Publications by authors named "Navjot Singh"

43 Publications

Regulatory roles of 5' UTR and ORF-internal RNAs detected by 3' end mapping.

Elife 2021 Jan 18;10. Epub 2021 Jan 18.

Wadsworth Center, New York State Department of Health, Albany, United States.

Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium . Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of - and -acting RNA regulators in bacterial 5´ UTRs and internal to ORFs.
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http://dx.doi.org/10.7554/eLife.62438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815308PMC
January 2021

RecipeDB: a resource for exploring recipes.

Database (Oxford) 2020 11;2020

Complex Systems Laboratory, Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi), New Delhi, India 110020.

Cooking is the act of turning nature into the culture, which has enabled the advent of the omnivorous human diet. The cultural wisdom of processing raw ingredients into delicious dishes is embodied in their cuisines. Recipes thus are the cultural capsules that encode elaborate cooking protocols for evoking sensory satiation as well as providing nourishment. As we stand on the verge of an epidemic of diet-linked disorders, it is eminently important to investigate the culinary correlates of recipes to probe their association with sensory responses as well as consequences for nutrition and health. RecipeDB (https://cosylab.iiitd.edu.in/recipedb) is a structured compilation of recipes, ingredients and nutrition profiles interlinked with flavor profiles and health associations. The repertoire comprises of meticulous integration of 118 171 recipes from cuisines across the globe (6 continents, 26 geocultural regions and 74 countries), cooked using 268 processes (heat, cook, boil, simmer, bake, etc.), by blending over 20 262 diverse ingredients, which are further linked to their flavor molecules (FlavorDB), nutritional profiles (US Department of Agriculture) and empirical records of disease associations obtained from MEDLINE (DietRx). This resource is aimed at facilitating scientific explorations of the culinary space (recipe, ingredient, cooking processes/techniques, dietary styles, etc.) linked to taste (flavor profile) and health (nutrition and disease associations) attributes seeking for divergent applications. Database URL:  https://cosylab.iiitd.edu.in/recipedb.
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http://dx.doi.org/10.1093/database/baaa077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7687679PMC
November 2020

Nanopore MinION Sequencing Reveals Possible Transfer of Plasmid Across Bacterial Species in Two Healthcare Facilities.

Front Microbiol 2020 19;11:2007. Epub 2020 Aug 19.

Wadsworth Center, New York State Department of Health, Albany, NY, United States.

Carbapenemase-producing are a major threat to global public health. carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the gene in four bacterial isolates belonging to three different species (, , and ). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.
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http://dx.doi.org/10.3389/fmicb.2020.02007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466660PMC
August 2020

Origin of 3 Rabid Terrestrial Animals in Raccoon Rabies Virus-Free Zone, Long Island, New York, USA, 2016-2017.

Emerg Infect Dis 2020 06;26(6):1315-1319

During 2016-2017, three rabid terrestrial animals were discovered in the raccoon rabies virus-free zone of Long Island, New York, USA. Whole-genome sequencing and phylogenetic analyses revealed the likely origins of the viruses, enabling the rabies outbreak response (often costly and time-consuming) to be done less expensively and more efficiently.
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http://dx.doi.org/10.3201/eid2606.191700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7258491PMC
June 2020

May-Thurner syndrome: an uncommon and incidental finding in a postpartum female.

Pol J Radiol 2019 23;84:e365-e367. Epub 2019 Sep 23.

Government Medical College and Hospital, Sector 32, Chandigarh, India.

May-Thurner syndrome or Cockett syndrome is a pathological condition that arises due to extrinsic compression on iliocaval venous territory, leading to venous outflow obstruction. Here, author presents an incidental finding of left common iliac vein extrinsic compression by right common iliac artery with collateral vessels in the pelvis in a postpartum female.
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http://dx.doi.org/10.5114/pjr.2019.89193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6964327PMC
September 2019

Impact of Candida auris Infection in a Neutropenic Murine Model.

Antimicrob Agents Chemother 2020 02 21;64(3). Epub 2020 Feb 21.

Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, USA

has become a global public health threat due to its multidrug resistance and persistence. Currently, there are limited murine models to study infection. Those models use a combination of cyclophosphamide and cortisone acetate, suppressing both innate and adaptive immunity. Here, we compare infection in two neutrophil-depleted murine models in which innate immunity is targeted using the monoclonal antibodies 1A8 and RB6-8C5.
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http://dx.doi.org/10.1128/AAC.01625-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038241PMC
February 2020

Effects of Thermal Annealing Duration on the Film Morphology of Methylamine Lead Triiodide (MAPbI₃) Perovskite Thin Films in Ambient Air.

J Nanosci Nanotechnol 2020 Jun;20(6):3795-3801

Centre of Advanced Study in Physics, Department of Physics, Panjab University Chandigarh,160014, India.

In the present communication we have studied the effect of thermal annealing duration on morphology of methylamine lead triiodide (MAPbI₃) perovskite (prepared using single step method) semiconductor that changes into lead iodide (PbI₂). Furthermore, the effect of annealing duration on thin films is investigated and correlated with its potential photovoltaic application. Thin films characteristics study by X-ray diffraction and scanning electron microscopy results indicate MAPbI₃ degraded strongly by annealing duration. However, thin films (about 1.25 micron-thick) annealed at 80 °C for 10 min in ambient conditions cause minimum degradation with smooth and uniform surface morphology. It also shows a higher absorption coefficient with the band gap of °1.5 eV rendering this perovskite suitable for practical applications.
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http://dx.doi.org/10.1166/jnn.2020.17494DOI Listing
June 2020

Laparoscopic Versus Open Sigmoid Loop Colostomy: A Comparative Study from a Cohort of 62 Patients Requiring Temporary Faecal Diversion at a Tertiary Care Center in North India.

Niger J Surg 2019 Jul-Dec;25(2):139-145

Department of Surgery, Christian Medical College and Hospital, Affliated to the Baba Farid University of Health Sciences-Faridkot, Ludhiana, Punjab, India.

Background: Over decades, colostomies have been done through open method, but laparoscopic creation of an intestinal stoma is safe, feasible and has distinct advantages over conventional techniques in specific procedures. The aim of this study compares operative and short-term outcomes of laparoscopic and open sigmoid loop colostomy formation for temporary fecal diversion.

Subjects And Methods: A single institution, comparative study conducted in the department of surgery for patients who underwent either laparoscopic or open sigmoid loop colostomy. The 2 years' study was from December 1, 2013, to November 30, 2015. Subjects were prospectively enrolled in the study after informed consent, both genders of >12 years of age. Data analysis was done using Statistical Package for Social Sciences version 21.0. Variables were tested by Kolmogorov-Smirnov test, compared using unpaired -test/Mann-Whitney Test, Chi-square test/Fisher's exact test. < 0.05 was considered statistically significant.

Results: Sixty-two patients were enrolled; laparoscopy group - 29 patients (46.77%) versus open group - 33 patients (53.22%). Laparoscopic group/open surgery group showed less blood loss (20.69 + 17.71 ml / 121.97 + 35.29ml, -value 0.0005), lower requirement of analgesics (4.28 ± 1.76 days/6.88 ± 2.75 days), shorter hospital stay (8.79 ± 5.57 days and 11.73 ± 6.61 days, = 0.001), early return of the bowel function and tolerance to diet. Complications and readmission requirement for any complication was lower in the laparoscopic group.

Conclusions: Laparoscopic sigmoid loop colostomy is a simple alternative to open sigmoid loop colostomy with respect to postoperative pain, earlier return of bowel function, lower analgesic requirement, and lesser hospital stay.
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http://dx.doi.org/10.4103/njs.NJS_13_19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771189PMC
October 2019

Monocarbonyl Curcumin-Based Molecular Hybrids as Potent Antibacterial Agents.

ACS Omega 2019 Jul 5;4(7):11673-11684. Epub 2019 Jul 5.

Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India.

Keeping in view various pharmacological attributes of curcumin, coumarin, and isatin derivatives, triazole-tethered monocarbonyl curcumin-coumarin and curcumin-isatin molecular hybrids have been synthesized and evaluated for their antibacterial potential against Gram-positive ( and ) and Gram-negative ( and ) human pathogenic bacterial strains. Among all hybrid molecules, and showed the most potent antibacterial activity with inhibition zones of 29 and 31 mm along with MIC values of 12.50 and 6.25 μg/mL, respectively. Structure-activity relationship that emerged from biological data revealed that the two-carbon alkyl chain between triazole and coumarin/isatin moiety is well tolerable for the activity. Bromo substitution at the fifth position of isatin, para-cholo substitution in the case of curcumin-isatin, and para-methoxy in the case of curcumin-coumarin hybrids on ring A of curcumin are most suitable groups for the antibacterial activity. Various types of binding interactions of and within the active site of dihydrofolate reductase (DHFR) of are also streamlined by molecular modeling studies, suggesting their capability in completely blocking DHFR.
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http://dx.doi.org/10.1021/acsomega.9b01109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6682034PMC
July 2019

RNA isolation from Peyer's patch lymphocytes and mononuclear phagocytes to determine gene expression profiles using NanoString technology.

J Biol Methods 2018 2;5(3):e95. Epub 2018 Jul 2.

Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany NY, USA.

Sampling and immune surveillance within gut-associated lymphoid tissues such as the intestinal Peyer's patch (PP) occurs by an elegantly orchestrated effort that involves the epithelial barrier, B and T lymphocytes, and an extensive network of mononuclear phagocytes. Although we now understand more about the dynamics of antigen and microbial sampling within PPs, the gene expression changes that occur in individual cell subsets during sampling are not well characterized. This protocol describes the isolation of high-quality RNA from sorted PP, B and T-lymphocytes, and CD11c phagocytes for use with nCounter-NanoString technology. This method allows investigators to study gene expression changes within PPs in response to antigens, microbes, and oral vaccine delivery vehicles of interest that are sampled.
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http://dx.doi.org/10.14440/jbm.2018.246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706143PMC
July 2018

Candida albicans Elicits Pro-Inflammatory Differential Gene Expression in Intestinal Peyer's Patches.

Mycopathologia 2019 Aug 22;184(4):461-478. Epub 2019 Jun 22.

Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA.

The details of how gut-associated lymphoid tissues such as Peyer's patches (PPs) in the small intestine play a role in immune surveillance, microbial differentiation and the mucosal barrier protection in response to fungal organisms such as Candida albicans are still unclear. We particularly focus on PPs as they are the immune sensors and inductive sites of the gut that influence inflammation and tolerance. We have previously demonstrated that CD11c phagocytes that include dendritic cells and macrophages are located in the sub-epithelial dome within PPs sample C. albicans. To gain insight on how specific cells within PPs sense and respond to the sampling of fungi, we gavaged naïve mice with C. albicans strains ATCC 18804 and SC5314 as well as Saccharomyces cerevisiae. We measured the differential gene expression of sorted CD45 B220 B-cells, CD3 T-cells and CD11c DCs within the first 24 h post-gavage using nanostring nCounter technology. The results reveal that at 24 h, PP phagocytes were the cell type that displayed differential gene expression. These phagocytes were able to sample C. albicans and discriminate between strains. In particular, strain ATCC 18804 upregulated fungal-specific pro-inflammatory genes pertaining to innate and adaptive immune responses. Interestingly, PP CD11c phagocytes also differentially expressed genes in response to C. albicans that were important in the protection of the mucosal barrier. These results highlight that the mucosal barrier not only responds to C. albicans, but also aids in the protection of the host.
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http://dx.doi.org/10.1007/s11046-019-00349-4DOI Listing
August 2019

Whole-Genome Single-Nucleotide Polymorphism (SNP) Analysis Applied Directly to Stool for Genotyping Shiga Toxin-Producing Escherichia coli: an Advanced Molecular Detection Method for Foodborne Disease Surveillance and Outbreak Tracking.

J Clin Microbiol 2019 07 25;57(7). Epub 2019 Jun 25.

New York State Department of Health (NYSDOH), Wadsworth Center, Albany, New York, USA

Whole-genome sequencing (WGS) of pathogens from pure culture provides unparalleled accuracy and comprehensive results at a cost that is advantageous compared with traditional diagnostic methods. Sequencing pathogens directly from a primary clinical specimen would help circumvent the need for culture and, in the process, substantially shorten the time to diagnosis and public health reporting. Unfortunately, this approach poses significant challenges because of the mixture of multiple sequences from a complex fecal biomass. The aim of this project was to develop a proof of concept protocol for the sequencing and genotyping of Shiga toxin-producing (STEC) directly from stool specimens. We have developed an enrichment protocol that reliably achieves a substantially higher DNA yield belonging to , which provides adequate next-generation sequencing (NGS) data for downstream bioinformatics analysis. A custom bioinformatics pipeline was created to optimize and remove non- reads, assess the STEC versus commensal population in the samples, and build consensus sequences based on population allele frequency distributions. Side-by-side analysis of WGS from paired STEC isolates and matched primary stool specimens reveal that this method can reliably be implemented for many clinical specimens to directly genotype STEC and accurately identify clusters of disease outbreak when no STEC isolate is available for testing.
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http://dx.doi.org/10.1128/JCM.00307-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6595464PMC
July 2019

Protein Engineered Triblock Polymers Composed of Two SADs: Enhanced Mechanical Properties and Binding Abilities.

Biomacromolecules 2018 05 2;19(5):1552-1561. Epub 2018 Apr 2.

Chemical and Biomolecular Engineering Department , New York University Tandon School of Engineering , 6 Metrotech Center , Brooklyn , New York 11201 , United States.

Recombinant methods have been used to engineer artificial protein triblock polymers composed of two different self-assembling domains (SADs) bearing one elastin (E) flanked by two cartilage oligomeric matrix protein coiled-coil (C) domains to generate CEC. To understand how the two C domains improve small molecule recognition and the mechanical integrity of CEC, we have constructed CEC, which bears an impaired C domain that is unstructured as a negative control. The CEC triblock polymer demonstrates increased small molecule binding and ideal elastic behavior for hydrogel formation. The negative control CEC does not exhibit binding to small molecule and is inelastic at lower temperatures, affirming the favorable role of C domain and its helical conformation. While both CEC and CEC assemble into micelles, CEC is more densely packed with C domains on the surface enabling the development of networks leading to hydrogel formation. Such protein engineered triblock copolymers capable of forming robust hydrogels hold tremendous promise for biomedical applications in drug delivery and tissue engineering.
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http://dx.doi.org/10.1021/acs.biomac.7b01259DOI Listing
May 2018

Identification of regulatory targets for the bacterial Nus factor complex.

Nat Commun 2017 12 11;8(1):2027. Epub 2017 Dec 11.

Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.

Nus factors are broadly conserved across bacterial species, and are often essential for viability. A complex of five Nus factors (NusB, NusE, NusA, NusG and SuhB) is considered to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent transcription termination. Here, we identify an additional cellular function for the Nus factor complex in Escherichia coli: repression of the Nus factor-encoding gene, suhB. This repression occurs primarily by translation inhibition, followed by Rho-dependent transcription termination. Thus, the Nus factor complex can prevent or promote Rho activity depending on the gene context. Conservation of putative NusB/E binding sites upstream of Nus factor genes suggests that Nus factor autoregulation occurs in many bacterial species. Additionally, many putative NusB/E binding sites are also found upstream of other genes in diverse species, and we demonstrate Nus factor regulation of one such gene in Citrobacter koseri. We conclude that Nus factors have an evolutionarily widespread regulatory function beyond ribosomal RNA, and that they are often autoregulatory.
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http://dx.doi.org/10.1038/s41467-017-02124-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5725501PMC
December 2017

FlavorDB: a database of flavor molecules.

Nucleic Acids Res 2018 01;46(D1):D1210-D1216

Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi), New Delhi, India.

Flavor is an expression of olfactory and gustatory sensations experienced through a multitude of chemical processes triggered by molecules. Beyond their key role in defining taste and smell, flavor molecules also regulate metabolic processes with consequences to health. Such molecules present in natural sources have been an integral part of human history with limited success in attempts to create synthetic alternatives. Given their utility in various spheres of life such as food and fragrances, it is valuable to have a repository of flavor molecules, their natural sources, physicochemical properties, and sensory responses. FlavorDB (http://cosylab.iiitd.edu.in/flavordb) comprises of 25,595 flavor molecules representing an array of tastes and odors. Among these 2254 molecules are associated with 936 natural ingredients belonging to 34 categories. The dynamic, user-friendly interface of the resource facilitates exploration of flavor molecules for divergent applications: finding molecules matching a desired flavor or structure; exploring molecules of an ingredient; discovering novel food pairings; finding the molecular essence of food ingredients; associating chemical features with a flavor and more. Data-driven studies based on FlavorDB can pave the way for an improved understanding of flavor mechanisms.
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http://dx.doi.org/10.1093/nar/gkx957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753196PMC
January 2018

Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation.

Nucleic Acids Res 2017 Jul;45(12):7474-7486

Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada.

Riboswitches are regulatory elements that control gene expression by altering RNA structure upon the binding of specific metabolites. Although Bacillus subtilis riboswitches have been shown to control premature transcription termination, less is known about regulatory mechanisms employed by Escherichia coli riboswitches, which are predicted to regulate mostly at the level of translation initiation. Here, we present experimental evidence suggesting that the majority of known E. coli riboswitches control transcription termination by using the Rho transcription factor. In the case of the thiamin pyrophosphate-dependent thiM riboswitch, we find that Rho-dependent transcription termination is triggered as a consequence of translation repression. Using in vitro and in vivo assays, we show that the Rho-mediated regulation relies on RNA target elements located at the beginning of thiM coding region. Gene reporter assays indicate that relocating Rho target elements to a different gene induces transcription termination, demonstrating that such elements are modular domains controlling Rho. Our work provides strong evidence that translationally regulating riboswitches also regulate mRNA levels through an indirect control mechanism ensuring tight control of gene expression.
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http://dx.doi.org/10.1093/nar/gkx434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499598PMC
July 2017

Unusual Glomus Tumor of the Penis.

Curr Urol 2016 Oct 20;9(3):113-118. Epub 2016 Sep 20.

Department of Physiology and Biophysics, SUNY at Stony Brook, New York, USA; Department of Urology, SUNY at Stony Brook, New York, USA.

Introduction: Glomus tumors are benign neoplasms commonly found in subungual regions of the extremities and rarely located in the penis. Misdiagnosis of glomus tumors is common; therefore, symptoms and clinical presentations should be reviewed.

Objective: The primary objective of this review article is to emphasize the pathogenesis, pathology, clinical presentation, symptoms, diagnosis, and treatment methods of glomus tumors in order to better identify and manage the condition.

Materials And Methods: Research was conducted using PubMed/Medline. The inclusion criteria required glomus tumor to be present on the penis.

Results: Glomus tumors, which appear as symptomatic or asymptomatic lesions, are attributed to dispersion grouping of neoplastic or non-neoplastic lesions in a particular area.

Conclusion: Differential diagnosis of glomus tumors includes hemangiomas, neurofibromatosis, epithelial lesions, and spindle-cell lesions. Physical examination and histological findings should be used for diagnosis. Treatment options can be either conservative or invasive, in which the patient undergoes surgical excision.
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http://dx.doi.org/10.1159/000442864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109964PMC
October 2016

Detecting diseases of neglected seminal vesicles using imaging modalities: A review of current literature.

Int J Reprod Biomed 2016 May;14(5):293-302

Department of Physiology and Biophysics, SUNY at Stony Brook, New York, USA.; Department of Urology, SUNY at Stony Brook, New York, USA.

Seminal vesicles (SVs) are sex accessory organs and part of male genitourinary system. They play a critical role in male fertility. Diseases of the SVs, usually results in infertility. Diseases of the SVs are extremely rare and are infrequently reported in the literature. We address the current literature of SV pathologies, symptoms, diagnosis, and treatment options. We review the clinical importance of SVs from PubMed. The current imaging modalities and instrumentation that help diagnose SV diseases are reviewed. Common pathologies including, infection, cysts, tumors, and congenital diseases of the SVs are addressed. Many times symptoms of hematospermia, pain, irritative and obstructive lower urinary tract symptoms, and infertility are presented in patients with SV diseases.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910035PMC
May 2016

SuhB Associates with Nus Factors To Facilitate 30S Ribosome Biogenesis in Escherichia coli.

mBio 2016 Mar 15;7(2):e00114. Epub 2016 Mar 15.

Wadsworth Center, New York State Department of Health, Albany, New York, USA Department of Biomedical Sciences, University at Albany, Albany, New York, USA

Unlabelled: A complex of highly conserved proteins consisting of NusB, NusE, NusA, and NusG is required for robust expression of rRNA in Escherichia coli. This complex is proposed to prevent Rho-dependent transcription termination by a process known as "antitermination." The mechanism of this antitermination in rRNA is poorly understood but requires association of NusB and NusE with a specific RNA sequence in rRNA known as BoxA. Here, we identify a novel member of the rRNA antitermination machinery: the inositol monophosphatase SuhB. We show that SuhB associates with elongating RNA polymerase (RNAP) at rRNA in a NusB-dependent manner. Although we show that SuhB is required for BoxA-mediated antitermination in a reporter system, our data indicate that the major function of the NusB/E/A/G/SuhB complex is not to prevent Rho-dependent termination of rRNA but rather to promote correct rRNA maturation. This occurs through formation of a SuhB-mediated loop between NusB/E/BoxA and RNAP/NusA/G. Thus, we have reassigned the function of these proteins at rRNA and identified another key player in this complex.

Importance: As RNA polymerase transcribes the rRNA operons in E. coli, it complexes with a set of proteins called Nus that confer enhanced rates of transcription elongation, correct folding of rRNA, and rRNA assembly with ribosomal proteins to generate a fully functional ribosome. Four Nus proteins were previously known, NusA, NusB, NusE, and NusG; here, we discover and describe a fifth, SuhB, that is an essential component of this complex. We demonstrate that the main function of this SuhB-containing complex is not to prevent premature transcription termination within the rRNA operon, as had been long claimed, but to enable rRNA maturation and a functional ribosome fully competent for translation.
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http://dx.doi.org/10.1128/mBio.00114-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807359PMC
March 2016

Urological complications of uterine leiomyoma: a review of literature.

Int Urol Nephrol 2016 Jun 27;48(6):941-8. Epub 2016 Feb 27.

Department of Physiology and Biophysics, SUNY at Stony Brook, Stony Brook, NY, 11794, USA.

Introduction: Uterine leiomyomas are common gynecologic tumor in reproductive-aged women, by age 50, diagnosis shared by urologist, gynecologists and radiologists.

Objective: The goal of this article is to review the current literature, study the impact of leiomyoma on female lower urinary tract, examine the cause female sexual dysfunction and provide a comprehensive review of current diagnostic, imaging studies, and current treatment of leiomyoma.

Methods: Clinical leiomyoma studies published from 1956 through 2015 were identified using the PubMed search engines and the key words leiomyoma, fibroid in the current literature. Impact of leiomyoma on the lower urinary tract including female sexual dysfunction was reviewed with terms of "urinary retention", "bladder", "urethra", "dyspareunia", "incontinence", "incomplete bladder emptying", "female sexual dysfunction", and "lower urinary tract" to study the urological and sexual effects of leiomyoma. Literature related to leiomyoma was reviewed from 1965 to present.

Results: Women with uterine leiomyomata complained of pelvic pain, menstrual irregularities, infertility, lower urinary tract symptoms and sexual dysfunction.

Conclusion: Leiomyoma is a common tumor of the uterus that often clinically impacts on the lower urinary tract and results in urological and sexual symptoms. Leiomyoma can compress and grow into and become adherent to the bladder and surrounding pelvic organs or metastasize into peritoneal organs. Leiomyoma can enlarge and compress the urinary bladder, urethra, and lower end of the ureters. Leiomyoma can cause embarrassing sexual dysfunction in females. Current literature of non-surgical and surgical therapy of leiomyoma is described.
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http://dx.doi.org/10.1007/s11255-016-1248-5DOI Listing
June 2016

Widespread suppression of intragenic transcription initiation by H-NS.

Genes Dev 2014 Feb 21;28(3):214-9. Epub 2014 Jan 21.

Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom:

Widespread intragenic transcription initiation has been observed in many species. Here we show that the Escherichia coli ehxCABD operon contains numerous intragenic promoters in both sense and antisense orientations. Transcription from these promoters is silenced by the histone-like nucleoid structuring (H-NS) protein. On a genome-wide scale, we show that 46% of H-NS-suppressed transcripts in E. coli are intragenic in origin. Furthermore, many intergenic promoters repressed by H-NS are for noncoding RNAs (ncRNAs). Thus, a major overlooked function of H-NS is to prevent transcription of spurious RNA. Our data provide a molecular description for the toxicity of horizontally acquired DNA and explain how this is counteracted by H-NS.
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http://dx.doi.org/10.1101/gad.234336.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923964PMC
February 2014

Identification of regulatory RNA in bacterial genomes by genome-scale mapping of transcription start sites.

Methods Mol Biol 2014 ;1103:1-10

Wadsworth Center, New York State Department of Health, Albany, NY, USA.

The ability to map transcription start sites is critical for studies of gene regulation and for identification of novel RNAs. Conventional RNA-seq is often insufficient for identification of transcription start sites due to low coverage and/or RNA processing events. We have developed a highly sensitive, genome-scale method for detection of transcription start sites in bacteria. This method uses deep sequencing of cDNA libraries to identify transcription start sites with strand specificity at nucleotide resolution. Here, we describe the application of this method for transcription start site identification in Escherichia coli.
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http://dx.doi.org/10.1007/978-1-62703-730-3_1DOI Listing
July 2014

Formulation development and optimization of sustained release matrix tablet of Itopride HCl by response surface methodology and its evaluation of release kinetics.

Saudi Pharm J 2013 Apr 12;21(2):201-13. Epub 2012 Apr 12.

Particle Design Research Group, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia ; Non-Destructive Biomedical and Pharmaceutical Research Centre, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia.

The objective of this present investigation was to develop and formulate sustained release (SR) matrix tablets of Itopride HCl, by using different polymer combinations and fillers, to optimize by Central Composite Design response surface methodology for different drug release variables and to evaluate drug release pattern of the optimized product. Sustained release matrix tablets of various combinations were prepared with cellulose-based polymers: hydroxy propyl methyl cellulose (HPMC) and polyvinyl pyrolidine (pvp) and lactose as fillers. Study of pre-compression and post-compression parameters facilitated the screening of a formulation with best characteristics that underwent here optimization study by response surface methodology (Central Composite Design). The optimized tablet was further subjected to scanning electron microscopy to reveal its release pattern. The in vitro study revealed that combining of HPMC K100M (24.65 MG) with pvp(20 mg)and use of LACTOSE as filler sustained the action more than 12 h. The developed sustained release matrix tablet of improved efficacy can perform therapeutically better than a conventional tablet.
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http://dx.doi.org/10.1016/j.jsps.2012.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744972PMC
April 2013

Identification and characterization of small RNAs in Yersinia pestis.

RNA Biol 2013 Mar 16;10(3):397-405. Epub 2013 Jan 16.

Wadsworth Center; New York State Department of Health; Albany, NY USA.

Yersinia pestis, the etiologic agent of plague, is closely related to Yersinia pseudotuberculosis evolutionarily but has a very different mode of infection. The RNA-binding regulatory protein, Hfq, mediates regulation by small RNAs (sRNAs) and is required for virulence of both Y. pestis and Y. pseudotuberculosis. Moreover, Hfq is required for growth of Y. pestis, but not Y. pseudotuberculosis, at 37°C. Together, these observations suggest that sRNAs play important roles in the virulence and survival of Y. pestis, and that regulation by sRNAs may account for some of the differences between Y. pestis and Y. pseudotuberculosis. We have used a deep sequencing approach to identify 31 sRNAs in Y. pestis. The majority of these sRNAs are not conserved outside the Yersiniae. Expression of the sRNAs was confirmed by Northern analysis and we developed deep sequencing approaches to map 5' and 3' ends of many sRNAs simultaneously. Expression of the majority of the sRNAs we identified is dependent upon Hfq. We also observed temperature-dependent effects on the expression of many sRNAs, and differences in expression patterns between Y. pestis and Y. pseudotuberculosis. Thus, our data suggest that regulation by sRNAs plays an important role in the lifestyle switch from flea to mammalian host, and that regulation by sRNAs may contribute to the phenotypic differences between Y. pestis and Y. pseudotuberculosis.
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http://dx.doi.org/10.4161/rna.23590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672283PMC
March 2013

Disseminated cryptococcosis presenting with generalized lymphadenopathy.

J Cytol 2012 Jul;29(3):200-2

Departments of Pathology, Christian Medical College and Hospital, Ludhiana, Punjab, India.

Cryptococcosis is a common opportunistic infection among immunocompromised individuals. Some of the commonly affected sites are respiratory and central nervous system. Lymph node is an unusual site of involvement which could mimic tuberculosis, as seen in our case. We report a 32-year-old male immunocompromised patient presenting with generalized lymphadenopathy who was clinically suspected to have tuberculous lymphadenitis. He was diagnosed to have disseminated cryptococcosis on fine needle aspiration cytology and fungal isolation on culture.
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http://dx.doi.org/10.4103/0970-9371.101175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3480772PMC
July 2012

FRUIT, a scar-free system for targeted chromosomal mutagenesis, epitope tagging, and promoter replacement in Escherichia coli and Salmonella enterica.

PLoS One 2012 27;7(9):e44841. Epub 2012 Sep 27.

Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.

Recombineering is a widely-used approach to delete genes, introduce insertions and point mutations, and introduce epitope tags into bacterial chromosomes. Many recombineering methods have been described, for a wide range of bacterial species. These methods are often limited by (i) low efficiency, and/or (ii) introduction of "scar" DNA into the chromosome. Here, we describe a rapid, efficient, PCR-based recombineering method, FRUIT, that can be used to introduce scar-free point mutations, deletions, epitope tags, and promoters into the genomes of enteric bacteria. The efficiency of FRUIT is far higher than that of the most widely-used recombineering method for Escherichia coli. We have used FRUIT to introduce point mutations and epitope tags into the chromosomes of E. coli K-12, Enterotoxigenic E. coli, and Salmonella enterica. We have also used FRUIT to introduce constitutive and inducible promoters into the chromosome of E. coli K-12. Thus, FRUIT is a versatile, efficient recombineering approach that can be applied in multiple species of enteric bacteria.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044841PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459970PMC
March 2013

FDA advisory committee meeting outcomes.

Nat Rev Drug Discov 2012 Jun 29;11(7):513-4. Epub 2012 Jun 29.

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http://dx.doi.org/10.1038/nrd3747DOI Listing
June 2012

Evaluation of mandibular morphology in different facial types.

Contemp Clin Dent 2011 Jul;2(3):200-6

Departments of Orthodontics and Dentofacial Orthopedics, M.M. College of Dental Sciences and Research, Mullana, Dist Ambala, India.

The purpose of this study was to evaluate mandibular morphology in different facial types using various parameters. This study was conducted on lateral cephalograms of a total of 110 subjects, which included 55 males and 55 females between the age of 18-25 years having a mean of 22.3 years for males and 21.5 years for females. The sample was divided into normodivergent, hypodivergent, and hyperdivergent subgroups based on Jarabak's ratio. Symphysis height, depth, ratio (height/depth) and angle, antegonial notch depth, ramal height and width, mandibular depth, upper, lower, and total gonial angle, and mandibular arc angle were analyzed statistically and graphically. It was found that the mandible with the vertical growth pattern was associated with a symphysis with large height, small depth, large ratio, small angle, decreased ramus height and width, smaller mandibular depth, increased gonial angle, and decreased mandibular arc angle in contrast to mandible with a horizontal growth pattern. Sexual dichotomy was found with mean symphysis height and depth in the female sample being smaller than in the male sample, but symphysis ratio was larger in the female sample; males having greater ramus height and width, mandibular depth than females. The mandible seemed to have retained its infantile characteristics with all its processes underdeveloped in hyperdivergent group.
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http://dx.doi.org/10.4103/0976-237X.86458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214527PMC
July 2011

Management of a case of ectodermal dysplasia: a multidisciplinary approach.

J Dent Child (Chic) 2011 Jul;78(2):107-10

Department of Pedodontics at Kothiwal Dental College and Research Center, Moradabad, India.

Ectodermal dysplasia (ED) is a rare disorder involving 2 or more of the ectodermal structures, which include the skin, hair, nails, teeth, mucus glands, and sweat glands. Each person with ectodermal dysplasia may have a different combination of defects. The most common form of ED is linked to the X chromosome and usually affects men. Another form of the disease affects men and women equally. The patient's special needs are taken into consideration in a treatment plan. The purpose of this case report was to describe the dental management of a 9-year-old boy with ectodermal dysplasia whose maxilla showed the presence of mobile, conical teeth that were unrestorable and a solitary permanent left molar, while his mandible was completely edentulous. These mobile, conical teeth were extracted, and a complete denture was constructed to restore the patient's esthetics, form, and function.
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July 2011