Evolutionary history and functional implications of protein domains and their combinations in eukaryotes

A rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no similar trends were observed in other clades of eukaryotes

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments

Expressed sequence tag (EST) sequencing has proven to be an economically feasible alternative for gene discovery in species lacking a draft genome sequence. Ongoing large-scale EST sequencing projects feel the need for bioinformatics tools to facilitate uniform EST handling. This brings about a renewed importance for a universal tool for processing and functional annotation of large sets of ESTs. EGassembler () is a web server, which provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling of ESTs and genomic fragments. The web server is publicly available and provides the community a unique all-in-one online application web service for large-scale ESTs and genomic DNA clustering and assembling. Running on a Sun Fire 15K supercomputer, a significantly large volume of data can be processed in a short period of time. The results can be used to functionally annotate genes, to facilitate splice alignment analysis, to link the transcripts to genetic and physical maps, design microarray chips, to perform transcriptome analysis and to map to KEGG metabolic pathways. The service provides an excellent bioinformatics tool to research groups in wet-lab as well as an all-in-one-tool for sequence handling to bioinformatics researchers

Recombination Activating Gene (RAG)-1 and 2 Encoding Proteins Expressed by the Baculovirus System

We have been attempting to obtain mouse recombination activating gene-1 (RAG-1) and RAG-2 protein for biochemical analyses. First of all, we obtained truncated products of these genes expressed and purified using the E. coli expression system and then established the polyclonal and monoclonal antibodies by means of E. coli expressed peptides as antigens. Subsequently, whole RAG-1 and RAG-2 gene products were expressed the baculovirus expression system. Since it has been difficult to achieve the significant gene expression of full-lenght cDNA, we employed the glutathione S-transferase (GST)-fused gene-expression system which facilitated the massive expression of gene products. This system was also advantageous in that we could detect the expressed protein molecules not only with anti-RAG antibody but also with anti-GST antibody

A POS-based preordering approach for English-to-Arabic statistical machine translation

In this work, we present a POS-based preordering approach that tackles both long- and short-distance reordering phenomena. Syntactic unlexicalized reordering rules are automatically extracted from a parallel corpus using only word alignment and a source-side language tagging. The reordering rules are used in a deterministic manner; this prevents the decoding speed from being bottlenecked in the reordering procedure. A new approach for both rule filtering and rule application is used to ensure a fast and efficient reordering. The tests performed on the IWSLT2016 English-to-Arabic evaluation benchmark show a noticeable increase in the overall Blue Score for our system over the baseline PSMT system

Anatomical liver segmentectomy 2 for combined hepatocellular carcinoma and cholangiocarcinoma with tumor thrombus in segment 2 portal branch

<p>Abstract</p> <p>Background</p> <p>Hepatic resection is the only effective treatment for combined hepatocellular carcinoma and cholangiocarcinoma.</p> <p>Case presentation</p> <p>A 52-year-old man was preoperatively diagnosed with hepatocellular carcinoma in segment 2 with tumor thrombus in the segment 2 portal branch. Anatomical liver segmentectomy 2, including separation of the hepatic arteries, portal veins, and bile duct, enabled us to remove the tumor and portal thrombus completely. Modified selective hepatic vascular exclusion, which combines extrahepatic control of the left and middle hepatic veins with occlusion of left hemihepatic inflow, was used to reduce blood loss. A pathological examination revealed combined hepatocellular carcinoma and cholangiocarcinoma with tumor thrombus in the segment 2 portal branch. No postoperative liver failure occurred, and remnant liver function was adequate.</p> <p>Conclusion</p> <p>The separation method of the hepatic arteries, portal veins, and bile duct is safe and feasible for a liver cancer patient with portal vein tumor thrombus. Modified selective hepatic vascular exclusion was useful to control bleeding during liver transection. Anatomical liver segmentectomy 2 using these procedures should be considered for a patient with a liver tumor located at segment 2 arising from a damaged liver.</p

Generation of Germline-Competent Rat Induced Pluripotent Stem Cells

Recent progress in rat pluripotent stem cell technology has been remarkable. Particularly salient is the demonstration that embryonic stem cells (ESCs) in the rat (rESCs) can contribute to germline transmission, permitting generation of gene-modified rats as is now done using mouse ESCs (mESCs) or mouse induced pluripotent stem cells (iPSCs; miPSCs). However, determinations of whether rat iPSCs (riPSCs) can contribute to germ cells are not published. Here we report the germline competency of riPSCs.We generated riPSCs by transducing three mouse reprogramming factors (Oct3/4, Klf4, and Sox2) into rat somatic cells, followed by culture in the presence of exogenous rat leukemia inhibitory factor (rLIF) and small molecules that specifically inhibit GSK3, MEK, and FGF receptor tyrosine kinases. We found that, like rESCs, our riPSCs can contribute to germline transmission. Furthermore we found, by immunostaining of testis from mouse-rat interspecific chimeras with antibody against mouse vasa homolog, that riPSCs can contribute to embryonic development with chimera formation in mice (rat-mouse interspecific chimeras) and to interspecific germlines.Our data clearly demonstrate that using only three reprogramming factors (Oct3/4, Klf4, and Sox2) rat somatic cells can be reprogrammed into a ground state. Our generated riPSCs exhibited germline transmission in either rat-rat intraspecific or mouse-rat interspecific chimeras

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

<p>Abstract</p> <p>Background</p> <p>The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009.</p> <p>Results</p> <p>Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs.</p> <p>Conclusions</p> <p>Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.</p

セイジン カンゴガク ジッシュウ オヨビ ロウネン カンゴガク ジッシュウ ニオイテ カンゴガクセイ ガ ケンガク マタハ ジッシ シタ カンゴ キホン ギジュツ ノ ジッタイ ガクセイ ニヨル ジコヒョウカ チョウサ ノ ブンセキヨリ

看護系大学一校の成人看護学実習および老年看護学実習における看護学生の看護基本技術についてその見学または実施状況を明らかにし, 今後の講義・演習の内容や, 実習カリキュラムと実習施設, 実習指導の在り方等を検討するための基礎資料とすることを目的に, 文献等から選定した看護基本技術118項目の「見学」または「指導者の助言・監督下で実施」について調査した. 同大学で領域別看護学実習を履修した4年生のうち協力の得られた79名(回答率98.8%)のデータを分析した結果, 成人看護学実習・老年看護学実習の全般において, 環境整備, 清潔ケア, バイタルサイン測定, 病態・症状観察等の看護基本技術を見学または実施した学生が過半数を超えた. 一方, 呼吸, 排泄, 与薬, 救急, 症状・生体機能管理, 感染予防面の看護基本技術の見学または実施は, 全体の4分の1程度にとどまった. 学生が, 多様な治療を受ける患者の看護を学ぶことを通し, 臨地実習の場で見学や実施したことを振り返り, そして現象を関連付けて理解できる実習を編成することの重要性が示唆された.The purpose of this survey is to identify the current status of fundamental nursing skills performed by nursing students in adult and gerontological nursing practicums incorporated as part of a four-year baccalaureate nursing program. There were 118 survey items about fundamental nursing skills selected from the related literature. For each fundamental nursing skill the respondents were asked to answer, "have observed demonstration of this skill", "have performed this skill under the supervision of clinical nurse instructors" or "have not had any chance for observation or performance". Seventy-nine senior students (response rate: 98.8%) agreed to fill in and submit the survey sheet. The survey showed that more than half of the respondents had observed demonstration of, or had performed under supervision, such fundamental skills as management of the environment of care (cleanliness and safety of hospital beds and rooms), personal and hygiene care, vital sign measurement, assessment and monitoring of signs and symptoms in either adult or gerontological nursing practicum, or in both. In addition, about less than one-fourths of the respondents reported that they had observed demonstration of, or had performed under supervision, skills like respiratory care, elimination care, medication, monitoring and maintenance of vital functions and infection control. These results indicate the importance of arranging nursing practicums in such a way that students can learn a variety of nursing interventions and clinical skills in diverse care settings. Furthermore, nursing students need to be encouraged to learn through observation, performance under supervision and reflection so that they can understand the meaning of a variety of interconnected phenomena