Identification of MYH6 as the potential gene for human ischaemic cardiomyopathy

The present study aimed to explore the potential hub genes and pathways of ischaemic cardiomyopathy (ICM) and to investigate the possible associated mechanisms. Two microarray data sets ( GSE5406 and GSE57338 ) were downloaded from the Gene Expression Omnibus (GEO) database. The limma package was used to analyse the differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, Disease Ontology (DO) and Gene Ontology (GO) annotation analyses were performed. A protein-protein interaction (PPI) network was set up using Cytoscape software. Significant modules and hub genes were identified by the Molecular Complex Detection (MCODE) app. Then, further functional validation of hub genes in other microarrays and survival analysis were performed to judge the prognosis. A total of 1065 genes were matched, with an adjusted p < 0.05, and 17 were upregulated and 25 were downregulated with|log₂ (fold change)|≥1.2. After removing the lengthy entries, GO identified 12 items, and 8 pathways were enriched at adjusted p < 0.05 (false discovery rate, FDR set at <0.05). Three modules with a score >8 after MCODE analysis and MYH6 were ultimately identified. When validated in GSE23561 , MYH6 expression was lower in patients with CAD than in healthy controls (p < 0.05). GSE60993 data suggested that MYH6 expression was also lower in AMI patients (p < 0.05). In the GSE59867 data set, MYH6 expression was lower in CAD patients than in AMI patients and lower in heart failure (HF) patients than in non-HF patients. However, there was no difference at different periods within half a year, and HF was increased when MYH6 expression was low (p < 0.05–0.01). We performed an integrated analysis and validation and found that MYH6 expression was closely related to ICM and HF. However, whether this marker can be used as a predictor in blood samples needs further experimental verification.     

Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing

High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.     

Issues in using whole slide imaging for diagnostic pathology: “routine” stains,immunohistochemistry and predictive markers

The traditional microscope, together with the “routine” hematoxylin and eosin (H & E) stain, remains the “gold standard” for diagnosis of cancer and other diseases; remarkably, it and the majority of associated biological stains are more than 150 years old. Immunohistochemistry has added to the repertoire of “stains” available. Because of the need for specific identification and even measurement of “biomarkers,” immunohistochemistry has increased the demand for consistency of performance and interpretation of staining results. Rapid advances in the capabilities of digital imaging hardware and software now offer a realistic route to improved reproducibility, accuracy and quantification by utilizing whole slide digital images for diagnosis, education and research. There also are potential efficiencies in work flow and the promise of powerful new analytical methods; however, there also are challenges with respect to validation of the quality and fidelity of digital images, including the standard H & E stain, so that diagnostic performance by pathologists is not compromised when they rely on whole slide images instead of traditional stained tissues on glass slides.     

DNA replication stress: Causes,resolution and disease

DNA replication is a fundamental process of the cell that ensures accurate duplication of the genetic information and subsequent transfer to daughter cells. Various pertubations, originating from endogenous or exogenous sources, can interfere with proper progression and completion of the replication process, thus threatening genome integrity. Coordinated regulation of replication and the DNA damage response is therefore fundamental to counteract these challenges and ensure accurate synthesis of the genetic material under conditions of replication stress. In this review, we summarize the main sources of replication stress and the DNA damage signaling pathways that are activated in order to preserve genome integrity during DNA replication. We also discuss the association of replication stress and DNA damage in human disease and future perspectives in the field.     

Effects of maternal depression on family food insecurity

We use data from the Early Childhood Longitudinal Study—Birth Cohort to estimate the effects of maternal depression, a condition that is fairly common and can be severe, on food insecurity, a hardship that has increased substantially in the U.S. Using various model specifications, we find convincing evidence that severe maternal depression increases the likelihood that young children experience food insecurity by 23–79%, with estimates depending on model specification and measures of depression and food insecurity. For household food insecurity, the corresponding estimates are 11–69%. We also find that maternal depression increases reliance on several types of public programs, suggesting that the programs play a buffering role.     

Methods for rapid screening and isolation of bacteria producing acidic lipase: feasibility studies and novel activity assay protocols

Acidic lipase finds its commercial values in medical applications and bioremediation of food wastes. In this work, approaches for rapid screening of lipase-producing bacteria were developed and the feasibility assessment of the screening methods was performed. From food waste samples, the proposed screening procedures allowed isolation of sixteen pure bacterial strains expressing higher lipase activity at acidic pH (pH 6.0) than at alkaline pH (pH 9.0). To enhance the accuracy of lipase activity determination under acidic conditions, a novel assay procedure was also developed by deactivating lipase activity by microwave treatment prior to back titration. This additional step could minimize interferences arising from residual lipase activity during conventional direct back-titration methods in measuring lipase activity at acidic pH. Using the four strategies proposed in this work, the best acidic-lipase-producing isolate was obtained by strategy C (SSC) and was identified as Aeromonas sp. C14, displaying an optimal lipase activity of 0.7 U/ml at an acidic pH of 6.0.     

Feeding ecology of common carp (Cyprinus carpio L.) in a rice–fish culture system of the Apatani plateau (Arunachal Pradesh, India)

For two years (2002, 2003) selective feeding ecology of the common carp (Cyprinus carpio L.) has been studied in carp-integrated rice fields in Apatani Plateau of Arunachal Pradesh (India). Sampling strategy was based on the water depths in the fields and on the flood phases: early flood phase (June–July), mid flood phase (July–August), and late flood phase (September–October). In 2003 the water level was higher and therefore periphyton availability was better. This resulted in larger gut contents and better growth of the carp compared with 2002 when the water levels were lower. Gut contents analyses revealed a total of 60 food items of which 22 belonged to the Chlorophycea, 12 to the Cyanobacteria, 10 to the Bacillariophycea and 16 to several zooplankton taxa. With the progress of flood phases, the fish increased its feeding on periphyton food items; simultaneously, feeding on plankton items gradually declined. This was caused by the increasing periphyton availability on the rice-stems. Selective feeding on plankton and periphyton taxa was studied, selectivity changed with the flood phases. Periphytic Chlorophycea and Cyanobacteria, especially, were strongly positively selected. Generally, periphyton was the most important resource for the common carp in the rice fields.     

The hidden face of food phenolic composition

Plant polyphenols are extremely diverse, due to the occurrence of several basic structures, numerous substitutions and, for some groups, of polymers (tannins). Plant polyphenol composition depends on the plant species and organ, with some molecules specific of particular plant families while others are ubiquitous. The polyphenol content is classically assessed by global analysis methods, which lack specificity and accuracy. These methods have been replaced with high performance liquid chromatography (HPLC), that enables accurate determination of individual molecules, provided they can be unambiguously identified and calibration curves can be established. However, HPLC analysis is restricted to simple compounds and difficult to apply in the case of complex extracts. Further difficulties encountered in the case of polymers include irreversible adsorption on the stationary phases. Proanthocyanidin analysis by HPLC after acid-catalysed depolymerisation in the presence of a nucleophile permits to overcome these problems and shows that proanthocyanidins predominate in the polyphenol composition of most plants. Large varietal differences in tannin quantitative and qualitative composition were observed for all plant species studied. Moreover, analysis is usually performed after extraction, which may lead to significant underestimation of the polyphenol content, since a large proportion is not extracted by usual solvents. This may be due to covalent binding to other plant constituents and to non-covalent adsorption on plant solids. Such matrix effect also influences the taste perception of polyphenols and their fate in the digestive tract, from in-mouth interactions with salivary proteins to their metabolism by colon microflora, with potential influence on bioavailability.     

黑龙江省通河乌龙狩猎场野猪冬季食性的初步研究

野生动物食性的研究,在野生动物保护和管理方面具有重要的基础理论意义。野猪（Sus scrofa）是一种经济价值较高的有蹄类动物。国内对野猪食性的报道,仅见综述性献（巫露平,1980;李振营和罗泽殉,1983;杨伯然,1984）,野猪食性方面的研究尚未多见;国外对野猪食性的研究主要集中在食物组成的定量分析和食物营养质量的评价（Eriksson and Petrov,1995;Foumier-chambrillon et al．,1995;朝日念,1985）。因此,作从2000～2001年,分别在黑龙江省通河乌龙狩猎场收集粪样,利用粪便显微组织学分析方法并结合野外掘食痕迹对野猪冬季食性进行了初步研究。