Effect of temperature, relative humidity and moisture content on germination percentage of wheat stored in different storage structures

The paper presents information regarding the pattern of changes in the environmental conditions (i.e. temperature, relative humidity and moisture content) on the stored wheat in Galvanized Iron Corrugated (GIC) silo, Godown storage and CAP storage.  The grain moisture content in the silo increased from 11.20% to 17.08% wet basis (w.b.), in bag storage increased from 11.20% to 17.25%, and in CAP storage increased from 11.20% to 17.19% wet basis (w.b.) during the storage period from April 06 to November 06.  The moisture content of the wheat grain then slightly decreased during the storage period from November 06 to April 07.  The temperature of the grain inside silo was 29.30℃ while at the end of the storage period, the temperature was 42.90℃.  The initial grain temperature inside Godown storage was 29.30℃ and at the end of the storage period, it was 32.31℃.  The initial grain temperature inside CAP storage was 29.10℃ and it increased to 39.94℃ at the end of the storage period.  The relative humidity in the silo was 16.1% lower than the ambient relative humidity.  The germination percentage of grain inside the silo was decreased from 86.70% to 78.60%, in Godown storage it decreased from 86.70% to 53.30%, and in CAP storage it decreased from 86.70% to 46.60% during the storage period from April to September. Keywords: temperature, moisture content, relative humidity, germination percentage, wheat, GIC, silo, Godown, CA

Diagnostic accuracy of an integrated approach using conventional ultrasonography, and Doppler and strain elastography in the evaluation of superficial soft tissue lesions

Introduction: To assess the diagnostic accuracy of an integrated approach using conventional ultrasonography, colour Doppler ultrasonography, and elastography strain ratios in tandem in the evaluation of superficial soft tissue lesions. Material and methods: Sixty-five subjects were included in this prospective cross-sectional study. Greyscale features and Doppler parameters were recorded. Strain elastography of the non-vascular and non-cystic lesions was performed and strain ratios were calculated. Fine-needle aspiration or biopsy of all the lesions was performed depending on their site and condition. Inter-rater k agreement was used to determine the strength of agreement between imaging-based diagnosis and histopathological diagnosis. A diagnostic test was used to calculate the sensitivity, specificity, positive predictive value, and negative predictive value. A p value of < 0.05 was considered statistically significant. Results: Multiple superficial soft tissue lesions were studied, the majority of which were lipomas, vascular anomalies, and epidermoid cysts. The diagnostic accuracy was very high and varied from 92.31% to 100% for various masses. The imaging-based diagnosis was in agreement with the histopathological diagnosis in 86.15% (n = 56) and disagreement in 13.85% (n = 9) of the cases (p < 0.007). There was very good inter-rater agreement between the imaging-based diagnosis and histopathological diagnosis (κ = 0.818). Conclusions: The combined use of conventional ultrasonography, colour Doppler, and elastography strain ratios provides a very effective non-invasive tool for the diagnosis of superficial soft tissue lesions and may negate the need for unnecessary biopsies. The advantage of this integrated approach using various ultrasound techniques needs no further emphasis

Clinical features, predisposing factors and radiological study of cerebral venous sinus thrombosis: experience from a tertiary care center in Southern India

Background: Cerebral venous thrombosis (CVT) is a less common cause of stroke with a wide range of clinical presentations, predisposing factors, radiological features and outcomes. A high index of suspicion is absolutely essential to diagnose cerebral venous thrombosis. In this article, we have reviewed the clinical spectrum and radiological profile of patients with cerebral venous thrombosis and attempted to identify the specific predisposing factors for developing cerebral venous thrombosis particularly in this region of India.Methods: 116 patients hospitalized from January 2015 to March 2017 with a final diagnosis of Cerebral Venous Thrombosis which was confirmed by imaging (MRI/MRV or CT angiography) were included. Patients who were initially diagnosed as CVT but imaging were not suggestive of the same were excluded.Results: The mean age of the study population was 35.21 years, with most patients aged between 21-30 years. 18.1% of the study population were puerperal women, much lower than earlier series. 54.54% of the men had a significant history of alcohol consumption and 10.34% of the non-puerperal women revealed a history of consuming oral contraceptive pills. Among men, seizures were the most common presenting symptom followed by headache. Women presented with headache followed by vomiting. Superior sagittal sinus, transverse sinus, cortical veins and sigmoid sinus involvement were quite common in comparison to the other sinuses.Conclusions: Accurate and prompt diagnosis of CVT is crucial because timely and appropriate therapy can reverse the disease process and significantly reduce the risk of acute complications and long-term sequelae. In this article, we have reviewed the epidemiology, causative factors, clinical features and as well as radiological pattern of CVT from an Indian perspective. Over the last decade, a relatively high incidence of CVT in fairly young individuals warrants further evaluation towards genetic predisposition for pro-thrombotic states particularly in this region of India

PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families

PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of ∼698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from the Pfam database. All the entries in PRODOC are represented as a sequence of functional domains, assigned using hidden Markov models, instead of as a sequence of amino acids. On average 69% of the proteins in the proteomes and 49% of the residues are covered by functional domain assignments. Software tools allow the user to query the dataset with a sequence of domains and identify proteins with the same or a jumbled or circularly permuted arrangement of domains. As it is proposed that proteins with jumbled or the same domain sequences have similar functions, this search tool is useful in assigning the overall function of a multi-domain protein. Unique features of PRODOC include the generation of alignments between multi-domain proteins on the basis of the sequence of domains and in-built information on distantly related domain families forming superfamilies. It is also possible using PRODOC to identify domain sharing and gene fusion events across organisms. An exhaustive genome–genome comparison tool in PRODOC also enables the detection of successive domain sharing and domain fusion events across two organisms. The tool permits the identification of gene clusters involved in similar biological processes in two closely related organisms. The URL for PRODOC is

Physical and sensory characteristics of Ready-To-Eat food prepared from finger millet based composite mixer by extrusion

Extrusion cooking process is a high temperature and short time process in which moist, soft food material is fed to the extruder for desired temperature, pressure, and residence time. &nbsp;Finger millet being a &ldquo;nutricereal&rdquo; was used to develop Ready-To-Eat (RTE) snack food through extrusion cooking. &nbsp;Seven composite mixes were prepared using brown finger millet flour, maize flour, rice flour, full fat soy flour, bengal gram flour, and skimmed milk powder in varying proportions. &nbsp;Extrusion cooking was carried out using a Twin Screw Extruder at a temperature of 140℃, screw speed of 300 r min-1 and die diameter of 3 mm. &nbsp;Physical properties of the extrudates namely bulk density, expansion ratio, Water Absorption Index (WAI), Water Solubility Index (WSI), colour and hardness were analyzed. &nbsp;Organoleptic qualities of the extruded products were also analyzed. &nbsp;The results indicated that the bulk density ranging from 0.1618 to 0.3946 g cm-3 while expansion ratio varied between 2.42 and 3.50. &nbsp;The water absorption index of the extrudates varied from 3.96% to 6.87%. &nbsp;The mix containing the least amount of finger millet flour (10%) had the lightest colour (highest L value) as indicated by Hunter Colour Flex Meter while the composite mix with the highest amount of brown finger millet flour (40%) had the least value for hardness as indicated by Food Texture Analyzer. &nbsp;The mean scores of organoleptic evaluation showed that all the extruded products prepared from the seven composite mixes were within the acceptable range. &nbsp;It is found that the composite mix comprising of brown finger millet flour, maize flour, rice flour, and full fat soy flour in the ratio of 20:50:20:10 produced the most acceptable RTE extrudates in terms of expansion ratio (3.5), hardness (23.37 N) and sensory characteristics (8.87). &nbsp; Keywords: extrusion, water absorption index, hardness, expansion rati

Ortho2ExpressMatrix—a web server that interprets cross-species gene expression data by gene family information

<p>Abstract</p> <p>Background</p> <p>The study of gene families is pivotal for the understanding of gene evolution across different organisms and such phylogenetic background is often used to infer biochemical functions of genes. Modern high-throughput experiments offer the possibility to analyze the entire transcriptome of an organism; however, it is often difficult to deduct functional information from that data.</p> <p>Results</p> <p>To improve functional interpretation of gene expression we introduce Ortho2ExpressMatrix, a novel tool that integrates complex gene family information, computed from sequence similarity, with comparative gene expression profiles of two pre-selected biological objects: gene families are displayed with two-dimensional matrices. Parameters of the tool are object type (two organisms, two individuals, two tissues, etc.), type of computational gene family inference, experimental meta-data, microarray platform, gene annotation level and genome build. Family information in Ortho2ExpressMatrix bases on computationally different protein family approaches such as EnsemblCompara, InParanoid, SYSTERS and Ensembl Family. Currently, respective all-against-all associations are available for five species: human, mouse, worm, fruit fly and yeast. Additionally, microRNA expression can be examined with respect to miRBase or TargetScan families. The visualization, which is typical for Ortho2ExpressMatrix, is performed as matrix view that displays functional traits of genes (differential expression) as well as sequence similarity of protein family members (BLAST e-values) in colour codes. Such translations are intended to facilitate the user's perception of the research object.</p> <p>Conclusions</p> <p>Ortho2ExpressMatrix integrates gene family information with genome-wide expression data in order to enhance functional interpretation of high-throughput analyses on diseases, environmental factors, or genetic modification or compound treatment experiments. The tool explores differential gene expression in the light of orthology, paralogy and structure of gene families up to the point of ambiguity analyses. Results can be used for filtering and prioritization in functional genomic, biomedical and systems biology applications. The web server is freely accessible at <url>http://bioinf-data.charite.de/o2em/cgi-bin/o2em.pl</url>.</p

Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase

Unlike classical 2-oxoglutarate and iron-dependent dioxygenases, which include several nucleic acid modifiers, the structurally similar jumonji-related dioxygenase superfamily was only known to catalyze peptide modifications. Using comparative genomics methods, we predict that a family of jumonji-related enzymes catalyzes wybutosine hydroxylation/peroxidation at position 37 of eukaryotic tRNAPhe. Identification of this enzyme raised questions regarding the emergence of protein- and nucleic acid-modifying activities among jumonji-related domains. We addressed these with a natural classification of DSBH domains and reconstructed the precursor of the dioxygenases as a sugar-binding domain. This precursor gave rise to sugar epimerases and metal-binding sugar isomerases. The sugar isomerase active site was exapted for catalysis of oxygenation, with a radiation of these enzymes in bacteria, probably due to impetus from the primary oxygenation event in Earth’s history. 2-Oxoglutarate-dependent versions appear to have further expanded with rise of the tricarboxylic acid cycle. We identify previously under-appreciated aspects of their active site and multiple independent innovations of 2-oxoacid-binding basic residues among these superfamilies. We show that double-stranded β-helix dioxygenases diversified extensively in biosynthesis and modification of halogenated siderophores, antibiotics, peptide secondary metabolites and glycine-rich collagen-like proteins in bacteria. Jumonji-related domains diversified into three distinct lineages in bacterial secondary metabolism systems and these were precursors of the three major clades of eukaryotic enzymes. The specificity of wybutosine hydroxylase/peroxidase probably relates to the structural similarity of the modified moiety to the ancestral amino acid substrate of this superfamily

Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes

A hallmark of the human immunodeficiency virus 1 (HIV-1) is its rapid rate of evolution within and among its various subtypes. Two complementary hypotheses are suggested to explain the sequence variability among HIV-1 subtypes. The first suggests that the functional constraints at each site remain the same across all subtypes, and the differences among subtypes are a direct reflection of random substitutions, which have occurred during the time elapsed since their divergence. The alternative hypothesis suggests that the functional constraints themselves have evolved, and thus sequence differences among subtypes in some sites reflect shifts in function. To determine the contribution of each of these two alternatives to HIV-1 subtype evolution, we have developed a novel Bayesian method for testing and detecting site-specific rate shifts. The RAte Shift EstimatoR (RASER) method determines whether or not site-specific functional shifts characterize the evolution of a protein and, if so, points to the specific sites and lineages in which these shifts have most likely occurred. Applying RASER to a dataset composed of large samples of HIV-1 sequences from different group M subtypes, we reveal rampant evolutionary shifts throughout the HIV-1 proteome. Most of these rate shifts have occurred during the divergence of the major subtypes, establishing that subtype divergence occurred together with functional diversification. We report further evidence for the emergence of a new sub-subtype, characterized by abundant rate-shifting sites. When focusing on the rate-shifting sites detected, we find that many are associated with known function relating to viral life cycle and drug resistance. Finally, we discuss mechanisms of covariation of rate-shifting sites

Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach

Symbiosis has been among the most important evolutionary steps to generate biological complexity. The establishment of symbiosis required an intimate metabolic link between biological systems with different complexity levels. The strict endo-cellular symbiotic bacteria of insects are beautiful examples of the metabolic coupling between organisms belonging to different kingdoms, a eukaryote and a prokaryote. The host (eukaryote) provides the endosymbiont (prokaryote) with a stable cellular environment while the endosymbiont supplements the host's diet with essential metabolites. For such communication to take place, endosymbionts' genomes have suffered dramatic modifications and reconfigurations of proteins' functions. Two of the main modifications, loss of genes redundant for endosymbiotic bacteria or the host and bacterial genome streamlining, have been extensively studied. However, no studies have accounted for possible functional shifts in the endosymbiotic proteomes. Here, we develop a simple method to screen genomes for evidence of functional divergence between two species clusters, and we apply it to identify functional shifts in the endosymbiotic proteomes. Despite the strong effects of genetic drift in the endosymbiotic systems, we unexpectedly identified genes to be under stronger selective constraints in endosymbionts of aphids and ants than in their free-living bacterial relatives. These genes are directly involved in supplementing the host's diet with essential metabolites. A test of functional divergence supports a strong relationship between the endosymbiosis and the functional shifts of proteins involved in the metabolic communication with the insect host. The correlation between functional divergence in the endosymbiotic bacterium and the ecological requirements of the host uncovers their intimate biochemical and metabolic communication and provides insights on the role of symbiosis in generating species diversity