Polysaccharide-rich fraction of Termitomyces eurhizus accelerate healing of indomethacin induced gastric ulcer in mice

The current study aims to determine the healing activity of water soluble polysaccharide-rich fraction of a wild mushroom, Termitomyces eurhizus (TEps) against the indomethacin induced gastric ulceration in mice model. Gastric tissue histology, myeloperoxidase (MPO) activity, cyclooxygenases (COX) 1 and 2 expression, prostaglandin E₂ (PGE₂) synthesis, and modulation of pro/anti inflammatory cytokines expression were studied for this purpose. Histological study shows that TEps (20 mg/kg) effectively healed the gastric ulceration. Based on biochemical results, the healing capacities of TEps could be attributed to reduction of MPO activity and protection of mucosal mucin content. Enhanced synthesis of PGE₂ by modulation of COX-1 and COX-2 expression and a prominent shift of cytokines expression from pro (TNF-α, IL-1ß) to anti inflammatory (IL-10) side are also held responsible for ulcer healing. The preliminary study highlights the anti-ulcerogenic property of polysaccharide-rich fraction of Termitomyces eurhizus and opens an alternative cure for NSAID induced gastroduodenal diseases.     

Evaluation of effects of arsenic on carbon, nitrogen, and sulfur metabolism in two contrasting varieties of Brassica juncea

This study evaluated the effects of arsenic (As) exposure on carbon, nitrogen, and sulfur (CNS) metabolism in Brassica juncea. Two contrasting, tolerant (TPM-1) and sensitive (TM-4), varieties of B. Juncea were selected and grown either in control sand (150 g) or in sand containing 10 mg of arsenate. Harvesting was performed at 7 and 15 days and various metabolites and enzymes of CNS as well as γ-aminobutyric acid (GABA) metabolism were analyzed. At 7 days, TM-4 showed significantly higher As accumulation and stressed phenotype with increase in superoxide radicals, malondialdehyde, and cell death, as compared with TPM-1. However, the level of hydrogen peroxide was higher in TPM-1 than in TM-4. The level of GABA and the activity of glutamate decarboxylase increased in both roots and shoots of TPM-1, but not in TM-4. The level of nitrate and sulfate increased and decreased in shoots of TPM-1 and TM-4, respectively. The supply of fumarate and succinate was maintained in both shoots and roots of TPM-1 while it was only in shoots of TM-4. There was significant alteration in the profile of amino acids and in sulfur and nitrogen metabolism. However, at 15 days, As accumulation of both varieties was found to be similar along with an increase in GABA, nitrate, and sulfate in both shoots and roots except sulfate in TM-4. Supply of fumarate and succinate was also maintained and other responses were found to be similar in TPM-1 and TM-4. The study demonstrates that responses of CNS metabolism differ in varietal and time-dependent manner.     

NHERF2 Protein Mobility Rate Is Determined by a Unique C-terminal Domain That Is Also Necessary for Its Regulation of NHE3 Protein in OK Cells

Na⁺/H⁺ exchanger regulatory factor (NHERF) proteins are a family of PSD-95/Discs-large/ZO-1 (PDZ)-scaffolding proteins, three of which (NHERFs 1-3) are localized to the brush border in kidney and intestinal epithelial cells. All NHERF proteins are involved in anchoring membrane proteins that contain PDZ recognition motifs to form multiprotein signaling complexes. In contrast to their predicted immobility, NHERF1, NHERF2, and NHERF3 were all shown by fluorescence recovery after photobleaching/confocal microscopy to be surprisingly mobile in the microvilli of the renal proximal tubule OK cell line. Their diffusion coefficients, although different among the three, were all of the same magnitude as that of the transmembrane proteins, suggesting they are all anchored in the microvilli but to different extents. NHERF3 moves faster than NHERF1, and NHERF2 moves the slowest. Several chimeras and mutants of NHERF1 and NHERF2 were made to determine which part of NHERF2 confers the slower mobility rate. Surprisingly, the slower mobility rate of NHERF2 was determined by a unique C-terminal domain, which includes a nonconserved region along with the ezrin, radixin, moesin (ERM) binding domain. Also, this C-terminal domain of NHERF2 determined its greater detergent insolubility and was necessary for the formation of larger multiprotein NHERF2 complexes. In addition, this NHERF2 domain was functionally significant in NHE3 regulation, being necessary for stimulation by lysophosphatidic acid of activity and increased mobility of NHE3, as well as necessary for inhibition of NHE3 activity by calcium ionophore 4-Br-{"type":"entrez-nucleotide","attrs":{"text":"A23187","term_id":"833253","term_text":"A23187"}}A23187. Thus, multiple functions of NHERF2 require involvement of an additional domain in this protein.     

Elemental stoichiometry of basal resources and benthic macroinvertebrates along a land use gradient in a Great Basin watershed

The effects of land use on the elemental stoichiometry of aquatic organisms have rarely been studied in semi-arid watersheds. In eight semi-arid sub-watersheds differing in land use, we determined which predictor variable(s) best explains the elemental variability in two basal food resources and benthic macroinvertebrates (BMI). The elemental composition of periphyton and seston was best explained by percentage of urban and agricultural areas, forested land and associated differences in SRP, DOC, and stream water N:P ratios. In contrast, consumer elemental stoichiometry was related to taxonomic identity and feeding mode. Elemental imbalances were higher for collector-gatherer than for scraper and collector-filterer. However, high spatial and temporal variability in the elemental composition of basal food resources obscured clear spatial patterns of imbalances between nutrient-poor upstream and nutrient-rich downstream sites. Results from this study suggest that land use can affect BMI due to alteration in stoichiometry of their food resources. However, taxonomy and allometry must be taken into account to better understand spatial and temporal changes in the elemental composition of BMI. Our results indicate the importance of considering multiple effects to accurately assess land use effects on producer and consumer stoichiometry, particularly the in highly variable Great Basin watersheds.     

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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Sex differences in kidney gene expression during the life cycle of F344 rats

Background

The kidney functions in key physiological processes to filter blood and regulate blood pressure via key molecular transporters and ion channels. Sex-specific differences have been observed in renal disease incidence and progression, as well as acute kidney injury in response to certain drugs. Although advances have been made in characterizing the molecular components involved in various kidney functions, the molecular mechanisms responsible for sex differences are not well understood. We hypothesized that the basal expression levels of genes involved in various kidney functions throughout the life cycle will influence sex-specific susceptibilities to adverse renal events.

Methods

Whole genome microarray gene expression analysis was performed on kidney samples collected from untreated male and female Fischer 344 (F344) rats at eight age groups between 2 and 104 weeks of age.

Results

A combined filtering approach using statistical (ANOVA or pairwise t test, FDR 0.05) and fold-change criteria (>1.5 relative fold change) was used to identify 7,447 unique differentially expressed genes (DEGs). Principal component analysis (PCA) of the 7,447 DEGs revealed sex-related differences in mRNA expression at early (2 weeks), middle (8, 15, and 21 weeks), and late (104 weeks) ages in the rat life cycle. Functional analysis (Ingenuity Pathway Analysis) of these sex-different genes indicated over-representation of specific pathways and networks including renal tubule injury, drug metabolism, and immune cell and inflammatory responses. The mRNAs that code for the qualified urinary protein kidney biomarkers KIM-1, Clu, Tff3, and Lcn2 were also observed to show sex differences.

Conclusions

These data represent one of the most comprehensive in-life time course studies to be published, assessing sex differences in global gene expression in the F344 rat kidney. PCA and Venn analyses reveal specific periods of sexually dimorphic gene expression which are associated with functional categories (xenobiotic metabolism and immune cell and inflammatory responses) of key relevance to acute kidney injury and chronic kidney disease, which may underlie sex-specific susceptibility. Analysis of the basal gene expression patterns of renal genes throughout the life cycle of the rat will improve the use of current and future renal biomarkers and inform our assessments of kidney injury and disease.

     

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.     

Genomic annotation and validation of bacterial consortium NDMC-1 for enhanced degradation of sugarcane bagasse

This study aims at designing a consortium using rumen bacterial isolates for enhancing the hydrolysis of sugarcane bagasse (SB) for efficient biofuel formation. The microbial population was screened through biochemical and molecular tools along with enzymatic activity to obtain potential isolates for diverse cellulolytic and hemicellulolytic carbohydrate active enzyme (CAZyme). Five strains (Paenibacillus, Bacillus, Enterobacter, and Microbacterium) were selected for designing the consortium NDMC-1. The hydrolytic efficiency of NDMC-1 was determined based on cellulase production with simultaneous rise in monosaccharides, oligosaccharides, and soluble chemical oxygen demand (sCOD) concentration. Cellulolytic machinery of these isolates was further explored using genome sequencing. The isolates selected for consortia NDMC-1 interacted synergistically leading to enhanced cellulase production. Maximal endoglucanase (1.67 μmol ml−1 min−1), exoglucanase (0.69 μmol ml−1 min−1), and β-glucosidase (2.03 μmol ml−1 min−1) activity were achieved with SB as a sole carbon source after 48 h of incubation. Enhancement in SB hydrolysis employing NDMC-1 was evident by the increase in sCOD from 609 to 2589 mg/l and release of 1295 mg/l reducing sugar, comprising 59.8%, 8.23%, and 6.16% of glucose, cellobiose, and cellotriose, respectively, which resulted in 5.5-fold rise in biogas production. On genome annotation, total 472 contigs from glycoside hydrolase family: 84 from Microbacterium arborescens ND21, 72 from Enterobacter cloacae ND22, 61 from Bacillus subtilis ND23, 116 from Paenibacillus polymyxa ND24, and 140 from Paenibacillus polymyxa ND25 were identified. On further analysis, total 33 cellulases, 59 hemicellulases, and 48 esterases were annotated in the reported genomes. This work proposes the application of consortia-based bioprocessing systems over the conventionally favorable single organism approach for efficient hydrolysis of cellulosic substrates to fermentable sugars.