

alphavbeta5 integrin sustains growth of human pre-B cells through an RGD-independent interaction with a basic domain of the CD23 protein

CD23 is a type II transmembrane glycoprotein synthesized by hematopoietic cells that has biological activity in both membrane-bound and freely soluble forms, acting via a number of receptors, including integrins. We demonstrate here that soluble CD23 (sCD23) sustains growth of human B cell precursors via an RGD-independent interaction with the alphavbeta5 integrin. The integrin recognizes a tripeptide motif in a small disulfide-bonded loop at the N terminus of the lectin head region of CD23, centered around Arg(172), Lys(173), and Cys(174) (RKC). This RKC motif is present in all forms of sCD23 with cytokine-like activity, and cytokine activity is independent of the lectin head, an "inverse RGD" motif, and the CD21 and IgE binding sites. RKC-containing peptides derived from this region of CD23 bind alphavbeta5 and are biologically active. The binding and activity of these peptides is unaffected by inclusion of a short peptide containing the classic RGD sequence recognized by integrins, and, in far-Western analyses, RKC-containing peptides bind to the beta subunit of the alphavbeta5 integrin. The interaction between alphavbeta5 and sCD23 indicates that integrins deliver to cells important signals initiated by soluble ligands without the requirement for interactions with RGD motifs in their common ligands. This mode of integrin signaling may not be restricted to alphavbeta5.     

HbS-Savaria: The Anti-polymerization Effect of a Single Mutation in Human α-chains

Recombinant α-Savaria globin (α^S49R) was assembled with β^S chains by the alloplex intermediate pathway to generate tetrameric rHbS-Sarvaria (α₂^S49Rβ₂^E6V) that exhibited normal O₂ affinity and co-operatively at pH 7.4. Allosteric effectors, 2,3-DPG, L35, and NaCl increased O₂ affinity by 15%. Bohr effects were similar for rHbS-Savaria and HbS (0.38 ± 0.025 vs. 0.46 ± 0.03, respectively). The C_SAT of HbS increased from 16.7 ± 0.8 to 27.0 ± 1.0 g/dL. Co-polymerization demonstrated inhibition predominantly by the Cis-dimer. Molecular modeling indicated that the positive charge at α-49 generated a strong anion-binding site and reduced flexibility of the CD-region by restricting movement in the E and F helices. The molecular distance between Arg-49 and Asn-78 in the neighboring double strand decreased, and electrostatic repulsion between the inter-double strands increased, resulting in inhibition of polymerization. The Savaria mutation may be useful for the design of super-inhibitory α-chains and gene therapy of sickle cell anemia.