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35 results on '"Samanta, Manoj P"'

1. Comparative Analysis of Plastid Genomes Using Pangenome Research ToolKit (PGR-TK)

Author

Jayanti, Richa, Kim, Andrew, Pham, Sean, Raghavan, Athreya, Sharma, Anish, and Samanta, Manoj P.

Subjects
Quantitative Biology - Genomics
Abstract

Plastid genomes (plastomes) of angiosperms are of great interest among biologists. High-throughput sequencing is making many such genomes accessible, increasing the need for tools to perform rapid comparative analysis. This exploratory analysis investigates whether the Pangenome Research Tool Kit (PGR-TK) is suitable for analyzing plastomes. After determining the optimal parameters for this tool on plastomes, we use it to compare sequences from each of the genera - Magnolia, Solanum, Fragaria and Cotoneaster, as well as a combined set from 20 rosid genera. PGR-TK recognizes large-scale plastome structures, such as the inverted repeats, among combined sequences from distant rosid families. If the plastid genomes are rotated to the same starting point, it also correctly groups different species from the same genus together in a generated cladogram. The visual approach of PGR-TK provides insights into genome evolution without requiring gene annotations., Comment: 15 pages, 4 figures

Published
2023

2. Genes Preferring Non-AUG Start Codons in Bacteria

Author

Gvozdjak, Anne and Samanta, Manoj P.

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Biomolecules
Abstract

Here we investigate translational regulation in bacteria by analyzing the distribution of start codons in fully assembled genomes. We report 36 genes (infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in evolutionarily diverse phyla ("non-AUG genes"). Most of the non-AUG genes are functionally associated with translation, transcription or replication. In E. coli, the percentage of essential genes among these 36 is significantly higher than among all genes. Furthermore, the functional distribution of these genes suggests that non-AUG start codons may be used to reduce gene expression during starvation conditions, possibly through translational autoregulation or IF3-mediated regulation.

Published
2020

3. Nucleotide Distribution Patterns in Insect Genomes

Author

Samanta, Manoj Pratim

Subjects
Quantitative Biology - Genomics
Abstract

This work analyzed genome-wide nucleotide distribution patterns in ten insect genomes. Two internal measures were applied: (i) GC variation and (ii) third codon nucleotide preference. Although the genome size and overall GC level did not show any correlation with insect order, the internal measures usually displayed higher levels of consistency. GC variations in genomes of hymenopteran insects, honeybee and wasp, ranked highest among all eukaryotic genomes analyzed by us. Genomes of honeybee and beetle, insects of different orders with similar overall GC levels, showed significant internal differences. Honeybee genome stood out as unusual due to its high GC variation and 'left-handed' gene locations.

Published
2007

4. Ultraconserved Sequences in the Honeybee Genome - Are GC-rich Regions Preferred?

Author

Samanta, Manoj Pratim

Subjects
Quantitative Biology - Genomics
Abstract

Among all insect genomes, honeybee displays one of the most unusual patterns with interspersed long AT and GC-rich segments. Nearly 75% of the protein-coding genes are located in the AT-rich segments of the genome, but the biological significance of the GC-rich regions is not well understood. Based on an observation that the bee miRNAs, actins and tubulins are located in the GC-rich segments, this work investigated whether other highly conserved genomic regions show similar preferences. Sequences ultraconserved between the genomes of honeybee and Nasonia, another hymenopteran insect, were determined. They showed strong preferences towards locating in the GC-rich regions of the bee genome.

Published
2007

5. Global Snapshot of Protein Interaction Network -- A Percolation Based Approach

Author

Chin, Chen-Shan and Samanta, Manoj Pratim

Subjects
Condensed Matter - Statistical Mechanics, Quantitative Biology - Molecular Networks
Abstract

In this paper, we study the large-scale protein interaction network of yeast uti lizing a stochastic method based upon percolation of random graphs. In order to find the global features of connectivities in the network, we introduce numeric al measures that quantify (1) how strongly a protein ties with the other parts o f the network and (2) how significantly an interaction contributes to the integr ity of the network. Our study shows that the distribution of essential proteins is distinct from the background in terms of global connectivities. This observ ation highlights a fundamental difference between the essential and the non-esse ntial proteins in the network. Furthermore, we find that the interaction data o btained from different experimental methods such as immunoprecipitation and two- hybrid techniques possess different characteristics. We discuss the biological implications of these observations.

Published
2003

6. Redundancies in Large-scale Protein Interaction Networks

Author

Samanta, Manoj Pratim and Liang, Shoudan

Subjects
Physics - Biological Physics, Condensed Matter - Soft Condensed Matter, Condensed Matter - Statistical Mechanics, Physics - Data Analysis, Statistics and Probability, Quantitative Biology - Molecular Networks
Abstract

Understanding functional associations among genes discovered in sequencing projects is a key issue in post-genomic biology. However, reliable interpretation of the protein interaction data has been difficult. In this work, we show that if two proteins share significantly larger number of common interaction partners than random, they have close functional associations. Analysis of publicly available data from Saccharomyces cerevisiae reveals more than 2800 reliable functional associations, 29% of which involve at least one unannotated protein. By further analyzing these associations, we derive tentative functions for 81 unannotated proteins with high certainty., Comment: 43 pages

Published
2003

7. Josephson Effect in Unconventional Superconductors

Author

Datta, Supriyo and Samanta, Manoj P.

Subjects
Condensed Matter
Abstract

In this letter we present a simple relation, that allows one to predict the Josephson current between two unconventional superconductors with arbitrary band-structure and pairing symmetry. We illustrate this relation with examples of s-wave and d-wave junctions and show a detailed numerical comparison with the phenomenological Sigrist and Rice relation commonly used to interpret tunneling experiments between d-wave superconductors. Our relation automatically accounts for `mid-gap states' that occur in d-wave superconductors and clearly shows how these states lead to a temperature-sensitive contribution to the Josephson current for certain orientations of the junction. This relation should be useful in exploring the effects of disordered junctions, multiple atomic orbitals and complicated order parameters., Comment: 10 pages, 4 figures

Published
1996

8. Genomic basis for the convergent evolution of electric organs

Author

Gallant, Jason R., Traeger, Lindsay L., Volkening, Jeremy D., Moffett, Howell, Chen, Po-Hao, Novina, Carl D., Phillips, George N., Anand, Rene, Wells, Gregg B., Pinch, Matthew, Güth, Robert, Unguez, Graciela A., Albert, James S., Zakon, Harold H., Samanta, Manoj P., and Sussman, Michael R.

Published
2014

11. Modeling of Switching and Hysteresis in Molecular Transport

Author

Samanta, Manoj P and Partridge, Harry

Subjects
Atomic And Molecular Physics
Abstract

The conventional way of modeling current transport in two and three terminal molecular devices could be inadequate for certain cases involving switching and hysteresis. Here we present an alternate approach. Contrary to the regular way where applied bias directly modulates the conducting energy levels of the molecule, our method introduces a nonlinear potential energy surface varying with the applied bias as a control parameter. A time-dynamics is also introduced properly accounting for switching and hysteresis behavior. Although the model is phenomenological at this stage, we believe any detailed model would contain similar descriptions at its core.

Published
2002

12. More Questions than Answers : Continued Critical Reanalysis of Fredrickson et al.'s Studies of Genomics and Well-Being

Author

Brown, Nicholas, MacDonald, Douglas A., Samanta, Manoj P., Friedman, Harris L., Coyne, James C., Brown, Nicholas, MacDonald, Douglas A., Samanta, Manoj P., Friedman, Harris L., and Coyne, James C.

Abstract

We critically re-examine Fredrickson et al.’s renewed claims concerning the differential relationship between hedonic and eudaimonic forms of well-being and gene expression, namely that people who experience a preponderance of eudaimonic well-being have gene expression profiles that are associated with more favorable health outcomes. By means of an extensive reanalysis of their data, we identify several discrepancies between what these authors claimed and what their data support; we further show that their different analysis models produce mutually contradictory results. We then show how Fredrickson et al.’s most recent article on this topic not only fails to adequately address our previously published concerns about their earlier related work, but also introduces significant further problems, including inconsistency in their hypotheses. Additionally, we demonstrate that regardless of which statistical model is used to analyze their data, Fredrickson et al.’s method can be highly sensitive to the inclusion (or exclusion) of data from a single subject. We reiterate our previous conclusions, namely that there is no evidence that Fredrickson et al. have established a reliable empirical distinction between their two delineated forms of well-being, nor that eudaimonic well-being provides any overall health benefits over hedonic well-being.

Published
2016
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17. Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus)

Author

Traeger, Lindsay L., Volkening, Jeremy D., Moffett, Howell, Gallant, Jason R., Chen, Po-Hao, Novina, Carl D., Phillips, George N., Anand, Rene, Wells, Gregg B., Pinch, Matthew, Guth, Robert, Unguez, Graciela A., Albert, James S., Zakon, Harold H., Sussman, Michael R., Samanta, Manoj P., Traeger, Lindsay L., Volkening, Jeremy D., Moffett, Howell, Gallant, Jason R., Chen, Po-Hao, Novina, Carl D., Phillips, George N., Anand, Rene, Wells, Gregg B., Pinch, Matthew, Guth, Robert, Unguez, Graciela A., Albert, James S., Zakon, Harold H., Sussman, Michael R., and Samanta, Manoj P.

Abstract

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 243, doi:10.1186/s12864-015-1288-8., With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs. We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs’ electric organ, main electric organ, and Hunter’s electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species. Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here., This project has been funded in part by NSF Grant MCB No. 1144012 (MRS), NSF Grant DEB No. 0741450 (JSA), NSF Grant CNS No. 1248109 (GAU), W.M. Keck Foundation Distinguished Young Scholars in Medical Research (CDN), NIH R01 GM084879 (HZ), NIH grant R01 GM088670 (RA), NIH grant 1SC1GM092297-01A1 (GAU), the Morgridge Graduate Fellowship (JDV and LLT), University of Wisconsin Genetics NIH Graduate Training Grant (LLT); and the Cornell University Center for Vertebrate Genomics (JRG).

Published
2015

20. Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus)

Author

Traeger, Lindsay L, primary, Volkening, Jeremy D, additional, Moffett, Howell, additional, Gallant, Jason R, additional, Chen, Po-Hao, additional, Novina, Carl D, additional, Phillips, George N, additional, Anand, Rene, additional, Wells, Gregg B, additional, Pinch, Matthew, additional, Güth, Robert, additional, Unguez, Graciela A, additional, Albert, James S, additional, Zakon, Harold, additional, Sussman, Michael R, additional, and Samanta, Manoj P, additional

Published
2015
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22. Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P.

Author

Samanta, Manoj P., Lai, Stella M., Daniels, Charles J., and Gopalan, Venkat

Subjects
RIBONUCLEASE P, LOCUS (Genetics), TRANSFER RNA, SEQUENCE analysis, COMPARATIVE studies, GENETIC code
Abstract

RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 51 -maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs. [ABSTRACT FROM AUTHOR]

Published
2016
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23. The genome of the sea urchin Strongylocentrotus purpuratus

Author

Sodergren, Erica, Weinstock, George M., Davidson, Eric H., Cameron, R. Andrew, Gibbs, Richard A., Angerer, Robert C., Angerer, Lynne M., Arnone, Maria Ina, Burgess, David R., Burke, Robert D., Coffman, James A., Dean, Michael, Elphick, Maurice R., Ettensohn, Charles A., Foltz, Kathy R., Hamdoun, Amro, Hynes, Richard O., Klein, William H., Marzluff, William, McClay, David R., Morris, Robert L., Mushegian, Arcady, Rast, Jonathan P., Smith, L. Courtney, Thorndyke, Michael C., Vacquier, Victor D., Wessel, Gary M., Wray, Greg, Zhang, Lan, Elsik, Christine G., Ermolaeva, Olga, Hlavina, Wratko, Hofmann, Gretchen, Kitts, Paul, Landrum, Melissa J., Mackey, Aaron J., Maglott, Donna, Panopoulou, Georgia, Poustka, Albert J., Pruitt, Kim, Sapojnikov, Victor, Song, Xingzhi, Souvorov, Alexandre, Solovyev, Victor, Wei, Zheng, Whittaker, Charles A., Worley, Kim, Durbin, K. James, Shen, Yufeng, Fedrigo, Olivier, Garfield, David, Haygood, Ralph, Primus, Alexander, Satija, Rahul, Severson, Tonya, Gonzalez-Garay, Manuel L., Jackson, Andrew R., Milosavljevic, Aleksandar, Tong, Mark, Killian, Christopher E., Livingston, Brian T., Wilt, Fred H., Adams, Nikki, Belle, Robert, Carbonneau, Seth, Cheung, Rocky, Cormier, Patrick, Cosson, Bertrand, Croce, Jenifer, Fernandez-Guerra, Antonio, Geneviere, Anne-Marie, Goel, Manisha, Kelkar, Hemant, Morales, Julia, Mulner-Lorillon, Odile, Robertson, Anthony J., Goldstone, Jared V., Cole, Bryan, Epel, David, Gold, Bert, Hahn, Mark E., Howard-Ashby, Meredith, Scally, Mark, Stegeman, John J., Allgood, Erin L., Cool, Jonah, Judkins, Kyle M., McCafferty, Shawn S., Musante, Ashlan M., Obar, Robert A., Rawson, Amanda P., Rossetti, Blair J., Gibbons, Ian R., Hoffman, Matthew P., Leone, Andrew, Istrail, Sorin, Materna, Stefan C., Samanta, Manoj P., Stolc, Viktor, Tongprasit, Waraporn, Tu, Qiang, Bergeron, Karl-Frederik, Brandhorst, Bruce P., Whittle, James, Berney, Kevin, Bottjer, David J., Calestani, Cristina, Peterson, Kevin, Chow, Elly, Yuan, Qiu Autumn, Elhaik, Eran, Graur, Dan, Reese, Justin T., Bosdet, Ian, Heesun, Shin, Marra, Marco A., Schein, Jacqueline, Anderson, Michele K., Brockton, Virginia, Buckley, Katherine M., Cohen, Avis H., Fugmann, Sebastian D., Hibino, Taku, Loza-Coll, Mariano, Majeske, Audrey J., Messier, Cynthia, Nair, Sham V., Pancer, Zeev, Terwilliger, David P., Agca, Cavit, Arboleda, Enrique, Chen, Nansheng, Churcher, Allison M., Hallböök, Finn, Humphrey, Glen W., Idris, Mohammed M., Kiyama, Takae, Liang, Shuguang, Mellott, Dan, Mu, Xiuqian, Murray, Greg, Olinski, Robert P., Raible, Florian, Rowe, Matthew, Taylor, John S., Tessmar-Raible, Kristin, Wang, D., Wilson, Karen H., Yaguchi, Shunsuke, Gaasterland, Terry, Galindo, Blanca E., Gunaratne, Herath J., Juliano, Celina, Kinukawa, Masashi, Moy, Gary W., Neill, Anna T., Nomura, Mamoru, Raisch, Michael, Reade, Anna, Roux, Michelle M., Song, Jia L., Su, Yi-Hsien, Townley, Ian K., Voronina, Ekaterina, Wong, Julian L., Amore, Gabriele, Branno, Margherita, Brown, Euan R., Cavalieri, Vincenzo, Duboc, Veronique, Duloquin, Louise, Flytzanis, Constantin, Gache, Christian, Lapraz, Francois, Lepage, Thierry, Locascio, Annamaria, Martinez, Pedro, Matassi, Giorgio, Matranga, Valeria, Range, Ryan, Rizzo, Francesca, Roettinger, Eric, Wilson, Karen, Beane, Wendy, Bradham, Cynthia, Byrum, Christine, Glenn, Tom, Hussain, Sofia, Loza, Mariano, Manning, Gerard, Miranda, Esther, Thomason, Rebecca, Walton, Katherine, Wikramanayke, Athula, Whittaker, Charles, Wu, Shu-Yu, Xu, Ronghui, Brown, C. Titus, Chen, Lili, Gray, Rachel F., Lee, Pei Yun, Nam, Jongmin, Oliveri, Paola, Smith, Joel, Muzny, Donna, Bell, Stephanie, Chacko, Joseph, Cree, Andrew, Curry, Stacey, Davis, Clay, Dinh, Huyen, Dugan-Rocha, Shannon, Fowler, Jerry, Gill, Rachel, Hamilton, Cerrissa, Hernandez, Judith, Hines, Sandra, Hume, Jennifer, Jackson, LaRonda, Jolivet, Angela, Kovar, Christie, Lee, Sandra, Lewis, Lora, Miner, George, Morgan, Margaret, Nazareth, Lynne V., Okwuonu, Geoffrey, Parker, David, Pu, Ling-Ling, Thom, Rachel, Wright, Rita, Sodergren, Erica, Weinstock, George M., Davidson, Eric H., Cameron, R. Andrew, Gibbs, Richard A., Angerer, Robert C., Angerer, Lynne M., Arnone, Maria Ina, Burgess, David R., Burke, Robert D., Coffman, James A., Dean, Michael, Elphick, Maurice R., Ettensohn, Charles A., Foltz, Kathy R., Hamdoun, Amro, Hynes, Richard O., Klein, William H., Marzluff, William, McClay, David R., Morris, Robert L., Mushegian, Arcady, Rast, Jonathan P., Smith, L. Courtney, Thorndyke, Michael C., Vacquier, Victor D., Wessel, Gary M., Wray, Greg, Zhang, Lan, Elsik, Christine G., Ermolaeva, Olga, Hlavina, Wratko, Hofmann, Gretchen, Kitts, Paul, Landrum, Melissa J., Mackey, Aaron J., Maglott, Donna, Panopoulou, Georgia, Poustka, Albert J., Pruitt, Kim, Sapojnikov, Victor, Song, Xingzhi, Souvorov, Alexandre, Solovyev, Victor, Wei, Zheng, Whittaker, Charles A., Worley, Kim, Durbin, K. James, Shen, Yufeng, Fedrigo, Olivier, Garfield, David, Haygood, Ralph, Primus, Alexander, Satija, Rahul, Severson, Tonya, Gonzalez-Garay, Manuel L., Jackson, Andrew R., Milosavljevic, Aleksandar, Tong, Mark, Killian, Christopher E., Livingston, Brian T., Wilt, Fred H., Adams, Nikki, Belle, Robert, Carbonneau, Seth, Cheung, Rocky, Cormier, Patrick, Cosson, Bertrand, Croce, Jenifer, Fernandez-Guerra, Antonio, Geneviere, Anne-Marie, Goel, Manisha, Kelkar, Hemant, Morales, Julia, Mulner-Lorillon, Odile, Robertson, Anthony J., Goldstone, Jared V., Cole, Bryan, Epel, David, Gold, Bert, Hahn, Mark E., Howard-Ashby, Meredith, Scally, Mark, Stegeman, John J., Allgood, Erin L., Cool, Jonah, Judkins, Kyle M., McCafferty, Shawn S., Musante, Ashlan M., Obar, Robert A., Rawson, Amanda P., Rossetti, Blair J., Gibbons, Ian R., Hoffman, Matthew P., Leone, Andrew, Istrail, Sorin, Materna, Stefan C., Samanta, Manoj P., Stolc, Viktor, Tongprasit, Waraporn, Tu, Qiang, Bergeron, Karl-Frederik, Brandhorst, Bruce P., Whittle, James, Berney, Kevin, Bottjer, David J., Calestani, Cristina, Peterson, Kevin, Chow, Elly, Yuan, Qiu Autumn, Elhaik, Eran, Graur, Dan, Reese, Justin T., Bosdet, Ian, Heesun, Shin, Marra, Marco A., Schein, Jacqueline, Anderson, Michele K., Brockton, Virginia, Buckley, Katherine M., Cohen, Avis H., Fugmann, Sebastian D., Hibino, Taku, Loza-Coll, Mariano, Majeske, Audrey J., Messier, Cynthia, Nair, Sham V., Pancer, Zeev, Terwilliger, David P., Agca, Cavit, Arboleda, Enrique, Chen, Nansheng, Churcher, Allison M., Hallböök, Finn, Humphrey, Glen W., Idris, Mohammed M., Kiyama, Takae, Liang, Shuguang, Mellott, Dan, Mu, Xiuqian, Murray, Greg, Olinski, Robert P., Raible, Florian, Rowe, Matthew, Taylor, John S., Tessmar-Raible, Kristin, Wang, D., Wilson, Karen H., Yaguchi, Shunsuke, Gaasterland, Terry, Galindo, Blanca E., Gunaratne, Herath J., Juliano, Celina, Kinukawa, Masashi, Moy, Gary W., Neill, Anna T., Nomura, Mamoru, Raisch, Michael, Reade, Anna, Roux, Michelle M., Song, Jia L., Su, Yi-Hsien, Townley, Ian K., Voronina, Ekaterina, Wong, Julian L., Amore, Gabriele, Branno, Margherita, Brown, Euan R., Cavalieri, Vincenzo, Duboc, Veronique, Duloquin, Louise, Flytzanis, Constantin, Gache, Christian, Lapraz, Francois, Lepage, Thierry, Locascio, Annamaria, Martinez, Pedro, Matassi, Giorgio, Matranga, Valeria, Range, Ryan, Rizzo, Francesca, Roettinger, Eric, Wilson, Karen, Beane, Wendy, Bradham, Cynthia, Byrum, Christine, Glenn, Tom, Hussain, Sofia, Loza, Mariano, Manning, Gerard, Miranda, Esther, Thomason, Rebecca, Walton, Katherine, Wikramanayke, Athula, Whittaker, Charles, Wu, Shu-Yu, Xu, Ronghui, Brown, C. Titus, Chen, Lili, Gray, Rachel F., Lee, Pei Yun, Nam, Jongmin, Oliveri, Paola, Smith, Joel, Muzny, Donna, Bell, Stephanie, Chacko, Joseph, Cree, Andrew, Curry, Stacey, Davis, Clay, Dinh, Huyen, Dugan-Rocha, Shannon, Fowler, Jerry, Gill, Rachel, Hamilton, Cerrissa, Hernandez, Judith, Hines, Sandra, Hume, Jennifer, Jackson, LaRonda, Jolivet, Angela, Kovar, Christie, Lee, Sandra, Lewis, Lora, Miner, George, Morgan, Margaret, Nazareth, Lynne V., Okwuonu, Geoffrey, Parker, David, Pu, Ling-Ling, Thom, Rachel, and Wright, Rita

Abstract

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Published
2006
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27. The Genome of the Sea Urchin Strongylocentrotus purpuratus

Author

Sodergren, Erica, primary, Weinstock, George M., additional, Davidson, Eric H, additional, Cameron, R. Andrew, additional, Gibbs, Richard A., additional, Angerer, Robert C., additional, Angerer, Lynne M., additional, Arnone, Maria Ina, additional, Burgess, David R., additional, Burke, Robert D., additional, Coffman, James A., additional, Dean, Michael, additional, Elphick, Maurice R., additional, Ettensohn, Charles A., additional, Foltz, Kathy R., additional, Hamdoun, Amro, additional, Hynes, Richard O., additional, Klein, William H., additional, Marzluff, William, additional, McClay, David R., additional, Morris, Robert L., additional, Mushegian, Arcady, additional, Rast, Jonathan P., additional, Smith, L. Courtney, additional, Thorndyke, Michael C., additional, Vacquier, Victor D., additional, Wessel, Gary M., additional, Wray, Greg, additional, Zhang, Lan, additional, Elsik, Christine G., additional, Ermolaeva, Olga, additional, Hlavina, Wratko, additional, Hofmann, Gretchen, additional, Kitts, Paul, additional, Landrum, Melissa J., additional, Mackey, Aaron J., additional, Maglott, Donna, additional, Panopoulou, Georgia, additional, Poustka, Albert J., additional, Pruitt, Kim, additional, Sapojnikov, Victor, additional, Song, Xingzhi, additional, Souvorov, Alexandre, additional, Solovyev, Victor, additional, Wei, Zheng, additional, Whittaker, Charles A., additional, Worley, Kim, additional, Durbin, K. James, additional, Shen, Yufeng, additional, Fedrigo, Olivier, additional, Garfield, David, additional, Haygood, Ralph, additional, Primus, Alexander, additional, Satija, Rahul, additional, Severson, Tonya, additional, Gonzalez-Garay, Manuel L., additional, Jackson, Andrew R., additional, Milosavljevic, Aleksandar, additional, Tong, Mark, additional, Killian, Christopher E., additional, Livingston, Brian T., additional, Wilt, Fred H., additional, Adams, Nikki, additional, Bellé, Robert, additional, Carbonneau, Seth, additional, Cheung, Rocky, additional, Cormier, Patrick, additional, Cosson, Bertrand, additional, Croce, Jenifer, additional, Fernandez-Guerra, Antonio, additional, Genevière, Anne-Marie, additional, Goel, Manisha, additional, Kelkar, Hemant, additional, Morales, Julia, additional, Mulner-Lorillon, Odile, additional, Robertson, Anthony J., additional, Goldstone, Jared V., additional, Cole, Bryan, additional, Epel, David, additional, Gold, Bert, additional, Hahn, Mark E., additional, Howard-Ashby, Meredith, additional, Scally, Mark, additional, Stegeman, John J., additional, Allgood, Erin L., additional, Cool, Jonah, additional, Judkins, Kyle M., additional, McCafferty, Shawn S., additional, Musante, Ashlan M., additional, Obar, Robert A., additional, Rawson, Amanda P., additional, Rossetti, Blair J., additional, Gibbons, Ian R., additional, Hoffman, Matthew P., additional, Leone, Andrew, additional, Istrail, Sorin, additional, Materna, Stefan C., additional, Samanta, Manoj P., additional, Stolc, Viktor, additional, Tongprasit, Waraporn, additional, Tu, Qiang, additional, Bergeron, Karl-Frederik, additional, Brandhorst, Bruce P., additional, Whittle, James, additional, Berney, Kevin, additional, Bottjer, David J., additional, Calestani, Cristina, additional, Peterson, Kevin, additional, Chow, Elly, additional, Yuan, Qiu Autumn, additional, Elhaik, Eran, additional, Graur, Dan, additional, Reese, Justin T., additional, Bosdet, Ian, additional, Heesun, Shin, additional, Marra, Marco A., additional, Schein, Jacqueline, additional, Anderson, Michele K., additional, Brockton, Virginia, additional, Buckley, Katherine M., additional, Cohen, Avis H., additional, Fugmann, Sebastian D., additional, Hibino, Taku, additional, Loza-Coll, Mariano, additional, Majeske, Audrey J., additional, Messier, Cynthia, additional, Nair, Sham V., additional, Pancer, Zeev, additional, Terwilliger, David P., additional, Agca, Cavit, additional, Arboleda, Enrique, additional, Chen, Nansheng, additional, Churcher, Allison M., additional, Hallböök, F., additional, Humphrey, Glen W., additional, Idris, Mohammed M., additional, Kiyama, Takae, additional, Liang, Shuguang, additional, Mellott, Dan, additional, Mu, Xiuqian, additional, Murray, Greg, additional, Olinski, Robert P., additional, Raible, Florian, additional, Rowe, Matthew, additional, Taylor, John S., additional, Tessmar-Raible, Kristin, additional, Wang, D., additional, Wilson, Karen H., additional, Yaguchi, Shunsuke, additional, Gaasterland, Terry, additional, Galindo, Blanca E., additional, Gunaratne, Herath J., additional, Juliano, Celina, additional, Kinukawa, Masashi, additional, Moy, Gary W., additional, Neill, Anna T., additional, Nomura, Mamoru, additional, Raisch, Michael, additional, Reade, Anna, additional, Roux, Michelle M., additional, Song, Jia L., additional, Su, Yi-Hsien, additional, Townley, Ian K., additional, Voronina, Ekaterina, additional, Wong, Julian L., additional, Amore, Gabriele, additional, Branno, Margherita, additional, Brown, Euan R., additional, Cavalieri, Vincenzo, additional, Duboc, Véronique, additional, Duloquin, Louise, additional, Flytzanis, Constantin, additional, Gache, Christian, additional, Lapraz, François, additional, Lepage, Thierry, additional, Locascio, Annamaria, additional, Martinez, Pedro, additional, Matassi, Giorgio, additional, Matranga, Valeria, additional, Range, Ryan, additional, Rizzo, Francesca, additional, Röttinger, Eric, additional, Beane, Wendy, additional, Bradham, Cynthia, additional, Byrum, Christine, additional, Glenn, Tom, additional, Hussain, Sofia, additional, Manning, Gerard, additional, Miranda, Esther, additional, Thomason, Rebecca, additional, Walton, Katherine, additional, Wikramanayke, Athula, additional, Wu, Shu-Yu, additional, Xu, Ronghui, additional, Brown, C. Titus, additional, Chen, Lili, additional, Gray, Rachel F., additional, Lee, Pei Yun, additional, Nam, Jongmin, additional, Oliveri, Paola, additional, Smith, Joel, additional, Muzny, Donna, additional, Bell, Stephanie, additional, Chacko, Joseph, additional, Cree, Andrew, additional, Curry, Stacey, additional, Davis, Clay, additional, Dinh, Huyen, additional, Dugan-Rocha, Shannon, additional, Fowler, Jerry, additional, Gill, Rachel, additional, Hamilton, Cerrissa, additional, Hernandez, Judith, additional, Hines, Sandra, additional, Hume, Jennifer, additional, Jackson, LaRonda, additional, Jolivet, Angela, additional, Kovar, Christie, additional, Lee, Sandra, additional, Lewis, Lora, additional, Miner, George, additional, Morgan, Margaret, additional, Nazareth, Lynne V., additional, Okwuonu, Geoffrey, additional, Parker, David, additional, Pu, Ling-Ling, additional, Thorn, Rachel, additional, and Wright, Rita, additional

Published
2006
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28. In-Depth Query of Large Genomes Using Tiling Arrays.

Author

Walker, John M., Korenberg, Michael J., Samanta, Manoj Pratim, Tongprasit, Waraporn, and Stolc, Viktor

Abstract

Identification of the transcribed regions in the newly sequenced genomes is one of the major challenges of postgenomic biology. Among different alternatives for empirical transcriptome mapping, whole-genome tiling array experiment emerged as the most comprehensive and unbiased approach. This relatively new method uses high-density oligonucleotide arrays with probes chosen uniformly from both strands of the entire genomes including all genic and intergenic regions. By hybridizing the arrays with tissue specific or pooled RNA samples, a genome-wide picture of transcription can be derived. This chapter discusses computational tools and techniques necessary to successfully conduct genome tiling array experiments. [ABSTRACT FROM AUTHOR]

Published
2007
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32. Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis.

Author

Qing-Jun Luo, Samanta, Manoj P., Fatih Köksal, Janda, Jaroslav, Galbraith, David W., Richardson, Casey R., Fangqian Ou-Yang, and Rock, Christopher D.

Subjects
*ANTISENSE RNA, *GENETIC transcription, *DNA microarrays, *GENES, *ARABIDOPSIS, *HEREDITY
Abstract

Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA cleavage site. Antisense smRNAs were also found associated with MIRNA genes. This suggests that miRNA-associated ''transitivity'' (production of small interfering RNAs through antisense transcription) is more common than previously reported. High-resolution (3 nt) custom tiling microarray transcriptome analysis was performed with probes 400 bp 59 upstream and 39 downstream of the miRNA cleavage sites (direction relative to the mRNA) for 22 select miRNA target genes. We hybridized RNAs labeled from the smRNA pathway mutants, including hen1-1, dcl1-7, hyl1-2, rdr6-15, and sgs3-14. Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants. This was corroborated by semi-quantitative reverse transcription PCR; however, a direct correlation of antisense transcript abundance in MIR164 gene knockouts was not observed. Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation. HEN1 and SGS3 may be links for miRNA target entry into different RNA processing pathways. [ABSTRACT FROM AUTHOR]

Published
2009
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33. Global snapshot of a protein interaction network--a percolation based approach

Author

Chin, Chen-Shan and Samanta, Manoj Pratim

Abstract

Motivation: Biologically significant information can be revealed by modeling large-scale protein interaction data using graph theory based network analysis techniques. However, the methods that are currently being used draw conclusions about the global features of the network from local connectivity data. A more systematic approach would be to define global quantities that measure (1) how strongly a protein ties with the other parts of the network and (2) how significantly an interaction contributes to the integrity of the network, and connect them with phenotype data from other sources. In this paper, we introduce such global connectivity measures and develop a stochastic algorithm based upon percolation in random graphs to compute them. Results: We show that, in terms of global connectivities, the distribution of essential proteins is distinct from the background. This observation highlights a fundamental difference between the essential and the non-essential proteins in the network. We also find that the interaction data obtained from different experimental methods such as immunoprecipitation and two-hybrid techniques contribute differently to network integrities. Such difference between different experimental methods can provide insight into the systematic bias present among these techniques. Supplementary information: The full list of our results can be found in the supplemental web site http://www.nas.nasa.gov/Groups/SciTech/nano/msamanta/projects/percolation/index.php

Published
2003
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34. Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds.

Author

Hedgecock, Dennis, Shin, Grace, Gracey, Andrew Y., Van Den Berg, David, and Samanta, Manoj P.

Subjects
*PACIFIC oysters, *GENOTYPES, *GENOMICS
Abstract

The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-density, linkage and gene-centromere maps mostly constructed from microsatellite DNA markers. Here, higher density, second- generation, linkage maps are constructed from more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), as well as 66 previously mapped microsatellite DNA markers, all typed in five families of Pacific oysters (nearly 172,000 genotypes). The map comprises 10 linkage groups, as expected, has an average total length of 588 cM, an average marker-spacing of 1.0 cM, and covers 86% of a genome estimated to be 616 cM. All but seven of the mapped SNPs map to 618 genome scaffolds; 260 scaffolds contain two or more mapped SNPs, but for 100 of these scaffolds (38.5%), the contained SNPs map to different linkage groups, suggesting widespread errors in scaffold assemblies. The 100 misassembled scaffolds are significantly longer than those that map to a single linkage group. On the genetic maps, marker orders and intermarker distances vary across families and mapping methods, owing to an abundance of markers segregating from only one parent, to widespread distortions of segregation ratios caused by early mortality, as previously observed for oysters, and to genotyping errors. Maps made from framework markers provide stronger support for marker orders and reasonable map lengths and are used to produce a consensus high-density linkage map containing 656 markers. [ABSTRACT FROM AUTHOR]

Published
2015
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35. The myogenic electric organ of Sternopygus macrurus: a non-contractile tissue with a skeletal muscle transcriptome.

Author

Pinch M, Güth R, Samanta MP, Chaidez A, and Unguez GA

Abstract

In most electric fish species, the electric organ (EO) derives from striated muscle cells that suppress many muscle properties. In the gymnotiform Sternopygus macrurus, mature electrocytes, the current-producing cells of the EO, do not contain sarcomeres, yet they continue to make some cytoskeletal and sarcomeric proteins and the muscle transcription factors (MTFs) that induce their expression. In order to more comprehensively examine the transcriptional regulation of genes associated with the formation and maintenance of the contractile sarcomere complex, results from expression analysis using qRT-PCR were informed by deep RNA sequencing of transcriptomes and miRNA compositions of muscle and EO tissues from adult S. macrurus. Our data show that: (1) components associated with the homeostasis of the sarcomere and sarcomere-sarcolemma linkage were transcribed in EO at levels similar to those in muscle; (2) MTF families associated with activation of the skeletal muscle program were not differentially expressed between these tissues; and (3) a set of microRNAs that are implicated in regulation of the muscle phenotype are enriched in EO. These data support the development of a unique and highly specialized non-contractile electrogenic cell that emerges from a striated phenotype and further differentiates with little modification in its transcript composition. This comprehensive analysis of parallel mRNA and miRNA profiles is not only a foundation for functional studies aimed at identifying mechanisms underlying the transcription-independent myogenic program in S. macrurus EO, but also has important implications to many vertebrate cell types that independently activate or suppress specific features of the skeletal muscle program.

Published
2016
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