Day 1 :
Keynote Forum
Henry M Sobell
University of Rochester, USA
Keynote: The centers of premeltons signal the beginning and ends of genes
Time : 10:05-11:10
Biography:
Henry M Sobell has completed his studies at Brooklyn Technical High School (1948-1952), Columbia College (1952-1956) and the University of Virginia, School of Medicine (1956-1960) in Brooklyn New York. Instead of practicing Clinical Medicine, he then went to the Massachusetts Institute of Technology, Cambridge to join Professor Alexander Rich in the Department of Biology (1960-1965) as a Helen Hay Whitney Postdoctoral fellow; he learned the technique of single Crystal X- Ray Analysis. He then joined the Chemistry Department at the University of Rochester and was then jointly appointed to the Department of Biophysics School of Medicine and Dentistry becoming a full Professor in both departments (1965-1993). He is now retired and living in New York, USA.
Abstract:
Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A- DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A- transition), which differs from either A- or B- DNA. Called beta-DNA, this is both metastable and hyperflexible – and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A- DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5’ and 3’ ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions – all readily testable – as will be described in this talk.
Keynote Forum
David L Perkins
University of Illinois at Chicago, USA
Keynote: Microbiome functions identified by the metatranscriptome
Time : 11:30-12:30
Biography:
David L Perkins is a MD, PhD who is currently a Professor of Medicine at University of Illinois at Chicago. He obtained his PhD in Immunology and is also a Practicing Kidney Transplant Nephrologist. His current research focuses on the role of the microbiome in immunosuppressed subjects. He has published more than 100 papers in reputed journals, serves on numerous editorial boards and has been a standing member of a NIH study section.
Abstract:
The human microbiome plays an important role in regulating human health and disease. Previous studies have relied on 16S rRNA amplicon and shotgun metagenome sequencing to investigate the bacterial composition of the microbiome. These approaches provide a taxonomic assignment that is used to predict microbial functions based on known genome sequences. Here we report an extremely deep shotgun sequencing and comparative analysis of the human fecal microbiome using metatranscriptomics and metagenomics. In our previous study, we analyzed the human fecal microbiome using a shotgun metagenomic approach, and in the present study we compiled a total of 139.6 million reads using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared the metagenome and metatranscriptome with following parameters: 1) the Illumina HiSeq versus MiSeq platforms, 2) the sequence reads versus de novo assembled contigs, and 3) the effect of shorter versus longer reads. Interestingly, our analysis identified differential expression of bacterial genes indicating over- and under-represented bacterial functions in the fecal microbiome.