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849 results on '"Bajic, Vladimir B"'

2. Author Correction: Bioprospecting desert plant Bacillus endophytic strains for their potential to enhance plant stress tolerance

Author

Bokhari, Ameerah, Essack, Magbubah, Lafi, Feras F, Andres-Barrao, Cristina, Jalal, Rewaa, Alamoudi, Soha, Razali, Rozaimi, Alzubaidy, Hanin, Shah, Kausar H, Siddique, Shahid, Bajic, Vladimir B, Hirt, Heribert, and Saad, Maged M

Subjects
Agricultural, Veterinary and Food Sciences, Crop and Pasture Production
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

3. Bioprospecting desert plant Bacillus endophytic strains for their potential to enhance plant stress tolerance

Author

Bokhari, Ameerah, Essack, Magbubah, Lafi, Feras F, Andres-Barrao, Cristina, Jalal, Rewaa, Alamoudi, Soha, Razali, Rozaimi, Alzubaidy, Hanin, Shah, Kausar H, Siddique, Shahid, Bajic, Vladimir B, Hirt, Heribert, and Saad, Maged M

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Microbiology, Plant Biology, Crop and Pasture Production
Abstract

Plant growth-promoting bacteria (PGPB) are known to increase plant tolerance to several abiotic stresses, specifically those from dry and salty environments. In this study, we examined the endophyte bacterial community of five plant species growing in the Thar desert of Pakistan. Among a total of 368 culturable isolates, 58 Bacillus strains were identified from which the 16 most divergent strains were characterized for salt and heat stress resilience as well as antimicrobial and plant growth-promoting (PGP) activities. When the 16 Bacillus strains were tested on the non-host plant Arabidopsis thaliana, B. cereus PK6-15, B. subtilis PK5-26 and B. circulans PK3-109 significantly enhanced plant growth under salt stress conditions, doubling fresh weight levels when compared to uninoculated plants. B. circulans PK3-15 and PK3-109 did not promote plant growth under normal conditions, but increased plant fresh weight by more than 50% when compared to uninoculated plants under salt stress conditions, suggesting that these salt tolerant Bacillus strains exhibit PGP traits only in the presence of salt. Our data indicate that the collection of 58 plant endophytic Bacillus strains represents an important genomic resource to decipher plant growth promotion at the molecular level.

Published
2019

4. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

Author

Baillie, J Kenneth, Bretherick, Andrew, Haley, Christopher S, Clohisey, Sara, Gray, Alan, Neyton, Lucile PA, Barrett, Jeffrey, Stahl, Eli A, Tenesa, Albert, Andersson, Robin, Brown, J Ben, Faulkner, Geoffrey J, Lizio, Marina, Schaefer, Ulf, Daub, Carsten, Itoh, Masayoshi, Kondo, Naoto, Lassmann, Timo, Kawai, Jun, IIBDGC Consortium, Mole, Damian, Bajic, Vladimir B, Heutink, Peter, Rehli, Michael, Kawaji, Hideya, Sandelin, Albin, Suzuki, Harukazu, Satsangi, Jack, Wells, Christine A, Hacohen, Nir, Freeman, Thomas C, Hayashizaki, Yoshihide, Carninci, Piero, Forrest, Alistair RR, and Hume, David A

Subjects
IIBDGC Consortium, Humans, Crohn Disease, Genetic Predisposition to Disease, Gene Expression Profiling, Genomics, Databases, Genetic, Promoter Regions, Genetic, Transcriptome, Databases, Genetic, Promoter Regions, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn's disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.

Published
2018

10. An optimized recursive learning algorithm for three-layer feedforward neural networks for mimo nonlinear system identifications

Author

Sha, Daohang and Bajic, Vladimir B.

Subjects
Computer Science - Neural and Evolutionary Computing, Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Learning
Abstract

Back-propagation with gradient method is the most popular learning algorithm for feed-forward neural networks. However, it is critical to determine a proper fixed learning rate for the algorithm. In this paper, an optimized recursive algorithm is presented for online learning based on matrix operation and optimization methods analytically, which can avoid the trouble to select a proper learning rate for the gradient method. The proof of weak convergence of the proposed algorithm also is given. Although this approach is proposed for three-layer, feed-forward neural networks, it could be extended to multiple layer feed-forward neural networks. The effectiveness of the proposed algorithms applied to the identification of behavior of a two-input and two-output non-linear dynamic system is demonstrated by simulation experiments., Comment: 15 pages, 5 figures

Published
2010

25. DES-Amyloidoses “Amyloidoses through the looking-glass”: A knowledgebase developed for exploring and linking information related to human amyloid-related diseases

Author

Bajic, Vladan P., primary, Salhi, Adil, additional, Lakota, Katja, additional, Radovanovic, Aleksandar, additional, Razali, Rozaimi, additional, Zivkovic, Lada, additional, Spremo-Potparevic, Biljana, additional, Uludag, Mahmut, additional, Tifratene, Faroug, additional, Motwalli, Olaa, additional, Marchand, Benoit, additional, Bajic, Vladimir B., additional, Gojobori, Takashi, additional, Isenovic, Esma R., additional, and Essack, Magbubah, additional

Published
2022
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31. Intelligent Extraction Versus Advanced Query: Recognize Transcription Factors from Databases

Author

Zhang, Zhuo, Veronika, Merlin, Ng, See-Kiong, Bajic, Vladimir B, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Rajapakse, Jagath C., editor, Wong, Limsoon, editor, and Acharya, Raj, editor

Published
2006
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38. Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

Author

Roy, Sugata, Schmeier, Sebastian, Arner, Erik, Alam, Tanvir, Parihar, Suraj P., Ozturk, Mumin, Tamgue, Ousman, Kawaji, Hideya, de Hoon, Michiel J. L., Itoh, Masayoshi, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Bajic, Vladimir B., Guler, Reto, Brombacher, Frank, and Suzuki, Harukazu

Published
2015
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45. A promoter-level mammalian expression atlas

Author

Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., ’t Hoen, Peter A. C., Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero, and Hayashizaki, Yoshihide

Published
2014
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46. The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network

Author

Meier, Stuart, Gehring, Chris, MacPherson, Cameron Ross, Kaur, Mandeep, Maqungo, Monique, Reuben, Sheela, Muyanga, Samson, Shih, Ming-Der, Wei, Fu-Jin, Wanchana, Samart, Mauleon, Ramil, Radovanovic, Aleksandar, Bruskiewich, Richard, Tanaka, Tsuyoshi, Mohanty, Bijayalaxmi, Itoh, Takeshi, Wing, Rod, Gojobori, Takashi, Sasaki, Takuji, Swarup, Sanjay, Hsing, Yue-ie, and Bajic, Vladimir B.

Published
2008
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47. Genes and comorbidities of thyroid cancer

Author

Ljubic, Branimir, primary, Pavlovski, Martin, additional, Roychoudhury, Shoumik, additional, Van Neste, Christophe, additional, Salhi, Adil, additional, Essack, Magbubah, additional, Bajic, Vladimir B., additional, and Obradovic, Zoran, additional

Published
2021
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49. Genome insights of the plant-growth promoting bacterium Cronobacter muytjensii JZ38 with volatile-mediated antagonistic activity against Phytophthora infestans

Author

Eida, Abdul Aziz, Bougouffa, Salim, L’Haridon, Floriane, Alam, Intikhab, Weisskopf, Laure, Bajic, Vladimir B., Saad, Maged M., and Hirt, Heribert

Subjects
fungi, food and beverages
Abstract

Salinity stress is a major challenge to agricultural productivity and global food security in light of a dramatic increase of human population and climate change. Plant growth promoting bacteria can be used as an additional solution to traditional crop breeding and genetic engineering. In the present work, the induction of plant salt tolerance by the desert plant endophyte Cronobacter sp. JZ38 was examined on the model plant Arabidopsis thaliana using different inoculation methods. JZ38 promoted plant growth under salinity stress via contact and emission of volatile compounds. Based on the 16S rRNA and whole genome phylogenetic analysis, fatty acid analysis and phenotypic identification, JZ38 was identified as Cronobacter muytjensii and clearly separated and differentiated from the pathogenic C. sakazakii. Full genome sequencing showed that JZ38 is composed of one chromosome and two plasmids. Bioinformatic analysis and bioassays revealed that JZ38 can grow under a range of abiotic stresses. JZ38 interaction with plants is correlated with an extensive set of genes involved in chemotaxis and motility. The presence of genes for plant nutrient acquisition and phytohormone production could explain the ability of JZ38 to colonize plants and sustain plant growth under stress conditions. Gas chromatography–mass spectrometry analysis of volatiles produced by JZ38 revealed the emission of indole and different sulfur volatile compounds that may play a role in contactless plant growth promotion and antagonistic activity against pathogenic microbes. Indeed, JZ38 was able to inhibit the growth of two strains of the phytopathogenic oomycete Phytophthora infestans via volatile emission. Genetic, transcriptomic and metabolomics analyses, combined with more in vitro assays will provide a better understanding the highlighted genes’ involvement in JZ38’s functional potential and its interaction with plants. Nevertheless, these results provide insight into the bioactivity of C. muytjensii JZ38 as a multi-stress tolerance promoting bacterium with a potential use in agriculture.

Published
2020

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