Analysis of Utilization of Biological Resources Using Text Mining Based on Freshwater Biodiversity Information Platform

The Nagoya Protocol on access to genetic resources and fair and equitable sharing of benefits arising from their utilization in the convention on biological diversity entered into force on October 12, 2014. Accordingly, attention toward securing the sovereignty and discovering the utilization value of biological resources has been increasing to secure national competitiveness. We are developing a freshwater biodiversity information platform for the systematic conservation and industrialization of freshwater biodiversity in South Korea. The platform comprises an integrated management system of freshwater bioresources for systematic registration and management of freshwater biodiversity information based on databases; a management system of storage for managing freshwater biological specimen; a utilization information system that manages efficacy, experimental method, and activity produced by the Nakdonggang National Institute of Biological Resources and external big data such as literature and patent; and a freshwater bioresources culture collection for preservation, ordering and deposition of biological resources. These systems are connected organically. Text mining, one of the big data technologies, helps to determine the utility of biological resources through comprehensive analysis. We tried to establish utilization foundations by predicting the usability of biological resources through systematic collection, processing, and analyzing external data, such as abstract, in order to support industrialization of national freshwater bioresources. Through text mining, we constructed a literature-based corpus and preprocessed the corpus with lowercase conversion and removal of stop word. Then, a word cloud was created and statistical analysis was performed. As a result, genes and diseases associated with specific biological resources have been identified. In this study, through a comprehensive analysis of species, genes, and disease information using text mining, we were able to determine the utilization value of biological resources. This study will help the freshwater biodiversity researchers by adding a function for utilization analysis in the utilization information system of the platform in the future

Population Genetic Structure and Evidence of Demographic Expansion of the Ayu (Plecoglossus altivelis) in East Asia

Plecoglossus altivelis (ayu) is an amphidromous fish widely distributed in Northeastern Asia from the East China Sea to the northern Japanese coastal waters, encompassing the Korean Peninsula within its range. The shore lines of northeastern region in Asia have severely fluctuated following glaciations in the Quaternary. In the present study, we investigate the population genetic structure and historical demographic change of P. altivelis at a population level in East Asia. Analysis of molecular variance (AMOVA) based on 244 mitochondrial control region DNA sequences clearly showed that as the sampling scope extended to a larger geographic area, genetic differentiation began to become significant, particularly among Northeastern populations. A series of hierarchical AMOVA could detect the genetic relationship of three closely located islands between Korea and Japan that might have been tightly connected by the regional Tsushima current. Neutrality and mismatch distribution analyses revealed a strong signature of a recent population expansion of P. altivelis in East Asia, estimated at 126 to 391 thousand years ago during the late Pleistocene. Therefore it suggests that the present population of P. altivelis traces back to its approximate demographic change long before the last glacial maximum. This contrasts our a priori expectation that the most recent glacial event might have the most crucial effect on the present day demography of marine organisms through bottleneck and subsequent increase of effective population size in this region

Freshwater Biodiversity Platform (FBP): an Integrated Information Management System of Freshwater Ecosystem for the Conservation and Sustainable Use of Biodiversity

Since the Nagoya Protocol on Access to genetic resources and Benefit Sharing (ABS) came into force in 2014, the conservation and assurance of national biodiversity has been internationally stressed. The Government of South Korea is exercising significant efforts to integrate and manage the information pertaining to biological resources in line with this global trend. However, connecting and sharing biodiversity data has certain challenges because the existing databases and information systems are being operated using different standards. In the present study, we established an integrated management system for freshwater biodiversity information, the Freshwater Biodiversity Platform (FBP), to support the conservation and sustainable use of biodiversity. This platform allows the management of various types of biodiversity data, such as occurrences, habitats and genetics, for freshwater species inhabiting South Korea. The data fields are based on a global biodiversity data standard, Darwin Core, and national biodiversity standards of South Korea in order to share our data more efficiently, both nationally and internationally. It is important to note that the platform deals with information related to the utilization of biological resources as well as information representing the national biodiversity. We have collected bibliographical data, such as papers and patents, from databases, including information on the use of biological resources. The data have been refined by applying a national species list of South Korea and ontology terms in (MeSH) to compile valuable information for biological industries. Furthermore, our platform is open source and is compatible with multiple language packs to facilitate the availability of biodiversity data for other countries and institutions. Currently, the Freshwater Biodiversity Platform is being used to collect and standardize various types of existing freshwater biodiversity data to build foundations for data management. Based on these data, we will improve the platform by adding new systems that can analyze and release data for public access. This platform will provide integrated information on freshwater species from the Korean Peninsula to the world and contribute to the conservation and sustainable use of biological resources

Endosulfine alpha maintains spindle pole integrity by recruiting Aurora A during mitosis

Abstract Background The maintenance of spindle pole integrity is essential for spindle assembly and chromosome segregation during mitosis. However, the underlying mechanisms governing spindle pole integrity remain unclear. Methods ENSA was inhibited by siRNA or MKI-2 treatment and its effect on cell cycle progression, chromosome alignment and microtubule alignment was observed by immunohistochemical staining and western blotting. PP2A-B55α knockdown by siRNA was performed to rescue the phenotype caused by ENSA inhibition. The interaction between ENSA and Aurora A was detected by in situ PLA. Furthermore, orthotopic implantation of 4Tl-luc cancer cells was conducted to confirm the consistency between the in vitro and in vivo relationship of the ENSA-Aurora A interaction. Results During mitosis, p-ENSA is localized at the spindle poles, and the inhibition of ENSA results in mitotic defects, such as misaligned chromosomes, multipolar spindles, asymmetric bipolar spindles, and centrosome defects, with a delay in mitotic progression. Although the mitotic delay caused by ENSA inhibition was rescued by PP2A-B55α depletion, spindle pole defects persisted. Notably, we observed a interaction between ENSA and Aurora A during mitosis, and inhibition of ENSA reduced Aurora A expression at the mitotic spindle poles. Injecting MKI-2-sensitized tumors led to increased chromosomal instability and downregulation of the MASTL-ENSA-Aurora A pathway in an orthotopic breast cancer mouse model. Conclusions These findings provide novel insights into the regulation of spindle pole integrity by the MASTL-ENSA-Aurora A pathway during mitosis, highlighting the significance of ENSA in recruiting Aurora A to the spindle pole, independent of PP2A-B55α

Identification of Cichlid Fishes from Lake Malawi Using Computer Vision

<div><p>Background</p><p>The explosively radiating evolution of cichlid fishes of Lake Malawi has yielded an amazing number of haplochromine species estimated as many as 500 to 800 with a surprising degree of diversity not only in color and stripe pattern but also in the shape of jaw and body among them. As these morphological diversities have been a central subject of adaptive speciation and taxonomic classification, such high diversity could serve as a foundation for automation of species identification of cichlids.</p><p>Methodology/Principal Finding</p><p>Here we demonstrate a method for automatic classification of the Lake Malawi cichlids based on computer vision and geometric morphometrics. For this end we developed a pipeline that integrates multiple image processing tools to automatically extract informative features of color and stripe patterns from a large set of photographic images of wild cichlids. The extracted information was evaluated by statistical classifiers Support Vector Machine and Random Forests. Both classifiers performed better when body shape information was added to the feature of color and stripe. Besides the coloration and stripe pattern, body shape variables boosted the accuracy of classification by about 10%. The programs were able to classify 594 live cichlid individuals belonging to 12 different classes (species and sexes) with an average accuracy of 78%, contrasting to a mere 42% success rate by human eyes. The variables that contributed most to the accuracy were body height and the hue of the most frequent color.</p><p>Conclusions</p><p>Computer vision showed a notable performance in extracting information from the color and stripe patterns of Lake Malawi cichlids although the information was not enough for errorless species identification. Our results indicate that there appears an unavoidable difficulty in automatic species identification of cichlid fishes, which may arise from short divergence times and gene flow between closely related species.</p></div

Multi-locus phylogenetic analyses support the monophyly and the Miocene diversification of <i>Iksookimia</i> (Teleostei: Cypriniformes: Cobitidae)

<p>The genus <i>Iksookimia</i> contains six species of primary freshwater fishes that are endemic to South Korea. Previous phylogenetic studies, based on DNA sequence data from three or fewer loci, have suggested non-monophyly of the genus, providing inconsistent resolutions of the relationships of <i>Iksookimia</i>. Our coalescent and concatenation-based phylogenetic analyses, utilizing seven unlinked nuclear-encoded genes, strongly supported <i>Iksookimia</i> as a monophyletic group, emphasizing the importance of multi-locus data in investigating complicated phylogenetic relationships. A relaxed molecular clock analysis using fossil calibrations, indicated that the origin of the major lineages of <i>Iksookimia</i> occurred between ∼12 to 5 Ma, which is consistent with the Miocene uplift of the Taebaek and Sobaek Mountains and the Miocene activation of the major south-eastern faults. These palaeogeographic events may have served as vicariant events in the diversification of <i>Iksookimia</i>.</p

Plot of the two most frequent colors among species.

<p>The plot conforms to Deutsch's observation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077686#pone.0077686-Larsen1" target="_blank">[26]</a> which states that all significant variation in male cichlid color occurs within species, rather than between species.</p

Accuracy of classification based on different information and methods.

<p>Statistics in percentage (%) of mean and standard deviation of 100 results of 100 repetitions of randomized tests. The numbers in parenthesis are standard deviation.</p

An example of the most frequently confused images.

<p>(A) A sample image of tm_f and (B) toc_f.</p

The F-scores of features.

<p>F-scores for non-color features. Features with higher F-scores are more likely to provide useful information to the SVM classifier.</p