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Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes. - PloS one
Metagenomic analyses have been widely used in the last decade to describe viral communities in various environments or to identify the etiology of human, animal, and plant pathologies. Here, we present a simple and standardized protocol that allows for the purification and sequencing of RNA viromes from complex biological samples with an important reduction of host DNA and RNA contaminants, while preserving the infectivity of viral particles.We evaluated different viral purification steps, random reverse transcriptions and sequence-independent amplifications of a pool of representative RNA viruses. Viruses remained infectious after the purification process. We then validated the protocol by sequencing the RNA virome of human body lice engorged in vitro with artificially contaminated human blood. The full genomes of the most abundant viruses absorbed by the lice during the blood meal were successfully sequenced. Interestingly, random amplifications differed in the genome coverage of segmented RNA viruses. Moreover, the majority of reads were taxonomically identified, and only 7-15% of all reads were classified as "unknown", depending on the random amplification method.The protocol reported here could easily be applied to generate RNA viral metagenomes from complex biological samples of different origins. Our protocol allows further virological characterizations of the described viral communities because it preserves the infectivity of viral particles and allows for the isolation of viruses.
Non-contiguous finished genome sequence and description of Clostridium ihumii sp. nov. - Standards in genomic sciences
Clostridium ihumii strain AP5(T) sp. nov. is a new species within the genus Clostridium. This strain, whose genome is described here, was isolated from the stool sample of a 21-year-old French Caucasian female with anorexia nervosa. C. ihumii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,433,668Â bp long genome contains 4,076 protein-coding and 85 RNA genes, including 9 rRNA genes.
A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity. - PloS one
Few studies have tested the small intestine microbiota in humans, where most nutrient digestion and absorption occur. Here, our objective was to examine the duodenal microbiota between obese and normal volunteers using metagenomic techniques.We tested duodenal samples from five obese and five normal volunteers using 16S rDNA V6 pyrosequencing and Illumina MiSeq deep sequencing. The predominant phyla of the duodenal microbiota were Firmicutes and Actinobacteria, whereas Bacteroidetes were absent. Obese individuals had a significant increase in anaerobic genera (p < 0.001) and a higher abundance of genes encoding Acyl-CoA dehydrogenase (p = 0.0018) compared to the control group. Obese individuals also had a reduced abundance of genes encoding sucrose phosphorylase (p = 0.015) and 1,4-alpha-glucan branching enzyme (p = 0.05). Normal weight people had significantly increased FabK (p = 0.027), and the glycerophospholipid metabolism pathway revealed the presence of phospholipase A1 only in the control group (p = 0.05).The duodenal microbiota of obese individuals exhibit alterations in the fatty acid and sucrose breakdown pathways, probably induced by diet imbalance.
Myositis Mimics. - Current rheumatology reports
Patients with autoimmune myositis typically present with muscle weakness, elevated serum levels of muscle enzymes, and abnormal muscle biopsies. However, patients with other acquired myopathies or genetic muscle diseases may have remarkably similar presentations. Making the correct diagnosis of another muscle disease can prevent these patients from being exposed to the risks of immunosuppressive medications, which benefit those with myositis, but not those with other types of muscle disease. Here, we review some of the most common acquired and inherited muscle diseases that can mimic autoimmune myositis, including inclusion body myositis, limb girdle muscular dystrophies, metabolic myopathies, mitochondrial myopathies, and endocrine myopathies. We emphasize aspects of the medical history, physical exam, laboratory evaluation, and muscle biopsy analysis that can help clinicians distinguish myositis mimics from true autoimmune myositis.
A Malaysia 97 monovalent foot-and-mouth disease vaccine (>6PD50/dose) protects pigs against challenge with a variant FMDV A SEA-97 lineage virus, 4 and 7 days post vaccination. - Vaccine
Pigs play a significant role during outbreaks of foot-and-mouth disease (FMD) due to their ability to amplify the virus. It is therefore essential to determine what role vaccination could play to prevent clinical disease and lower virus excretion into the environment. In this study we investigated the efficacy of the double oil emulsion A Malaysia 97 vaccine (>6PD50/dose) against heterologous challenge with an isolate belonging to the A SEA-97 lineage at 4 and 7 days post vaccination (dpv). In addition, we determined whether physical separation of pigs in the same room could prevent virus transmission. Statistically there was no difference in the level of protection offered by 4 and 7 dpv. However, no clinical disease or viral RNA was detected in the blood of pigs challenged 4 dpv, although three of the pigs had antibodies to the non-structural proteins (NSPs), indicating viral replication. Viral RNA was also detected in nasal and saliva swabs, but on very few occasions. Two of the pigs vaccinated seven days prior to challenge had vesicles distal from the injection site, but on the inoculated foot, and two pigs had viral RNA detected in the blood. One pig sero-converted to the NSPs. In contrast, all unvaccinated and inoculated pigs had evidence of infection. No infection occurred in any of the susceptible pigs in the same room, but separated from the infected pigs, indicating that strict biosecurity measures were sufficient under these experimental conditions to prevent virus transmission. However, viral RNA was detected in the nasal swabs of one group of pigs, but apparently not at sufficient levels to cause clinical disease. Vaccination led to a significant decrease in viral RNA in vaccinated pigs compared to unvaccinated and infected pigs, even with this heterologous challenge, and could therefore be considered as a control option during outbreaks.Copyright Â© 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
Draft Genome Sequence of Mycobacterium tuberculosis Strain MT43, a Representative of the Manu2 Genotype. - Genome announcements
We announce the draft genome sequence of Mycobacterium tuberculosis strain MT43, isolated from a pulmonary form of tuberculosis in French Polynesia. Analyzing its 4,145,007-bp, 65.17% G+C chromosome confirmed a fully antibiotic-susceptible Manu2 spoligotype.Copyright Â© 2015 Aboubaker Osman et al.
Draft Genome Sequence of Mycobacterium tuberculosis Strain MT11, Which Represents a New Lineage. - Genome announcements
We sequenced the genome of Mycobacterium tuberculosis strain MT11, which exhibits a specific 16S rRNA gene mutation found in 6% of French Polynesian M. tuberculosis isolates. It comprises a 4,110,293-bp chromosome with 65.15% G+C content, and it encodes 3,949 proteins and contains 85 predicted RNA genes. The TbD1 region is absent in strain MT11 as in modern M.Â tuberculosis strains.Copyright Â© 2015 Aboubaker Osman et al.
Absence of Annexin A1 impairs host adaptive immunity against Mycobacterium tuberculosis in vivo. - Immunobiology
The role of Annexin A1 (ANXA1) in counter-regulating the activities of innate immune cells, such as the migration of neutrophils and monocytes, and the generation of pro-inflammatory mediators in various models of inflammatory and autoimmune diseases is well documented. However, while ANXA1 has been proposed as an important mediator of the adaptive immune response, its involvement in this respect has been less studied. Furthermore, while there have been numerous studies on the role of ANXA1 in inflammatory diseases, less has been reported on its influence in immunity against infection. A recent study reported a link between ANXA1 and tuberculosis, and proposed a model in which Mycobacterium tuberculosis exerts its virulence by manipulating the ANXA1-mediated host apoptotic response. This has prompted us to further investigate the role of ANXA1 in the pathogenesis of tuberculosis in vivo. Here, we show that ANXA1(-/-) mice are more susceptible to M. tuberculosis infection, as evidenced by a transient increase in the pulmonary bacterial burden, and exacerbated and disorganized granulomatous inflammation. These pathological manifestations correlated with an impaired ability of ANXA1(-/-) dendritic cells to activate naÃ¯ve T cells, thereby supporting a role for ANXA1 in shaping the adaptive immunity against M. tuberculosis.Copyright Â© 2014 Elsevier GmbH. All rights reserved.
Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov. - Standards in genomic sciences
Paucisalibacillus algeriensis strain EB02(T) is the type strain of Paucisalibacillus algeriensis sp. nov., a new species within the genus Paucisalibacillus. This strain, whose genome is described here, was isolated from soil sample from the hypersaline lake Ezzemoul Sabkha in northeastern Algeria. Paucisalibacillus algeriensis is a Gram-positive and strictly aerobic bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,006,766 bp long genome (1 chromosome but no plasmid) exhibits a low G+C content of 36% and contains 3,956 protein-coding and 82 RNA genes, including 9 rRNA genes.
Genome sequence and description of Bacteroides timonensis sp. nov. - Standards in genomic sciences
Bacteroides timonensis strain AP1(T) (= CSUR P194 = DSM 26083) is the type strain of B. timonensis sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasoid female who suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative, obligate anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 7,130,768 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains 5,786 protein-coding and 59 RNA genes, including 2 rRNA genes.
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