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Integrated functional visualization of eukaryotic genomes
Rohit Ghai, Hannes Lindemann, Trinad Chakraborty
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-348
Abstract: STRIPE and GFFtool (General Feature Format Tool) are softwares designed to support integration, visualization and exploration of whole genome data from eukaryotic genomes. STRIPE, in addition to providing a highly customizable and interactive data plot, provides access to numerous well-selected databases with updated information on all genes of a genome. GFFtool provides a user-friendly solution to integrating experimental data with the genomic information available in public databases. They also obviate the need for users to maintain large annotation resources, as they link to well-known resources using standard gene and protein identifiers.The programs provide the user with broad genomic overviews of data distribution, fast access to data of interest, and the ability to navigate speedily from one resource to another, and gain a better understanding of result of whole genome analysis experiments.The continuously growing availability of genomic information exercises pressure on the systems used to capture it and on users concerned with its interpretation. Analysis of large scale genomic data is a demanding task, requiring extensive input from diverse sources of biological significance, statistical methodologies and data exchange standards. To answer interesting biological questions, biologists need accessible interfaces that enable convenient visualization of information, searching multiple databases and flexible maneuvering within the data. When confronted with the lists of significantly differentially expressed genes from the microarray experiments performed, it is important to get a feel for the genome-wide distribution of the data and to be able to quickly navigate between diverse sources of information. Visualization on a genomic scale is also helpful in identifying and representing clusters of genes that are co-regulated and map close to each other in the genome. There are several examples of regions in the genome where genes implicated in the same biological
GenomeViz: visualizing microbial genomes
Rohit Ghai, Torsten Hain, Trinad Chakraborty
BMC Bioinformatics , 2004, DOI: 10.1186/1471-2105-5-198
Abstract: Here we describe a program that allows visualization of both qualitative and quantitative information from complete and partially sequenced microbial genomes. Using GenomeViz, data deriving from studies on genomic islands, gene/protein classifications, GC content, GC skew, whole genome alignments, microarrays and proteomics may be plotted. Several genomes can be visualized interactively at the same time from a comparative genomic perspective and publication quality circular genome plots can be created.GenomeViz should allow researchers to perform visualization and comparative analysis of up to eight different microbial genomes simultaneously.Current efforts in genome sequencing have led to a rapid increase in the number of microbial genome sequences. A total of 522 ongoing microbial genome projects are listed in the GOLD database [1] and while 167 microbes have been completely sequenced. These sequencing projects now include several bacterial pathogens and different isolates of the same bacterial species that differ with respect to virulence and physiology. Thus, complete and partial genome sequences of a number of closely related species/strains from various genera such as Escherichia, Bacillus, Helicobacter, Mycobacterium, Streptococcus, Staphylococcus and Listeria are available. Genomic data too, is diverse, ranging from COG functional classification data [2], genomic islands [3,4], expression data from microarrays and proteomics, GC skew, AT skew, GC%, to whole genome alignments. Such rapid increase in genomic information necessitates the development of tools that offer rapid and convenient visualization capabilities. Furthermore, it is important to contrast and compare data deriving from several different sources (computational, genomic, proteomic) to have a better understanding of genome function.Several genome visualization tools have been developed in the last few years. The Microbial Genomes Viewer [5] offers a good online solution to genomic visualization,
Protective Immunity to Listeria Monocytogenes Infection Mediated by Recombinant Listeria innocua Harboring the VGC Locus
Walid Mohamed, Shneh Sethi, Svetlin Tchatalbachev, Ayub Darji, Trinad Chakraborty
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035503
Abstract: In this study we propose a novel bacterial vaccine strategy where non-pathogenic bacteria are complemented with traits desirable for the induction of protective immunity. To illustrate the proof of principle of this novel vaccination strategy, we use the model organism of intracellular immunity Listeria. We introduced a, low copy number BAC-plasmid harbouring the virulence gene cluster (vgc) of L. monocytogenes (Lm) into the non-pathogenic L. innocua (L.inn) strain and examined for its ability to induce protective cellular immunity. The resulting strain (L.inn::vgc) was attenuated for virulence in vivo and showed a strongly reduced host detrimental inflammatory response compared to Lm. Like Lm, L.inn::vgc induced the production of Type I Interferon's and protection was mediated by Listeria-specific CD8+ T cells. Rational vaccine design whereby avirulent strains are equipped with the capabilities to induce protection but lack detrimental inflammatory effects offer great promise towards future studies using non-pathogenic bacteria as vectors for vaccination.
Erythema caused by a localised skin infection with Arthrobacter mysorens
Can Imirzalioglu, Torsten Hain, Hamid Hossain, Trinad Chakraborty, Eugen Domann
BMC Infectious Diseases , 2010, DOI: 10.1186/1471-2334-10-352
Abstract: Here we report a case of an erythema resembling the erythema migrans manifestation of Lyme disease, but with atypical symptoms like persistent pruritus. The patient had no history of a recent tick-bite but displayed a positive serology for an advanced stage of Lyme borreliosis, which stood in contrast to the clinical manifestation of erythema migrans as a symptom of early Lyme disease. Three skin swabs and soil samples, collected in the area where the patient possibly acquired the infection, were examined by bacterial and fungal culture methods. Microorganisms were identified by using 16 S rRNA gene sequencing and bioinformatics. The patient and soil isolates were compared by employing RAPD analysis. The serum samples of the patient were examined by immunoblotting. Arthrobacter mysorens, a soil bacterium, was isolated from the collected skin and soil samples. The identity of both isolates was determined by molecular fingerprinting methods. A. mysorens was proven to be causative for the erythema by direct isolation from the affected skin and a positive serology, thus explaining the atypical appearance of the erythema compared to erythema migrans caused by Borrelia infection.Infections with A.mysorens might be underreported and microbiological diagnostic techniques should be applied in cases of patients with unclear erythemas, resembling erythema migrans, without a history of tick bites.Skin erythemas of unknown origin are a frequent reason for consulting the general practitioner or dermatologist. Among many clinicians, laminary spreading erythemas often lead to the diagnosis of a tick bite-associated erythema migrans (EM), a symptom of early localized infection with Borrelia burgdorferi (sensu lato) [1,2]. As the development of an immunologic response to this infection usually takes 4 to 6 weeks and the incubation period for EM is typically 7 to 14 days, early Lyme borreliosis often presents itself with a negative serology [3,4]. In addition, tick bites are not alway
Gram-positive pathogenic bacteria induce a common early response in human monocytes
Svetlin Tchatalbachev, Rohit Ghai, Hamid Hossain, Trinad Chakraborty
BMC Microbiology , 2010, DOI: 10.1186/1471-2180-10-275
Abstract: Activation of monocytes was demonstrated by the upregulation of chemokine rather than interleukin genes except for the prominent expression of interleukin 23, marking it as the early lead cytokine. This activation was accompanied by cytoskeleton rearrangement signals and a general anti-oxidative stress and anti-apoptotic reaction. Remarkably, the expression profiles also provide evidence that monocytes participate in the regulation of angiogenesis and endothelial function in response to these pathogens.Regardless of the invasion properties and survival mechanisms of the pathogens used, we found that the early response comprised of a consistent and common response. The common response was hallmarked by the upregulation of interleukin 23, a rather unexpected finding regarding Listeria infection, as this cytokine has been linked primarily to the control of extracellular bacterial dissemination.The percentage of patients with severe infections caused by gram-positive bacteria has increased in recent years, accounting for almost half of the incidents of septicemia and severe systemic infections [1-5]. A number of recent publications have investigated the transcriptional response to killed or inactive gram-positive pathogens, or the contribution of gram-positive cell wall constituents such as peptidoglycan (PepG), lipopeptide (LP) and lipoteichoic acid (LTA) to the triggering of specific host defense responses [6-10]. Though such studies are crucial for identifying stimulus specific effects, they are unable to account for the immunomodulatory effects of live bacteria, which frequently employ multiple survival strategies in parallel. Viable pathogenic bacteria secrete active components in the intercellular space and in the invaded cells in order to modulate the cellular response. In order to track the early events of gram-positive induced immune activation, we examined the total transcriptional response of isolated peripheral human CD14+/CD11b+ monocytes, infected with the
Comparative Analysis of Plasmids in the Genus Listeria
Carsten Kuenne,Sonja Voget,Jordan Pischimarov,Sebastian Oehm,Alexander Goesmann,Rolf Daniel,Torsten Hain,Trinad Chakraborty
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0012511
Abstract: We sequenced four plasmids of the genus Listeria, including two novel plasmids from L. monocytogenes serotype 1/2c and 7 strains as well as one from the species L. grayi. A comparative analysis in conjunction with 10 published Listeria plasmids revealed a common evolutionary background.
microRNA Response to Listeria monocytogenes Infection in Epithelial Cells
Benjamin Izar,Gopala Krishna Mannala,Mobarak Abu Mraheil,Trinad Chakraborty,Torsten Hain
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms13011173
Abstract: microRNAs represent a family of very small non-coding RNAs that control several physiologic and pathologic processes, including host immune response and cancer by antagonizing a number of target mRNAs. There is limited knowledge about cell expression and the regulatory role of microRNAs following bacterial infections. We?investigated whether infection with a Gram-positive bacterium leads to altered expression of microRNAs involved in the host cell response in epithelial cells. Caco-2 cells were infected with Listeria monocytogenes EGD-e, a mutant strain (? inlAB or ? hly) or incubated with purified listeriolysin (LLO). Total RNA was isolated and microRNA and target gene expression was compared to the expression in non-infected cells using microRNA microarrays and qRT-PCR. We identified and validated five microRNAs (miR-146b, miR-16, let-7a1, miR-145 and miR-155) that were significantly deregulated following listerial infection. We show that expression patterns of particular microRNAs strongly depend on pathogen localization and the presence of bacterial effector proteins. Strikingly, miR-155 which was shown to have an important role in inflammatory responses during infection was induced by wild-type bacteria, by LLO-deficient bacteria and following incubation with purified LLO. It was downregulated following ? inlAB infection indicating a new potent role for internalins in listerial pathogenicity and miRNA regulation. Concurrently, we observed differences in target transcript expression of the investigated miRNAs. We provide first evidence that L. monocytogenes infection leads to deregulation of a set of microRNAs with important roles in host response. Distinct microRNA expression depends on both LLO and pathogen localization.
Prevalence of multiresistant gram-negative organisms in a tertiary hospital in Mwanza, Tanzania
Stephen E Mshana, Erasmus Kamugisha, Mariam Mirambo, Trinad Chakraborty, Eligius F Lyamuya
BMC Research Notes , 2009, DOI: 10.1186/1756-0500-2-49
Abstract: A total of 800 clinical samples (urine, wound swab, pus, blood, aspirate, sputum etc) were processed over a period of 6 months. Gram-negative bacteria were identified using conventional in-house biochemical tests and susceptibility to common antibiotics done using disc diffusion methods. The disc approximation method was used to identify ESBL producers.A total of 377 Gram-negative bacteria (GNB) recovered from 377 clinical specimens were analyzed of which 76.9% were Enterobacteriaceae. Among all GNB, 110/377 (29.2%) were found to be ESBL producers. Species specific ESBLs rate among Klebsiella pneumoniae, Escherichia coli, Acinetobacter spp, Proteus spp and other enterobacteria were 63.7%, 24.4%, 17.7%, 6.4% and 27.9% respectively. A statistically significant higher number of inpatients 100/283 (35.3%) compared to 10/94 (10.6%) of outpatients had ESBL-producing organisms (p = 0.000023). Rates of resistances to gentamicin, tetracycline, sulphamethaxazole/trimethoprim and ciprofloxacin were significantly higher among ESBLs isolates than non-ESBL isolates (p = 0.000001).ESBL producing organisms are common at BMC (Bugando Medical Center) and pose a challenge to antibiotic therapy. Successful implementation of a routine detection of ESBL production is essential in designing appropriate antibiotic prescribing policies and infection control intervention programmes.Antimicrobial resistance among enteric Gram negative bacteria is fast becoming a global public health concern with rapid increase in multidrug resistant organisms [1]. Gram negative bacteria (GNB) are a common cause of urinary tract infections, neonatal sepsis and post surgical infections in hospitalized patients [1,2]. Resistance of Enterobacteriaceae to broad spectrum β-lactam antibiotics via ESBL production is an increasing problem worldwide [2].The prevalence of ESBL producing clinical isolates is more than 20% in Asia and South Africa [3]. ESBLs have been found in 30 to 60% of klebsiellae from intensive care
Conjugative IncFI plasmids carrying CTX-M-15 among Escherichia coli ESBL producing isolates at a University hospital in Germany
Stephen E Mshana, Can Imirzalioglu, Hamid Hossain, Torsten Hain, Eugen Domann, Trinad Chakraborty
BMC Infectious Diseases , 2009, DOI: 10.1186/1471-2334-9-97
Abstract: We analysed 63 non-duplicate clinical ESBL isolates obtained over an 8-month period using PCR and sequence-based ESBL allele typing, plasmid replicon typing, phylogenetic group typing. Pulsed-field gel electrophoresis (PFGE) based genotyping and plasmid profiling was performed, as well as confirmatory DNA-based hybridization assays.Examination of the 63 Escherichia coli isolates revealed an almost equal distribution among the E. coli phylogenetic groups A, B1, B2 and D. High prevalence (36/63) of the CTX-M-15 gene was observed and an analysis of PFGE-based patterns revealed the presence of this CTX-M allele in multiple clones. Resistance to cefotaxime was a transferable trait and a commonly occurring 145.5 kb conjugative IncFI plasmid was detected in 65% of E. coli carrying the CTX-M-15 allele. The rate of transferable antibiotic resistances for GM, SXT, TET, GM-SXT-TET, SXT-TET and GM-TET was 33%, 61%, 61%, 27%, 44% and 11%, respectively. The remaining strains did not have a common IncFI plasmid but harboured transferable IncFI plasmids with sizes that ranged from 97 to 242.5 kb.Our data demonstrate the presence of IncFI plasmids within the prevailing E. coli population in a hospital setting and suggest that the dissemination of CTX-M-15 allele is associated to lateral transfer of these well-adapted, conjugative IncFI plasmids among various E. coli genotypes.Emergence of resistance to β-lactam antibiotics was described even before the first β-lactam penicillin was developed. The first β-lactamase was identified in E. coli prior to the use of penicillin in medical practice [1]. In 1983, a Klebsiella ozaenae isolate from Germany was found to secrete a SHV-2 β-lactamase which efficiently hydrolyzed cefotaxime and to a lesser extent ceftazidime [2]. Many ESBL-producing enterobacterial isolates express enzyme variants that are derived from TEM-1 and SHV-1 by mutations. Recently, different types of ESBL such as CTX-M have been detected. These enzymes hydrolyze cefepime w
Necrosis Is the Dominant Cell Death Pathway in Uropathogenic Escherichia coli Elicited Epididymo-Orchitis and Is Responsible for Damage of Rat Testis
Yongning Lu, Sudhanshu Bhushan, Svetlin Tchatalbachev, Marcelo Marconi, Martin Bergmann, Wolfgang Weidner, Trinad Chakraborty, Andreas Meinhardt
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0052919
Abstract: Male infertility is a frequent medical condition, compromising approximately one in twenty men, with infections of the reproductive tract constituting a major etiological factor. Bacterial epididymo-orchitis results in acute inflammation most often caused by ascending canalicular infections from the urethra via the continuous male excurrent ductal system. Uropathogenic Escherichia coli (UPEC) represent a relevant pathogen in urogenital tract infections. To explore how bacteria can cause damage and cell loss and thus impair fertility, an in vivo epididymo-orchitis model was employed in rats by injecting UPEC strain CFT073 into the vas deference in close proximity to the epididymis. Seven days post infection bacteria were found predominantly in the testicular interstitial space. UPEC infection resulted in severe impairment of spermatogenesis by germ cell loss, damage of testicular somatic cells, a decrease in sperm numbers and a significant increase in TUNEL (+) cells. Activation of caspase-8 (extrinsic apoptotic pathway), caspase-3/?6 (intrinsic apoptotic pathway), caspase-1 (pyroptosis pathway) and the presence of 180 bp DNA fragments, all of which serve as indicators of the classical apoptotic pathway, were not observed in infected testis. Notably, electron microscopical examination revealed degenerative features of Sertoli cells (SC) in UPEC infected testis. Furthermore, the passive release of high mobility group protein B1 (HMGB1), as an indication of necrosis, was observed in vivo in infected testis. Thus, necrosis appears to be the dominant cell death pathway in UPEC infected testis. Substantial necrotic changes seen in Sertoli cells will contribute to impaired spermatogenesis by loss of function in supporting the dependent germ cells.
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