User:Jarle Pahr

The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

Contact Info

Jarle Pahr
Norwegian University of Science and Technology

jarlemag@stud.ntnu.no

Email me through OpenWetWare

Education

2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology

Research interests

Omega-3/poly-unsaturated fatty acid biosynthesis
Metabolic networks & Metabolic engineering
Molecular genetics of lactate utilization in bacteria
Bacterial stringent response

Notes

Projects

ppGpp MSc. project

Organisms

C. glutamicum

Lactobacillus bulgaricus

http://en.wikipedia.org/wiki/Lactobacillus_delbrueckii_subsp._bulgaricus

Interesting articles

Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

Environmentally controlled invasion of cancer cells by engineered bacteria

Dual role of lldR in regulation of the lldPRD operon, involved in L-lactate metabolism in E. coli

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Genetic programs constructed from layered logic gates in single cells

Research centres/labs

Laboratory for Molecular Infection Medicine Sweden - Umeå: http://www.mims.umu.se/

Cold Spring Harbor Laboratory: http://www.cshl.edu/

Wellcome Trust Sanger Institute: http://www.sanger.ac.uk/

Synthetic Biology

http://www.synbioproject.org/

http://www.synbiont.org/

Competitions and challenges:

http://igem.org

http://genocon.org/

http://www.ia-sb.eu/go/synthetic-biology/

LabGenius: www.labgeni.us

http://synbio.org.uk/

Synthetic Biology timeline: http://www.labgeni.us/synbiotimeline/

Invitrogen synthetic biology webinars: http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/synthetic-biology/Synthetic-Biology-Webinars.html

DYI Bio/Citizen science

http://diybioftw.com/

http://dyibio.org

DYI Bio Europe: http://www.diybio.eu/

http://genefoo.com/

Open PCR: http://openpcr.org/

www.indiebiotech.com

Ask a Biosafety expert: http://ask.diybio.org/

Public Laboratory: http://publiclaboratory.org/home

BOSSLAB: http://bosslab.org/

http://biocurious.org/

http://genspace.org/

Science hideout: http://www.youtube.com/user/ScienceHideout

http://basementbiotech.org/

http://www.biotinker.com/

Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs

Programming

Beginning Python fro bioinformatics Wiki: http://wiki.genedrift.org/doku.php?id=beginning_python_for_bioinformatics

Art and Strategy

Xenotext: http://www.law.ed.ac.uk/ahrc/script-ed/vol5-2/editorial.asp http://en.wikipedia.org/wiki/Christian_B%C3%B6k#The_Xenotext_experiment

Personal genomics

https://www.23andme.com/

http://www.23andyou.com

http://www.genomesunzipped.org/

uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome

http://www.personalgenomes.org/

Companies

http://www.syntheticgenomics.com/

BGI: http://www.genomics.cn/en/index

Gen9: http://gen9bio.com/

DNA 2.0: https://www.dna20.com

Integrated DNA Technologies (IDT): http://eu.idtdna.com/site

GenScript: http://www.genscript.com/

Desktop Genetics: http://www.deskgen.com

Ginkgo Bioworks: http://ginkgobioworks.com/

Biofab: http://www.biofab.org/

Suppliers

DongSheng Biotech: http://dongshengbio.com/en/index.asp

Macrogen Inc.: http://www.macrogen.com/eng/index/

Carolina Biological: http://www.carolina.com/

Epoch Life Sciences: http://www.epochlifescience.com/Default.aspx

http://www.hometrainingtools.com/

http://www.labsupplymall.com/

United Nuclear: http://www.unitednuclear.com/

New England Biolabs: www.neb.com

Elemental Scientific: http://www.elementalscientific.net/store/Scripts/default.asp

Books

Gene Synthesis: http://link.springer.com/book/10.1007/978-1-61779-564-0/page/1

http://www.dummies.com/store/product/Bioinformatics-For-Dummies-2nd-Edition.productCd-0470089857.html

Useful links

Educational resources

http://www.bioinformatics.nl/molbi/SimpleCloningLab/index.htm

ROSALIND Bioinformatics challenges: http://rosalind.info/problems/locations/

Project Euler: http://projecteuler.net/

AddGene molecular biology reference: http://www.addgene.org/mol_bio_reference/

Discussion and communities

http://molecularbiology.forums.biotechniques.com/

DYI Bio Google Group: https://groups.google.com/forum/?fromgroups#!forum/diybio

http://www.americanbiotechnologist.com/blog/

BioStar - questions and answers on bioinformatics and genomics: http://www.biostars.org/

Persons

Tom Ellis: http://openwetware.org/wiki/User:Ellis

George Church: http://arep.med.harvard.edu/gmc/

Jay Keasling

Chris Voigt

Pallsson

Tom Knight

Drew Endy: http://openwetware.org/wiki/User:Endy

Journals

Bioengineered (Previously: Bioengineered bugs): http://dev.landesbioscience.com/journals/bioe/

Metabolic Engineering: http://www.journals.elsevier.com/metabolic-engineering/

PLOS One: http://nar.oxfordjournals.org/

BMC Systems Biology: http://www.biomedcentral.com/bmcsystbiol/

Molecular Systems Biology: http://www.nature.com/msb/index.html

BMC Microbiology

PLOS Computational Biology: PLOS Computational Biology

Proceedings of the National Academy of Sciences: http://www.pnas.org/

Journal of molecular biology:

Journal of biological chemistry:

Journal of bacteriology

The EMBO Journal

ACS Synthetic Biology: http://pubs.acs.org/journal/asbcd6

Databases/Repositories

PlasmID database: http://plasmid.med.harvard.edu/PLASMID/

Addgene plasmid repository: http://www.addgene.org/

DNASU plasid repository: http://dnasu.asu.edu/DNASU/

The Open Construct Database: http://www.the-odin.com

Bionumbers - The database of useful biological numbers

EcoCyc - E. coli K-12 MG1655 database: http://www.ecocyc.org/

EcoGene: http://www.ecogene.org

JWS Online model database: http://jjj.biochem.sun.ac.za/database/

http://systems-biology.org/resources/model-repositories/

Genome-Scale metabolic network database: http://synbio.tju.edu.cn/GSMNDB/gsmndb.htm

Array express: http://www.ebi.ac.uk/arrayexpress/

Rebase restriction enzyme database: http://rebase.neb.com/rebase/rebase.html

Codon usage

http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333

Codon usage analyzer: http://www.bioinformatics.org/sms2/codon_usage.html

Other informational resources

http://seqanswers.com

NCBI vs EMBL vs DDBJ.: http://lib.bioinfo.pl/courses/view/151

The DDBJ/EMBL/GenBank Feature Table Definition: http://www.insdc.org/files/feature_table.html#1

http://openwetware.org/wiki/DNA - Contains many protocols

Bite Size Bio: http://bitesizebio.com/

Programming

BioPython: http://biopython.org/wiki/Main_Page

Law and ethics

http://www.genomicslawreport.com/

American journal of Bioethics: http://www.tandfonline.com/toc/uajb20/current

IASB Code of Conduct for best practices in gene synthesis: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/code-of-conduct-for-best-practices-in-gene-synthesis/

IASB - About Biosafety & Security: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/biosafety-biosecurity/

Andrew W Torrance on DNA copyright: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2017670

Cloning

SLIC, Gibson, CPEC and SLiCE assembly methods: http://j5.jbei.org/j5manual/pages/22.html

RF cloning: http://www.rf-cloning.org/QandA.php

PCR Primer design: http://bioweb.uwlax.edu/genweb/molecular/seq_anal/primer_design/primer_design.htm

PCR: http://www.molbiol-tools.ca/PCR.htm

OpenWetWare - designing primers: http://openwetware.org/wiki/Designing_primers

PCR Guide: http://medicine.yale.edu/labs/henegariu/www/tavi/Guide.html

PCR troubleshooting: http://medicine.yale.edu/labs/henegariu/www/tavi/Trblesht.html

DNA Tm estimation methods: http://openwetware.org/wiki/Primer_Tm_estimation_methods

DNA stability: http://openwetware.org/wiki/DNA_stability

E. coli cloning checklist: http://openwetware.org/wiki/Cloning_Checklist

Guide to Gibson assembly: http://www.synbio.org.uk/dna-assembly/guidetogibsonassembly.html

Primer design guidelines: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html

Sequencing

Design of sequencing primers: http://seqcore.brcf.med.umich.edu/doc/dnaseq/primers.html

Conserved primer sequences for PCR amplification and sequencing from nuclear ribosomal RNA in fungi: http://biology.duke.edu/fungi/mycolab/primers.htm

GenScript DNA Sequencing Primers Design Tool: http://www.genscript.com/cgi-bin/tools/sequencing_primer_design