Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants—the ‘Keio collection'—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/)

Health Checkup and Telemedical Intervention Program for Preventive Medicine in Developing Countries: Verification Study

Background: The prevalence of non-communicable diseases is increasing throughout the world, including developing countries. / Objective: The intent was to conduct a study of a preventive medical service in a developing country, combining eHealth checkups and teleconsultation as well as assess stratification rules and the short-term effects of intervention. / Methods: We developed an eHealth system that comprises a set of sensor devices in an attaché case, a data transmission system linked to a mobile network, and a data management application. We provided eHealth checkups for the populations of five villages and the employees of five factories/offices in Bangladesh. Individual health condition was automatically categorized into four grades based on international diagnostic standards: green (healthy), yellow (caution), orange (affected), and red (emergent). We provided teleconsultation for orange- and red-grade subjects and we provided teleprescription for these subjects as required. / Results: The first checkup was provided to 16,741 subjects. After one year, 2361 subjects participated in the second checkup and the systolic blood pressure of these subjects was significantly decreased from an average of 121 mmHg to an average of 116 mmHg (P<.001). Based on these results, we propose a cost-effective method using a machine learning technique (random forest method) using the medical interview, subject profiles, and checkup results as predictor to avoid costly measurements of blood sugar, to ensure sustainability of the program in developing countries. / Conclusions: The results of this study demonstrate the benefits of an eHealth checkup and teleconsultation program as an effective health care system in developing countries

VSOP Data Archive System

Abstract We present the new VSOP data archive system installed on the Data ARchive and Transmission System (DARTS) at ISAS. The current test archive for VSOP visibility data started in June 2002, and about 50 datasets are available now (http://www.darts.isas.ac.jp)

Clinical application of removable partial dentures using thermoplastic resin—Part I: Definition and indication of non-metal clasp dentures

AbstractThis position paper proposes a definition and naming standard for removable partial dentures (RPDs) using thermoplastic resin, and presents a guideline for clinical application. A panel of 14 experts having broad experience with clinical application of RPDs using thermoplastic resin was selected from members of the Japan Prosthodontic Society. At a meeting of the panel, “non-metal clasp denture” was referred as the generic name of RPDs with retentive elements (resin clasps) made of thermoplastic resin. The panel classified non-metal clasp dentures into two types: one with a flexible structure that lacks a metal framework and the other having a rigid structure that includes a metal framework. According to current prosthetic principles, flexible non-metal clasp dentures are not recommended as definitive dentures, except for limited cases such as patients with a metal allergy. Rigid non-metal clasp dentures are recommended in cases where patients will not accept metal clasps for esthetic reasons. Non-metal clasp dentures should follow the same design principles as conventional RPDs using metal clasps

Phylogenetic groups and cephalosporin resistance genes of Escherichia coli from diseased food-producing animals in Japan

A total of 318 Escherichia coli isolates obtained from different food-producing animals affected with colibacillosis between 2001 and 2006 were subjected to phylogenetic analysis: 72 bovine isolates, 89 poultry isolates and 157 porcine isolates. Overall, the phylogenetic group A was predominant in isolates from cattle (36/72, 50%) and pigs (101/157, 64.3%) whereas groups A (44/89, 49.4%) and D (40/89, 44.9%) were predominant in isolates from poultry. In addition, group B2 was not found among diseased food-producing animals except for a poultry isolate. Thus, the phylogenetic group distribution of E. coli from diseased animals was different by animal species. Among the 318 isolates, cefazolin resistance (minimum inhibitory concentrations: ≥32 μg/ml) was found in six bovine isolates, 29 poultry isolates and three porcine isolates. Of them, 11 isolates (nine from poultry and two from cattle) produced extended spectrum β-lactamase (ESBL). The two bovine isolates produced blaCTX-M-2, while the nine poultry isolates produced blaCTX-M-25 (4), blaSHV-2 (3), blaCTX-M-15 (1) and blaCTX-M-2 (1). Thus, our results showed that several types of ESBL were identified and three types of β-lactamase (SHV-2, CTX-M-25 and CTX-M-15) were observed for the first time in E. coli from diseased animals in Japan

Abnormal spermatogenesis and male infertility in testicular zinc finger protein Zfp318-knockout mice

Zfp318, a mouse gene with a Cys2/His2 zinc finger motif, is mainly expressed in germ cells in the testis. It encodes two alternative transcripts, which regulate androgen receptor-mediated transcriptional activation or repression by overexpression of them. However, the role of Zfp318 is still obscure in vivo, especially in spermatogenesis. To elucidate the role of Zfp318 during gamete production, we established a knockout mouse line. Zfp318-null male mice exhibited infertility, whereas Zfp318-null female mice displayed normal fertility. ZFP318 was expressed during multiple stages of spermatogenesis, from spermatocytes to round spermatids. The nuclei of secondary spermatocytes showed high levels of expression. Histological analysis and quantitative analysis of DNA content showed decreased numbers of both spermatids in the seminiferous tubules and mature spermatozoa in the epididymides of Zfp318-null mice. These results suggest that Zfp318 is expressed as a functional protein in testicular germ cells and plays an important role in meiosis during spermatogenesis

Clinical application of removable partial dentures using thermoplastic resin. Part II: Material properties and clinical features of non-metal clasp dentures

This position paper reviews physical and mechanical properties of thermoplastic resin usedfor non-metal clasp dentures, and describes feature of each thermoplastic resin in clinicalapplication of non-metal clasp dentures and complications based on clinical experience ofexpert panels. Since products of thermoplastic resin have great variability in physical andmechanical properties, clinicians should utilize them with careful consideration of thespecific properties of each product. In general, thermoplastic resin has lower color-stabilityand higher risk for fracture than polymethyl methacrylate. Additionally, the surface ofthermoplastic resin becomes roughened more easily than polymethyl methacrylate. Studiesrelated to material properties of thermoplastic resin, treatment efficacy and follow-up areinsufficient to provide definitive conclusions at this time. Therefore, this position papershould be revised based on future studies and a clinical guideline should be provided

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

<p>Abstract</p> <p>Background</p> <p>In <it>Escherichia coli</it>, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we analysed the low-molecular-weight RNAs (< 200 nt) of <it>E. coli </it>with deep sequencing, because the regulatory RNAs in bacteria are usually 50-200 nt in length.</p> <p>Results</p> <p>We discovered 229 novel candidate sRNAs (≥ 50 nt) with computational or experimental evidence of transcription initiation. Among them, the expression of seven intergenic sRNAs and three <it>cis</it>-antisense sRNAs was detected by northern blot analysis. Interestingly, five novel sRNAs are expressed from prophage regions and we note that these sRNAs have several specific characteristics. Furthermore, we conducted an evolutionary conservation analysis of the candidate sRNAs and summarised the data among closely related bacterial strains.</p> <p>Conclusions</p> <p>This comprehensive screen for <it>E. coli </it>sRNAs using a deep sequencing approach has shown that many as-yet-undiscovered sRNAs are potentially encoded in the <it>E. coli </it>genome. We constructed the <it>Escherichia coli </it>Small RNA Browser (ECSBrowser; <url>http://rna.iab.keio.ac.jp/</url>), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.</p