Sep

14

material lecture:

1. DNA fingerprinting and barcoding (fat-UB 2015)

2. Lecture Intro Forensic Science DNA Testing

3. 5.dbSnp of nucleotide Seq Variation

4. Lecture DNA Barcode (taxmol or molEvo)

5. dbSNP variation

Sep

6

Matriks Rencana Pembelajaran Semester Mata Kuliah Sidik Jari Molekuler.

 

Minggu

ke

Kemampuan Akhir

yang Diharapkan (CLO)

Bahan kajian

Pokok Bahasan

(topics)

Sub Pokok Bahasan

(subtopics)

Bentuk Pembelajaran

(Learning methods)

Indikator/Kriteria Penilaian

(Value Criteria)

Bobot Nilai

(%)

Fasilitas Pembelajaran

(learning Facility)

1 Menjelaskan Dasar-dasar sidik jari DNA dan DNA typing dalam forensik Dasar-dasar sidik jari DNA dan DNA typing dalam forensik Overview Dasar-dasar sidik jari DNA dan DNA typing dalam forensik DNA Fingerprinting & DNA typing on Forensic Biology Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module
2 Melakukan pengambilan sampel, purifikasi, penyimpanan Pengambilan sampel, purifikasi, penyimpanan Sample tracking Sample collection, extraction, purification & storage Presentation, Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam
3 Menetapkan metode isolasi dan analysis sampel molecular dan sekuensing Molecular sample preparation isolasi dan analysis sampel molecular dan sekuensing DNA isolation, PCR, DDGE and Sequencing Presentation, Lecture and discussion Kebenaran dan ketepatan analisis

10

Laptop, LCD, module, paper exam
4 Memahami perbedaan genome dan mitokodria typing Genetic basis  of DNA typing Basic Analysis of DNA typing Genomic or mitokondria DN A Presentation, Mini Project Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam
5 Membedakan Fingerprinting DNA  & Forensic DNA system Comparation of Fingerprinting DNA  & Forensic DNA system Fingerprinting DNA  & Forensic DNA system CODIS, Y-chromosome, SNP, STR, SSP, HLA typing Presentation, Mini Project Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam
6 Menganlisis data molekuler secara in silico Analisis data molekuler secara in silico Bioinformatic Analysis DNA Seq analysis, alignment, phylogenetic tree Presentation, mini project, Lecture and discussion Kebenaran dan ketepatan analisis

10

Laptop, LCD, module, paper exam
7 Menjelasakan Dasar teori DNA Barcoding Dasar teori DNA Barcoding DNA Barcoding analysis What is DNA Barcoding? Biomarker for DNA animal barcode Presentation, Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam
8     Middle test      

 
9 Membandingkan analisis DNA Barcoding pada biodiversitas dan kekerabatan hewan Analisis DNA Barcoding pada biodiversitas dan kekerabatan hewan DNA Barcoding analysis on animal molecular biodiversity and taxonomy Barcode of Life Data Systems (BOLD) database

GeneBank  Database for DNA & Protein

Presentation, Mini Project Lecture and discussion Kebenaran dan ketepatan analisis

16

Laptop, LCD, module, paper exam
10 Membandingkan dasar analisis kekerabatan spesies Dasar-dasar analisis kekerabatan spesies Molecular data Interpretation UPGM, statistics analysis, Clad Presentation, Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam
11 Membandingkan analisis DNA Barcoding pada biodiversitas dan kekerabatan pada mikrobia Analisis DNA Barcoding pada biodiversitas dan kekerabatan pada mikrobia Biomarker for microbe DNA Barcoding analysis 16SRNA, SNP, SST Presentation, Mini Project Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam
12 Membandingkan  dasar analisis DNA Barcoding utuk kekerabatan spesies Dasar analisis DNA Barcoding utuk kekerabatan spesies DNA Barcoding analysis on molecular biodiversity and taxonomy of microbe Bacteri, Virus, Jamur Presentation, Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam
13-14 Menenetapkan biomarker untuk analisis sisdik jari pada tanaman Type biomarker untuk analisis sisdik jari pada tanaman Biomarker for plant DNA Fingertyping and Barcoding analysis Minisatelite, microsatelite Presentation, Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam
15 Membandingkan analisis DNA Barcoding pada biodiversitas dan kekerabatan pada tanaman Analisis DNA Barcoding pada biodiversitas dan kekerabatan pada tanaman DNA Fingerprinting analayis on molecular biodiversity and taxonomy of plant RFLP, Simple sequence length polymorphisms (SSLP), RAPD Presentation, Mini Project, Lecture and discussion Kebenaran dan ketepatan analisis

6

Laptop, LCD, module, paper exam

 

Daftar Pustaka

John M Butler. 2009. Fundamentals of Forensic DNA Typing 1st Edition. Academic Press. ISBN-13: 978-0123749994. ISBN-10: 0123749999

Richads Li. 2015. Forensic Biology. 2nd Edition. CRS. ·  ISBN-10: 1439889708 ·  ISBN-13: 978-1439889701

Jörg Epplen and Thomas Lubjuhnn. 1999. DNA Profiling and DNA Fingerprinting. Birkhäuser. ISBN-10: 3764360186. ISBN-13: 978-3764360184

Ricki Lewis. 2011. Human Genetics concepts and application. McGraw-Hill Education; 10 edition ISBN-13: 978-0073525303, ISBN-10: 0073525308 or ISBN: 007246268x

Tom Strachan & Andrew Read.2003. Human Molecular genetics. Garland Science; 3 edition. ·  ISBN-10: 0815341822 ·  ISBN-13: 978-0815341826

Julian Knight.2009. Human Genetic Diversity. Oxford Univrsity Press. London.

Robert Nussbaum, Roderick R. McInnes, and Huntington F Willard. 2007. Genetics in Medicine, 7th Edition. Sounders. ·  ISBN: 9781416030805

Ida Lopez and David L. Erickson. 2012. DNA Barcodes: Methods and Protocols (Methods in Molecular Biology). Human Press. ISBN-13: 978-1617795909. ISBN-10: 1617795909

Nikolaus J. Sucher and James R. Hennell. 2012. Plant DNA Fingerprinting and Barcoding: Methods and Protocols (Methods in Molecular Biology).  Human Press. ISBN-13: 978-1617796081. ISBN-10: 1617796085

Erich Grotewold and Joseph Chappel. 2015. Plant Genes, Genomes and Genetics. Willey Blackwell. ISBN-13: 978-1119998877. ISBN-10: 1119998875

Cecie Starr,  Ralph Taggart,  Christine Evers, & Lisa Starr.  Biology: The Unity and Diversity of Life 14th Edition. Brooks Cole. ISBN-13: 978-1305073951. ISBN-10: 1305073959

Gene Helfman and Bruce B. Collette. 2009. The Diversity of Fishes: Biology, Evolution, and Ecology. Wiley-Blackwell; 2 edition. ISBN-10: 1405124946. ISBN-13: 978-1405124942

Jacques Izard and Maria Rivera. 2014. Metagenomics for Microbiology. !rst Ed. Academic Press. ISBN-13: 978-0124104723. ISBN-10: 012410472X

Sandra Tscherwizek. 2008. 16S Ribosomal RNA Gene Sequencing: Establishment of a Method for the Identification of Microorganisms in Biopharmaceutical Production Areas. VDM Verlag Dr Muller. ISBN-13: 978-3639109030. ISBN-10: 3639109031

Sep

17

 

JADUAL KULIAH MK TEKNIK ANALISIS DNA FORENSIK DAN BARCODING

PASCASARJANA BIOLOGI FMIPA MALANG

Pertemuan ke

Sub pokok bahasan

Metoda pembelajaran

Dosen
1 Overview DNA Fingerprinting & DNA typing on Forensic Biology Lecture F
2 Genetic basis  of DNA typing (genomic or mtDNA) Lecture F
3 Forensic DNA typing system (CODIS, Y-chromosome, SNP, STR, SSP, DDGE) discussion of articles on forensic DNA testing F
4 Sample collection. extraction, purification, & storage Practice F/NK
5 DNA preparation and Sequensing Practice F/NK
6 Bioinformatic Analysis: DNA Seq analysis, alignment, phylogenetic tree Practice, online F/NK
7 Molecular data Interpretation (UPGM, stat analysis, Clad) Practice, online F/NK
8 Middle test    
9 Biomarker for animal DNA Barcoding analysis Lecture SH
10 DNA Barcoding analysis on animal molecular biodiversity and taxonomy discussion of articles on insect DNA Barcoding SH
11 DNA Barcoding analysis on animal molecular biodiversity and taxonomy discussion of articles on insect DNA Barcoding SH
12 Biomarker for microbe DNA Barcoding analysis Lecture NK
12 DNA Barcoding analysis on molecular biodiversity and taxonomy of microbe discussion of articles on microbe DNA typing & Barcoding NK
14 Biomarker for plant DNA Fingertyping and Barcoding analysis Lecture ELA
15 DNA Fingerprinting analayis on molecular biodiversity and taxonomy of plant discussion of articles on Plant DNA Fingerprinting ELA
16 DNA Fingerprinting analayis on molecular biodiversity and taxonomy of plant discussion of articles on Plant DNA Fingerprinting ELA

Tim Dosen:

Fatchiyah, M.Kes., PhD. (F, Koordinator), Dr.Ir.Estri Laras Arumingtyas, MScSt (ELA), Dr.Suharjono, MS (SH), dan Nia Kurniawan, MP, Ph.D. (NK)

Acuan Bacaan

Bashinski, J. “Laboratory Standards: Accreditation, Training, and Certification of Staff in the Forensic Context.” p. 159-173. Ballantyne J, Sensabaugh G. DNA Technology and Forensic Science, Cold Spring Harbor, NY: Cold Spring Harbor Press, 1989.

Balke,  M. and Schmidt S. 2012. Training of Trainers and Students Module II: DNA Barcoding Course material. Implementation of  Indonesian-German Network for Teaching, Training and Research Collaborations (IGN-TTRC) UB Councils. Zoologische Staatssammlung, Munchen. German

Hughey, J. Bio 13- Introduction To Forensic DNA Analysis Lecture Manual: Section 5052, Fall 2011.

Kobilinsky, L., Liotti, T. F. & Oeser-Sweat, J. DNA: Forensic and Legal Applications. Wiley-Interscience, New Jersey, 2004.  ISBN: 0471414786.

Kirby, L.T. 1990. DNA Fingerprinting: An Introduction.     W. H. Freeman.

Krawczak, M. & J. Schmidtke. 1994. DNA Fingerprinting.  Books International, Inc.

Moriniere, Jerome. 2012. Apractical lab manual for  molecularphylogenetics, barcoding and friends. Bavarian state collection of zoology. Zoologische Staatssammlung, Munchen. German

OSHA Bloodborne Pathogen Standard. 1992. Fisher Scientific.

Saferstein, R. 2001. Forensic Science Handbook.  Prentice Hall

Weedn VW, Roby RK. Forensic DNA Testing. Arch Pathol Lab Med 1993;117:486-491

 

Weblink:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0014448

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028832

http://fatchiyah.lecture.ub.ac.id

Feb

21

This July, the IGN-TTRC lecture will be take by Prof Michael Blake (who one famous professor of DNA Barcoding in the World)  and DR.Stefan Smith from Munich University German

Let’s send Your Application as soon as possible!

If you need the application form –>please send email to ignttrc.ub.council@gmail.com or praba.sanjaya@gmail.com, or take a soft copy on LSIH UB lt 2

 

Implementation IGN for TTR Biodiversity Curricula

Training of Trainers and Students Course of Module II on DNA Barcoding

Brawijaya University

Malang, July 1-14, 2012

At the Second Year activity, The Indonesian – German Network for Teaching, Training and Research Collaborations (IGN-TTRC), a consortium to improve teaching, training and research collaborations within Indonesian universities and between those of Indonesia and Germany, will give a competitive, merit-based scholarship program that provides opportunities for two weeks: one week Training of Trainers (Lecturers) and a one week Students Course in Module II on DNA Barcoding, conducted at the University of Brawijaya. The ToT and Student Course consist of lectures and a practical class given by German and Indonesian tutors. Candidates from the following Universities are eligible participants for the program and involve UB and UNAND (main course Universities), UNSRAT, UNEJ, IPB, UNMUL, and UNAIR (associated Universities). This program is supported by the German Academic Exchange Service (Deutscher Akademischer Austausch Dienst, DAAD), by the Ministry of National Education of the Republic Indonesia, and several other funding sources.

The biological diversity of each country is a valuable and vulnerable natural resource. Sampling, identifying, and studying biological specimens are among the first steps towards protecting and benefiting from this biodiversity. DNA Barcoding is new tool for taxonomic research based on sequence diversity in short, standardized genomic regions. The international DNA Barcoding initiative is generating a global, open access library of reference barcode sequences that will allow the reliable identification of biological specimens by non-taxonomists. In principle, DNA Barcoding requires three consecutive steps: a. obtaining and preparing organisms (collecting, identification, preparation, and preserving), b. Laboratory procedure: sampling and processing specimen samples to obtain DNA barcode gene sequences, and c. data management using a dedicated database.

Program Objectives

  1. To give an overview of the role of molecular biology methods in biodiversity research. The course modules will be integrated into the biodiversity curricula at the participating universities. The final goal would be a joint the M.Sc and/or PhD curriculum.
  2. To establish a curriculum that is equivalent to a German MSc degree and that enables Indonesian students to rapidly integrate into a German PhD program. Credits will be awarded by the IGN-TTRC. The participating universities may accept these certificates as partial fulfillment of an Indonesian PhD degree.

Eligibility Requirements

-       Student Applicants must have Grade Transcripts of (≥3.25) proven by a certified original or certified photocopy of academic records (transcripts) from any previous university work

-       Applicant must have active English language proficiency and a TOEFL/TOEIC/IELTS score of min. 450/550/5.5

-       Applicants should provide a motivation letter of 2-3 pages (including CV) describing their scientific interest.

-       Lecturer Applicants must fill in and sign a Commitment Letter of Module Implementation

-       Applicants, except UB participants, should include a statement by the University/Faculty if costs for travel and subsistence can be (partially) covered if the available funding is not sufficient.

-       Applicant should fill in IGN-TTRC application form and send it together with the other material by E-Mail to ignttrc.ub.council@gmail.com along.

 

Selection Process of Module II on DNA Barcoding

Selection of students and graduate students

All participating institutions will motivate their best students to apply for the courses. Candidates will write a letter of motivation accompanied by a brief evaluation by their mentor. The council will decide on acceptance based on excellence of the candidates. In the case of equal qualification, we will try to accommodate students from different partner universities. It is understood that gender issues will be strictly observed.

Funding for travel and subsistence is limited to approx. 10 persons. Up to 20 (max.) students/lecturers may be accepted for each course if additional funding is provided by the faculty/university.

Selection will be made by the IGN-TTRC Council academic review committee that includes UNKA, UB, UNAND, IPB, UNSRAT, UNMUL, UNEJ and UNAIR.  In selecting eligible candidates, the review committee will consider academic merit as well as evidence of leadership potential and experience capacity for change; adaptability; ability to pursue independent study; English language proficiency; creativity; initiative; self-expression.

Application Deadline
·         A complete application must be received by IGN-TTRC Council of the University of Brawijaya, Fatchiyah, PhD: ignttrc.ub.council@gmail.com no later than April 20th 2012. Please write the subject email ToT UB Module 2 for lecturers or SC UB Module 2 for students.

 

Award Provisions and Conditions

Scholarship recipients will receive the following:

  • Free tuition fee for TOT and student course
  • Credits Certificate will be awarded by the IGN-TTRC
  • For participants from outside UB (UNSRAT, UNEJ, IPB, UNMUL, and UNAIR) will be reimbursed for transportation from their university to UB

 

Award Decision, Start Dates and Venue

Award decisions are expected to be announced on Website http://lsih.ub.ac.id and/or email to inviting participant by June 1, 2012.

Courses take place on July 1-14, 2012 (UB Malang)

UB Venue: at Central Lab of Life Sciences UB (LSIH UB)

 

Written and E-mail Inquiries

Email inquiries may be addressed to ignttrc.ub.council@gmail.com