PVAMU-CAHS-Seminar Series
What
Texas Aquatic Science
Who:
Leroy Davis, Postdoctoral Researcher, CARC at
Prairie View A & M University, Prairie View, Texas
Background
Dr. Davis is a recently hired Postdoctoral Scientist at Prairie View A & M University (PVAMU). His
prior research includes genetic engineering of plant bioreactors and his scientific interests include the development of
technology for writing novel DNA code. This is best illustrated in his 2014 publication in Biosystems, wherein he
introduced a novel in vitro evolution methodology “Template Assisted DNA Shuffling and in Vitro Recombination” based
upon the work of Dr. W.C. Stemmer. He has gone on to write algorithms that describe the stochastic and thermodynamic
mechanisms of DNA shuffling and has applied his algorithms to development of technology for optimization of in vitro
evolution experiments. In accordance to his interest in writing novel DNA code, he will introduce to PVAMU his recent
invention “GenEBiogenesis”, a neural network that utilizes high performance computing (HPC) to write novel DNA code.
The technology is a first of its kind and will be available on the Stampede Supercomputer at the Texas Advanced
Computing Center (TACC) for scientists throughout the world. The applications of this technology are broad including
synthesis of novel enzymes as well as the evolution of gene regulatory regions. His ambition is to apply these technologies
to the metabolic engineering of plant feedstock for advanced biofuels. Further, his long term goal is the integration of
synthetic biology and HPC technology into agricultural sciences for establishment of PVAMU as a National leader in
agricultural engineering technology.
When:
11:00 AM - 12:00 PM (Noon), Thursday, March 17, 2016
Where:
CAHS-CEP Auditorium
Abstract
GenEBiogenesis (GEB) performs gene engineering by re-engineering a DNA Secondary Code (DESC). Wherein, the GEB
algorithm transforms the genetic code into a DESC by partitioning into genomic alphabet of discrete size. Libraries
comprised of evolutionarily conserved genomic building blocks are constructed by simulating DNA shuffling within
genomic alphabet comprising the aforementioned DNA Secondary Code. GenEBiogenesis simulates DNA shuffling by
performing random hybridization of DNA sequences selected from across an orthologue sequence space constructed by a
NCBI-BLAST query. Building blocks are selected based on probability of formation derived from DNA binding states and
scored for evolutional conservation utilizing algorithms presented herein. The GEB algorithm identifies building blocks
dispersed over orthologue sequence space by solving variance of candidates from a universal domain of sequences
constructed utilizing a DNA shuffling based Monte Carlo simulation. The algorithm applies directionality to variance
creating sequence vectors that convey a color attribute, wherein sequences may possess (+) or (-) color. Genomic building
blocks are identified by constructing a homogeneous domain of (+) colored sequences formed by passing candidates thru a
theoretical filter, followed by quantile normalization using R. The formation of genomic building block libraries allows
GenEBiogenesis to perform random DNA shuffling, targeted gene engineering and De Novo gene engineering.
GenEBiogenesis is tethered to NCBI-Blast as well as a collection of microbial, plant and mammalian genome databases
that includes the human genome. The aforementioned allow GenEBiogenesis to target mutation within genes, introns,
exons and intergenic regions. GenEBiogenesis further allows 3D visualization and analysis of protein and DNA structures
as the platform contains I-TASSER and MFOLD wrapped within the GenEBiogenesis python shell. Prominently,
GenEBiogenesis offers a powerful and innovative genetic engineering tool for both evolutionally stable and intelligent
gene design.
Contact:
Ali Fares, Associate Director of Research (Interim) & Professor, CAHS-PVAMU
Phone: 936 261 5019, Email: AlFares@PVAMU.Edu