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Participants in the Advanced Bioinformatics annual training workshop conducted by BecA-ILRI Hub in collaboration with the Swedish University of Agriculture Sciences (SLU) in Nairobi, Kenya October 7th - 18th, 2013
Photo credit: BecA-ILRI/Tim Hall
Test of an art concept for an institutional fundraiser. The sharp-eyed and bored among you may recognize six of my previous photos in this mess.
The original composition was about the size of the "blackboard" in the centre. When I increased the canvas size to add a gray border, parts of the other layers magically appeared. Totally unintentional.
All feedback gratefully received. I tried brightening it, and increasing the contrast and colour, but it lost something in that process. So this is the working version, for now.
Best viewed large on black.
Aim: To analyze various single subunit DNA dependent RNA polymerases and identify conserved motifs, active site regions among them and propose a plausible mechanism of action for these polymerases using the T7 RNA polymerase as a model system.
Study Design: Bioinformatics, Biochemical, Site-directed mutagenesis and X-ray crystallographic data were analyzed.
Place and Duration of Study: Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai – 625 021, India, from 2010 to 2013.
Methodology: The advanced version of Clustal Omega was used for protein sequence analysis of various SSU DNA dependent RNA polymerases from viruses, mitochondria and chloroplasts. Along with the conserved motifs identified by the bioinformatics analysis and with the data obtained by X-ray crystallographic, biochemical and site-directed mutagenesis (SDM) were also used to confirm the possible amino acids involved in the active sites and catalysis of these RNA polymerases.
Results: Multiple sequence analyses of various single subunit (SSU) DNA dependent RNA polymerases from different sources showed only a few highly conserved motifs among them, except chloroplast RNA polymerases where a large number of highly conserved motifs were found. Possible catalytic regions in all these polymerases consist of a highly conserved amino acid K and a ‘gatekeeper’ YG pair. In addition to, these polymerases also use an invariant R at the -4 position from the YG pair and an invariant S/T, adjacent to the YG pair. Furthermore, two highly conserved Ds are implicated in the metal-binding site and thus might participate in the catalytic process. The YG pair appears to be specific for DNA templates as it is not reported in RNA dependent RNA polymerases.
Conclusion: The highly conserved amino acid K, the ‘gatekeeper’ YG pair and an invariant R which are reported in all DNA polymerases, are also found in these DNA dependent RNA polymerases. Therefore, these RNA polymerases might be using the same catalytic mechanism as DNA polymerases. The catalytic amino acid K could act as the proton abstractor and generate the necessary nucleophile at the 3’-OH and the YG pair, R and the S/T might involve in the template binding and selection of nucleoside triphosphates (NTPs) for polymerization reactions. The two highly conserved Ds could act as the ‘NTP charge shielder’ and orient the alpha phosphate of incoming NTPs for the reaction at the 3’-OH growing end.
Author(s) Details
Dr. Peramachi Palanivelu
Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai –625 021, India (Retd.).
Read full article: bp.bookpi.org/index.php/bpi/catalog/view/54/590/477-1
View More: www.youtube.com/watch?v=n1nk0tu3U3Q
Figure 2 from Computational Design of Targeted Inhibitors of Polo-Like Kinase 1 (Plk1) Published in Bioinformatics and Biology Insights
A BecA-ILRI Hub Africa Biosciences Challenge Fund Fellow undertakes a practical exercise at a bioinformatics workshop.
Photo Credit: BecA-ILRI Hub/Tim Hall
Participants in the Advanced Bioinformatics annual training workshop conducted by BecA-ILRI Hub in collaboration with the Swedish University of Agriculture Sciences (SLU) in Nairobi, Kenya October 7th - 18th, 2013
Photo credit: BecA-ILRI/Tim Hall
Original full Poster available here from the Research Collaboratory for Structural Bioinformatics (RCSB)
Participants in the Advanced Bioinformatics annual training workshop conducted by BecA-ILRI Hub in collaboration with the Swedish University of Agriculture Sciences (SLU) in Nairobi, Kenya October 7th - 18th, 2013
Photo credit: BecA-ILRI/Tim Hall
Dr Laura Purdie, PhD and BecA-ILRI Hub Africa Biosciences Challenge Fund Fellows at a bioinformatics workshop.
Photo Credit: BecA-ILRI Hub/Tim Hall
The introductory workshop in bioinformatics and genomics held at ILRI, Nairobi 24-28 February 2014, was conducted by BecA-ILRI Hub in collaboration with the National Science Foundation, the Fulbright Foundation, and Reed and Lewis & Clark Colleges. The workshop was facilitated by Prof Sarah Schaack, Assistant Professor of Biology, Reed College, USA . (photo credit BecA-ILRI Hub/Ethel Makila)
Belgium - Brussels - 10 March 2014 - Innovation Convention 2014 - Hearing your genes evolve - Deirdre GRIBBIN , Composer - Sarah TEICHMANN , Research Group Leader at EMBL-European Bioinformatics Institute and Wellcome Trust Sanger Institute ©EC/CE
BecA-ILRI Hub Africa Biosciences Challenge Fund Fellows at a bioinformatics workshop.
Photo Credit: BecA-ILRI Hub/Tim Hall
The introductory workshop in bioinformatics and genomics held at ILRI, Nairobi 24-28 February 2014, was conducted by BecA-ILRI Hub in collaboration with the National Science Foundation, the Fulbright Foundation, and Reed and Lewis & Clark Colleges. The workshop was facilitated by Prof Sarah Schaack, Assistant Professor of Biology, Reed College, USA . (photo credit BecA-ILRI Hub/Ethel Makila)
Joe and Bank hard at work. The Centre for Applied Genomics, in the Peter Gilgan Centre for Research and Learning, Toronto.
Voigtländer VF-101
Color-Skopar 40mm f/2.8
Ilford XP2 Super, ISO 400
Developing and scanning by Aden Camera, Toronto. I am really liking this film.
Participants on the final day of the Advanced Bioinformatics annual training workshop conducted by BecA-ILRI Hub in collaboration with the Swedish University of Agriculture Sciences (SLU) in Nairobi, Kenya on October 18th, 2013
Photo credit: BecA-ILRI/Tim Hall
DAVOS/SWITZERLAND, 21JAN15 - Nick Goldman , Research Group Leader and Senior Scientist, The Goldman Group, EMBL-EBI European Bioinformatics Institute, United Kingdom captured during the session Brain-Based Chips and DNA Hard Drives in the congress centre at the Annual Meeting 2015 of the World Economic Forum in Davos, January 21, 2015.
WORLD ECONOMIC FORUM/Benedikt von Loebell
Students in the biology class, Genomics and Bioinformatics, prepare their final projects in the Scripps Landstrum Laboratory at Knox College. Photo by Peter Bailley.
Participants in the Advanced Bioinformatics annual training workshop conducted by BecA-ILRI Hub in collaboration with the Swedish University of Agriculture Sciences (SLU) in Nairobi, Kenya October 7th - 18th, 2013
Photo credit: BecA-ILRI/Tim Hall
BecA Research Scientist Dr. Rob Skilton after hosting a workshop on bioinformatics for ABCF Fellows.
Photo Credit: BecA-ILRI Hub/Tim Hall
Belgium - Brussels - 10 March 2014 - Innovation Convention 2014 - Press point 3 Deirdre GRIBBIN , Composer - Sarah TEICHMANN , Research Group Leader at EMBL-European Bioinformatics Institute and Wellcome Trust Sanger Institute ©EC/CE
Students from the MS Biotechnology and Bioinformatics emphasis for Stem Cell Technology and Laboratory Management.
From left to right:
Front row: Jennifer Jones, Dr. Ching-Hua Wang, Anukriti Sharma, Shruti Iyer, Yifeng Yuan.
Back row: Elaheh Mohammad Asghari, Adrien Larsen, Ryder Paredes, Mahalakshmi Sridharan, Michael Silva, Eugene Babcock (not in emphasis), William Ferguson.
Attendees at the October 2013 Advanced Bioinformatics Workshop with BecA-ILRI Hub Acting Technology Manager Timothy Kingori (far left)
The Advanced Bioinformatics annual training workshop conducted by BecA-ILRI Hub in collaboration with the Swedish University of Agriculture Sciences (SLU) in Nairobi, Kenya October 7th - 18th, 2013
Photo Credit: BecA-ILRI/Tim Hall
Dictionary of Bioinformatics and Computational Biology edited by John M. Hancock and Marketa J. Zvelebil. A handy reference book fro any bioinformatician to have on their bookshelf.
isbn:0471436224 www.amazon.co.uk/exec/obidos/ASIN/0471436224
0752224700
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Effect of the Hxt on the transcription of other Fusarium oxysporum sugar transporter genes during consolidated bioprocessing (CBP) of wheat straw/bran.Wild type fungus 11C, Hxt-silenced mutant pSilent-1-Hxt-3 and overexpression mutant pBARGPE1-Hxt-6 were aerobically cultured on wheat straw/bran (10?1 ratio) and RT-PCR was conducted using RNA isolated from samples harvested 24 h post-inoculation. (A) Transcript accumulation in RNA extracts was quantified relative to that of the housekeeping gene ?-tubulin (FOXG_06228.2) by 2?-??Ct method, where ??Ct?=?(Ct, Target gene - Ct, ?-tubulin). Results are based on two experiments, each with three replicates per strain/mutant per medium. Bars indicate the SEM (LSD0.05?=?0.015) (B) A phylogenetic tree was constructed based on the protein sequence of 20 F. oxysporum strain 4287 sugar transporters. Protein sequences were aligned using European Bioinformatics Institutes?s ClustalW2 tool (www.ebi.ac.uk) [62] and a distance tree of 100 bootstrapped data sets was generated by using the Phylogeny.fr program and the neighbor-joining method [64]. Arrows indicated the three genes alluded to in part (A) above that were affected by Hxt expression.
Belgium - Brussels - 10 March 2014 - Innovation Convention 2014 - Hearing your genes evolve - Deirdre GRIBBIN , Composer - Sarah TEICHMANN , Research Group Leader at EMBL-European Bioinformatics Institute and Wellcome Trust Sanger Institute ©EC/CE
DAVOS/SWITZERLAND, 21JAN15 - Nick Goldman , Research Group Leader and Senior Scientist, The Goldman Group, EMBL-EBI European Bioinformatics Institute, United Kingdom captured during the session Brain-Based Chips and DNA Hard Drives in the congress centre at the Annual Meeting 2015 of the World Economic Forum in Davos, January 21, 2015.
WORLD ECONOMIC FORUM/Benedikt von Loebell
BecA-ILRI Hub Africa Biosciences Challenge Fund Fellows at a bioinformatics workshop.
Photo Credit: BecA-ILRI Hub/Tim Hall
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