Genome Science Course

Genome Science Course ID: 9919 (Spring), 9921 (Fall)

Aim
Designed for participants who expect to engage in both laboratory work and fieldwork. Beginner (direct sequencing) and advanced (next generation sequencing) courses are available. English is the official language as in the previous course. The samples from Yakushima will be used to perform various experiments and analyses. Students give a poster presentation at the international symposium scheduled on the last day of the course.
Place
- Kyoto University
- Primate Research Institute
Schedule
2017 FY
- Spring
May 22-26, 2017 & May 30, 2017


2016 FY
- Spring
May 30 - June 3, 7, 2016. View Photos

- Fall
October 24-28, 2016. View Photos

2015 FY
- Spring
2015/06/02-2015/06/07, 06/09 View Photos

- Fall
2015/10/26-2015/10/30, 11/05. View Photos

2014 FY
- Spring
2014/05/29 - 2014/06/06 (excluding 2014/05/31 - 2014/06/01) Presentation at the international seminar required at June 6.
View Photos

- Fall
2014/10/27 - 2014/10/31, View Photos

2017 FallNovember 13-17, 2017

2017 SpringMay 22-26, 2017 & May 31, 2017

Schedule
May 22-26, 2017 & May 30, 2017
Application Period
April 01, 2017 - April 09, 2017.
Presentation
On May 30, participants of the Yakushima/Genome Science Courses will give poster presentations of their results from both courses at "the 6th International Seminar on Biodiversity and Evolution: Wildlife Science by New Biologging Studies".
 
 

2016 FallOctober 24-28, 2016



Schedule
October 24-28, 2016

Introduction
Application
Application Period
August 22, 2016 - September 9, 2016.
We (Kinoshita, Kishida and Hayakawa) held PWS Genome Training Course last week (Oct 24-28). It successfully finished. 9 students joined to this course and made a presentation on the last day with Imai-sensei and Andrew.

Based on the fecal DNA from Japanese macaques in Yakushima, students analyzed DNA (for sex identification) and steroid hormone (for evaluation of the stress level). They compared these laboratory results with parasite infection data collected in Yakushima.

Unfortunately, they couldn't find obvious correlation between parasite infection and stress hormone levels, but could learn how to analyze parasite, DNA and hormone from identical feces and enjoy combining field and laboratory works.

Takashi Hayakawa


Report
 

2016 SpringMay 30 - June 3 & June 7, 2016


Schedule
May 30 - June 3, 7 2016

Introduction
Application
Presentation
Participants of the Yakushima/Genome Science Courses will have a presentation of the results of the courses at the 5th International Seminar on Biodiversity and Evolution:  New Methodology for Wildlife Science on June 7.
Reports

2015 Fall2015/10/26-2015/10/30, 11/05


Outline
Following the Field Science Course, we will have the Genome Science Course, which uses samples collected during the Field Science Course on Yakushima Island. We also recommend taking the following course that corresponds to that which you took during the Field Science course. These combinations enable you to analyze the samples you yourself have collected. Prior knowledge in molecular biology is not necessary for the Genome Science Course in fall. This course is open either at the Primate Research Institute, Kyoto University in Inuyama City (deer group) or at the Graduate School of Science, Kyoto University in Yoshida Campus (plant group).

A) Deer group
DNA and hormonal analyses of deer feces for the determination of sex and reproductive status By applying two molecular methods (DNA and hormonal analyses), participants will determine the sex and reproductive status of Yakushima deer from feces collected during the Field Science Course. First, deer genomic DNA will be extracted from the feces. The participants will determine the deer sex by amplification of genes located on the sex chromosomes. Second, participants will also analyze the sex steroid hormones (estrogen, progesterone, and testosterone) from the same deer feces to determine sex. In addition, by measuring the concentration of each hormone, the participants will estimate the reproductive status of deer. Because fall is the breeding season for deer, if female and male adults are in estrus and in rut, respectively, female (estrogen/progesterone) and male (testosterone) hormones will show high concentrations. Based on the results from these two molecular analyses, we will try to develop practical methods for estimating reproductive status of wild deer.

B) Plant group
Species composition and phenology in fern gametophyte For the gametophyte samples collected from Yakushima, we will try to identify the species or the genera to which they belong using molecular analysis. We will extract DNA from the samples and determine rbcL gene sequences from them. Subsequently, we will compare these sequences with registered DNA sequences in the gene bank.

Schedule
September 13
Deadline for application (both for the Field Science Course and Genome Science Course)
Middle of October
Guidance for the Field Science Course and Genome Science Course, at PRI, Inuyama.
October 26-30
Genome experiments, at several laboratories in Inuyama (animal) and Yoshida (plant) Campus of Kyoto Univ.
November 5
Presentation of the result of the courses at Primate Research Institute

Application
Reports
 

2015 Spring2015/06/02-2015/06/07, 06/09


Outline

Following the Field Science Course will be the Genome Science Course. If you are planning to take both the Field Science and Genome Science Courses, we will be using samples collected from the Field Science Course in Yakushima Island for the Genome Science Course. Therefore, we recommend that you take a Genome Science Course accordingly to the Field Science course you took (if you take the Field Science Course). In addition, if you do not have experience with genome experiments, we recommend Genome Science Courses A) - C). These combinations enable you to analyze the samples collected by yourselves. If you are interested in NGS and data analysis for NGS, take course D), regardless of the group you took in the Field Science Course (if you did take any Field Science Courses).


A) Individual identification of fecal DNA
We will focus on DNA individual identification method based on genotyping. DNA of monkeys and deer will be extracted from the feces collected during the Field Science Course. After DNA extraction, we will identify the sex using genetic marker and will identify individuals using several microsatellite loci.

B) Insect DNA barcoding
The Insect group will collect and identify insect species in Yakushima. Using these collected insects, we will sequence the mitochondrial DNA in order to provide a DNA barcode catalogue of insects in Yakushima. Based on the DNA barcode catalogue thus obtained, we will analyze the food repertories of Yakushima monkeys using the monkey feces-derived sequence data which were obtained by the members of 2014 Genome Training Course using MiSeq next generation sequencer.

C) Mushroom DNA barcoding
The Mushroom DNA group will collect and identify mushroom species in Yakushima. Using these collected mushrooms, we will sequence the ITS region of the genomic DNA in order to provide a DNA barcode catalogue of mushrooms in Yakushima Island.

D) Whole genome analyses of the Yakushima monkey
Lecturers will provide a whole genome shotgun (WGS) sequence of a Yakushima monkey, Macaca fuscata yakui determined by HiSeq2000 high-throughput sequencer. Using this data, we will try to analyze the functional gene sequences (e.g., sensory receptor gene repertoire), genetic diversity in the genome-wide scale, genetic differences with other macaque species, and historical changes of the effective population sizes of Yakushima monkeys in order to reveal the ecology and evolution of Yakushima monkeys. This group will not do "wet" laboratory experiments, but will focus on "dry" bioinformatics using personal- and super- computers.

International Seminar
Date: June 9 (Tue), 2015
Place: Science Seminar House, Yoshida Campus of Kyoto University.
We will have talks from visiting foreign students and host researchers. We will also present the results of Field Science Course and Genome Science Course in the poster session.

Application

Introduction.pdf


Application Form.doc

Please read Introduction.pdf, and submit Application Form by e-mail during the following period.
Mail to: Ms. Sakai, sakai.yoko.2e
Period: April 1 to April 16, 2015 (deadline is April 16)

Schedule
April 16
Deadline for application by students of Kyoto University (both for the Field Science Course and Genome Science Course)
May 18
4:00 p.m.
Guidance for the Field Science Course and Genome Science Course, at WRC in Yoshida Campus. We will have a welcome party for participants from abroad.
June 2-7
Genome experiments, at several laboratories in Yoshida Campus of Kyoto Univ.
June 8
Preparation for presentation
June 9
Presentation of the results of the courses at international symposium (held at Yoshida Campus)

International Seminar
      The 4th International Seminar on Biodiversity and Evolution


Please click on the pictures to see the full-sized versions.
 

2014 Fall2014/10/27 - 2014/10/31, 11/06


Date
2014/10/27 - 2014/10/31
October 9: 13:00- Guidance for the course at PRI seminar room
October 27-31: Practice course at PRI
November 6: Presentation at PRI

Application
Please read Call for Yakushima and Genome training course 2014 fall , and submit Application form 2014 fall to Ms. Sakai (sakai.yoko.2e [at] kyoto-u.ac.jp).
Application Period: July 11 to July 31, 2014.
Reports
 

2014 Spring2014/05/29-2014/06/06 (excluding 2014/05/31 - 2014/06/01)


Date
2014/05/29 - 2014/06/06 (excluding 2014/05/31 - 2014/06/01)
Presentation at the international seminar required at June 6.
Outline
“Genome Science Course" aims to train students to analyze genomes using up-to-date molecular biological techniques, including next-generation sequencing. In this course, various samples collected in “Field Science Course" will be analyzed. Through the two courses, students will experience the whole process of scientific research, sampling in the field, analyzing in the laboratory, data analysis and presentation of the results.
Introduction
Soon after the Field Science Course, we will have Genome Science Course, using samples collected in the Field Science Course in Yakushima Island. We will analyze DNA of host animals, that of foods, and intestinal micro-biota from fecal samples, using next-generation sequencers and other apparatus. We will also lecture on the analysis of next-generation sequencing.

Target re-sequencing of genome of Japanese monkeys from their feces, collected in Yakushima Island. Survey of micro-biota in the intestine of Japanese monkeys by next-generation sequencing. Identify insects species predated by monkeys by next-generation sequencing of their feces. Determine DNA sequence of insects collected in Yakushima Island for DNA bar-coding. Determine DNA sequence of ferns collected in Yakushima Island for DNA bar-coding.
International Seminar
Date: June 6 (Fri), 2014
Place: Science Seminar House, Kyoto University.
We will have talks of visiting foreign students and host researchers. We will also present the results of Field Science Course and Genome Science Course.
Application
Please read Introduction.pdf, and submit Application Form to Ms. Maekawa (maekawa.youko.8e [at] kyoto-u.ac.jp) by April 18, 2014.
More info


Please click on the pictures to see the full-sized versions.