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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
Bryn Williams-Jones of Connected Discovery Ltd: "SME's form a huge percentage of the end-users of bioinformatics resources. I'm here to talk about what they need the data for, and how they need the services to evolve. I'm also very interested to learn about how biotech works in Italy. There are a lot of people doing very valuable work here, but they need to talk about it more widely."
Figure 2 from Computational Design of Targeted Inhibitors of Polo-Like Kinase 1 (Plk1) Published in Bioinformatics and Biology Insights
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
Trīs no šīm grāmatām ir manis pirktās. Lai arī mani tas daļēji ir iedzinis bankrotā, grāmatas šeit maksā daudz lētāk nekā jebkurā veikalā, kas būtu pieejams Eiropā vai Amerikā.
Introduction to Algorithms - 40 USD, Amazonē - 82 USD.
Bioinformatics - 35 USD, Amazonē 49 USD.
Natural Language Processing - 35 USD, Amazonē - 63 USD.
Pagājušosemestr bija Artificial Intelligence - 35 USD, Amazonē - 115 USD.
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
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)
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
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
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
Scientists used novel bioinformatics to investigate molecular-level changes over time and toxicity pathways in mahi-mahi embryos and larvae exposed to Deepwater Horizon oil. They observed that weathered oil (collected from slick skimming operations) induced more pronounced gene expression changes than a non-weathered source oil (collected from the subsea containment system directly over the wellhead). The tools predicted impairment of heart rates and increased pericardial edema which the researchers observed in the fish. The method also predicted disturbances in eye and nervous system development. These results suggest new genetic and developmental toxicity pathways targets associated with Deepwater Horizon oil.
Photo Caption: Mahi-mahi.
Photo provided by Dan DiNicola,
RECOVER Outreach Coordinator
Read More: gulfresearchinitiative.org/study-suggests-wider-range-mah...
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.
From an early age, Tom Hagen has enjoyed watching plants grow and solving complex problems. Now, as the enterprise breeding system manager at the International Maize and Wheat Improvement Center (CIMMYT), Hagen is combining his expertise in crop breeding and IT to help researchers and farmers be more successful.
“You could say I’m a hybrid scientific consultant – IT system architect,” said Hagen. “I will work with breeding teams to appropriately design software and then manage its development and deployment to facilitate breeding operations at CIMMYT and the International Rice Research Institute.”
The software will help breeders more effectively choose seed varieties, design field trials, collect data and analyze their outcomes. It is intended to assist farmers and extension agents as well.
“It will be able to give them advice about the appropriate seeds to use based on their specific environment and economic situation,” said Hagen. “It can also recommend ways to plant and manage their crop for better yields and higher income.”
Hagen’s interest in using computer programing to analyze large sets of biological data emerged shortly after obtaining a doctorate in plant genetics from the University of Georgia. It was the early 1990s, and bioinformatics was a new frontier. Hagen founded and managed the university’s Center for Scientific Computing and Visualization, and helped create the Bioinformatics Graduate Program.
To continue reading this story, click below:
www.cimmyt.org/breaking-ground-tom-hagen-brings-it-expert...