Looking for staffs

To launch new research projects at CDB in Kobe (details about my move)  regarding the evolution of vertebrate gene repertoire and its functional characterization, I am looking for staffs (PhD students or postdocs) with special focus detailed below:

・Bioinformatician with prior skills to analyze output of next-generation sequencers
・Pre-/post-doctoral researcher who is specialized in molecular evolution and phylogenetics
・Pre-/post-doctoral researcher who has prior experience in chromatin biochemistry for ChIP assays
・Pre-/post-doctoral researcher with skills of molecular developmental biology (RT-PCR, in situ hybridization, etc.)

At the moment, no position funded directly by CDB is advertized, but I welcome candidates applying for external fellowships/scholarships. Please don't hesitate to contact directly to me (shigehiro.kuraku (at) uni-konstanz.de).

'Good slip' into 2012 !

In this season, every German says 'Guten Rutsch!',
meaning 'Good slip (into the new year) !'. 

Today I organized several things to leave the apartment and the town soon.

I wish you all a happy new year.

About my move

I included the info about my move in the page 'Author info' linked above. I am widely looking for staffs (Ph.D. students and postdocs) who can join in my new team in Kobe. I will probably also announce that in this page later as wel as in other sites.

Turtle symposium

There will be a symposum about turtle evolution held in June 2012 in Tuebingen, Germany

Devo Meetings

Click on the images for details!

Academic positions in Germany

I found a few interesting web sites summarizing descriptions of various academic positions in Germany as well as in other countries.

European University Institute

Wikipedia

my science

Ensembl ASIA

I am now in the middle of a one-week trip in Japan to attend this conference.

I didn't know that if I access to the Ensembl here, I am automatically redirected to 'Ensembl ASIA'. Of course, the contents there are the same as what I normally see in Europe.

Guess what fish, frog and chicken have but we don't

The work I started in 2005 has just been published online.

Genome-wide Detection of Gene Extinction in Early Mammalian Evolution.
Kuraku S & Kuratani S.
Genome Biol Evol. 2011 Nov 17.

My team has been dealing with several examples of lineage-specific gene loss within vertebrates, including Hox14, Bmp16 and Pax4 . These are based on small-scale focus on selected examples of gene loss. The genome-wide assessment is the focus of the article just published. There I stick to gene loss in the early mammalian lineage. In addition to some gene loss already implicated by previous gene-level studies, I have identified many gene losses that require functional dissection.

There are still many questions to be addressed employing molecular phylogenetics.

I will move

It seems that I am still not allowed to say exactly where, but I am moving to a different place some time in February 2012.

Not simply because it is just my home, but also because of many other reasons, I decided to move to Japan.

It is a long story ...... which I can write here ...... maybe little by little.

Teaching Bioinformatics at High Schools

The journal PLoS Computational Biology published a series of articles about teaching bioinformatics at secondary schools.

This journal really likes article titles 'ten simple rules ...'

Coelacanth in Ensemble Pre!

Preliminary genome annotation for coelacanth (Latimeria chalumnae), the 'living fossil', is viewable at the Ensembl Pre! website.

PAG XX Meeting

'PAG' is abbreviation of 'Plant Animal Genomics', the world's largest genomic meeting, always held in San Diego in January.

Japan Week in Frankfurt

There will be some events about Japanese culture etc. in Frankfurt, starting this weekend.

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).

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.

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.

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.

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.

Busstreik!!

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.

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.

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.

'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)

Why???

I was at the foreigner's office in the city hall this morning. It turned out that the workers, probably in Berlin, were super slow, and new certificates of stay permit for me and my family were not ready.

So ........... , I had to pay extra because of their slow work, literally!
(Wir sind in Urlaubmeisterland, ich weiss)

I wish I could find a convincing reason for this and ................

I just want to choose the place to live in by myself. Of course, I can.

This is, too! (I was not the one who wrote the words at the bottom)

Report from 6th Intl Chick Meeting

As part of POULTRY GENOME NEWSLETTER posted in AnGenMap emailing list, I received a report from the 6th International Chicken Meeting.

 'The Sixth International Chicken Meeting, previously scheduled for Sendai, Japan, was held at the new Roslin Institute facility in Edinburgh, Scotland, September 17-20. Kudos to the outstanding organizational efforts of Dave Burt and his team (especially Liz Brown) from Roslin and thanks for their exceptional hospitality. Among the highlights: Wes Warren spoke of the on-going efforts to improve the chicken sequence assembly. He noted that the Galgal4 assembly was sent to browsers about 1.5 months ago and should be out soon, but there remains more to do to fill gaps and find missing microchromosome sequences. Almas Gheyas described the sequencing of 243 chickens, generating nearly 140M SNP and efforts to reduce this set to the most useful 675,000 SNP for a new Affymetrix genotyping array expected to be out middle of next year. There were several remarkable and even beautiful talks on cell labeling and imaging, and the use of these approaches to follow cell commitment and development pathways. Olivier Pourquie described the mechanism of somitogenesis and segmentation, along with numerous other excellent developmental biology talks. Tatsuo Fukagawa showed how the Z centromere could be deleted in DT40 cells and replaced with an engineered constitutive centromere or by selective   neocentromere evolution at a variety of locations along Z. Andrew Sinclair and Mike Clinton described the latest developments in chicken gonadal and cell autonomous somatic sex determination, respectively. Dave Burt discussed the soon-to-appear duck genome sequence and noted that reports collected at the meeting suggest that there are now at least 54 unique avian genome projects underway. Several excellent student talks and posters were also presented. The 7^th International meeting (soon to get a new, more pan-avian inclusive name) is to be held in Nagoya, Japan in November, 2012, and preliminary plans are underway for the 8^th meeting at Caltech (Pasadena, California) in 2014.'

Introduction to learning the Japanese language

Here is a web site explaining how different the Japanese language is from other languages, like English.

'Fascinating language of one of the world's largest economy and the best path into an utterly refined an complex culture. Japanese is a very difficult language to read and write, but it is very rewarding and can be put to many cultural and professional uses.'

They give the highest score for its difficulty to the Japanese language. I am proud of my command of this complicated language.

In this page, you can partly get why English spoken by Japanese people is often difficult to understand, in terms of their pronunciation. For example:

'Japanese pronunciation is dead easy, all the sounds are perfectly natural for the native English speaker, the only new sound is the Japanese R which is nothing like an English R and involves tapping your tongue just behind your teeth, similar to the English L.'

It is very difficult for many Japanese to differently pronounce L and R. Examples are:

long - wrong
lock - rock

Other typical confusions are:

shit - sit
very - bury

For those who are highly interested now, I present below a table of Japanese alphabets (obtained here). Be careful. We also use Chinese letters very often, and just learning the Japanese alphabets will not give you sufficient command of the Japanese language.

'Japanese, like Korean, borrowed most of its Kanjis (characters) from Chinese. This is good news if you already speak Chinese since the vast majority of characters are very similar or exactly the same in both languages. Furthermore, they are often pronounced in not totally different ways, which considerably helps when learning new vocabulary.'

I hope this is good news to you!

Special Issue 'Hox and ParaHox genes' in GPB

The journal Genomics Bioinformatics and Proteomics has published a special issue, titled 'Hox and ParaHox genes in Evolution, Development and Genomics'.



To this special issue, I contributed a mini review paper about Hox gene cluster evolution and expression patterns of cyclostomes (extant jawless fishes) and cartilaginous fishes (available upon request).

The main and associate Editors-in-Chief of this relatively new journal are all affiliated with the world's biggest sequencing center, BGI. I received free reprints of my review and free copies of the journal issue kindly gifted by the publisher. Thanks!