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Find video protocols related to scientific articles indexed in Pubmed.
C. pseudotuberculosis Phop confers virulence and may be targeted by natural compounds.
Integr Biol (Camb)
PUBLISHED: 09-13-2014
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The bacterial two-component system (TCS) regulates genes that are crucial for virulence in several pathogens. One of such TCS, the PhoPR system, consisting of a transmembrane sensory histidine kinase protein (PhoR) and an intracellular response regulator protein (PhoP), has been reported to have a major role in mycobacterial pathogenesis. We knocked out the phoP in C. pseudotuberculosis, the causal organism of caseous lymphadenitis (CLA), and using a combination of in vitro and in vivo mouse system, we showed for the first time, that the PhoP of C. pseudotuberculosis plays an important role in the virulence and pathogenicity of this bacterium. Furthermore, we modeled the PhoP of C. pseudotuberculosis and our docking results showed that several natural compounds including Rhein, an anthraquinone from Rheum undulatum, and some drug-like molecules may target PhoP to inhibit the TCS of C. pseudotuberculosis, and therefore may facilitate a remarkable attenuation of bacterial pathogenicity being the CLA. Experiments are currently underway to validate these in silico docking results.
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An improved interolog mapping-based computational prediction of protein-protein interactions with increased network coverage.
Integr Biol (Camb)
PUBLISHED: 09-12-2014
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Automated and efficient methods that map ortholog interactions from several organisms and public databases (pDB) are needed to identify new interactions in an organism of interest (interolog mapping). When computational methods are applied to predict interactions, it is important that these methods be validated and their efficiency proven. In this study, we compare six Blast+ metrics over three datasets to identify the best metric for protein-protein interaction predictions. Using Blast+ to align the protein pairs, the ortholog interactions from DIP were mapped to String, Intact and Psibase pDBs. For each interaction mapped to each pDBs, we retrieved the alignment score, e-value, bitscore, similarity, identity and coverage. We evaluated these Blast+ values, and combinations thereof, with the Receiver Operating Characteristic (ROC) curves and computed the Area Under Curve (AUC). To validate these predictions, we used a subset of the Database of Interacting Proteins (DIP) composed of experimental interactions curated by the International Molecular Exchange (IMEx). The cut-off point for each metric/pDB was computed aiming to identify the best one that separates the true and false predicted interactions. In contrast to other methods that only compute the first Blast hit, we considered the first 20 hits, thus increasing the number of predicted interaction pairs. In addition, we identified the contribution of each individual pDB, as well as their combined contribution to the prediction. The best metric had an AUC of 0.96 for a single pDB and AUC of 0.93 for combined pDBs. Compared to other studies, with a cut-off point of 0.70 representing a specificity of 0.95 and a sensitivity of 0.90 for individual pDB, our method efficiently predicts protein-protein interactions.
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Antioxidant, total phenolic contents and antinociceptive potential of Teucrium stocksianum methanolic extract in different animal models.
BMC Complement Altern Med
PUBLISHED: 05-20-2014
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Oxidative stress and analgesia are connected with different pathological conditions. The drug candidates from synthetic sources are associated with various side effects; therefore, researchers are giving priority to find novel, effective and safe phytomedicines. Teucrium species possesses antioxidant, analgesic, anti-inflammatory and hepatoprotective activities. The essential oils of Teucrium stocksianum have shown strong antinociceptive potential. Our current study is designed to embark total phenolic content (TPC), antioxidant and antinociceptive potential of the methanolic extract of Teucrium stocksianum (METS).
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A five years old girl child with takayasu arteritis.
J Coll Physicians Surg Pak
PUBLISHED: 12-06-2013
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Takayasu arteritis is a systemic vasulitis of large vessels that mainly involves the aorta and its branches. It normally presents in third decade of life and has rarely been reported in children under 10 years of age. We report here a case of Takayasu arteritis in a 5 years old girl who presented with headache, generalized body swelling, severe hypertension, proteinuria and minimal functioning kidneys. Conventional angiography demonstrated narrowing of descending aorta, right subclavian artery and right common iliac artery. She responded steroids, diuretics, antiplatelets and digoxin and discharged home on maintenance therapy.
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Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks.
Stand Genomic Sci
PUBLISHED: 06-15-2013
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Streptococcus agalactiae (Lancefield group B; GBS) is the causative agent of meningoencephalitis in fish, mastitis in cows, and neonatal sepsis in humans. Meningoencephalitis is a major health problem for tilapia farming and is responsible for high economic losses worldwide. Despite its importance, the genomic characteristics and the main molecular mechanisms involved in virulence of S. agalactiae isolated from fish are still poorly understood. Here, we present the genomic features of the 1,820,886 bp long complete genome sequence of S. agalactiae SA20-06 isolated from a meningoencephalitis outbreak in Nile tilapia (Oreochromis niloticus) from Brazil, and its annotation, consisting of 1,710 protein-coding genes (excluding pseudogenes), 7 rRNA operons, 79 tRNA genes and 62 pseudogenes.
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Exoproteome and secretome derived broad spectrum novel drug and vaccine candidates in Vibrio cholerae targeted by Piper betel derived compounds.
PLoS ONE
PUBLISHED: 01-30-2013
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Vibrio cholerae is the causal organism of the cholera epidemic, which is mostly prevalent in developing and underdeveloped countries. However, incidences of cholera in developed countries are also alarming. Because of the emergence of new drug-resistant strains, even though several generic drugs and vaccines have been developed over time, Vibrio infections remain a global health problem that appeals for the development of novel drugs and vaccines against the pathogen. Here, applying comparative proteomic and reverse vaccinology approaches to the exoproteome and secretome of the pathogen, we have identified three candidate targets (ompU, uppP and yajC) for most of the pathogenic Vibrio strains. Two targets (uppP and yajC) are novel to Vibrio, and two targets (uppP and ompU) can be used to develop both drugs and vaccines (dual targets) against broad spectrum Vibrio serotypes. Using our novel computational approach, we have identified three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from our identified two dual targets. These two targets were modeled and subjected to virtual screening against natural compounds derived from Piper betel. Seven compounds were identified first time from Piper betel to be highly effective to render the function of these targets to identify them as emerging potential drugs against Vibrio. Our preliminary validation suggests that these identified peptide vaccines and betel compounds are highly effective against Vibrio cholerae. Currently we are exhaustively validating these targets, candidate peptide vaccines, and betel derived lead compounds against a number of Vibrio species.
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Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by Piper b
Integr Biol (Camb)
PUBLISHED: 01-05-2013
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Although attempts have been made to unveil protein-protein and host-pathogen interactions based on molecular insights of important biological events and pathogenesis in various organisms, these efforts have not yet been reported in Corynebacterium pseudotuberculosis (Cp), the causative agent of Caseous Lymphadenitis (CLA). In this study, we used computational approaches to develop common conserved intra-species protein-protein interaction (PPI) networks first time for four Cp strains (Cp FRC41, Cp 316, Cp 3/99-5, and Cp P54B96) followed by development of a common conserved inter-species bacterial PPI using conserved proteins in multiple pathogens (Y. pestis, M. tuberculosis, C. diphtheriae, C. ulcerans, E. coli, and all four Cp strains) and E. Coli based experimentally validated PPI data. Furthermore, the interacting proteins in the common conserved inter-species bacterial PPI were used to generate a conserved host-pathogen interaction (HP-PPI) network considering human, goat, sheep, bovine, and horse as hosts. The HP-PPI network was validated, and acetate kinase (Ack) was identified as a novel broad spectrum target. Ceftiofur, penicillin, and two natural compounds derived from Piper betel were predicted to inhibit Ack activity. One of these Piper betel compounds found to inhibit E. coli O157:H7 growth similar to penicillin. The target specificity of these betel compounds, their effects on other studied pathogens, and other in silico results are currently being validated and the results are promising.
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Parents opinion of quality of life (QOL) in Pakistani thalassaemic children.
J Pak Med Assoc
PUBLISHED: 12-30-2011
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To find out the physical, social, psychological life aspects and overall quality of life among thalassaemic children in Pakistan.
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Incidence of methicillin resistant Staphylococcus aureus in Peshawar.
J Ayub Med Coll Abbottabad
PUBLISHED: 01-01-2011
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There is considerable variation in the percentage of isolates of methicillin resistant Staphylococcus aureus (MRSA). There are several mechanisms for methicillin resistance. The most important is low affinity of penicillin binding proteins for beta-lactam antibiotics. The objectives of this study were to establish the pattern of MRSA incidence in Peshawar in recent years, and to identify high risk groups for acquiring infection amongst the city population.
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Concepts of homeopathy among general population in Karachi, Pakistan.
J Pak Med Assoc
PUBLISHED: 08-24-2010
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To explore the characteristics of patients and their gender influences concerning the use of homeopathic medicine, visiting both homeopathic and conventional medicine (allopathic) clinics.
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Knowledge and practices among the general practitioners of Karachi regarding dog bite management.
J Pak Med Assoc
PUBLISHED: 07-21-2009
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To find out the knowledge and practices among the general practitioners (GPs) of Karachi regarding dog bite management.
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Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation sequencing technology.
Stand Genomic Sci
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The Actinobacteria, Corynebacterium pseudotuberculosis strain P54B96, a nonmotile, non-sporulating and a mesophile bacterium, was isolated from liver, lung and mediastinal lymph node lesions in an antelope from South Africa. This strain is interesting in the sense that it has been found together with non-tuberculous mycobacteria (NTMs) which could nevertheless play a role in the lesion formation. In this work, we describe a set of features of C. pseudotuberculosis P54B96, together with the details of the complete genome sequence and annotation. The genome comprises of 2.34 Mbp long, single circular genome with 2,084 protein-coding genes, 12 rRNA, 49 tRNA and 62 pseudogenes and a G+C content of 52.19%. The analysis of the genome sequence provides means to better understanding the molecular and genetic basis of virulence of this bacterium, enabling a detailed investigation of its pathogenesis.
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Analysis of chemical constituents and antinociceptive potential of essential oil of Teucrium Stocksianum bioss collected from the North West of Pakistan.
BMC Complement Altern Med
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Medicinal plants are used for the treatment of different diseases in almost all cultures. Teucrium species grow wildly at different geographical locations around the world. Teucrium stocksianum is used in folk medicine for the treatment of diarrhea, cough, jaundice and abdominal pain. Scientific study on Teucrium stocksianum shows that it possesses anthelmintic, cytotoxic and antispasmodic activity. The aim of our present study is to identify the chemical composition and antinociceptive potential of the essential oil extracted from Teucrium stocksianum bioss.
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Genome sequence of Exiguobacterium antarcticum B7, isolated from a biofilm in Ginger Lake, King George Island, Antarctica.
J. Bacteriol.
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Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus Exiguobacterium are extremophiles and have properties of biotechnological interest, e.g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of E. antarcticum B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.
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Whole-genome sequence of Corynebacterium pseudotuberculosis strain Cp162, isolated from camel.
J. Bacteriol.
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Corynebacterium pseudotuberculosis is a pathogen of great veterinary and economic importance, since it affects livestock, mainly sheep and goats, worldwide, together with reports of its presence in camels in several Arabic, Asiatic, and East and West African countries, as well as Australia. In this article, we report the genome sequence of Corynebacterium pseudotuberculosis strain Cp162, collected from the external neck abscess of a camel in the United Kingdom.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.