BioResource Newsletter  Vol.5 No.4

■ Information on
    Resource-related Events：

■ Hot News from Abroad
    No.27：

・Avoidance of Complexity in MTA
 and MTA Survey

 Mutsuaki Suzuki, Director,
 Intellectual Property Unit, NIG

・How are enteric bacterial flora
 formed in children ?

■ Hot News from Abroad
    No.28：

・Report on the 3rd International
 Biocuration Conference

 Human induced pluripotent stem (iPS) cell
     and embryonic stem (ES) cell bank project was initiated.
    Technical training on simple vitrification methods is organized.
     Dates: April 10, 24(Fri.), May 8, 15 , 22 , 29(Fri.), June 5, 19 (Fri.)
     Time: 13:00 - 16:00
     Place: Cell Engineering Division, RIKEN BioResource Center

 Lecture Series for the Standardization of
      Culturing and Analyzing Human Pluripotent Stem Cells: No. 1
      "Xeno-free Culturing"-- Possibilities, Issues,
      and Validations for the Applications of Pluripotent Stem Cells
     Date and Time: 11:00 - 17:30 on Thursday, June 25, 2009.
     Place：Auditorium (1F, Building C), Center for Developmental Biology, RIKEN

Details are available at: http://www.nbrp.jp/

  Japanese Association for Laboratory Animal Science will launch a serial article  
  on NBRP animal resources in "Experimental Animals"- the in-house journal -  
  in the second issue of Vol. 58 (published in the beginning of April 2009).   

  How Are Enteric Bacterial Flora Formed in Children？

   Natural delivery may contaminate a baby with bacteria in the parturient passage and even with enteric bacteria if the baby is covered with feces. If a baby makes contact with the mother's feces, the baby's enteric environment will be determined. In other words, if harmful bacteria are predominant in the mother's intestine, the enteric environment of the baby will probably be occupied predominantly by harmful bacteria. Although the enteric environment of the baby can obviously be altered by the diet after birth, it is predominantly affected by the enteric bacteria that are present immediately after birth.

   A particular group of Clostridium species resides in the colon of newborn infants and the extent of Clostridium propagation presumably associates with the probability of developing various diseases. Considering this vertical infection of harmful bacteria from a mother to her baby, we apprehend the condition of the feces of young ladies. Thus, ladies should realize that when they bear children, their unhealthy feces will be harmful not only to them but also to their children.

   Accordingly, a new mother's concern will be what to let her baby drink: breast milk, powdered milk, or mixed milk ? It is well known that babies that are fed breast milk have a lesser probability of developing disordered digestion or intestinal infections, catching common cold, or dying because of the cold than babies that are fed powdered milk. The feces of the babies nourished with breast milk are vitelline and smell mildly, whereas those of the babies nourished with powdered milk are brownish yellow and smell stronger. An investigation of the enteric bacteria of babies revealed that bifidobacteria are predominant in the babies nourished with either breast milk or powder milk; however, other enteric bacteria such as Escherichia coli, Enterococci, and Clostridium are less in the babies that are fed breast milk.

   The enteric environment and bacterial flora will be altered depending on the future diet. Nevertheless, the initial group of enteric bacteria in the intestine rather than the future alteration of the enteric environment primarily determines the entire life of the environment. The enteric environment of mothers during pregnancy and at delivery is extremely important in order to transfer preferable bacteria to their babies and let these bacteria grow in the babies.
I would like to draw the attention of young ladies to this question:"Are you ready to let your babies inherit your feces or bacteria ?"■

 Report on the Third International Biocuration Conference

        April 16 - 19, Berlin, Germany

Brandenburg Gate

   More than 200 people (including 11 Japanese people) working on databases gathered and actively discussed for 3 days the ways to enhance the quality and quantity of curations. In particular, the manual extraction of information from journal articles cannot cope with the rapid accumulation of scientific knowledge, whereas machine learning approaches cannot achieve the expected qualities. In order to resolve this issue, it is ideal to develop a system in which authors directly register information to databases on publication; however, the realization of such a system has been difficult. This time, it was reported that 2 journals - FEBS Letters and Plant Physiology - initiated the system in which authors register information to databases by cooperating with the Molecular INTeraction database (MINT) and the Arabidopsis Information Resource (TAIR), respectively; this was considered to be a giant step toward the realization of an ideal biocuration system.

In addition, Oxford Journal announced the publication of a new journal, DATABASE[1], indicating a widespread recognition of the importance of databases and curations. An intense discussion took place regarding curation errors, and the necessity of peer-reviews of the curations was also pointed out at the end (Cusick 2009[2]）). It was a fruitful conference, where we were stimulated by finding various databases and useful tools and by actively exchanging information with the affiliates. The contents of oral and poster presentations are published in Nature Precedings[3].

[1] http://database.oxfordjournals.org/
[2] Science 2008, 322(5898):104-10
[3] http://precedings.nature.com/collections/biocuration-09

Conference Site (Science & Conference Center)

(Yukiko Yamazaki)  

   This was the first time I participated in the conference. My first surprise was meeting so many people working on annotations (>200 people), who I rarely meet in Japan. Moreover, it was impressive to see many elderly women, including myself, communicating with each other at the conference.
   The conference consisted of seminars, workshops, and poster presentations. Many topics focused on the issue of the impossibility of manually annotating useful resources in the journal articles, which cover exponentially accumulating research achievements, and compiling them into databases. Many effective tools related to this issue were also introduced. One seminar presentation was concerned with the effective application of Textpresso to the annotation of Wormbase, which is a major database of Caenorhabditis elegans. Although I am working on developing the Textpresso for rice and thus far refer only to abstracts, the seminar inspired me to further improve the tool by incorporating full text information.
   In addition, I found the following 2 interesting tools at the conference: GoGene, a web-based tool (http://www.gopubmed.org/gogene/), which searches genes and journal articles with gene ontology (GO) terms, and Artemis, a java application for genome annotation provided by the Sanger Center, which easily loads DNA sequences and entry files in Genbank, EMBL, and DDBJ; visualize genomes; and annotates information by interactively associating the data.

(Rie Tsuchiya)  

Poster Session

Conference Hall

    I participated in the BioCuration Conference for the first time. It was a stimulating conference where I could share the excitement with curators and database developers from across the world. I could appreciate the efforts and concerns of each representative who maintains and provides high-quality curation data. In order to gain the contribution of annotations from end users, user-friendly tools have also been developed. Although a simpler tool makes it easier for the users to contribute, reducing the number of input items will decrease the data quality; hence, a balance between usability and the completeness of the data is crucial. In addition, a strategist reported that it was difficult to obtain the contribution from end users. It is ideal that researchers who write journal articles input the information into databases; however, the benefit of this contribution is not tangible for the researchers, which could be why the number of contributions is not increasing as expected.
   In the future, it is important to establish a system that prompts the authors to provide information to databases, for example, by extensively posting the journal article of the contributors on the top page of the database.

(Shingo Sakaniwa)