Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes.

abstract：BACKGROUND:Wolbachia, one of the most abundant taxa of intracellular Alphaproteobacteria, is widespread among arthropods and filarial nematodes. The presence of these maternally inherited bacteria is associated with modifications of host fitness, including a variety of reproductive abnormalities, such as cytoplasmic in...

journal_title：BMC microbiology

authors： Conte CA,Segura DF,Milla FH,Augustinos A,Cladera JL,Bourtzis K,Lanzavecchia SB

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:Nitric oxide (NO) is produced as part of the host immune response to bacterial infections, including urinary tract infections. The enzyme flavohemoglobin, coded by the hmp gene, is involved in protecting bacterial cells from the toxic effects of NO and represents a potentially interesting target for developm...

journal_title：BMC microbiology

authors： Bang CS,Kinnunen A,Karlsson M,Önnberg A,Söderquist B,Persson K

更新日期：2014-03-14 00:00:00

abstract：BACKGROUND:The Gifsy-I phage integrates into the Salmonella Typhimurium chromosome via an integrase mediated, site-specific recombination mechanism. Excision of the Gifsy-I phage requires three proteins, the Gifsy-I integrase (Int), the Gifsy-I excisionase (Xis) protein, and host encoded Integration Host Factor (IHF). ...

journal_title：BMC microbiology

authors： Flanigan A,Gardner J

更新日期：2008-11-17 00:00:00

abstract：BACKGROUND:Sigma factors are one of the components of RNA polymerase holoenzymes, and an essential factor of transcription initiation in bacteria. Corynebacterium glutamicum possesses seven genes coding for sigma factors, most of which have been studied to some detail; however, the role of SigD in transcriptional regul...

journal_title：BMC microbiology

authors： Taniguchi H,Busche T,Patschkowski T,Niehaus K,Pátek M,Kalinowski J,Wendisch VF

更新日期：2017-07-12 00:00:00

abstract：BACKGROUND:Burkholderia pseudomallei is the etiological agent of melioidosis and a CDC category B select agent with no available effective vaccine. Previous immunizations in mice have utilized the lipopolysaccharide (LPS) as a potential vaccine target because it is known as one of the most important antigenic epitopes ...

journal_title：BMC microbiology

authors： Stone JK,Mayo M,Grasso SA,Ginther JL,Warrington SD,Allender CJ,Doyle A,Georgia S,Kaestli M,Broomall SM,Karavis MA,Insalaco JM,Hubbard KS,McNew LA,Gibbons HS,Currie BJ,Keim P,Tuanyok A

更新日期：2012-11-05 00:00:00

abstract：BACKGROUND:Pseudomonas aeruginosa is the predominant pathogen associated with the decline of pulmonary function in cystic fibrosis (CF) patients. Both environment-to-host acquisition and patient-to-patient transmission have been described for P. aeruginosa infection. Epidemic clones and bacterial phenotypic adaptation ...

journal_title：BMC microbiology

authors： Cigana C,Melotti P,Baldan R,Pedretti E,Pintani E,Iansa P,De Fino I,Favari F,Bergamini G,Tridello G,Cirillo DM,Assael BM,Bragonzi A

更新日期：2016-07-11 00:00:00

abstract：BACKGROUND:Though important in the context of food microbiology and as potential pathogens in immuno-compromised humans, bacterial isolates belonging to the genus Pediococcus are best known for their association with contamination of ethanol fermentation processes (beer, wine, or fuel ethanol). Use of antimicrobial com...

journal_title：BMC microbiology

authors： Haakensen M,Vickers DM,Ziola B

更新日期：2009-09-07 00:00:00

abstract：BACKGROUND:Photorhabdus are Gram-negative nematode-symbiotic and insect-pathogenic bacteria. The species Photorhabdus asymbiotica is able to infect humans as well as insects. We investigated the secreted proteome of a clinical isolate of P. asymbiotica at different temperatures in order to identify proteins relevant to...

journal_title：BMC microbiology

authors： Jones RT,Sanchez-Contreras M,Vlisidou I,Amos MR,Yang G,Muñoz-Berbel X,Upadhyay A,Potter UJ,Joyce SA,Ciche TA,Jenkins AT,Bagby S,Ffrench-Constant RH,Waterfield NR

更新日期：2010-05-12 00:00:00

abstract：BACKGROUND:Rhodobacter sphaeroides 2.4.1 is a metabolically versatile organism that belongs to α-3 subdivision of Proteobacteria. The present study was to identify the extent, history, and role of gene duplications in R. sphaeroides 2.4.1, an organism that possesses two chromosomes. RESULTS:A protein similarity search...

journal_title：BMC microbiology

authors： Bavishi A,Lin L,Schroeder K,Peters A,Cho H,Choudhary M

更新日期：2010-12-30 00:00:00

abstract：BACKGROUND:Staphylococcus aureus is a food-borne pathogen and the most common cause of infections in hospitalized patients. The increase in the resistance of this pathogen to antibacterials has made necessary the development of new anti-staphylococcal agents. In this context, bacteriophage lytic enzymes such as endolys...

journal_title：BMC microbiology

authors： Rodríguez L,Martínez B,Zhou Y,Rodríguez A,Donovan DM,García P

更新日期：2011-06-17 00:00:00

abstract：BACKGROUND:The currently used genotyping system for the avian zoonotic pathogen Chlamydophila (C.) psittaci has evolved from serology and is based on ompA sequence variations. It includes seven avian and two non-avian genotypes. Restriction enzyme cleavage of the amplified ompA gene and, less frequently, ompA sequencin...

journal_title：BMC microbiology

authors： Sachse K,Laroucau K,Hotzel H,Schubert E,Ehricht R,Slickers P

更新日期：2008-04-17 00:00:00

abstract：BACKGROUND:Mycobacterium abscessus group includes antibiotic-resistant, opportunistic mycobacteria that are responsible for sporadic cases and outbreaks of cutaneous, pulmonary and disseminated infections. However, because of their close genetic relationships, accurate discrimination between the various strains of thes...

journal_title：BMC microbiology

authors： Sassi M,Ben Kahla I,Drancourt M

更新日期：2013-01-07 00:00:00

abstract：BACKGROUND:Lactobacillus plantarum, a versatile lactic acid-fermenting bacterium, isolated from the traditional pickles in Ningbo of China, was chosen for grass carp fermentation, which could also improve the flavor of grass carp. We here explored the central metabolic pathways of L. plantarum by using metabolomic appr...

journal_title：BMC microbiology

authors： Ming T,Han J,Li Y,Lu C,Qiu D,Li Y,Zhou J,Su X

更新日期：2018-12-18 00:00:00

abstract：BACKGROUND:The bacterial surface protein internalin (InlA) is a major virulence factor of the food-born pathogen Listeria monocytogenes. It plays a critical role in the bacteria crossing the host intestinal barrier by a species-specific interaction with the cell adhesion molecule E-cadherin. In mice, the interaction of...

journal_title：BMC microbiology

authors： Bergmann S,Beard PM,Pasche B,Lienenklaus S,Weiss S,Gahan CG,Schughart K,Lengeling A

更新日期：2013-04-23 00:00:00

abstract：BACKGROUND:Chlamydia pneumoniae is a common human pathogen that is associated with upper and lower respiratory tract infections. It has also been suggested that C. pneumoniae infection can trigger or promote a number of chronic inflammatory conditions, including asthma and atherosclerosis. Several strains of C. pneumon...

journal_title：BMC microbiology

authors： He X,Liang Y,LaValley MP,Lai J,Ingalls RR

更新日期：2015-10-23 00:00:00

abstract：BACKGROUND:Leptospires lack many of the homologs for oxidative defense present in other bacteria, but do encode homologs of the Bacteriodes aerotolerance (Bat) proteins, which have been proposed to fulfill this function. Bat homologs have been identified in all families of the phylum Spirochaetes, yet a specific functi...

journal_title：BMC microbiology

authors： Stewart PE,Carroll JA,Dorward DW,Stone HH,Sarkar A,Picardeau M,Rosa PA

更新日期：2012-12-13 00:00:00

abstract：BACKGROUND:With the growing demand for fossil fuels and the severe energy crisis, lignocellulose is widely regarded as a promising cost-effective renewable resource for ethanol production, and the use of lignocellulose residues as raw material is remarkable. Polar organisms have important value in scientific research a...

journal_title：BMC microbiology

authors： Cong B,Wang N,Liu S,Liu F,Yin X,Shen J

更新日期：2017-05-30 00:00:00

abstract：BACKGROUND:Hypervirulent K. pneumoniae (hvKp) causes severe community acquired infections, predominantly in Asia. Though initially isolated from liver abscesses, they are now prevalent among invasive infections such as bacteraemia. There have been no studies reported till date on the prevalence and characterisation of ...

journal_title：BMC microbiology

authors： Shankar C,Veeraraghavan B,Nabarro LEB,Ravi R,Ragupathi NKD,Rupali P

更新日期：2018-01-08 00:00:00

abstract：BACKGROUND:Although the most widely accepted mechanism of action for polymyxins is related to bacterial lysis via disruption, we hypothesized that this antimicrobial drug class could have other effects on Pseudomonas aeruginosa planktonic and sessile cells. Little is known regarding oxidative burst and zeta potential (...

journal_title：BMC microbiology

authors： Lima MR,Ferreira GF,Nunes Neto WR,Monteiro JM,Santos ÁRC,Tavares PB,Denadai ÂML,Bomfim MRQ,Dos Santos VL,Marques SG,de Souza Monteiro A

更新日期：2019-05-29 00:00:00

abstract：BACKGROUND:Streptococcus canis is an important opportunistic pathogen of dogs and cats that can also infect a wide range of additional mammals including cows where it can cause mastitis. It is also an emerging human pathogen. RESULTS:Here we provide characterization of the first genome sequence for this species, strai...

journal_title：BMC microbiology

authors： Richards VP,Zadoks RN,Pavinski Bitar PD,Lefébure T,Lang P,Werner B,Tikofsky L,Moroni P,Stanhope MJ

更新日期：2012-12-18 00:00:00

abstract：BACKGROUND:The KdpD/KdpE two-component system of Escherichia coli regulates expression of the kdpFABC operon encoding the high affinity K+ transport system KdpFABC. The input domain of KdpD comprises a domain that belongs to the family of universal stress proteins (Usp). It has been previously demonstrated that UspC bi...

journal_title：BMC microbiology

authors： Heermann R,Lippert ML,Jung K

更新日期：2009-07-09 00:00:00

abstract：BACKGROUND:The aminoglycoside antibiotic gentamicin was supposed to induce a crosstalk between the Cpx- and the Arc-two-component systems (TCS). Here, we investigated the physical interaction of the respective TCS components and compared the results with their respective gene expression and protein abundance. The findi...

journal_title：BMC microbiology

authors： Ćudić E,Surmann K,Panasia G,Hammer E,Hunke S

更新日期：2017-09-18 00:00:00

abstract：BACKGROUND:Coxiella burnetii is a Gram-negative intracellular bacterial pathogen that replicates within a phagolysosome-like parasitophorous vacuole (PV) of macrophages. PV formation requires delivery of effector proteins directly into the host cell cytoplasm by a type IVB secretion system. However, additional secretio...

journal_title：BMC microbiology

authors： Stead CM,Omsland A,Beare PA,Sandoz KM,Heinzen RA

更新日期：2013-10-05 00:00:00

abstract：BACKGROUND:The evolution of mycoplasmas from a common ancestor with Firmicutes has been characterized not only by genome down-sizing but also by horizontal gene transfer between mycoplasma species sharing a common host. The mechanisms of these gene transfers remain unclear because our knowledge of the mycoplasma mobile...

journal_title：BMC microbiology

authors： Breton M,Tardy F,Dordet-Frisoni E,Sagne E,Mick V,Renaudin J,Sirand-Pugnet P,Citti C,Blanchard A

更新日期：2012-11-12 00:00:00

abstract：BACKGROUND:Similar to Gram-negative bacteria, the outer membrane (OM) of the pathogenic spirochete, Borrelia burgdorferi, contains integral OM-spanning proteins (OMPs), as well as membrane-anchored lipoproteins. Although the mechanism of OMP biogenesis is still not well-understood, recent studies have indicated that a ...

journal_title：BMC microbiology

authors： Lenhart TR,Kenedy MR,Yang X,Pal U,Akins DR

更新日期：2012-04-20 00:00:00

abstract：BACKGROUND:Brucellosis is an important zoonosis caused by the genus Brucella. In addition Brucella represents potential biological warfare agents due to the high contagious rates for humans and animals. Therefore, the strain typing epidemiological tool may be crucial for tracing back source of infection in outbreaks an...

journal_title：BMC microbiology

authors： De Santis R,Ciammaruconi A,Faggioni G,D'Amelio R,Marianelli C,Lista F

更新日期：2009-04-07 00:00:00

abstract：ERRATUM:Upon publication of the original article (1) it was highlighted by the authors that a grant awarded to support the research work of the study was missed in the acknowledgements. It should also be acknowledged that the grant titled "Genotyping and Molecular Epidemiological Characteristic of Bacillus anthracis in...

journal_title：BMC microbiology

authors： Li S,Ma Q,Chen H,Wang D,Liu Y,Wei X,You L,Yao G,Tian K,Tang G

更新日期：2018-04-12 00:00:00

abstract：BACKGROUND:Bovine tuberculosis (bTB) caused by Mycobacterium bovis is the most serious endemic disease affecting livestock in the UK. The European badger (Meles meles) is the most important wildlife reservoir of bTB transmission to cattle, making eradication particularly difficult. In this respect, oral vaccination wit...

journal_title：BMC microbiology

authors： Stedman A,Maluquer de Motes C,Lesellier S,Dalley D,Chambers M,Gutierrez-Merino J

更新日期：2018-07-13 00:00:00

abstract：BACKGROUND:Salmonella enterica serovar Typhimurium (Typhimurium) is an important pathogen that infects a broad range of hosts. In humans, Typhimurium causes a gastroenteritis characterized by vomiting, diarrhea, and abdominal pains. Typhimurium infection occurs mainly through the ingestion of contaminated food includin...

journal_title：BMC microbiology

authors： Dieye Y,Ameiss K,Mellata M,Curtiss R 3rd

更新日期：2009-01-06 00:00:00

abstract：BACKGROUND:Staphylococcus aureus is an opportunistic commensal bacterium that mostly colonizes the skin and soft tissues. The pathogenicity of S. aureus is due to both its ability to resist antibiotics, and the production of toxins. Here, we characterize a group of genes responsible for toxin production and antibiotic ...

journal_title：BMC microbiology

authors： Sina H,Ahoyo TA,Moussaoui W,Keller D,Bankolé HS,Barogui Y,Stienstra Y,Kotchoni SO,Prévost G,Baba-Moussa L

更新日期：2013-08-08 00:00:00