Ashok Srinivasan

Bio: Ashok Srinivasan is an academic researcher from University of West Florida. The author has contributed to research in topics: Medicine & Magnetization. The author has an hindex of 29, co-authored 227 publications receiving 5823 citations. Previous affiliations of Ashok Srinivasan include University of Illinois at Urbana–Champaign & National Institutes of Health.

Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA

Abstract: Two small RNAs regulate the timing of Caenorhabditis elegans development. Transition from the first to the second larval stage fates requires the 22-nucleotide lin-4 RNA and transition from late larval to adult cell fates requires the 21-nucleotide let-7 RNA. The lin-4 and let-7 RNA genes are not homologous to each other, but are each complementary to sequences in the 3' untranslated regions of a set of protein-coding target genes that are normally negatively regulated by the RNAs. Here we have detected let-7 RNAs of ~21 nucleotides in samples from a wide range of animal species, including vertebrate, ascidian, hemichordate, mollusc, annelid and arthropod, but not in RNAs from several cnidarian and poriferan species, Saccharomyces cerevisiae, Escherichia coli or Arabidopsis. We did not detect lin-4 RNA in these species. We found that let-7 temporal regulation is also conserved: let-7 RNA expression is first detected at late larval stages in C. elegans and Drosophila , at 48 hours after fertilization in zebrafish, and in adult stages of annelids and molluscs. The let-7 regulatory RNA may control late temporal transitions during development across animal phylogeny.

Algorithm 806: SPRNG: a scalable library for pseudorandom number generation

Abstract: In this article we present background, rationale, and a description of the Scalable Parallel Random Number Generators (SPRNG) library. We begin by presenting some methods for parallel pseudorandom number generation. We will focus on methods based on parameterization, meaning that we will not consider splitting methods such as the leap-frog or blocking methods. We describe, in detail, parameterized versions of the following pseudorandom number generators: (i) linear congruential generators, (ii) shift-register generators, and (iii) lagged-Fibonacci generators. We briefly describe the methods, detail some advantages and disadvantages of each method, and recount results from number theory that impact our understanding of their quality in parallel applications. SPRNG was designed around the uniform implementation of different families of parameterized random number generators. We then present a short description of SPRNG. The description contained within this document is meant only to outline the rationale behind and the capabilities of SPRNG. Much more information, including examples and detailed documentation aimed at helping users with putting and using SPRNG on scalable systems is available at htt;//sprng.sc.fsu.edu. In this description of SPRNG we discuss the random-number generator library as well as the suite of tests of randomness that is an integral part of SPRNG. Random-number tools for parallel Monte Carlo applications must be subjected to classical as well as new types of empirical tests of randomness to eliminate generators that show defects when used in scalable envionments.

Tissue-engineered small intestine improves recovery after massive small bowel resection.

Abstract: Short bowel syndrome (SBS) includes a broad diversity of metabolic and physiologic disturbances, including fluid, nutrient, and weight loss secondary to unavailable functional surface area.1 Calcium, magnesium, zinc, iron, B12, and fat-soluble vitamin deficiencies are complicated by decreased absorption of carbohydrates and protein, which are linked as well to metabolic acidosis, formation of biliary and renal calculi, dehydration, and weight loss.2 SBS generally occurs with loss of approximately 70% to 75% of the small intestine.3–5 The severity of SBS is linked to the extent of resection, presence of an ileocecal valve, and presence of jejunum,2 as well as the health of the remaining small bowel.4 Our laboratory first reported making tissue-engineered small intestine (TESI) by the transplantation of organoid units on a polymer scaffold into the omentum of the Lewis rat.6 Organoid units are multicellular units derived from neonatal rat intestine, containing a mesenchymal core surrounded by a polarized intestinal epithelium, and contain all of the cells of a full-thickness intestinal section.7 We have recently transformed this protocol to yield significantly more organoid units in a shorter time from more specific areas of the gastrointestinal tract, beginning with the sigmoid colon as reported in this journal,8 leading to a greater viability, as production of tissue-engineered colon (TEC) occurs 100% of the time from autologous tissue, syngeneic tissue, or TEC itself. We have generated specific areas of the entire gastrointestinal tract including the abdominal esophagus,9 stomach,10 gastroesophageal junction,10 ileum and jejunum, and portions of the colon (Fig. 1). The sigmoid colon alone, harvested and grown into TEC and used in a replacement model, demonstrates resilient architecture, sodium and water absorption, short-chain fatty acid production, and ganglion cells.11 In the case of TEC, the model in which much of the protocol refinement was done, the histology has improved to be indistinguishable in some cases from native colon with an appropriate epithelial layer, actin-positive muscularis propria containing S100-positive cells in the distribution of Meissner and Auerbach's plexi, as well as lucent adjacent ganglion cells.8 FIGURE 1. A, Tissue engineered esophagus, original magnification 20 ×. B, Tissue engineered colon, original magnification 20 ×. C, Tissue engineered stomach; note large lucent parietal cells and glandular structure, original magnification ... Preliminary data showed that TESI generated by our new protocol has markedly improved tissue architecture, including a mucosal immune system with an immunocyte population similar to that of native small intestine.12,13 In addition, response of TESI to exogenous GLP-2 includes mucosal growth and enhanced SGLT1 epxression.14 We hypothesized that together these findings indicated TESI could aid in recovery of SBS. In addition, we sought to confirm the correct architecture of TESI seen on initial histology by performing computer morphometry and immunohistochemistry to assess for nerve and muscle components. To prove the donor origin of the TESI, we sought to label the progenitor cells with green fluorescent protein (GFP), which has additional implications for future more useful transfections, and we initiated confirmation of the differentiated state of the enterocytes in TESI after anastomosis by studying the villin and intestinal alkaline phosphatase content by Northern blot.

Oxygen octahedra distortion induced structural and magnetic phase transitions in Bi1−xCaxFe1−xMnxO3 ceramics

Abstract: The co-doping of Ca and Mn in respective Bi and Fe-sites of BiFeO3 lattice leads to structural transition from rhombohedral (R3c space group) to orthorhombic (Pbnm space group) crystal symmetry. The tilt angle for anti-phase rotation of the oxygen octahedra of BiFeO3 at room temperature is observed to be ∼13.8°. It decreases with the increase in the co-doping percentage which suggests the composition-driven structural phase transition. The remnant magnetization for sample with 15% of co-doping becomes about 16 times that of BiFeO3. It may be attributed to the suppression of cycloid spin structure and uncompensated spins at the surface of nanocrystallites. Further increase in co-doping percentage results in the sharp reduction of remnant magnetization due to the dominant contribution from the collinear antiferromagnetic ordering in the Pbnm space group. The Arrott plot analysis clearly indicates the composition-driven crossover from the antiferromagnetic to weak ferromagnetic ordering and vice versa. Electron spin resonance results provide the evidence for the composition-driven phase transitions from an incommensurate spin cycloidal modulated state to one with nearly homogeneous spin order. The band gap (2.17 eV) of BiFeO3 measured using UV-Vis spectra was supported by the resonance Raman spectra.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

MicroRNAs: small RNAs with a big role in gene regulation

Abstract: MicroRNAs are a family of small, non-coding RNAs that regulate gene expression in a sequence-specific manner. The two founding members of the microRNA family were originally identified in Caenorhabditis elegans as genes that were required for the timed regulation of developmental events. Since then, hundreds of microRNAs have been identified in almost all metazoan genomes, including worms, flies, plants and mammals. MicroRNAs have diverse expression patterns and might regulate various developmental and physiological processes. Their discovery adds a new dimension to our understanding of complex gene regulatory networks.

Oncomirs : microRNAs with a role in cancer

Abstract: I MicroRNAs (miRNAs) are an abundant class of small non-protein-coding RNAs that function as negative gene regulators. They regulate diverse biological processes, and bioinformatic data indicates that each miRNA can control hundreds of gene targets, underscoring the potential influence of miRNAs on almost every genetic pathway. Recent evidence has shown that miRNA mutations or mis-expression correlate with various human cancers and indicates that miRNAs can function as tumour suppressors and oncogenes. miRNAs have been shown to repress the expression of important cancer-related genes and might prove useful in the diagnosis and treatment of cancer.