Challenges in assessing pathogenicity based on frequency of variants in mismatch repair genes: an extreme case of a MSH2 variant and a meta-analysis

The clinical interpretation of variants in mismatch repair (MMR) genes associated with Lynch syndrome can be confusing when the functional nature of the variant is not clearly defined. We report an extreme case where a polymorphism in the MSH2 gene which had a low minor allele frequency, was misclassified as a mutation based on low evidential methods in the database and previous publications. We expanded this experience to perform a systematic meta-analysis in order to investigate other variants that have potentially been misclassified. Our results suggested that the interpretation of pathogenicity should be more cautious and emphasized the need for solid validation through multiple analyses including functional analysis for variants in MMR genes.     

Insect Barcode Information System

Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client– server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn.

Availability

http://www.nabg-nbaii.res.in/barcode     

New horizons in schizophrenia treatment: autophagy protection is coupled with behavioral improvements in a mouse model of schizophrenia

Autophagy plays a key role in the pathophysiology of schizophrenia as manifested by a 40% decrease in BECN1/Beclin 1 mRNA in postmortem hippocampal tissues relative to controls. This decrease was coupled with the deregulation of the essential ADNP (activity-dependent neuroprotector homeobox), a binding partner of MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 β) another major constituent of autophagy. The drug candidate NAP (davunetide), a peptide fragment from ADNP, enhanced the ADNP-LC3B interaction. Parallel genetic studies have linked allelic variation in the gene encoding MAP6/STOP (microtubule-associated protein 6) to schizophrenia, along with altered MAP6/STOP protein expression in the schizophrenic brain and schizophrenic-like behaviors in Map6-deficient mice. In this study, for the first time, we reveal significant decreases in hippocampal Becn1 mRNA and reversal by NAP but not by the antipsychotic clozapine (CLZ) in Map6-deficient (Map6^+/−) mice. Normalization of Becn1 expression by NAP was coupled with behavioral protection against hyperlocomotion and cognitive deficits measured in the object recognition test. CLZ reduced hyperlocomotion below control levels and did not significantly affect object recognition. The combination of CLZ and NAP resulted in normalized outcome behaviors. Phase II clinical studies have shown NAP-dependent augmentation of functional activities of daily living coupled with brain protection. The current studies provide a new mechanistic pathway and a novel avenue for drug development.     

从文献计量学角度评价我国干细胞产业发展历程

目的:通过分析我国有关干细胞科技论文被国际权威检索工具PubMed收录情况,评价我国干细胞领域的发展历程及应用前景。方法:应用文献计量学和数理统计方法对PubMed收录我国干细胞领域科技论文进行统计分析。结果:PubMed一共收录我国干细胞领域科技论文8039篇,其中中文文献2021篇,外文文献6018篇;北京、上海、广东、台湾四个地区发文量领先于其他地区;排名前三的发文机构为中山大学、上海交通大学和中国医学科学院北京协和医院;国际期刊分布中Biochem Biophys Res Commun、Biomaterials、PLoS One位列前三甲;国内期刊分布中中国实验血液学杂志、中国修复重建外科杂志、中华医学杂志位列前三甲;主题分布中高频主题词有间充质干细胞、骨髓细胞、造血干细胞,等;干细胞治疗疾病常见的有白血病、心肌梗死、肝肿瘤,等。结论:我国干细胞起步于1986年,于2000年后快速发展,发文量成几何倍数增长,干细胞的发展将对我国传统医疗手段和医疗观念造成一场重大的革命。     

In silico proteolysis and analysis of bioactive peptides from sequences of fatty acid desaturase 3 (FAD3) of flaxseed protein

Flaxseed (Linum usitatissimum), commonly known as linseed is an oilseed crop, emerging as an important and functional ingredient of food and has been paid more attention due to its nutritional value as well as beneficial effects. It is mainly rich in is α-linolenic acid (ALA, omega-3 fatty acid), fibres and lignans that have potential health benefits in reducing cardiovascular diseases, diabetes, osteoporosis, atherosclerosis, cancer, arthritis, neurological and autoimmune disorders. Due to its richness in omega-3 fatty acid, a group of enzymes known as fatty acid desaturases (FADs) mainly introduce double bonds into fatty acids’ (FAs) hydrocarbon chains that produce unsaturated fatty acids. Fatty acid desaturase 3 (FAD3), the commonest microsomal enzyme of omega-3 fatty acid, synthesizes linolenic acid (C18:3) from linoleic acid located in endoplasmic reticulum (ER) facing towards the cytosol. The emerging field of bioinformatics and large number of databases of bioactive peptides, helps in providing time-saving and efficient method for identification of potential bioactivities of any protein. In this study, 10 unique sequences of FAD3 from flaxseed protein have been used for in silico proteolysis and releasing of various bioactive peptides using three plant proteases, namely ficin, papain and stem bromelain, that are evaluated with the help of BIOPEP database. Overall, 20 biological activities were identified from these proteins. The results showed that FAD3 protein is a potential source of peptides with angiotensin-I-converting enzyme (ACE) inhibitory and dipeptidyl peptidase-IV (DPP-IV) activities, and also various parameters such as ∑A, ∑B, A_E, W, B_E, V and DHt were also calculated. Furthermore, PeptideRanker have been used for screening of novel promising bioactive peptides. Various bioinformatics tools also used to study protein’s physicochemical properties, peptide’s score, toxicity, allergenicity aggregation, water solubility, and drug likeliness. The present work suggests that flaxseed protein can be a good source of bioactive peptides for the synthesis of good quality and quantity of oil, and in silico method helps in investigating and production of functional peptides.     

上海昆虫多样性信息系统的设计与建立

利用Access＋ASP＋IIs技术,建立了集害虫信息管理与昆虫编目数据库为一体的上海昆虫多样性管理信息系统。用户可以通过浏览器访问http：／／www．insects．cn进行检索和查询。本文详细阐述了该系统的构建方法,并就目前昆虫多样性信息管理系统建设中存在的问题作了评述。     

Component manufacturing analysis

To date, numerous simplified Life Cycle Assessment methods and techniques have been developed to reduce complexities associated with practical application. However, these methods often identify critical elements according to subjective considerations. In this paper, we develop and apply a new type of Life Cycle Inventory method — Component Manufacturing Analysis (CMA) — that is easy to implement and less arbitrary. Application of CMA requires identification of all product components and their associated weights, which are then entered into a factory-type database. Because the factory database has a rigorous yet generic structure and because calculation is done automatically, the application of CMA tends to be less arbitrary and more complete than other simplified methods. Results of a case study on beverage vending machines show that the manufacturing stage is a significant phase in the whole life-cycle inventory of a product. We conclude that CMA shows promise for further development and future application.