Proposing Genes for Gap Reactions in Metabolic Pathways

A metabolic model is a map of the biochemical reactions that take place in an organism. These reactions are catalyzed by enzymes, which are encoded by genes in the organism’s genome. However, there are reactions that are known to exist and needed to complete the metabolic model, but are not associated with any genes. These are called “gap reactions”. Our goal is to find the genes that encode the enzymes that catalyze these gap reactions. We have researched two approaches: a knowledge-driven approach that focuses on finding a small set of good candidates, and a data-driven approach that focuses on scoring all candidates to rank their plausibility. Identifying the genes that are associated with gap reactions produces better predictive models and directs laboratory experimentation

Freshwater mussels (Bivalvia: Unionidae) from the rising sun (Far East Asia): phylogeny, systematics, and distribution

Freshwater mussels (Bivalvia: Unionidae) is a diverse family with around 700 species being widespread in the Northern Hemisphere and Africa. These animals fulfill key ecological functions and provide important services to humans. Unfortunately, populations have declined dramatically over the last century, rendering Unionidae one of the world’s most imperiled taxonomic groups. In Far East Asia (comprising Japan, Korea, and Eastern Russia), conservation actions have been hindered by a lack of basic information on the number, identity, distribution and phylogenetic relationships of species. Available knowledge is restricted to studies on national and sub-national levels. The present study aims to resolve the diversity, biogeography and evolutionary relationships of the Far East Asian Unionidae in a globally comprehensive phylogenetic and systematic context.We reassessed the systematics of all Unionidae species in the region, including newly collected specimens from across Japan, South Korea, and Russia, based on molecular (including molecular species delineation and a COI + 28S phylogeny) and comparative morphological analyses. Biogeographical patterns were then assessed based on available species distribution data from the authors and previous reference works.We revealed that Unionidae species richness in Far East Asia is 30% higher than previously assumed, counting 43 species (41 native + 2 alien) within two Unionidae subfamilies, the Unioninae (32 + 1) and Gonideinae (9 + 1). Four of these species are new to science, i.e. Beringiana gosannensis sp. nov., Beringiana fukuharai sp. nov., Buldowskia kamiyai sp. nov., and Koreosolenaia sitgyensis gen. & sp. nov. We also propose a replacement name for Nodularia sinulata, i.e. Nodularia breviconcha nom. nov. and describe a new tribe (Middendorffinaiini tribe nov.) within the Unioninae subfamily. Biogeographical patterns indicate that this fauna is related to that from China south to Vietnam until the Mekong River basin. The Japanese islands of Honshu, Shikoku, Kyushu, Hokkaido, and the Korean Peninsula were identified as areas of particularly high conservation value, owing to high rates of endemism, diversity and habitat loss. The genetically unique species within the genera Amuranodonta, Obovalis, Koreosolenaia gen. nov., and Middendorffinaia are of high conservation concern

Modeling Bacterial Metabolism and Genetic Regulation

A number of methods have been proposed to incorporate gene expression data to improve metabolic modeling with Flux Balance Analysis (FBA). With the idea of using probabilities of specific genes to be on or off which are computed from gene expression data, one of such methods, PROM (the Probabilistic Regulation of Metabolism) is known to produce better results than traditional methods. However, it suffers from the lack of biological explanation why it uses such probabilities to limit fluxes of reactions instead of setting genes to be on or off. In our method, we use the probabilities to penalize inconsistent gene usage by incorporating gene use variables into the objective function during FBA. We also decided to implement the method on KBase, an open platform for genomics and systems biology, to utilize existing methods and data, and to make it easier to publish and share our method and results in future

Epidermal Cyst in the Scrotum Successfully Treated while Preserving the Testis: A Case Report

A 66-year-old male was referred to our hospital for further examination of a scrotal mass. Because of the risk of testicular cancer, we first clamped the vessels as a course of higher orchiectomy. Then, we approached the tumor through the scrotum and successfully resected it while preserving the testis. A histopathological diagnosis revealed an epidermal cyst. We herein report a rare case of an intrascrotal epidermal cyst successfully treated while preserving the testis

The DOE Systems Biology Knowledgebase (KBase)

The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology — predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing infrastructure; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities that currently include genome assembly, annotation, ontology assignment, comparative genomics, transcriptomics, and metabolic modeling; (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software development kit allowing the community to add functionality to the system