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Maria Magdalane C, Kaviyarasu K, Raja A, Arularasu MV, Mola GT, Isaev AB, Al-Dhabi NA, Arasu MV, Jeyaraj B, Kennedy J, Maaza M. Photocatalytic decomposition effect of erbium doped cerium oxide nanostructures driven by visible light irradiation: Investigation of cytotoxicity, antibacterial growth inhibition using catalyst. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 185:275-282. [PMID: 30012250 DOI: 10.1016/j.jphotobiol.2018.06.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/04/2018] [Accepted: 06/20/2018] [Indexed: 01/13/2023]
Abstract
Cerium (IV) oxide (CeO2) is the most accessible noble rare earth metal oxide for the excitation of the excitons by light-harvesting performance. The present work is focused on Erbium doped ceria nanoparticles that were beneficially obtained by hydrothermal method from cerium nitrate and Erbium nitrate as precursors for decomposition of Rhodamine-B (RhB) dye in the polluted waste water removed from the industries. Dye removal efficiency of the catalyst was found to be nearly ~94%. The structural phases, functional groups and the transitions are identified with the help of various techniques. XRD pattern determines the development of cubic phase with the particle size is 20 nm. Highly crystalline nature of as-synthesized nanomaterials with an average diameter of 35 nm was investigated by HRSEM. The crystalline size, shape and textural morphology, of the Erbium doped ceria nanostructures were analysed by HRTEM. Our results suggest, that the concentration of OH- ion determines the lattice constants and oxygen vacancy in the nanostructures which stimulate the probability of photocatalytic decomposition effect of organic pollutants, due to synergistic approach. In this context, both unhydrolyzed things and their swiftly drip from deceased or scratched cells with conceded membranes, even when the cells embrace some are outstanding attention. Although, the loss of viable cells also depends on epithelial cell dynamically conceal of numerous molar matrix.
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Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. High-resolution comparative analysis of great ape genomes. Science 2018; 360:eaar6343. [PMID: 29880660 PMCID: PMC6178954 DOI: 10.1126/science.aar6343] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/02/2018] [Indexed: 12/22/2022]
Abstract
Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.
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Zhou L, Raja A, Malik K, Pavel A, Glickman J, Guttman-Yassky E. 1071 Age-specific changes in the atopic dermatitis molecular phenotype. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.1084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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54
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Raja A, Ashokkumar S, Pavithra Marthandam R, Jayachandiran J, Khatiwada CP, Kaviyarasu K, Ganapathi Raman R, Swaminathan M. Eco-friendly preparation of zinc oxide nanoparticles using Tabernaemontana divaricata and its photocatalytic and antimicrobial activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 181:53-58. [DOI: 10.1016/j.jphotobiol.2018.02.011] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/03/2018] [Accepted: 02/08/2018] [Indexed: 10/18/2022]
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Maheshwari SU, Govindan K, Raja M, Raja A, Pravin MBS, Kumar SV. Synthesis and Characterization of Calcium Phosphate Ceramic/(Poly(vinyl alcohol)-Polycaprolactone) Bilayer Nanocomposites-A Bone Tissue Regeneration Scaffold. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY 2018; 18:1548-1556. [PMID: 29448629 DOI: 10.1166/jnn.2018.14259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
β Tricalcium phosphate ceramic was used to reinforce nanofibers in composite mats produced via electrospinning of poly(vinyl alcohol) (PVA), polycaprolactone (PCL) and (PVA: PCL) bilayers. The role of TCP ceramic on morphology of nanocomposites, crystalline structure, functional groups and thermal behaviour of nanocomposites were characterized by SEM, EDAX, XRD, FTIR and DSC analysis. Ultrathin cross-sections of the obtained nanocomposites were morphologically investigated with SEM and all fabricated composites consisted of fibers with average fiber diameter (AFD) around 100 nm except PCL-TCP fibers having AFD in the range of 608 nm. XRD profile presented the main peaks of β-TCP (JCPDS 090169 and JCPDS 70-2065). The characteristic absorption bands of TCP were also identified by FTIR in all the composites. The thermal stability was enhanced after adding TCP filler particles in all the polymer composites. The porosity of PCL-TCP was found around 63% and (PVA-PCL: TCP) composite was found to be 58%. The biocompatibility of the (PVA-PCL: TCP) composite scaffold has also been investigated by culturing MG-63 osteoblast cells on it; primary results showed that the cells adhered and proliferated well on the composite scaffold.
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Pai K M, Naidu RC, Raja A, Rai YS, Kumar N, Kini A, Joseph S, Hegde V, Ballal HS, Rao R, Sharma S, Valakatte V. Surgical nuances in the separation of craniopagus twins - Our experience and a follow up of 15 years. Neurol India 2018; 66:426-433. [DOI: 10.4103/0028-3886.227289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Varun A, Karthikeyan N, Muthusamy P, Raja A, Vijayarani K, Saranya S. Effect of zinc oxide and zinc oxide nano particles on performance, carcass characteristics and metallotheionine (MTmRNA) expression in broiler chicken. ACTA ACUST UNITED AC 2018. [DOI: 10.5958/0974-8180.2018.00061.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Joseph Daniel D, Raja A, Lee JY, Balaji D, Kim HJ, Ramasamy P. Synthesis, crystal growth and characterization of Zn 0.5Mn 0.5Te single crystal grown via the Bridgman technique. CrystEngComm 2018. [DOI: 10.1039/c8ce00772a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single crystal of Zn0.5Mn0.5Te has been grown by the vertical Bridgman method.
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Sakthivel M, Balasubramanyam D, Kumarasamy P, Gopi H, Raja A, Anilkumar R, Devaki A. Estimates of (co)variance components and genetic parameters for body weights and growth efficiency traits in the New Zealand white rabbit. WORLD RABBIT SCIENCE 2017. [DOI: 10.4995/wrs.2017.7057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The genetic parameters of growth traits in the New Zealand White rabbits kept at Sheep Breeding and Research Station, Sandynallah, The Nilgiris, India were estimated by partitioning the variance and covariance components. The (co)variance components of body weights at weaning (W42), post-weaning (W70) and marketing (W135) age and growth efficiency traits viz., average daily gain (ADG), relative growth rate (RGR) and Kleiber ratio (KR) estimated on a daily basis at different age intervals (42 to 70 d; 70 to 135 d and 42 to 135 d) from weaning to marketing were estimated by restricted maximum likelihood, fitting 6 animal models with various combinations of direct and maternal effects. Data were collected over a period of 15 yr (1998 to 2012). A log-likelihood ratio test was used to select the most appropriate univariate model for each trait, which was subsequently used in bivariate analysis. Heritability estimates for W42, W70 and W135 were 0.42±0.07, 0.40±0.08 and 0.27±0.07, respectively. Heritability estimates of growth efficiency traits were moderate to high (0.18 to 0.42). Of the total phenotypic variation, maternal genetic effect contributed 14 to 32% for early body weight traits (W42 and W70) and ADG1. The contribution of maternal permanent environmental effect varied from 6 to 18% for W42 and for all the growth efficiency traits except for KR2. Maternal permanent environmental effect on most of the growth efficiency traits was a carryover effect of maternal care during weaning. Direct maternal genetic correlations, for the traits in which maternal genetic effect was significant, were moderate to high in magnitude and negative in direction. Maternal effect declined as the age of the animal increased. The estimates of total heritability and maternal across year repeatability for growth traits were moderate and an optimum rate of genetic progress seems possible in the herd by mass selection. The genetic and phenotypic correlations among body weights and between growth efficiency traits were also estimated. Moderate to high heritability and higher genetic correlation in body weight traits promise good scope for genetic improvement provided measures are taken to keep the inbreeding at the lowest level.
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Mannebach EM, Nyby C, Ernst F, Zhou Y, Tolsma J, Li Y, Sher MJ, Tung IC, Zhou H, Zhang Q, Seyler KL, Clark G, Lin Y, Zhu D, Glownia JM, Kozina ME, Song S, Nelson S, Mehta A, Yu Y, Pant A, Aslan B, Raja A, Guo Y, DiChiara A, Mao W, Cao L, Tongay S, Sun J, Singh DJ, Heinz TF, Xu X, MacDonald AH, Reed E, Wen H, Lindenberg AM. Dynamic Optical Tuning of Interlayer Interactions in the Transition Metal Dichalcogenides. NANO LETTERS 2017; 17:7761-7766. [PMID: 29119791 DOI: 10.1021/acs.nanolett.7b03955] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Modulation of weak interlayer interactions between quasi-two-dimensional atomic planes in the transition metal dichalcogenides (TMDCs) provides avenues for tuning their functional properties. Here we show that above-gap optical excitation in the TMDCs leads to an unexpected large-amplitude, ultrafast compressive force between the two-dimensional layers, as probed by in situ measurements of the atomic layer spacing at femtosecond time resolution. We show that this compressive response arises from a dynamic modulation of the interlayer van der Waals interaction and that this represents the dominant light-induced stress at low excitation densities. A simple analytic model predicts the magnitude and carrier density dependence of the measured strains. This work establishes a new method for dynamic, nonequilibrium tuning of correlation-driven dispersive interactions and of the optomechanical functionality of TMDC quasi-two-dimensional materials.
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Gopalan A, Deka G, Prabhavathi M, Savithri HS, Murthy MRN, Raja A. Structural and biophysical characterization of Rv3716c, a hypothetical protein from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2017; 495:982-987. [PMID: 29154992 DOI: 10.1016/j.bbrc.2017.11.093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 10/18/2022]
Abstract
Latent tuberculosis (TB) is the main hurdle in reaching the goal of "Stop TB 2050". Tuberculin skin and Interferon-gamma release assay tests used currently for the diagnosis of TB infection cannot distinguish between active disease and latent tuberculosis infection (LTBI) and hence new and sensitive protein markers need to be identified for the diagnosis. A protein Rv3716c from Mycobacterium tuberculosis (MtbRv3716c) has been identified as a potential surrogate marker for the diagnosis of LTBI. Here, we present characterization of MtbRv3716c (∼13 kDa) using both biophysical and X-Ray crystallographic methods. EMSA study showed that MtbRv3716c binds to double stranded DNA. X-ray diffraction data collected on a crystal of MtbRv3716c at 1.9 Å resolution was used for structure determination using the molecular replacement method. Significant electron density was not observed for the N-terminal 21 and C-terminal 41 residues in the final electron density map. The C- terminal disordered region is proline rich and displays characteristics of intrinsically disordered proteins. Although the crystal asymmetric unit contained a protomer, a tight dimer could be generated by the application of the crystal two-fold symmetry parallel to the b axis. Packing of dimers in the crystal is mediated by a cadmium ion (Cd2+) occurring at the interface of two dimers. Molecular packing analysis reveals large cavities that are probably occupied by the disordered segments of the N- and C-termini. Structural comparison with other homologous hypothetical DNA binding proteins (PDB codes: 1PUG, 1YBX) highlights structural features that might be significant for DNA binding.
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Jin LE, Wang M, Yang ST, Yang Y, Galvin VC, Lightbourne TC, Ottenheimer D, Zhong Q, Stein J, Raja A, Paspalas CD, Arnsten AFT. mGluR2/3 mechanisms in primate dorsolateral prefrontal cortex: evidence for both presynaptic and postsynaptic actions. Mol Psychiatry 2017; 22:1615-1625. [PMID: 27502475 PMCID: PMC5298940 DOI: 10.1038/mp.2016.129] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/04/2016] [Accepted: 06/15/2016] [Indexed: 01/12/2023]
Abstract
Cognitive deficits in psychiatric and age-related disorders generally involve dysfunction of the dorsolateral prefrontal cortex (dlPFC), but there are few treatments for these debilitating symptoms. Group II metabotropic glutamate receptors (mGluR2/3), which couple to Gi/Go, have been a focus of therapeutics based on rodent research, where mGluR2/3 have been shown to reduce axonal glutamate release and increase glial glutamate uptake. However, this strategy has had mixed results in patients, and understanding mGluR2/3 mechanisms in primates will help guide therapeutic interventions. The current study examined mGluR2/3 localization and actions in the primate dlPFC layer III circuits underlying working memory, where the persistent firing of 'Delay cells' is mediated by N-methyl-d-aspartate receptors and weakened by cAMP-PKA-potassium channel signaling in dendritic spines. Immunoelectron microscopy identified postsynaptic mGluR2/3 in the spines, in addition to the traditional presynaptic and astrocytic locations. In vivo iontophoretic application of the mGluR2/3 agonists (2R, 4R)-APDC or LY379268 onto dlPFC Delay cells produced an inverted-U effect on working memory representation, with enhanced neuronal firing following low doses of mGluR2/3 agonists. The enhancing effects were reversed by an mGluR2/3 antagonist or by activating cAMP signaling, consistent with mGluR2/3 inhibiting postsynaptic cAMP signaling in spines. Systemic administration of these agonists to monkeys performing a working memory task also produced an inverted-U dose-response, where low doses improved performance but higher doses, similar to clinical trials, had mixed effects. Our data suggest that low doses of mGluR2/3 stimulation may have therapeutic effects through unexpected postsynaptic actions in dlPFC, strengthening synaptic connections and improving cognitive function.
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Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE. Genomic Patterns of De Novo Mutation in Simplex Autism. Cell 2017; 171:710-722.e12. [PMID: 28965761 PMCID: PMC5679715 DOI: 10.1016/j.cell.2017.08.047] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/25/2017] [Indexed: 12/22/2022]
Abstract
To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10-8 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends. Probands carry more gene-disruptive CNVs and SNVs, resulting in severe missense mutations and mapping to predicted fetal brain promoters and embryonic stem cell enhancers. These differences become more pronounced for autism genes (p = 1.8 × 10-3, OR = 2.2). Patients are more likely to carry multiple coding and noncoding DNMs in different genes, which are enriched for expression in striatal neurons (p = 3 × 10-3), suggesting a path forward for genetically characterizing more complex cases of autism.
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Uma Maheshwari S, Govindan K, Raja M, Raja A, Pravin M, Vasanth Kumar S. Preliminary studies of PVA/PVP blends incorporated with HAp and β-TCP bone ceramic as template for hard tissue engineering. Biomed Mater Eng 2017; 28:401-415. [DOI: 10.3233/bme-171682] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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65
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Manjunath BN, Shenvi S, Raja A, Reddy GC. New water soluble glycosides of 11-keto-β-boswellic acid: A paradigm. Nat Prod Res 2017. [DOI: 10.1080/14786419.2017.1342084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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66
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Sumesh A, Rameshkumar K, Raja A, Mohandas K, Santhakumari A, Shyambabu R. Establishing Correlation Between Current and Voltage Signatures of the Arc and Weld Defects in GMAW Process. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2017. [DOI: 10.1007/s13369-017-2609-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Raja A, Daly A, Harper R, Senghore N, White D, Ravaghi V. Characteristics of children undergoing dental extractions under general anaesthesia in Wolverhampton: 2007-2012. Br Dent J 2017; 220:407-11. [PMID: 27103291 DOI: 10.1038/sj.bdj.2016.297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2016] [Indexed: 11/09/2022]
Abstract
INTRODUCTION Studying characteristics of children requiring extractions under dental general anaesthesia (DGA) can help identify trends, which can be used to facilitate future planning of healthcare services. OBJECTIVE To report on the profile of children who underwent extractions under DGA between 2007 and 2012 at the New Cross Hospital in Wolverhampton, England.Methods Retrospective analyses of hospital records. RESULTS Of the 2692 patients seen between 2007 and 2012, 49.6% were boys and 50.4% were girls. The mean age was 7.1 and 7 to 12 years was the largest age group (43%). The majority of the sample was White British (67%). Of the 8,286 teeth extracted, 85% were primary teeth and 15% permanent. More teeth were extracted in boys than girls (P = 0.002) and 'Other' ethnicities had a higher mean number of extractions compared to White British (P <0.001) and South Asians (P = 0.046). The mean age of the patients has decreased over the years (P = 0.001) and the mean number of primary teeth extracted has increased (P = 0.001). CONCLUSIONS A clear dental public health issue has been reinforced through the relatively high level of DGA activity reported. Though rigorous caries prevention remains the ultimate goal, a better assessment and discharge process may help reduce the need for first time DGAs as well as repeats.
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Raja A, Chaves A, Yu J, Arefe G, Hill HM, Rigosi AF, Berkelbach TC, Nagler P, Schüller C, Korn T, Nuckolls C, Hone J, Brus LE, Heinz TF, Reichman DR, Chernikov A. Coulomb engineering of the bandgap and excitons in two-dimensional materials. Nat Commun 2017; 8:15251. [PMID: 28469178 PMCID: PMC5418602 DOI: 10.1038/ncomms15251] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/14/2017] [Indexed: 12/21/2022] Open
Abstract
The ability to control the size of the electronic bandgap is an integral part of solid-state technology. Atomically thin two-dimensional crystals offer a new approach for tuning the energies of the electronic states based on the unusual strength of the Coulomb interaction in these materials and its environmental sensitivity. Here, we show that by engineering the surrounding dielectric environment, one can tune the electronic bandgap and the exciton binding energy in monolayers of WS2 and WSe2 by hundreds of meV. We exploit this behaviour to present an in-plane dielectric heterostructure with a spatially dependent bandgap, as an initial step towards the creation of diverse lateral junctions with nanoscale resolution. Electronic bandgap tuning in semiconductors enables key functionalities in solid-state devices. Here, the authors present a strategy to control the bandgap of atomically thin WS2 and WSe2 semiconductors via manipulation of the surrounding dielectric environment rather than by modifications of the materials themselves.
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Sahu AR, Jeichitra V, Rajendran R, Raja A. Polymorphism in exon 3 of myostatin ( MSTN ) gene and its association with growth traits in Indian sheep breeds. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Dennis MY, Harshman L, Nelson BJ, Penn O, Cantsilieris S, Huddleston J, Antonacci F, Penewit K, Denman L, Raja A, Baker C, Mark K, Malig M, Janke N, Espinoza C, Stessman HAF, Nuttle X, Hoekzema K, Lindsay-Graves TA, Wilson RK, Eichler EE. The evolution and population diversity of human-specific segmental duplications. Nat Ecol Evol 2017; 1:69. [PMID: 28580430 PMCID: PMC5450946 DOI: 10.1038/s41559-016-0069] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed “core duplicons”, and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (e.g., TCAF1/2), we highlight ten gene families (e.g., ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing, and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits.
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Raja MMM, Raja A, Salique SM, Gajalakshmi P. Comparative Studies on Effect of Carbon and Nitrogen Sources on L -Asparaginase Production. ACTA ACUST UNITED AC 2017. [DOI: 10.3126/ijasbt.v4i4.16241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Marine actinomycetes sediment samples were collected from Gulf of Mannar costal region, Kayalpatinam, located at Tuticorin district, Tamilnadu, India. Marine actinomycetes were isolated and evaluated for activity of L-asparaginase production. A total of 10 marine actinomycetes strains were isolated. Among 10 isolates, six were belongs to Streptomyces sp, three were belongs to Micromonospora sp and one was to Micropolyspora sp. Based on phenotypic characteristics, actinomycetes strains were screened for L-asparaginase production. Streptomyces sp KPMS5 and Micromonospora sp KPMS10 were showed large pink coloration on L-asparaginase production medium. The strains were further studied for maximum production and characterizations of culture condition of L-asparaginase enzyme were evaluated. Effect of substrate on L-asparaginase production was evaluated by enzyme assy. Maximum enzyme assay (1.4 mM) was observed on glucose followed by starch (1.12Mm) by Micromonospora sp KPMS10. In Streptomyces sp KPMS5 showed maximum of 1.25mM of enzyme assay on glucose substrate followed by lactose 1.17mM. Yeast extract was effectively used as substrate for maximum production of L-asparaginase by submerged fermentation. Further studies on purification and characterization are required to support the application of enzyme. The finding concludes isolates belongs to non-Streptomyces sp like Micromonospora sp is a potential novel source for L-asparaginase production.Int J Appl Sci Biotechnol, Vol 4(4): 452-457
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Sahu AR, Jeichitra V, Rajendran R, Raja A. Polymorphism of growth hormone receptor (GHR) gene in Nilagiri sheep. Trop Anim Health Prod 2016; 49:281-285. [PMID: 27885492 DOI: 10.1007/s11250-016-1189-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/16/2016] [Indexed: 11/24/2022]
Abstract
The allelic variation in the regulatory sequence of growth hormone receptor (GHR) gene influences the growth traits of sheep. A study was carried out to find out the polymorphisms associated with exon 10 of GHR gene and its association with growth traits of Nilagiri sheep. The blood samples were collected from Nilagiri sheep (n = 103) reared at Sheep Breeding Research Station, Sandynallah, Tamil Nadu, India. DNA was isolated using the phenol-chloroform extraction procedure and eight samples having amplified product of part of exon 10 (895 bp) sequenced. The results indicated transitions of nucleotide G>A at loci G177624A and G177878A. The genotyping frequencies estimated using the tetra-primer amplification refractory mutation system-PCR for GG, GA and AA were 0.262, 0.544 and 0.194, and 0.349, 0.505 and 0.146, respectively. The estimated allele frequencies of G and A nucleotides were 0.5340 and 0.4660, and 0.6015 and 0.3985, respectively, at loci G177624A and G177878A. The effects of both the mutations on growth-related traits viz., birth, weaning (3 months) 6, 9 and 12 months weight in Nilagiri sheep were found to be non-significant. This can be a novel approach to assess growth of sheep using the mutation in GHR gene. Thus, this approach can be useful for further investigation as a molecular marker associated with genetic improvement.
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Delisle T, Stillman J, Raja A. The relevance of endoscopy readmissions and mortality. Int J Surg 2016. [DOI: 10.1016/j.ijsu.2016.08.293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mohajeri K, Cantsilieris S, Huddleston J, Nelson BJ, Coe BP, Campbell CD, Baker C, Harshman L, Munson KM, Kronenberg ZN, Kremitzki M, Raja A, Catacchio CR, Graves TA, Wilson RK, Ventura M, Eichler EE. Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region. Genome Res 2016; 26:1453-1467. [PMID: 27803192 PMCID: PMC5088589 DOI: 10.1101/gr.211284.116] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022]
Abstract
Recurrent rearrangements of Chromosome 8p23.1 are associated with congenital heart defects and developmental delay. The complexity of this region has led to inconsistencies in the current reference assembly, confounding studies of genetic variation. Using comparative sequence-based approaches, we generated a high-quality 6.3-Mbp alternate reference assembly of an inverted Chromosome 8p23.1 haplotype. Comparison with nonhuman primates reveals a 746-kbp duplicative transposition and two separate inversion events that arose in the last million years of human evolution. The breakpoints associated with these rearrangements map to an ape-specific interchromosomal core duplicon that clusters at sites of evolutionary inversion (P = 7.8 × 10−5). Refinement of microdeletion breakpoints identifies a subgroup of patients that map to the same interchromosomal core involved in the evolutionary formation of the duplication blocks. Our results define a higher-order genomic instability element that has shaped the structure of specific chromosomes during primate evolution contributing to rearrangements associated with inversion and disease.
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Caputo N, Donner L, Williams A, West J, Ryan M, Raja A, Kanter M, Scott S. 9 The Use of Emergency Department Diffuse Apneic Oxygenation Versus Usual Care During Rapid Sequence Intubation of Emergency Department Patients: A Randomized Controlled Trial (Preliminary Results of the ENDAO Study). Ann Emerg Med 2016. [DOI: 10.1016/j.annemergmed.2016.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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