Ephemeroptericola cinctiostellae gen. nov., sp. nov., isolated from gut of an aquatic insect.

A Gram-stain-negative, catalase- and oxidase-positive, non-motile bacterium, designated F02T, was isolated from of gut of Cincticostellalevanidovae (Tshernova). Growth occurred at a temperature range of 4-30 °C, at pH 6-9 and in the presence of 0-0.5 % (w/v) NaCl. Phylogenetic analysis demonstrated that the 16S rRNA gene sequence of strain F02T shared the highest similarity to that of the type strain of Hydromonas duriensis A2P5T (96.82 %). The major isoprenoid quinone was Q-8. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and iso-C13 : 0 3-OH. The polyamines were cadaverine and putrescine. Combined data from phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain F02T represents a novel genus and species, for which the name Ephemeroptericolacinctiostellae gen. nov., sp. nov. is proposed. The type strain of Ephemeroptericola cinctiostellae gen. nov., sp. nov. is F02T (=FBCC 500047T=KCTC 62567T=JCM 32722T).

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr.

Complete genome of Kangiella geojedonensis KCTC 23420(T), putative evidence for recent genome reduction in marine environments.

Kangiella geojedonensis KCTC 23420(T) is an aerobic, Gram-negative, non-motile, non-spore-forming, rod-shaped bacterium that was isolated from seawater off the southern coast of Korea. We here report the complete genome of K. geojedonensis KCTC 23420(T), which consists of 2,495,242 bp (G+C content of 43.78%) with 2,257 protein-coding genes, 41 tRNAs, 2 rRNA operons. The genome is smaller than the other closely related genomes, indicating that K. geojedonensis has recently experienced reductive evolution.

Complete genome of a coastal marine bacterium Muricauda lutaonensis KCTC 22339(T).

Muricauda lutaonensis KCTC 22339(T) is a yellow-pigmented, gram-negative, rod-shaped bacterium that was isolated from a coastal hot spring of a volcanic island in the Pacific Ocean, off the eastern coast of Taiwan. We here report the complete genome of M. lutaonensis KCTC 22339(T), which consists of 3,274,259bp with the G+C content of 44.97%. The completion of the M. lutaonensis genome sequence is expected to provide a valuable resource for understanding the secondary metabolic pathways related to bacterial pigmentation.

Zinc regulates meiotic resumption in porcine oocytes via a protein kinase C-related pathway.

Zinc is an extremely important trace element that plays important roles in several biological processes. However, the function of zinc in meiotic division of porcine oocytes is unknown. In this study, we investigated the role of zinc during meiotic resumption in in vitro matured porcine oocytes. During meiotic division, a massive release of zinc was observed. The level of free zinc in the cytoplasm significantly increased during maturation. Depletion of zinc using N, N, N', N'-tetrakis (2-pyridylmethyl) ethylenediamine (TPEN), a Zn2+ chelator, blocked meiotic resumption in a dose dependent manner. The level of phosphorylated mitogen activated protein kinase (MAPK) and p34cdc2 kinase activity were reduced when zinc was depleted. Moreover, zinc depletion reduced the levels of phosphorylated protein kinase C (PKC) substrates in a dose dependent manner. Real-time PCR analysis showed that expression of the MAPK- and maturation promoting factor related genes C-mos, CyclinB1, and Cdc2 was downregulated following zinc depletion. Treatment with the PKC agonist phorbol 12-myristate 13-acetate (PMA) increased phosphorylation of PKC substrates and MAPK and increased p34cdc2 kinase activity. This rescued the meiotic arrest, even in the presence of TPEN. Activation of PKC by PMA increased the level of zinc in the cytoplasm. These data demonstrate that zinc is required for meiotic resumption in porcine oocytes, and this appears to be regulated via a PKC related pathway.

(Z)-Ethyl 2-cyano-3-(1H-imidazol-2-yl)acrylate.

The crystal structure of the title compound, C9H9N3O2, features N-H⋯N and C-H⋯O inter-actions. The N-H⋯N inter-action generates a chain running along the a axis and the C-H⋯O inter-action generates a chain along the c axis. An intra-molecular C-H⋯O inter-action is also observed.

CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization.

The recent nucleic acid sequencing revolution driven by shotgun and high-throughput technologies has led to a rapid increase in the number of sequences for microbial communities. The availability of 16S ribosomal RNA (rRNA) gene sequences from a multitude of natural environments now offers a unique opportunity to study microbial diversity and community structure. The large volume of sequencing data however makes it time consuming to assign individual sequences to phylotypes by searching them against public databases. Since ribosomal sequences have diverged across prokaryotic species, they can be grouped into clusters that represent operational taxonomic units. However, available clustering programs suffer from overlap of sequence spaces in adjacent clusters. In natural environments, gene sequences are homogenous within species but divergent between species. This evolutionary constraint results in an uneven distribution of genetic distances of genes in sequence space. To cluster 16S rRNA sequences more accurately, it is therefore essential to select core sequences that are located at the centers of the distributions represented by the genetic distance of sequences in taxonomic units. Based on this idea, we here describe a novel sequence clustering algorithm named CLUSTOM that minimizes the overlaps between adjacent clusters. The performance of this algorithm was evaluated in a comparative exercise with existing programs, using the reference sequences of the SILVA database as well as published pyrosequencing datasets. The test revealed that our algorithm achieves higher accuracy than ESPRIT-Tree and mothur, few of the best clustering algorithms. Results indicate that the concept of an uneven distribution of sequence distances can effectively and successfully cluster 16S rRNA gene sequences. The algorithm of CLUSTOM has been implemented both as a web and as a standalone command line application, which are available at http://clustom.kribb.re.kr.

PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences.

The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct low-quality sequences. We have developed a program called PyroTrimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.

Bacterial diversity in ornithogenic soils compared to mineral soils on King George Island, Antarctica.

In the Narebski Point area of King George Island of Antarctica, ornithogenic soils form on land under Chinstrap and Gentoo Penguin rookeries. The purpose of this study was to compare the bacterial community compositions in the gradient of contamination by penguin feces; mineral soil with no contamination, and soils with medium or high contamination. The discrimination between mineral soils and ornithogenic soils by characterization of physicochemical properties and bacterial communities was notable. Physicochemical analyses of soil properties showed enrichment of carbon and nitrogen in ornithogenic soils. Firmicutes were present abundantly in active ornithogenic soils, Bacteroidetes and Proteobacteria in a formerly active one, and several diverse phyla such as Proteobacteria, Actinobacteria, and Acidobacteria in mineral soils. Some predominant species belonging to the Firmicutes and Gammaproteobacteria may play an important role for the mineralization of nutrients in ornithogenic soils. Results of this study indicate that dominant species may play an important role in mineralization of nutrients in these ecosystems.

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization.

We propose a novel, efficient and intuitive approach of estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data. Our method, NEUMA (Normalization by Expected Uniquely Mappable Area), is based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. Quantitative RT-PCR based on 27 randomly selected genes in two human cell lines and computer simulation experiments demonstrated superior accuracy of NEUMA over other recently developed methods. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency ('consistency coefficient') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. We propose that NEUMA could make a standard method in quantifying gene transcript levels from RNA-Seq data.

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

BACKGROUND: Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases. RESULTS: To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page http://diseasome.kobic.re.kr/, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes. CONCLUSION: Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.

Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals.

Mitome is a specialized mitochondrial genome database designed for easy comparative analysis of various features of metazoan mitochondrial genomes such as base frequency, A+T skew, codon usage and gene arrangement pattern. A particular function of the database is the automatic reconstruction of phylogenetic relationships among metazoans selected by a user from a taxonomic tree menu based on nucleotide sequences, amino acid sequences or gene arrangement patterns. Mitome also enables us (i) to easily find the taxonomic positions of organisms of which complete mitochondrial genome sequences are publicly available; (ii) to acquire various metazoan mitochondrial genome characteristics through a graphical genome browser; (iii) to search for homology patterns in mitochondrial gene arrangements; (iv) to download nucleotide or amino acid sequences not only of an entire mitochondrial genome but also of each component; and (v) to find interesting references easily through links with PubMed. In order to provide users with a dynamic, responsive, interactive and faster web database, Mitome is constructed using two recently highlighted techniques, Ajax (Asynchronous JavaScript and XML) and Web Services. Mitome has the potential to become very useful in the fields of molecular phylogenetics and evolution and comparative organelle genomics. The database is available at: http://www.mitome.info.