An Integrated Korean Biodiversity and Genetic Information Retrieval System

Background: On-line biodiversity information databases are growing quickly and being integrated into general bioinformatics systems due to the advances of fast gene sequencing technologies and the Internet. These can reduce the cost and effort of performing biodiversity surveys and genetic searches, which allows scientists to spend more time researching and less time collecting and maintaining data. This will cause an increased rate of knowledge build-up and improve conservations. The biodiversity databases in Korea have been scattered among several institutes and local natural history museums with incompatible data types. Therefore, a comprehensive database and a nation wide web portal for biodiversity information is necessary in order to integrate diverse information resources, including molecular and genomic databases. Results: The Korean Natural History Research Information System (NARIS) was built and serviced as the central biodiversity information system to collect and integrate the biodiversity data of various institutes and natural history museums in Korea. This database aims to be an integrated resource that contains additional biological information, such as genome sequences and molecular level diversity. Currently, twelve institutes and museums in Korea are integrated by the DiGIR (Distributed Generic Information Retrieval) protocol, with Darwin Core2.0 format as its metadata standard for data exchange. Data quality control and statistical analysis functions have been implemented. In particular, integrating molecular and genetic information from the National Center for Biotechnology Information (NCBI) databases with NARIS was recently accomplished. NARIS can also be extended to accommodate other institutes abroad, and the whole system can be exported to establish local biodiversity management servers. Conclusion: A Korean data portal, NARIS, has been developed to efficiently manage and utilize biodiversity data, which includes genetic resources. NARIS aims to be integral in maximizing biofrom resource utilization for conservation, management, research, education, industrial applications, and integration with other bioinformation data resources. It can be found at http://www.naris.go.krclose1

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources

<p>Abstract</p> <p>Background</p> <p>DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases.</p> <p>Results</p> <p>We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses.</p> <p>Conclusion</p> <p>Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system <url>http://www.asianbarcode.org</url>.</p

Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity

The red-crowned crane (Grus japonensis) is an endangered, large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is known to be positively correlated with body size and negatively correlated with metabolic rate, though the genetic mechanisms for the red-crowned crane&apos;s long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, including the long-lived common ostrich, we identified red-crowned crane candidate genes with known associations with longevity. Among these are positively selected genes in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12, SOD3, CTH, RPA1, PHAX, HNMT, HS2ST1, PPCDC, PSTK CD8B, GP9, IL-9R, and PTPRC). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and this genome should provide a useful genetic resource for future conservation studies of this rare and iconic species

The Korean Bird Information System (KBIS) through open and public participation

<p>Abstract</p> <p>Background</p> <p>The importance of biodiversity conservation has been increasing steadily due to its benefits to human beings. Recently, producing and managing biodiversity databases have become much easier because of the information technology (IT) advancement. This made the general public's participation in biodiversity conservation much more practical than ever. For example, an openfree web service can be devised for a wider spectrum of people to collaborate with each other for sharing biodiversity information. Bird migration is one such area of the collaboration. Korean migratory birds are usually traceable in the important routes of the East Asian-Australia Flyway (EAAF), and they play a key role as an environmental change indicator of the Earth. Therefore, the preservation of migratory birds requires an information system which involves a broader range of voluntary and interactive knowledge network to process bird information production, circulation, and dissemination.</p> <p>Results</p> <p>The Korean Bird Information System (KBIS) aims to construct a cooperative partnership domestically and internationally through the acquisition, management, and sharing of Korean bird information involving both expert and non-expert groups. KBIS has six goals: data standard, system linkage, data diversity, utilization, bird knowledge network, and statistics. The key features of KBIS are to provide a simple search, gallery (photographs), and community to lead the participation of numerous non-experts, especially amateur bird watchers. The function of real-time observation data submission through the internet has been accomplished. It also provides bird banding database, statistics, and taxon network for experts. Especially, the statistics part provides the user with easy understanding of ecological trends of species based on the time and region.</p> <p>Conclusion</p> <p>KBIS is a tool for the conservation and management of bird diversity and ecosystem that encourages users to participate by providing the openfree data access and real-time data input web-interface. It will enhance bird knowledge networking activities locally, nationally, and internationally. In addition, it provides opportunities to enhance the public awareness for the preservation of bird diversity and species information in relevant localities through the database construction and networking activities. It can be found at <url>http://korbird.naris.go.kr</url>.</p

Whole genome sequence and analysis of the Marwari horse breed and its genetic origin

Background: The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. Results: We generated 101 Gb (similar to 30 x coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of similar to 98% and with similar to 95% of the genome having at least 10 x coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344&gt;Val) associated with the inward-turning ear tip shape of the Marwari horses. Conclusions: Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.open1

Exopolysaccharide and lactic acid bacteria: Perception, functionality and prospects

Lactic acid bacteria exhibit the most effective potential to divert significant amount of fermentable sugars towards the biosynthesis of functional exopolysaccharide. Exopolysaccharides from lactic acid bacteria are receiving a renewed interest due to the claims of human health benefits. This review provides an update on multiple uses and production of exopolysaccharides with major emphasis on their chemical properties, characterization, and some other molecular strategies adopted for their genetics and biological tailoring to better understand the process of exopolysaccharide production along with their antiviral efficacy with multiple modes of action. Additionally, microbiological, biochemical, nutritional and biotechnological aspects of exopolysaccharide production have also been discussed. Moreover, appro-priate suggestions have been made on lactic acid bacteria improvements, leading to enhanced production with advanced modification and production process that may contribute to the economic soundness of applications in food and pharmacological industries with this promising group of biomolecules.

The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Background: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging. Results: We sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene. Conclusions: We present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vulturesopen

Diversity of bioactive polysaccharide originated from marine sources: A review

1857-1869<span style="font-size:9.0pt;mso-bidi-font-size: 12.0pt;font-family:" times="" new="" roman";mso-fareast-font-family:palatinoltstd-roman;="" mso-bidi-font-family:"times="" roman";mso-ansi-language:en-gb;mso-fareast-language:="" en-us;mso-bidi-language:hi"="" lang="EN-GB">A multitude of marine organisms, including shellfish, sponge, seaweed, marine fungi, microalgae, and corals, are very efficient sources of polysaccharides with number of interesting functional properties. Marine-based polysaccharides as the counterparts of terrestrial animals have great potential to be used for food processing, long-term storage, and fortification, as well as in medicine industry as carriers of drugs and as nutraceuticals. This review will encounter the recent findings on the different mechanisms of anti-viral actions of marine polysaccharides. Their potential for therapeutic application is also summarized to a certain level. The potential food applications of marine polysaccharides along with their chemical nature is discussed in later half. This review covers a significant amount of vital information on the chemistry and biological potential of the bioactive brominated compounds, heterocyclics (nitrogen and nitrogen-sulphur) and sulfated polysaccharides isolated from marine algae, fungi and bacteria.</span

The Sources of Chemical Contaminants in Food and Their Health Implications

Food contamination is a matter of serious concern, as the high concentration of chemicals present in the edibles poses serious health risks. Protecting the public from the degrees of the harmfulness of contaminated foods has become a daunting task. This article highlights the causes, types, and health implications of chemical contamination in food. The food contamination could be due to naturally occurring contaminants in the environment or artificially introduced by the human. The phases of food processing, packaging, transportation, and storage are also significant contributors to food contamination. The implications of these chemical contaminants on human health are grave, ranging from mild gastroenteritis to fatal cases of hepatic, renal, and neurological syndromes. Although, the government regulates such chemicals in the eatables by prescribing minimum limits that are safe for human consumption yet measures still need to be taken to curb food contamination entirely. Therefore, a variety of food needs to be inspected and measured for the presence of chemical contaminants. The preventative measures pertaining about the food contaminants problems are pointed out and discussed