MPDB 1.0: a medicinal plant database of Bangladesh

The term of medicinal plants include a various types of plants used in herbalism with medicinal activities. These plants are considered as rich resources of ingredients which can be used as complementary and alternative medicines and, also in drug developments and synthesis. In addition, some plants regarded as valuable origin of nutrition. Thus, all these plants are recommended as therapeutic agents. Information related to medicinal plants and herbal drugs accumulated over the ages are scattered and unstructured which make it prudent to develop a curated database for medicinal plants. MPDB 1.0 database is dedicated to provide the first window to find the plants around Bangladesh claimed to have medicinal and/or nutritive values by accumulating data from the published literatures. This database contains 406 medicinal plants with their corresponding scientific, family and local names as well as utilized parts for treatment from different districts of Bangladesh. Information regarding ailments is available for 353 plants. In addition, we have found active compounds for 78 plants with their corresponding PubMed ID.

Availability

www.medicinalplantbd.net     

InDiaMed: A Comprehensive Database of Indian Medicinal plants for Diabetes

According to International Diabetes Federation (IDF), India has 62.4 million people with diabetes and by 2030 it is predicted that the number will rise to 100 million. Studies claim that there are around 410 experimentally proven Indian medicinal plants which have anti-diabetic activity, of which the mechanism of action of 109 plants has been elucidated or reported. So, the need of the hour is to explore the claims of Indian medicinal flora and open up the facets of many Indian plants which are being examined for their beneficial role in diabetes. So, we created a database (InDiaMed) of Indian medicinal plants that captures their role in anti-diabetic activity. InDiaMed''s features include chemical, pharmacological, biochemical and geographical information of the medicinal plant, scientifically relevant information of the plant, and the coherent research done on it in the field of diabetes. The database also includes the list of poly-herbal formulations which are used for treatment of diabetes in India.

Availability

http://www.indiamed.info     

Bamboo-infoline: A database for North Bengal Bamboo's

Bamboo, the "Green Gold", included in the non-timber forest products has both ecological and economic importance. Here is an attempt to describe a database named "Bambooinfoline" , which provides enumeration of the different species of bamboos found in North Bengal, with special emphasis on taxonomy, edible properties, chemical constituents, morphological features along with tissue culture specifications, which in turn benefits of scientific community. AVAILABILITY: The database is freely available at http://www.bamboodb.ind.in/     

A database for medicinal plants used in the treatment of diabetes and its secondary complications

Effective treatment of diabetes is increasingly dependent on active constituents of medicinal plants capable of controlling hyperglycemia as well as its secondary complications. Sensing the importance of documenting such medicinal plants, here we describe a web database containing information (name, literature citation, active compounds and few related full text articles) of the diabetes medicinal plants exhibiting hypoglycemic, antioxidant and antimicrobial effects. AVAILABILITY: http://www.autogeneralfilters.com/holycross/Home.html.     

A database for anti-diabetic plants with clinical / experimental trials

A number of plants have been described in Ayurveda and other traditional medicine for the management of diabetes. However, information about them is not easily available. Active constituents of any medicinal plant define the efficacy and safety of treatment to control hyperglycemia. We describe the database to maintain the record of medicinal plants having anti-hyperglycemic or anti-diabetic activity. The database contains information such as plant name, its geographical distribution, useful plant part, known dosage, active constituents, mechanism of action and clinical/experimental data. The database also includes information about plant raw material suppliers or manufacturers in India. The current database includes 238 plants species and 123 Indian industries using them. AVAILABILITY: The database is freely available at http://www.biotechpark.org.in/antidia/index.html.     

Ectomychorrizal DB: a symbiotic association database

Ectomycorrhizal (ECM) fungal species, a "Symbiotic" relationship between tress and fungi in forest has a great ecological and economic importance. Here is an attempt to describe database named "EctomycorrhizalDB", addressing ECM diversity of Central Himalaya (Kumaun region), with special emphasis on their characterization, physical properties and morphological features along with specifications. This database would help the scientific community to draw a better understanding of the environmental factors that affects species diversity. AVAILABILITY: The database is available for free at http://www.kubic.nic.in/ectomychorhiza.     

Ethnopharmacological Survey of Plants Used for the Treatment of Stomach,Diabetes, and Ophthalmic Diseases in Sudhan Gali,Kashmir , Pakistan

The present paper represents the ethnopharmacological survey of Sudhan Gali, Kashmir, Pakistan. The study revealed that 12 plant species belonging to 11 families were used for the treatment of stomach, diabetes and ophthalmic diseases by the local people in Sudhan Gali. Achillea millefolium , Aconitum heterophyllum, Berberis lycium, Polygonum amplexicaule, Mentha longifolia, Paeonia emodi, Plantago lanceolata were locally used for stomach related problems treatment; Berberis lycium, Skimmia lareola, Solanum dulcamara for diabetes and Geranium wallichianum, Artemisia vulgaris, Solanum dulcamara, and Corydalis crassifolia used for the treatment of ophthalmic diseases. Two species Berberis lycium and Solanum dulcamara have multipurpose value. Former is used to treat stomach as well as diabetes while latter is used to treat not only to diabetes but also ophthalmic diseases. According to IUCN categories , out of these 12 plant species collected and marketed, Polygonum amplexicaule and Paeonia emodi are endangered, Aconitum heterophyllum; Berberis lycium species are vulnerable while Plantago lanceolata and Skimmia lareola species are rare.The availability of these medicinal plants has decreased during the past 20 years and these are facing a drastic biotic pressure due to their extensive usage and non-scientific methods of collection. It is quite evident that these valuable native medicinal plants species are going to decline in number and ultimately will become extinct if no timely proper conservation strategies are adopted.     

一种用于构建表达载体的合成生物学数据库

由于基因测序及DNA合成技术与工具的突破性进展,生物工程正在加速发展,导致合成生物学的出现。本文介绍了一种用于构建表达载体的合成生物学数据库。阐述了如何利用MySQL数据库管理系统(DBMS)对合成生物学数据库gene_bank进行查询,并借助BioEdit软件对其中的多克隆位点(MCS)进行序列分析,通过查询与分析找出这一合成生物学数据库的特点。     

In-vitro phytochemical and pharmacological bio-efficacy studies on Azadirachta indica A. Juss and Melia azedarach Linn for anticancer activity

In this study, phyto-constituents, anti-bacterial and anticancer activity of Azadirachta indica A. Juss and Melia azedarach Linn was analyzed. High Performance Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) fingerprint profile of methanol extract of A. indica and M. azedarach was carried out. The present findings showed the presence of phytochemicals such as, steroids, alkaloids, phenols, flavonoids, saponins, tannins, anthraquinone and aminoacids in A. indica and M. azedarach extracts. HPLC profiling of methanolic extract of A. indica and M. azaderach revealed eleven and ten fractions of compounds were visualized in the form of peak. In TLC methanolic extract of A. indica was separated by eight distinct phenolic and three steroidal bands and M. azaderach showed sixteen distinct phenolic and three different steroidal bands. In antibacterial activity, Among the various extracts 50 µg/ml methanolic extracts of A. indica showed high activity against K. pneumoniae (14 mm) and M. azedarach showed high activity against S. aureus (15 mm). The results suggest that the crude methanolic extracts of A. indica and M. azedarach possess significant phytochemical properties compared to other extracts and hence the phytochemicals of M. azedarach and A. indica can be exploited for plant based anticancer and antimicrobial agents in the near future.     

GPDE: A biological proteomic database for biomarker discovery and evaluation

Clinical proteomics faces extremely complex and variable data. Here, we present an updated version of the Griss Proteomics Database Engine (GPDE): A free biological proteomic database specifically designed for clinical proteomics and biomarker discovery (http://gpde.sourceforge.net). It combines experiments based on investigated cell types thereby supporting customizable biological meta-analyses. Through the new features described here, the GPDE now became a powerful yet easy-to-use tool to support the fast identification and reliable evaluation of biomarker candidates.     

A relational database for cryoEM: experience at one year and 50 000 images

For the past year we have been using a relational database as part of an automated data collection system for cryoEM. The database is vital for keeping track of the very large number of images collected and analyzed by the automated system and essential for quantitatively evaluating the utility of methods and algorithms used in the data collection. The database can be accessed using a variety of tools including specially developed Web-based interfaces that enable a user to annotate and categorize images using a Web-based form.     

Antagonistic,Anti-oxidant,Anti-inflammatory and Anti-diabetic Probiotic Potential of Lactobacillus agilis Isolated From the Rhizosphere of the Medicinal Plants

Potential probiotic bacteria can be used as a biotherapeutic agent and a sustainable alternative to antibiotics, as an anti-oxidative, anti-inflammatory, and anti-diabetic agent without causing any serious side effects. Mostly human-friendly Lactic acid bacteria (LAB) have been isolated from the animal-human origin to be used as biotherapeutic agents or to produce useful metabolites (nutraceutical). However, less information is known about the role of medicinal plants associated LAB as biotherapeutic agents. The isolation of 115 human-friendly Lactobacillus strains was done from the rhizosphere of the medicinal plants Ocimum tenuiflorum, Azadirachta indica, Ficus carica. The obtained bacteria were then tested for their safe status before being using it for a beneficial purpose. Out of 115 strains, 29 (25%) were negative for blood hemolytic activities. Among these 29 isolates, three isolates did not show a breakdown of gelatin and were recognized as safe. Antibiotic resistance assay showed resistance of two of them against antibiotics discs of Streptomycin (10 µg), Ciprofloxacin (20 µg), Vancomycin (30 µg), Metronidazole (10 µg), Ampicillin (5 µg), Chloramphenicol (30 µg), Kanamycin (30 µg), Erythromycin (15 µg), Penicillin (10 µg) and Tetracycline (30 µg). The bacterial isolate (T-2) was found safe that was identified as Lactobacillus agilis by sequence analysis of 16 s rRNA gene and processed in vitro as an anti-bacterial, anti-oxidant, anti-diabetic, and anti-inflammatory agent. Free radical scavenging activities and inhibition of α-amylase activities for Lactobacillus agilis were found relative to standard drug values as 68% and 73% and 51.3% and 65.3%, respectively. The in-vitro anti-inflammatory assay showed 61.6% (Lactobacillus agilis) while showed 69% (aspirin) activity for denaturation albumin protein. The results suggested that Lactobacillus agilis can be used as a potential probiotic strain as well as can be used to produce nutraceuticals.     

Peripartum cardiomyopathy: the need for a national database

Peripartum cardiomyopathy (PPCM) is a rare and life-threatening disease that affects young women in the last month of pregnancy or within 5 months of delivery. It is a form of dilated cardiomyopathy with left-sided systolic dysfunction. The incidence rate in the Western world is estimated to be 1:3000. Symptoms of PPCM vary greatly and may be obscured by common physiological aspects of pregnancy. Therefore, the incidence rate might be higher. Echocardiography or MRI can confirm or rule out PPCM. Unfortunately, there is no specific risk factor profile available. The clinical course varies from complete recovery to deterioration of cardiac function. Patients with PPCM, especially those whose ventricular function has not returned to normal, are advised against further pregnancy. Recently, more disease-specific therapeutic strategies have been developed with promising results for prolactin blockade by bromocriptine. Increasing awareness for PPCM among general practitioners, gynaecologists and cardiologists may help to diagnose patients efficiently in order to start adequate treatment. A national registry is warranted to identify risk factor profiles and to optimise treatment strategies.     

HORA suite: a database and software for human metabolomics

HORA suite (Human blOod Range vAlidator) consists of a Java application used to validate the metabolomic analysis of human blood against a database that stores the normal plasma and serum range concentrations of metabolites. The goal of HORA is to find the metabolites that are outside the normal range and to show those not present in the list provided by the user, for different thresholds of concentration. Moreover it supplies a graphical interface to manage the data. The software can also be used to compare different metabolomic techniques. HORA is open-source software and it can be accessed at . A separate file contains instructions for the installation and a brief tutorial.     

Transgenic Plant Monitor (TPM): a relational database for the management and analysis of information in plant tissue culture and transformation laboratories

Increased public concern and strict statutory regulations relating tothe generation and exploitation of genetically modified organisms, make itimperative to track accurately individual plants through DNA transformationprogrammes. The ability to rapidly retrieve information associated withspecifictransgenic events and to provide accurate reports on demand is an increasinglyimportant feature for public research laboratories. Transgenic Plant Monitor(TPM) has been developed as a database structured to allow efficient recording,monitoring and analysis of the extensive and complex data generated in planttissue culture and transformation experiments. TPM is built upon the widelyavailable Microsoft Access database engine and can be readily adoptedand/or adapted by other users. The key features and the utility of TPM as aresearch tool are discussed in this article.     

Ssa miRNAs DB: Online repository of in silico predicted miRNAs in Salmo salar

The Atlantic salmon (Salmo salar) is a very valuable commercial salmonid species. As with other aquaculture species, intensive aquaculture of Atlantic salmon often faces disease problems especially in early life stages which can limit stable production of the species. 'Ssa miRNAs DB', a bioinformatics and manually curated database, aims at providing a comprehensive resource of microRNA in Altantic salmon, with a user friendly interface for a convenient retrieval of each entry by microRNA ID or target gene. The current version of Ssa miRNAs DB involved the prediction of 41 and 266 homologous and novel microRNAs, respectively. AVAILABILITY: The database is available for free at http://www.molgenv.com/ssa_mirnas_db_home.php.     

A standardized format for handling data on plasmids,viruses and transposons: The PVT database format

The PVT format described here has been designed to store and retrieve genetic data on plasmids, viruses or transposons with special focus on their applications. Both naturally-occurring and engineered elements can be included in it. A variety of data can be accommodated in fields that are grouped in blocks: name and type of element, database administration, element administration, history, propagation, selection and host, biological properties, cloned insert and applications. The number of fields, now 157, can be expanded as required. Most properties can be described in simple logical fields. The format is organized to permit rapid searches and to facilitate communication between database and user; connection with culture and/or DNA collections is also envisaged and adequate fields for these tasks have been provided. The format allows cross-reference with that originated by the Microbial Information Network Europe (MINE) for computer storage and handling of bacterial or fungal strain data.     

BiomarkerDigger: A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers

We have developed a proteome database (DB), BiomarkerDigger ( http://biomarkerdigger.org ) that automates data analysis, searching, and metadata‐gathering function. The metadata‐gathering function searches proteome DBs for protein–protein interaction, Gene Ontology, protein domain, Online Mendelian Inheritance in Man, and tissue expression profile information and integrates it into protein data sets that are accessed through a search function in BiomarkerDigger. This DB also facilitates cross‐proteome comparisons by classifying proteins based on their annotation. BiomarkerDigger highlights relationships between a given protein in a proteomic data set and any known biomarkers or biomarker candidates. The newly developed BiomarkerDigger system is useful for multi‐level synthesis, comparison, and analyses of data sets obtained from currently available web sources. We demonstrate the application of this resource to the identification of a serological biomarker for hepatocellular carcinoma by comparison of plasma and tissue proteomic data sets from healthy volunteers and cancer patients.