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Microbial genetics, genomics and proteomics

This section aims to publish studies relating to all aspects of microbial genomics, transcriptomics, proteomics, metabolomics and microbial genome editing.

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  1. As bacterial cells enter stationary phase, they adjust their growth rate to comply with nutrient restriction and acquire increased resistance to several stresses. These events are regulated by controlling gene...

    Authors: Carolina A. P. T. da Silva, Rogério F. Lourenço, Ricardo R. Mazzon, Rodolfo A. Ribeiro and Marilis V. Marques

    Citation: BMC Microbiology 2016 16:66

    Content type: Research article

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  2. Predictive genomics is the translation of raw genome sequence data into a phenotypic assessment of the organism. For bacterial pathogens, these phenotypes can range from environmental survivability, to the sev...

    Authors: Matthew D. Whiteside, Chad R. Laing, Akiff Manji, Peter Kruczkiewicz, Eduardo N. Taboada and Victor P. J. Gannon

    Citation: BMC Microbiology 2016 16:65

    Content type: Software

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  3. Low-copy-number vectors of potential wide application in biotechnology need to encode stabilization modules ensuring their stable inheritance. The efficiency of stabilization may vary depending on the plasmid ...

    Authors: Aneta A. Bartosik, Krzysztof Glabski, Anna Kulinska, Ewa Lewicka, Jolanta Godziszewska, Aleksandra Markowska and Grazyna Jagura-Burdzy

    Citation: BMC Microbiology 2016 16:59

    Content type: Methodology article

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  4. RNA helicases are enzymes that catalyze the separation of double-stranded RNA (dsRNA) using the free energy of ATP binding and hydrolysis. DEAD/DEAH families participate in many different aspects of RNA metabo...

    Authors: Laís Moreira Granato, Simone Cristina Picchi, Maxuel de Oliveira Andrade, Marco Aurélio Takita, Alessandra Alves de Souza, Nian Wang and Marcos Antonio Machado

    Citation: BMC Microbiology 2016 16:55

    Content type: Research article

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  5. Bifidobacterium thermophilum RBL67 (RBL67), a human fecal isolate and health promoting candidate shows antagonistic and protective effects against Salmonella and Listeria spec. in vitr...

    Authors: Sabine A. Tanner, Christophe Chassard, Eugenia Rigozzi, Christophe Lacroix and Marc J. A. Stevens

    Citation: BMC Microbiology 2016 16:46

    Content type: Research article

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  6. The Cerrado—an edaphic type of savannah— comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land convers...

    Authors: Renata Carolini Souza, Iêda Carvalho Mendes, Fábio Bueno Reis-Junior, Fabíola Marques Carvalho, Marco Antonio Nogueira, Ana Tereza Ribeiro Vasconcelos, Vânia Aparecida Vicente and Mariangela Hungria

    Citation: BMC Microbiology 2016 16:42

    Content type: Research article

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  7. Clostridium difficile infections (CDI) are a significant health problem to humans and food animals. Clostridial toxins ToxA and ToxB encoded by genes tcdA and tcdB are located on a pat...

    Authors: Piklu Roy Chowdhury, Matthew DeMaere, Toni Chapman, Paul Worden, Ian G. Charles, Aaron E. Darling and Steven P. Djordjevic

    Citation: BMC Microbiology 2016 16:41

    Content type: Research article

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  8. Diazotrophic (nitrogen-fixing) Gram-positive and endospore-formed Paenibacillus spp. have potential uses as a bacterial fertilizer in agriculture. The transcriptional analysis of nitrogen fixation in Paenibacillu...

    Authors: Hao-wen Shi, Li-ying Wang, Xin-xin Li, Xiao-meng Liu, Tian-yi Hao, Xiao-juan He and San-feng Chen

    Citation: BMC Microbiology 2016 16:25

    Content type: Research article

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  9. Bloom-forming cyanobacteria cause toxic algae outbreaks in lakes and reservoirs. We aimed to explore and quantify mutation events occurring within the large mcy gene cluster (55 kbp) encoding microcystin (MC) bio...

    Authors: Qin Chen, Guntram Christiansen, Li Deng and Rainer Kurmayer

    Citation: BMC Microbiology 2016 16:23

    Content type: Methodology article

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  10. Anaerobic digestion is a biological process in which a consortium of microorganisms transforms a complex substrate into methane and carbon dioxide. A good understanding of the interactions between the populati...

    Authors: Vimac Nolla-Ardèvol, Miriam Peces, Marc Strous and Halina E. Tegetmeyer

    Citation: BMC Microbiology 2015 15:277

    Content type: Research article

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  11. Chromobacterium violaceum (C. violaceum) occurs abundantly in a variety of ecosystems, including ecosystems that place the bacterium under stress. This study assessed the adaptability ...

    Authors: Diogo Castro, Isabelle Bezerra Cordeiro, Paula Taquita, Marcos Nogueira Eberlin, Jerusa Simone Garcia, Gustavo Henrique M. F. Souza, Marco Aurélio Zezzi Arruda, Edmar V. Andrade, Spartaco A. Filho, J. Lee Crainey, Luis Lopez Lozano, Paulo A. Nogueira and Patrícia P. Orlandi

    Citation: BMC Microbiology 2015 15:272

    Content type: Research article

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  12. The zoonosis bovine tuberculosis (TB) is known to be responsible for a considerable proportion of extrapulmonary TB. In Mozambique, bovine TB is a recognised problem in cattle, but little has been done to eval...

    Authors: Sofia Omar Viegas, Solomon Ghebremichael, Leguesse Massawo, Matos Alberto, Fabíola Couto Fernandes, Eliane Monteiro, David Couvin, José Maiane Matavele, Nalin Rastogi, Margarida Correia-Neves, Adelina Machado, Carla Carrilho, Ramona Groenheit, Gunilla Källenius and Tuija Koivula

    Citation: BMC Microbiology 2015 15:268

    Content type: Research article

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  13. Proliferating cell nuclear antigen (PCNA/POL30) an essential protein forms a homotrimeric ring encircling dsDNA and serves as a molecular scaffold to recruit various factors during DNA replication, repair and ...

    Authors: Kodavati Manohar and Narottam Acharya

    Citation: BMC Microbiology 2015 15:257

    Content type: Research article

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  14. The denitrifying betaproteobacterium "Aromatoleum aromaticum" EbN1 anaerobically utilizes a multitude of aromatic compounds via specific peripheral degradation routes. Compound-specific formation of these catabol...

    Authors: Imke Büsing, Mirjam Kant, Marvin Dörries, Lars Wöhlbrand and Ralf Rabus

    Citation: BMC Microbiology 2015 15:251

    Content type: Research article

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  15. Duck viral pathogens primarily include the avian influenza virus (AIV) subtypes H5, H7, and H9; duck hepatitis virus (DHV); duck tembusu virus (DTMUV); egg drop syndrome virus (EDSV); duck enteritis virus (DEV...

    Authors: Yan-fang Zhang, Zhi-xun Xie, Li-ji Xie, Xian-wen Deng, Zhi-qin Xie, Si-si Luo, Li Huang, Jiao-ling Huang and Ting-ting Zeng

    Citation: BMC Microbiology 2015 15:247

    Content type: Methodology article

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  16. Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. or...

    Authors: Xiang-Na Niu, Zhi-Qiong Wei, Hai-Fan Zou, Gui-Gang Xie, Feng Wu, Kang-Jia Li, Wei Jiang, Ji-Liang Tang and Yong-Qiang He

    Citation: BMC Microbiology 2015 15:233

    Content type: Research article

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  17. Vibrio (V.) parahaemolyticus causes seafood-borne gastro-intestinal bacterial infections in humans worldwide. It is widely found in marine environments and is isolated frequently from ...

    Authors: Sara Urmersbach, Tommi Aho, Thomas Alter, Syeda Sakira Hassan, Reija Autio and Stephan Huehn

    Citation: BMC Microbiology 2015 15:229

    Content type: Research article

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  18. A number of bacterial species are capable of growing in various life history modes that enable their survival and persistence in both planktonic free-living stages as well as in biofilm communities. Mechanisms...

    Authors: Alba Chavez-Dozal, Clayton Gorman and Michele K. Nishiguchi

    Citation: BMC Microbiology 2015 15:226

    Content type: Research article

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  19. Clostridium perfringens is a widespread pathogen, but the precise quantification of this subdominant gut microbe remains difficult due to its low fecal count (particularly in asymptoma...

    Authors: Ravinder Nagpal, Kiyohito Ogata, Hirokazu Tsuji, Kazunori Matsuda, Takuya Takahashi, Koji Nomoto, Yoshio Suzuki, Kazunari Kawashima, Satoru Nagata and Yuichiro Yamashiro

    Citation: BMC Microbiology 2015 15:219

    Content type: Research article

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  20. Chronic infection with Pseudomonas aeruginosa is a major cause of morbidity and mortality in cystic fibrosis (CF) patients, and a more complete understanding of P. aeruginosa within-host genomic evolution, transm...

    Authors: Rasmus Lykke Marvig, Daniela Dolce, Lea M. Sommer, Bent Petersen, Oana Ciofu, Silvia Campana, Søren Molin, Giovanni Taccetti and Helle Krogh Johansen

    Citation: BMC Microbiology 2015 15:218

    Content type: Research article

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  21. The application of molecular based diagnostics in sepsis has had limited success to date. Molecular community profiling methods have indicated that polymicrobial infections are more common than suggested by st...

    Authors: MMP Faria, JM Conly and MG Surette

    Citation: BMC Microbiology 2015 15:215

    Content type: Methodology article

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  22. Bacteria use transcriptional regulation to respond to environmental stresses. Specifically, exposure to antibacterial drugs is deemed to be an atypical stress, and altering transcriptional regulation in respon...

    Authors: Jialing Hu, Lei Zhao and Min Yang

    Citation: BMC Microbiology 2015 15:214

    Content type: Research article

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  23. The genus Brachyspira currently encompasses seven valid species that colonize the intestines of mammals and birds. In a previous study a group of strongly haemolytic isolates from pigs and mallards was provisiona...

    Authors: Mamoona Mushtaq, Saima Zubair, Therese Råsbäck, Erik Bongcam-Rudloff and Désirée S. Jansson

    Citation: BMC Microbiology 2015 15:208

    Content type: Research article

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  24. To screen whether E. coli strains encoding type 1 fimbriae, isolated from fecal microflora, produce bacteriocins more often relative to fimA-negative E. coli strains of similar origin.

    Authors: Barbora Štaudová, Lenka Micenková, Juraj Bosák, Kristýna Hrazdilová, Eva Slaninková, Martin Vrba, Alena Ševčíková, Darina Kohoutová, Vladana Woznicová, Jan Bureš and David Šmajs

    Citation: BMC Microbiology 2015 15:201

    Content type: Research article

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  25. Chlamydia (C.) trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness. Genetic approaches to investigate C....

    Authors: James W. Marsh, Bryan A. Wee, Joel D.A. Tyndall, William B. Lott, Robert J. Bastidas, Harlan D. Caldwell, Raphael H. Valdivia, L. Kari and Wilhelmina M. Huston

    Citation: BMC Microbiology 2015 15:194

    Content type: Research article

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  26. Flavobacterium psychrophilum is the etiologic agent of bacterial coldwater disease in salmonids. Earlier research showed that a rifampicin-passaged strain of F. psychrophilum (CSF 259-...

    Authors: Karol Gliniewicz, Mark Wildung, Lisa H. Orfe, Gregory D. Wiens, Kenneth D. Cain, Kevin K. Lahmers, Kevin R. Snekvik and Douglas R. Call

    Citation: BMC Microbiology 2015 15:179

    Content type: Research article

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  27. Mannheimia haemolytica is a commensal bacterium that resides in the upper respiratory tract of cattle that can play a role in bovine respiratory disease. Prophages are common in the M....

    Authors: Yan D. Niu, Shaun R. Cook, Jiaying Wang, Cassidy L. Klima, Yu-hung Hsu, Andrew M. Kropinski, Dann Turner and Tim A. McAllister

    Citation: BMC Microbiology 2015 15:175

    Content type: Research article

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  28. Classical bacteriological characteristics of Salmonella enterica indicate that the members of this species are unable to utilize lactose as a carbon source. However, lactose-fermenting (Lac+) strains of several S...

    Authors: Susan R. Leonard, David W. Lacher and Keith A. Lampel

    Citation: BMC Microbiology 2015 15:173

    Content type: Research article

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  29. Neisseria meningitidis is an inhabitant of the mucosal surfaces of the human nasopharynx. We recently demonstrated that the secreted meningococcal Two-partner secretion protein A (TpsA...

    Authors: Jesús Arenas, Vincent de Maat, Laura Catón, Massis Krekorian, Juan Cruz Herrero, Flavio Ferrara and Jan Tommassen

    Citation: BMC Microbiology 2015 15:156

    Content type: Research article

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  30. Almond witches’-broom (AlmWB), a devastating disease of almond, peach and nectarine in Lebanon, is associated with ‘Candidatus Phytoplasma phoenicium’. In the present study, we generated a draft genome sequence o...

    Authors: Fabio Quaglino, Michael Kube, Maan Jawhari, Yusuf Abou-Jawdah, Christin Siewert, Elia Choueiri, Hana Sobh, Paola Casati, Rosemarie Tedeschi, Marina Molino Lova, Alberto Alma and Piero Attilio Bianco

    Citation: BMC Microbiology 2015 15:148

    Content type: Research article

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  31. Pseudorabies virus is a widely-studied model organism of the Herpesviridae family, with a compact genome arrangement of 72 known coding sequences. In order to obtain an up-to-date genetic map of the virus, a comb...

    Authors: Péter Oláh, Dóra Tombácz, Nándor Póka, Zsolt Csabai, István Prazsák and Zsolt Boldogkői

    Citation: BMC Microbiology 2015 15:130

    Content type: Research article

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  32. Non-typeable H. influenzae (NTHi) is a nasopharyngeal commensal that can become an opportunistic pathogen causing infections such as otitis media, pneumonia, and bronchitis. NTHi is known to form biofilms. Resist...

    Authors: Deborah MB Post, Jason M Held, Margaret R Ketterer, Nancy J Phillips, Alexandria Sahu, Michael A Apicella and Bradford W Gibson

    Citation: BMC Microbiology 2014 14:329

    Content type: Research article

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  33. The human pathogen Vibrio cholerae normally enters the developmental program of natural competence for transformation after colonizing chitinous surfaces. Natural competence is regulated by at least three pathway...

    Authors: Mirella Lo Scrudato, Sandrine Borgeaud and Melanie Blokesch

    Citation: BMC Microbiology 2014 14:327

    Content type: Research article

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  34. Mesorhizobium alhagi CCNWXJ12-2 is a α-proteobacterium which could be able to fix nitrogen in the nodules formed with Alhagi sparsifolia in northwest of China. Desiccation and high salinity are the two major env...

    Authors: Xiaodong Liu, Yantao Luo, Osama Abdalla Mohamed, Dongying Liu and Gehong Wei

    Citation: BMC Microbiology 2014 14:319

    Content type: Research article

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  35. The Rhizobiaceae family of Gram-negative bacteria often engage in symbiosis with plants of economic importance. Historically, genetic studies to identify the function of individual genes, and characterize the bio...

    Authors: Benjamin J Perry and Christopher K Yost

    Citation: BMC Microbiology 2014 14:298

    Content type: Methodology article

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  36. Phenotypic data are routinely used to elucidate gene function in organisms amenable to genetic manipulation. However, previous to this work, there was no generalizable system in place for the structured storag...

    Authors: Marcus C Chibucos, Adrienne E Zweifel, Jonathan C Herrera, William Meza, Shabnam Eslamfam, Peter Uetz, Deborah A Siegele, James C Hu and Michelle G Giglio

    Citation: BMC Microbiology 2014 14:294

    Content type: Software

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  37. In recent years novel human respiratory disease agents have been described for Southeast Asia and Australia. The causative pathogens were classified as pteropine orthoreoviruses with a strong phylogenetic rela...

    Authors: Tingsong Hu, Wei Qiu, Biao He, Yan Zhang, Jing Yu, Xiu Liang, Wendong Zhang, Gang Chen, Yingguo Zhang, Yiyin Wang, Ying Zheng, Ziliang Feng, Yonghe Hu, Weiguo Zhou, Changchun Tu, Quanshui Fan…

    Citation: BMC Microbiology 2014 14:293

    Content type: Research article

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  38. The HilA protein is the master regulator of the Salmonella pathogenicity island 1 (SPI1). EilA and YgeH proteins show a moderate similarity to HilA and are encoded in pathogenicity islands from several E. coli st...

    Authors: Mário Hüttener, Manuela Dietrich, Sònia Paytubi and Antonio Juárez

    Citation: BMC Microbiology 2014 14:268

    Content type: Research article

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  39. Chromobacterium violaceum is a bacterium commonly found in tropical and subtropical regions and is associated with important pharmacological and industrial attributes such as producing substances with therapeuti...

    Authors: Daniel C Lima, Fbio T Duarte, Viviane KS Medeiros, Diogo B Lima, Paulo C Carvalho, Diego Bonatto and Silvia R Batistuzzo de Medeiros

    Citation: BMC Microbiology 2014 14:267

    Content type: Research article

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  40. Botrytis cinerea secretes a high number of proteins that are predicted to have numerous O-glycosylation sites, frequently grouped in highly O-glycosylated regions, and analysis of mutants affected in O-glycosyla...

    Authors: Mario González, Nélida Brito and Celedonio González

    Citation: BMC Microbiology 2014 14:254

    Content type: Research article

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  41. Sclerotinia sclerotiorum is a necrotrophic fungus that is pathogenic to many plants. Genomic analysis of its revealed transposable element expansion that has strongly influenced the evolutionary trajectory of se...

    Authors: Mateus F Santana, Jos C F Silva, Eduardo S G Mizubuti, Elza F Arajo and Marisa V Queiroz

    Citation: BMC Microbiology 2014 14:256

    Content type: Research article

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  42. Rhodococcus equi is an important pulmonary pathogen in foals and in immunocompromised individuals. Virulent R. equi strains carry an 80-90 kb virulence plasmid that expresses the virulence-associated protein A (...

    Authors: Tsutomu Kakuda, Takuya Hirota, Tatsuya Takeuchi, Hirofumi Hagiuda, Shiko Miyazaki and Shinji Takai

    Citation: BMC Microbiology 2014 14:243

    Content type: Research article

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  43. Aspergillus sojae has been an important filamentous fungus in Biotechnology due to its use in diverse fermentative processes for the production of various food products. Furthermore, this fungus is a common expr...

    Authors: Rodrigo Mora-Lugo, Judith Zimmermann, Amira M Rizk and Marcelo Fernandez-Lahore

    Citation: BMC Microbiology 2014 14:247

    Content type: Research article

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  44. Escherichia coli is the most predominant Gram-negative bacterial pathogen associated with neonatal meningitis. Previous studies indicated that the prototypic neonatal meningitis E. coli (NMEC) strain RS218 (O18:...

    Authors: Dona Saumya S Wijetunge, Kurundu Hewage Eranda M Karunathilake, Atul Chaudhari, Robab Katani, Edward G Dudley, Vivek Kapur, Chitrita DebRoy and Subhashinie Kariyawasam

    Citation: BMC Microbiology 2014 14:203

    Content type: Research article

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  45. The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate...

    Authors: Jessica L Linville, Miguel Rodriguez, Steven D Brown, Jonathan R Mielenz and Chris D Cox

    Citation: BMC Microbiology 2014 14:215

    Content type: Research article

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  46. The hapalindole-type family of natural products is a group of hybrid isoprenoid-indole alkaloids, produced solely by members of the Subsection V cyanobacterial strains. This family broadly includes the hapalindol...

    Authors: Melinda L Micallef, Deepti Sharma, Brittney M Bunn, Lena Gerwick, Rajesh Viswanathan and Michelle C Moffitt

    Citation: BMC Microbiology 2014 14:213

    Content type: Research article

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  47. Two-component systems have emerged as compelling targets for antibacterial drug design for a number of reasons including the distinct histidine phosphorylation property of their constituent sensor kinases. The...

    Authors: Kohinoor Kaur, Neetu Kumra Taneja, Sakshi Dhingra and Jaya S Tyagi

    Citation: BMC Microbiology 2014 14:195

    Content type: Research article

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