Sunday, October 30, 2011

Hagfish predation and slime defense

The journal Scientific Reports published an article about hagfish predation and slime defense. The article provides two movies showing hagfishes' predators behaviors against hagfish slime.

There are also many related news out there (for example, this) based on this article.

Unforgettable moments, things and places in Germany

 I was sorting out photo files in my mobile phone, and found some special (funny or unpleasant) photos there. Those are pasted below (sorry, without any comments).

Wednesday, October 26, 2011

From TV news in Japan

I was back in Japan last week for 5 days. I had some chances to watch news on TV. I expected to see a lot of news on continuous danger of radioactivity and so on, but saw more often about European financial crisis (see below). That could have been a kind of media control based on national policy to hide shocking information about domestic situation.

Tuesday, October 25, 2011

Galeaspids, a 435–370-million-year-old ostracoderm published in Nature

There was an article about fossil jawless fish published recently in Nature.

Fossil jawless fish from China foreshadows early jawed vertebrate anatomy.
Gai Z, Donoghue PC, Zhu M, Janvier P, Stampanoni M.
Nature. 2011 Aug 17;476(7360):324-7. doi: 10.1038/nature10276.

I remember I listened to a talk by the first author at a meeting held in Kobe, Japan.

Friday, October 21, 2011

Funding opportunities

The research support office of our university is doing a quite good job. They make a collection of funding opportunities in science in Konstanz and distribute that to researchers in the university.

The collection includes opportunities for researchers in other parts of Germany or Europe, although written in German. This can help many people.

Monday, October 10, 2011

Short autumn before cold winter

The warm summer has gone, and the temperature went down. It is sometimes dark and foggy outside in the morning. We are right in the middle of very short autumn before cold winter comes.

A big annual event here in Konstanz is Christmas market (Weihnachtsmarkt). This year the market starts on November 24.

A wide pedestrian path in the middle of the street called 'Laube'.

The church St. Stephan. Very quiet place.

Friday, October 7, 2011


There was a notice sent today from an administration office that bus drivers in our town are planning to have a strike next Monday and Tuesday. I am sort of used to this kind of things here ... . I just knew that it is often seen in France.

Tuesday, October 4, 2011

Excellent Japanese restaurants in Germany

I list top 3 based on my actual experience. I need to admit that my experience is still quite limited.

1. 'Basho-an Tsubaki' in Freiburg

2. 'Konomi' in Heidelberg (Waitresses are in Kimono!!)

3. 'Kaito' in Munich

They have nice sushi as well as other traditional Japanese dishes.

Monday, October 3, 2011

Tag der deutschen Einheit

Today is a national holiday of Germany, 'Tag der deutschen Einheit (day of German unity)'.

I was sorting out my old stuffs in my room today, and found the pin below. It was gifted to all participants of the Joint Meeting between German Developmental Biology Society (GfE) and Japanese Society of Developmental Biologist (JSDB) held in Dresden in March this year.

Sunday, October 2, 2011

'Orthology' matters in all fields of molecular biology

It is not a maniac lingo of the field of molecular phylogenetics any more. The idea of 'orthology' has spread throughout molecular biology, and has been a basis of comparative approaches of analyzing molecular sequences, although not fully recognized sometimes.

The journal Briefings in Bioinformatics, whose latest impact factor is 9.283, published a special issue titled 'Orthology and Applications'. This issue includes an obituary for Walter M. Fitch who passed away in March this year, focusing on his milestone of providing the idea of orthology and paralogy for the first time in his paper in 1970 (see below).

The 1st page of the paper by Fitch (1970) introducing the concept of orthology and paralogy (Systematic Zoology. 19: 99-113)
I also contributed a research paper based on a collaborative study to this special issue. This article reports an approach to scaffold separate coding regions of the same protein-coding gene split into multiple sequence segments with an aid of molecular phylogenetic information. In particular, my team provided a set of predicted peptide sequences on the low-coverage genome assembly of the ghost shark (aka, elephant shark, Callorhinchus milii). This gene prediction was achieved with the utility of the setting for gene prediction program, Augustus, trained for this species also by my team (also introduced here). I had tight communication with Christophe Dessimoz, the first author (and also the guest editor of this special journal issue) to examine the performance of the algorithm ESPRIT introduced in this article. It was a big excitement to work with him for the paper and to be part of this special issue.

(please also another obituary for W.M. Fitch in Science)