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Sample records for salmonella small non-coding

  1. Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli

    DEFF Research Database (Denmark)

    Boysen, Anders; Møller-Jensen, Jakob; Kallipolitis, Birgitte H.

    2010-01-01

    Small non-coding RNAs (sRNA) have emerged as important elements of gene regulatory circuits. In enterobacteria such as Escherichia coli and Salmonella many of these sRNAs interact with the Hfq protein, an RNA chaperone similar to mammalian Sm-like proteins and act in the post...... that adaptation to anaerobic growth involves the action of a small regulatory RNA....... of at least one sRNA regulator. Here, we extend this view by the identification and characterization of a highly conserved, anaerobically induced small sRNA in E. coli, whose expression is strictly dependent on the anaerobic transcriptional fumarate and nitrate reductase regulator (FNR). The sRNA, named Fnr...

  2. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

    Energy Technology Data Exchange (ETDEWEB)

    Ansong, Charles; Tolic, Nikola; Purvine, Samuel O.; Porwollik, Steffen; Jones, Marcus B.; Yoon, Hyunjin; Payne, Samuel H.; Martin, Jessica L.; Burnet, Meagan C.; Monroe, Matthew E.; Venepally, Pratap; Smith, Richard D.; Peterson, Scott; Heffron, Fred; Mcclelland, Michael; Adkins, Joshua N.

    2011-08-25

    Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. For example systems biology-oriented genome scale modeling efforts greatly benefit from accurate annotation of protein-coding genes to develop proper functioning models. However, determining protein-coding genes for most new genomes is almost completely performed by inference, using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no information on biologically important post-translational processing events critical for protein function. With the ability to directly measure peptides arising from expressed proteins, mass spectrometry-based proteomics approaches can be used to augment and verify coding regions of a genomic sequence and importantly detect post-translational processing events. In this study we utilized “shotgun” proteomics to guide accurate primary genome annotation of the bacterial pathogen Salmonella Typhimurium 14028 to facilitate a systems-level understanding of Salmonella biology. The data provides protein-level experimental confirmation for 44% of predicted protein-coding genes, suggests revisions to 48 genes assigned incorrect translational start sites, and uncovers 13 non-annotated genes missed by gene prediction programs. We also present a comprehensive analysis of post-translational processing events in Salmonella, revealing a wide range of complex chemical modifications (70 distinct modifications) and confirming more than 130 signal peptide and N-terminal methionine cleavage events in Salmonella. This study highlights several ways in which proteomics data applied during the primary stages of annotation can improve the quality of genome annotations, especially with regards to the annotation of mature protein products.

  3. Non-Typhoidal Salmonella Aortitis in a transplant patient

    International Nuclear Information System (INIS)

    Tarif, N.; Azam, M.N.; Mitwalli, Ahmad H.; Al-Wakeel, Jamal S.; El-Kheder, A. Al-Aboud

    2002-01-01

    Non-typhoidal salmonella bacteremia may result in extra gastrointestinallocalization of infection. Aortitis due to non-typhoidal salmonella wasreported to be the cause of 38-42% of all infected abdominal aortitis.Underlying atherosclerosis is a frequent site for salmonella aortitis. Wedescribe here a case of possible salmonella aortitis in a renal transplantpatient. (author)

  4. 76 FR 22667 - Availability of Salmonella Compliance Guide for Small and Very Small Meat and Poultry...

    Science.gov (United States)

    2011-04-22

    ...] Availability of Salmonella Compliance Guide for Small and Very Small Meat and Poultry Establishments That... production of ready-to-eat (RTE) meat and poultry products with respect to Salmonella and other pathogens... This document provides small and very small meat and poultry establishments \\1\\ that manufacture RTE...

  5. 77 FR 58089 - Availability of FSIS Salmonella Compliance Guidelines for Small and Very Small Meat and Poultry...

    Science.gov (United States)

    2012-09-19

    ...] Availability of FSIS Salmonella Compliance Guidelines for Small and Very Small Meat and Poultry Establishments... revised compliance guide for small and very small meat and poultry establishments on the safe production of ready-to-eat (RTE) meat and poultry products with respect to Salmonella and other pathogens. FSIS...

  6. A rabbit model of non-typhoidal Salmonella bacteremia.

    Science.gov (United States)

    Panda, Aruna; Tatarov, Ivan; Masek, Billie Jo; Hardick, Justin; Crusan, Annabelle; Wakefield, Teresa; Carroll, Karen; Yang, Samuel; Hsieh, Yu-Hsiang; Lipsky, Michael M; McLeod, Charles G; Levine, Myron M; Rothman, Richard E; Gaydos, Charlotte A; DeTolla, Louis J

    2014-09-01

    Bacteremia is an important cause of morbidity and mortality in humans. In this study, we focused on the development of an animal model of bacteremia induced by non-typhoidal Salmonella. New Zealand White rabbits were inoculated with a human isolate of non-typhoidal Salmonella strain CVD J73 via the intra-peritoneal route. Blood samples were collected at specific time points and at euthanasia from infected rabbits. Additionally, tissue samples from the heart, lungs, spleen, gastrointestinal tract, liver and kidneys were obtained at euthanasia. All experimentally infected rabbits displayed clinical signs of disease (fever, dehydration, weight loss and lethargy). Tissues collected at necropsy from the animals exhibited histopathological changes indicative of bacteremia. Non-typhoidal Salmonella bacteria were detected in the blood and tissue samples of infected rabbits by microbiological culture and real-time PCR assays. The development of this animal model of bacteremia could prove to be a useful tool for studying how non-typhoidal Salmonella infections disseminate and spread in humans. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Exploration of small RNA-seq data for small non-coding RNAs in Human Colorectal Cancer.

    Science.gov (United States)

    Koduru, Srinivas V; Tiwari, Amit K; Hazard, Sprague W; Mahajan, Milind; Ravnic, Dino J

    2017-01-01

    Background: Improved healthcare and recent breakthroughs in technology have substantially reduced cancer mortality rates worldwide. Recent advancements in next-generation sequencing (NGS) have allowed genomic analysis of the human transcriptome. Now, using NGS we can further look into small non-coding regions of RNAs (sncRNAs) such as microRNAs (miRNAs), Piwi-interacting-RNAs (piRNAs), long non-coding RNAs (lncRNAs), and small nuclear/nucleolar RNAs (sn/snoRNAs) among others. Recent studies looking at sncRNAs indicate their role in important biological processes such as cancer progression and predict their role as biomarkers for disease diagnosis, prognosis, and therapy. Results: In the present study, we data mined publically available small RNA sequencing data from colorectal tissue samples of eight matched patients (benign, tumor, and metastasis) and remapped the data for various small RNA annotations. We identified aberrant expression of 13 miRNAs in tumor and metastasis specimens [tumor vs benign group (19 miRNAs) and metastasis vs benign group (38 miRNAs)] of which five were upregulated, and eight were downregulated, during disease progression. Pathway analysis of aberrantly expressed miRNAs showed that the majority of miRNAs involved in colon cancer were also involved in other cancers. Analysis of piRNAs revealed six to be over-expressed in the tumor vs benign cohort and 24 in the metastasis vs benign group. Only two piRNAs were shared between the two cohorts. Examining other types of small RNAs [sn/snoRNAs, mt_rRNA, miscRNA, nonsense mediated decay (NMD), and rRNAs] identified 15 sncRNAs in the tumor vs benign group and 104 in the metastasis vs benign group, with only four others being commonly expressed. Conclusion: In summary, our comprehensive analysis on publicly available small RNA-seq data identified multiple differentially expressed sncRNAs during colorectal cancer progression at different stages compared to normal colon tissue. We speculate that

  8. 75 FR 18849 - Small Entity Compliance Guide: Prevention of Salmonella Enteritidis in Shell Eggs During...

    Science.gov (United States)

    2010-04-13

    ...] Small Entity Compliance Guide: Prevention of Salmonella Enteritidis in Shell Eggs During Production... ``Prevention of Salmonella Enteritidis in Shell Eggs During Production, Storage, and Transportation--Small... requiring shell egg producers to implement measures to prevent Salmonella Enteritidis (SE) from...

  9. Small non coding RNAs in adipocyte biology and obesity.

    Science.gov (United States)

    Amri, Ez-Zoubir; Scheideler, Marcel

    2017-11-15

    Obesity has reached epidemic proportions world-wide and constitutes a substantial risk factor for hypertension, type 2 diabetes, cardiovascular diseases and certain cancers. So far, regulation of energy intake by dietary and pharmacological treatments has met limited success. The main interest of current research is focused on understanding the role of different pathways involved in adipose tissue function and modulation of its mass. Whole-genome sequencing studies revealed that the majority of the human genome is transcribed, with thousands of non-protein-coding RNAs (ncRNA), which comprise small and long ncRNAs. ncRNAs regulate gene expression at the transcriptional and post-transcriptional level. Numerous studies described the involvement of ncRNAs in the pathogenesis of many diseases including obesity and associated metabolic disorders. ncRNAs represent potential diagnostic biomarkers and promising therapeutic targets. In this review, we focused on small ncRNAs involved in the formation and function of adipocytes and obesity. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome.

    Science.gov (United States)

    Ferlaino, Michael; Rogers, Mark F; Shihab, Hashem A; Mort, Matthew; Cooper, David N; Gaunt, Tom R; Campbell, Colin

    2017-10-06

    Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome.

  11. Antibiotic resistance, integrons and Salmonella genomic island 1 among non-typhoidal Salmonella serovars in The Netherlands.

    NARCIS (Netherlands)

    Vo, An T T; Duijkeren, Engeline van; Fluit, Ad C; Wannet, Wim J B; Verbruggen, Anjo J; Maas, Henny M E; Gaastra, Wim

    2006-01-01

    The objective of this study was to investigate the antimicrobial resistance patterns, integron characteristics and gene cassettes as well as the presence of Salmonella genomic island 1 (SGI1) in non-typhoidal Salmonella (NTS) isolates from human and animal origin. Epidemiologically unrelated Dutch

  12. Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes.

    Science.gov (United States)

    Sittka, Alexandra; Sharma, Cynthia M; Rolle, Katarzyna; Vogel, Jörg

    2009-01-01

    The bacterial Sm-like protein, Hfq, is a key factor for the stability and function of small non-coding RNAs (sRNAs) in Escherichia coli. Homologues of this protein have been predicted in many distantly related organisms yet their functional conservation as sRNA-binding proteins has not entirely been clear. To address this, we expressed in Salmonella the Hfq proteins of two eubacteria (Neisseria meningitides, Aquifex aeolicus) and an archaeon (Methanocaldococcus jannaschii), and analyzed the associated RNA by deep sequencing. This in vivo approach identified endogenous Salmonella sRNAs as a major target of the foreign Hfq proteins. New Salmonella sRNA species were also identified, and some of these accumulated specifically in the presence of a foreign Hfq protein. In addition, we observed specific RNA processing defects, e.g., suppression of precursor processing of SraH sRNA by Methanocaldococcus Hfq, or aberrant accumulation of extracytoplasmic target mRNAs of the Salmonella GcvB, MicA or RybB sRNAs. Taken together, our study provides evidence of a conserved inherent sRNA-binding property of Hfq, which may facilitate the lateral transmission of regulatory sRNAs among distantly related species. It also suggests that the expression of heterologous RNA-binding proteins combined with deep sequencing analysis of RNA ligands can be used as a molecular tool to dissect individual steps of RNA metabolism in vivo.

  13. Salmonella Weltevreden in integrated and non-integrated tilapia aquaculture systems in Guangdong, China.

    Science.gov (United States)

    Li, Kang; Petersen, Gitte; Barco, Lisa; Hvidtfeldt, Kristian; Liu, Liping; Dalsgaard, Anders

    2017-08-01

    Integrated tilapia-pig farming, which uses manure from pigs as fertilizers in fish pond, is a traditional and common production system practised by small-scale farmers in South-east Asia. Although such systems may be environmentally sustainable, they also pose potential food safety hazards including transmission of faecal zoonotic pathogens and accumulation of antimicrobial and other chemical residues. This study aimed to determine differences in occurrence and characteristics of Salmonella spp. isolated from tilapia-pig and non-integrated aquaculture systems in Guangdong province, China. A total of 77 samples (9 pig feed, 19 fish feed, 9 pig faeces, 20 fish mucus and 20 fish intestine) from 10 tilapia-pig ponds and 10 non-integrated ponds were analysed. Salmonella spp. was found in fish mucus (20.0%), fish intestine (40.0%) and pig faeces (11.1%) from integrated ponds, and from fish mucus (40.0%) and fish intestine (40.0%) from non-integrated ponds. S. Weltevreden (76.5%) was by far the most common serovar showing limited antimicrobial resistance. One pig faeces sample contained S. Typhimurium whereas feed samples were found free of Salmonella spp.. DNA fingerprinting by the PFGE method showed a clonal relationship of S. Weltevreden which was supported by similar antimicrobial resistance patterns (sulfamethoxazole and trimethoprim resistance) as well as most isolates harbouring a 147-kb sized plasmid. The common finding of S. Weltevreden in both tilapia production systems indicates that this serovar may have a different ecology and increased survival in aquaculture environments in comparison with other Salmonella serovars. Further in vivo studies of the ecology of S. Weltevreden in aquaculture environments are needed. Copyright © 2017. Published by Elsevier Ltd.

  14. Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection

    Science.gov (United States)

    It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs ...

  15. Small RNAs controlling outer membrane porins

    DEFF Research Database (Denmark)

    Valentin-Hansen, Poul; Johansen, Jesper; Rasmussen, Anders A

    2007-01-01

    are key regulators of environmental stress. Recent work has revealed an intimate interplay between small RNA regulation of outer membrane proteins and the stress-induced sigmaE-signalling system, which has an essential role in the maintenance of the integrity of the outer membrane.......Gene regulation by small non-coding RNAs has been recognized as an important post-transcriptional regulatory mechanism for several years. In Gram-negative bacteria such as Escherichia coli and Salmonella, these RNAs control stress response and translation of outer membrane proteins and therefore...

  16. Non-Coding RNAs in Hodgkin Lymphoma

    Directory of Open Access Journals (Sweden)

    Anna Cordeiro

    2017-05-01

    Full Text Available MicroRNAs (miRNAs, small non-coding RNAs that regulate gene expression by binding to the 3’-UTR of their target genes, can act as oncogenes or tumor suppressors. Recently, other types of non-coding RNAs—piwiRNAs and long non-coding RNAs—have also been identified. Hodgkin lymphoma (HL is a B cell origin disease characterized by the presence of only 1% of tumor cells, known as Hodgkin and Reed-Stenberg (HRS cells, which interact with the microenvironment to evade apoptosis. Several studies have reported specific miRNA signatures that can differentiate HL lymph nodes from reactive lymph nodes, identify histologic groups within classical HL, and distinguish HRS cells from germinal center B cells. Moreover, some signatures are associated with survival or response to chemotherapy. Most of the miRNAs in the signatures regulate genes related to apoptosis, cell cycle arrest, or signaling pathways. Here we review findings on miRNAs in HL, as well as on other non-coding RNAs.

  17. The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression

    Directory of Open Access Journals (Sweden)

    Ramachandran Vinoy K

    2012-01-01

    Full Text Available Abstract Background Invasion of intestinal epithelial cells by Salmonella enterica serovar Typhimurium (S. Typhimurium requires expression of the extracellular virulence gene expression programme (STEX, activation of which is dependent on the signalling molecule guanosine tetraphosphate (ppGpp. Recently, next-generation transcriptomics (RNA-seq has revealed the unexpected complexity of bacterial transcriptomes and in this report we use differential RNA sequencing (dRNA-seq to define the high-resolution transcriptomic architecture of wild-type S. Typhimurium and a ppGpp null strain under growth conditions which model STEX. In doing so we show that ppGpp plays a much wider role in regulating the S. Typhimurium STEX primary transcriptome than previously recognised. Results Here we report the precise mapping of transcriptional start sites (TSSs for 78% of the S. Typhimurium open reading frames (ORFs. The TSS mapping enabled a genome-wide promoter analysis resulting in the prediction of 169 alternative sigma factor binding sites, and the prediction of the structure of 625 operons. We also report the discovery of 55 new candidate small RNAs (sRNAs and 302 candidate antisense RNAs (asRNAs. We discovered 32 ppGpp-dependent alternative TSSs and determined the extent and level of ppGpp-dependent coding and non-coding transcription. We found that 34% and 20% of coding and non-coding RNA transcription respectively was ppGpp-dependent under these growth conditions, adding a further dimension to the role of this remarkable small regulatory molecule in enabling rapid adaptation to the infective environment. Conclusions The transcriptional architecture of S. Typhimurium and finer definition of the key role ppGpp plays in regulating Salmonella coding and non-coding transcription should promote the understanding of gene regulation in this important food borne pathogen and act as a resource for future research.

  18. Annotating non-coding regions of the genome.

    Science.gov (United States)

    Alexander, Roger P; Fang, Gang; Rozowsky, Joel; Snyder, Michael; Gerstein, Mark B

    2010-08-01

    Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and networks. Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis.

  19. Non-binary Hybrid LDPC Codes: Structure, Decoding and Optimization

    OpenAIRE

    Sassatelli, Lucile; Declercq, David

    2007-01-01

    In this paper, we propose to study and optimize a very general class of LDPC codes whose variable nodes belong to finite sets with different orders. We named this class of codes Hybrid LDPC codes. Although efficient optimization techniques exist for binary LDPC codes and more recently for non-binary LDPC codes, they both exhibit drawbacks due to different reasons. Our goal is to capitalize on the advantages of both families by building codes with binary (or small finite set order) and non-bin...

  20. Long non-coding RNAs: Mechanism of action and functional utility

    OpenAIRE

    Bhat, Shakil Ahmad; Ahmad, Syed Mudasir; Mumtaz, Peerzada Tajamul; Malik, Abrar Ahad; Dar, Mashooq Ahmad; Urwat, Uneeb; Shah, Riaz Ahmad; Ganai, Nazir Ahmad

    2016-01-01

    Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs) are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA), small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs) are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological ...

  1. Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs.

    LENUS (Irish Health Repository)

    Weissenmayer, Barbara A

    2011-01-01

    Second generation sequencing has prompted a number of groups to re-interrogate the transcriptomes of several bacterial and archaeal species. One of the central findings has been the identification of complex networks of small non-coding RNAs that play central roles in transcriptional regulation in all growth conditions and for the pathogen\\'s interaction with and survival within host cells. Legionella pneumophila is a gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila during exponential and post-exponential broth growth and during the replicative and transmissive phase of infection inside A. castellanii. We extend previous microarray based studies as well as uncovering evidence of a complex regulatory architecture underpinned by numerous non-coding RNAs. Over seventy new non-coding RNAs could be identified; many of them appear to be strain specific and in configurations not previously reported. We discover a family of non-coding RNAs preferentially expressed during infection conditions and identify a second copy of 6S RNA in L. pneumophila. We show that the newly discovered putative 6S RNA as well as a number of other non-coding RNAs show evidence for antisense transcription. The nature and extent of the non-coding RNAs and their expression patterns suggests that these may well play central roles in the regulation of Legionella spp. specific traits and offer clues as to how L. pneumophila adapts to its intracellular niche. The expression profiles outlined in the study have been deposited into Genbank\\'s Gene Expression Omnibus (GEO) database under the series accession GSE27232.

  2. Diagnostic and prognostic signatures from the small non-coding RNA transcriptome in prostate cancer

    DEFF Research Database (Denmark)

    Martens-Uzunova, E S; Jalava, S E; Dits, N F

    2011-01-01

    Prostate cancer (PCa) is the most frequent male malignancy and the second most common cause of cancer-related death in Western countries. Current clinical and pathological methods are limited in the prediction of postoperative outcome. It is becoming increasingly evident that small non-coding RNA...... signatures of 102 fresh-frozen patient samples during PCa progression by miRNA microarrays. Both platforms were cross-validated by quantitative reverse transcriptase-PCR. Besides the altered expression of several miRNAs, our deep sequencing analyses revealed strong differential expression of small nucleolar...... RNAs (snoRNAs) and transfer RNAs (tRNAs). From microarray analysis, we derived a miRNA diagnostic classifier that accurately distinguishes normal from cancer samples. Furthermore, we were able to construct a PCa prognostic predictor that independently forecasts postoperative outcome. Importantly...

  3. Function and Application Areas in Medicine of Non-Coding RNA

    Directory of Open Access Journals (Sweden)

    Figen Guzelgul

    2009-06-01

    Full Text Available RNA is the genetic material converting the genetic code that it gets from DNA into protein. While less than 2 % of RNA is converted into protein , more than 98 % of it can not be converted into protein and named as non-coding RNAs. 70 % of noncoding RNAs consists of introns , however, the rest part of them consists of exons. Non-coding RNAs are examined in two classes according to their size and functions. Whereas they are classified as long non-coding and small non-coding RNAs according to their size , they are grouped as housekeeping non-coding RNAs and regulating non-coding RNAs according to their function. For long years ,these non-coding RNAs have been considered as non-functional. However, today, it has been proved that these non-coding RNAs play role in regulating genes and in structural, functional and catalitic roles of RNAs converted into protein. Due to its taking a role in gene silencing mechanism, particularly in medical world , non-coding RNAs have led to significant developments. RNAi technolgy , which is used in designing drugs to be used in treatment of various diseases , is a ray of hope for medical world. [Archives Medical Review Journal 2009; 18(3.000: 141-155

  4. Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.

    Science.gov (United States)

    Ragan, Chikako; Mowry, Bryan J; Bauer, Denis C

    2012-09-01

    Recent advances in RNA sequencing technology (RNA-Seq) enables comprehensive profiling of RNAs by producing millions of short sequence reads from size-fractionated RNA libraries. Although conventional tools for detecting and distinguishing non-coding RNAs (ncRNAs) from reference-genome data can be applied to sequence data, ncRNA detection can be improved by harnessing the full information content provided by this new technology. Here we present NorahDesk, the first unbiased and universally applicable method for small ncRNAs detection from RNA-Seq data. NorahDesk utilizes the coverage-distribution of small RNA sequence data as well as thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, we evaluated our method with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). We compared our method with Dario and mirDeep2 and found that NorahDesk produces longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs.

  5. Repression of Salmonella enterica phoP Expression by Small Molecules from Physiological Bile

    Science.gov (United States)

    Antunes, L. Caetano M.; Wang, Melody; Andersen, Sarah K.; Ferreira, Rosana B. R.; Kappelhoff, Reinhild; Han, Jun; Borchers, Christoph H.

    2012-01-01

    Infection with Salmonella enterica serovar Typhi in humans causes the life-threatening disease typhoid fever. In the laboratory, typhoid fever can be modeled through the inoculation of susceptible mice with Salmonella enterica serovar Typhimurium. Using this murine model, we previously characterized the interactions between Salmonella Typhimurium and host cells in the gallbladder and showed that this pathogen can successfully invade gallbladder epithelial cells and proliferate. Additionally, we showed that Salmonella Typhimurium can use bile phospholipids to grow at high rates. These abilities are likely important for quick colonization of the gallbladder during typhoid fever and further pathogen dissemination through fecal shedding. To further characterize the interactions between Salmonella and the gallbladder environment, we compared the transcriptomes of Salmonella cultures grown in LB broth or physiological murine bile. Our data showed that many genes involved in bacterial central metabolism are affected by bile, with the citric acid cycle being repressed and alternative respiratory systems being activated. Additionally, our study revealed a new aspect of Salmonella interactions with bile through the identification of the global regulator phoP as a bile-responsive gene. Repression of phoP expression could also be achieved using physiological, but not commercial, bovine bile. The biological activity does not involve PhoPQ sensing of a bile component and is not caused by bile acids, the most abundant organic components of bile. Bioactivity-guided purification allowed the identification of a subset of small molecules from bile that can elicit full activity; however, a single compound with phoP inhibitory activity could not be isolated, suggesting that multiple molecules may act in synergy to achieve this effect. Due to the critical role of phoP in Salmonella virulence, further studies in this area will likely reveal aspects of the interaction between Salmonella

  6. Progressive changes in non-coding RNA profile in leucocytes with age

    Science.gov (United States)

    Muñoz-Culla, Maider; Irizar, Haritz; Gorostidi, Ana; Alberro, Ainhoa; Osorio-Querejeta, Iñaki; Ruiz-Martínez, Javier; Olascoaga, Javier; de Munain, Adolfo López; Otaegui, David

    2017-01-01

    It has been observed that immune cell deterioration occurs in the elderly, as well as a chronic low-grade inflammation called inflammaging. These cellular changes must be driven by numerous changes in gene expression and in fact, both protein-coding and non-coding RNA expression alterations have been observed in peripheral blood mononuclear cells from elder people. In the present work we have studied the expression of small non-coding RNA (microRNA and small nucleolar RNA -snoRNA-) from healthy individuals from 24 to 79 years old. We have observed that the expression of 69 non-coding RNAs (56 microRNAs and 13 snoRNAs) changes progressively with chronological age. According to our results, the age range from 47 to 54 is critical given that it is the period when the expression trend (increasing or decreasing) of age-related small non-coding RNAs is more pronounced. Furthermore, age-related miRNAs regulate genes that are involved in immune, cell cycle and cancer-related processes, which had already been associated to human aging. Therefore, human aging could be studied as a result of progressive molecular changes, and different age ranges should be analysed to cover the whole aging process. PMID:28448962

  7. iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

    Science.gov (United States)

    Giurato, Giorgio; De Filippo, Maria Rosaria; Rinaldi, Antonio; Hashim, Adnan; Nassa, Giovanni; Ravo, Maria; Rizzo, Francesca; Tarallo, Roberta; Weisz, Alessandro

    2013-12-13

    Qualitative and quantitative analysis of small non-coding RNAs by next generation sequencing (smallRNA-Seq) represents a novel technology increasingly used to investigate with high sensitivity and specificity RNA population comprising microRNAs and other regulatory small transcripts. Analysis of smallRNA-Seq data to gather biologically relevant information, i.e. detection and differential expression analysis of known and novel non-coding RNAs, target prediction, etc., requires implementation of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. As a consequence, the analytical workflow is slowed down by the need for continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. We designed a novel modular pipeline (iMir) for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow. As statistics is crucial in deep-sequencing data analysis, we devised and integrated in iMir tools based on different statistical approaches to allow the operator to analyze data rigorously. The pipeline created here proved to be efficient and time-saving than currently available methods and, in addition, flexible enough to allow the user to select the preferred combination of analytical steps. We present here the results obtained by applying this pipeline to analyze simultaneously 6 smallRNA-Seq datasets from either exponentially growing or growth-arrested human breast cancer MCF-7 cells, that led to the rapid and accurate identification, quantitation and differential expression analysis of ~450 miRNAs, including several novel miRNAs and isomiRs, as well as identification of the putative mRNA targets of differentially expressed mi

  8. Genotypic and phenotypic characterization of multidrug resistant Salmonella Typhimurium and Salmonella Kentucky strains recovered from chicken carcasses.

    Directory of Open Access Journals (Sweden)

    Rizwana Tasmin

    Full Text Available Salmonella Typhimurium is the leading cause of human non-typhoidal gastroenteritis in the US. S. Kentucky is one the most commonly recovered serovars from commercially processed poultry carcasses. This study compared the genotypic and phenotypic properties of two Salmonella enterica strains Typhimurium (ST221_31B and Kentucky (SK222_32B recovered from commercially processed chicken carcasses using whole genome sequencing, phenotype characterizations and an intracellular killing assay. Illumina MiSeq platform was used for sequencing of two Salmonella genomes. Phylogenetic analysis employing homologous alignment of a 1,185 non-duplicated protein-coding gene in the Salmonella core genome demonstrated fully resolved bifurcating patterns with varying levels of diversity that separated ST221_31B and SK222_32B genomes into distinct monophyletic serovar clades. Single nucleotide polymorphism (SNP analysis identified 2,432 (ST19 SNPs within 13 Typhimurium genomes including ST221_31B representing Sequence Type ST19 and 650 (ST152 SNPs were detected within 13 Kentucky genomes including SK222_32B representing Sequence Type ST152. In addition to serovar-specific conserved coding sequences, the genomes of ST221_31B and SK222_32B harbor several genomic regions with significant genetic differences. These included phage and phage-like elements, carbon utilization or transport operons, fimbriae operons, putative membrane associated protein-encoding genes, antibiotic resistance genes, siderophore operons, and numerous hypothetical protein-encoding genes. Phenotype microarray results demonstrated that ST221_31B is capable of utilizing certain carbon compounds more efficiently as compared to SK222_3B; namely, 1,2-propanediol, M-inositol, L-threonine, α-D-lactose, D-tagatose, adonitol, formic acid, acetoacetic acid, and L-tartaric acid. ST221_31B survived for 48 h in macrophages, while SK222_32B was mostly eliminated. Further, a 3-fold growth of ST221_31B was

  9. Identification by PCR of non-typhoidal Salmonella enterica serovars associated with invasive infections among febrile patients in Mali.

    Directory of Open Access Journals (Sweden)

    Sharon M Tennant

    2010-03-01

    Full Text Available In sub-Saharan Africa, non-typhoidal Salmonella (NTS are emerging as a prominent cause of invasive disease (bacteremia and focal infections such as meningitis in infants and young children. Importantly, including data from Mali, three serovars, Salmonella enterica serovar Typhimurium, Salmonella Enteritidis and Salmonella Dublin, account for the majority of non-typhoidal Salmonella isolated from these patients.We have extended a previously developed series of polymerase chain reactions (PCRs based on O serogrouping and H typing to identify Salmonella Typhimurium and variants (mostly I 4,[5],12:i:-, Salmonella Enteritidis and Salmonella Dublin. We also designed primers to detect Salmonella Stanleyville, a serovar found in West Africa. Another PCR was used to differentiate diphasic Salmonella Typhimurium and monophasic Salmonella Typhimurium from other O serogroup B, H:i serovars. We used these PCRs to blind-test 327 Salmonella serogroup B and D isolates that were obtained from the blood cultures of febrile patients in Bamako, Mali.We have shown that when used in conjunction with our previously described O-serogrouping PCR, our PCRs are 100% sensitive and specific in identifying Salmonella Typhimurium and variants, Salmonella Enteritidis, Salmonella Dublin and Salmonella Stanleyville. When we attempted to differentiate 171 Salmonella Typhimurium (I 4,[ 5],12:i:1,2 strains from 52 monophasic Salmonella Typhimurium (I 4,[5],12:i:- strains, we were able to correctly identify 170 of the Salmonella Typhimurium and 51 of the Salmonella I 4,[5],12:i:- strains.We have described a simple yet effective PCR method to support surveillance of the incidence of invasive disease caused by NTS in developing countries.

  10. Biocomputational prediction of small non-coding RNAs in Streptomyces

    Czech Academy of Sciences Publication Activity Database

    Pánek, Josef; Bobek, Jan; Mikulík, Karel; Basler, Marek; Vohradský, Jiří

    2008-01-01

    Roč. 9, č. 217 (2008), s. 1-14 ISSN 1471-2164 R&D Projects: GA ČR GP204/07/P361; GA ČR GA203/05/0106; GA ČR GA310/07/1009 Grant - others:XE(XE) EC Integrated Project ActinoGEN, LSHM-CT-2004-005224. Institutional research plan: CEZ:AV0Z50200510 Keywords : non-coding RNA * streptomyces * biocomputational prediction Subject RIV: IN - Informatics, Computer Science Impact factor: 3.926, year: 2008

  11. Non-Coding RNAs and Endometrial Cancer

    Directory of Open Access Journals (Sweden)

    Cristina Vallone

    2018-03-01

    Full Text Available Non-coding RNAs (ncRNAs are involved in the regulation of cell metabolism and neoplastic transformation. Recent studies have tried to clarify the significance of these information carriers in the genesis and progression of various cancers and their use as biomarkers for the disease; possible targets for the inhibition of growth and invasion by the neoplastic cells have been suggested. The significance of ncRNAs in lung cancer, bladder cancer, kidney cancer, and melanoma has been amply investigated with important results. Recently, the role of long non-coding RNAs (lncRNAs has also been included in cancer studies. Studies on the relation between endometrial cancer (EC and ncRNAs, such as small ncRNAs or micro RNAs (miRNAs, transfer RNAs (tRNAs, ribosomal RNAs (rRNAs, antisense RNAs (asRNAs, small nuclear RNAs (snRNAs, Piwi-interacting RNAs (piRNAs, small nucleolar RNAs (snoRNAs, competing endogenous RNAs (ceRNAs, lncRNAs, and long intergenic ncRNAs (lincRNAs have been published. The recent literature produced in the last three years was extracted from PubMed by two independent readers, which was then selected for the possible relation between ncRNAs, oncogenesis in general, and EC in particular.

  12. Prevalence and concentration of Salmonella and Campylobacter in the processing environment of small-scale pastured broiler farms.

    Science.gov (United States)

    Trimble, Lisa M; Alali, Walid Q; Gibson, Kristen E; Ricke, Steven C; Crandall, Philip; Jaroni, Divya; Berrang, Mark; Habteselassie, Mussie Y

    2013-11-01

    A growing niche in the locally grown food movement is the small-scale production of broiler chickens using the pasture-raised poultry production model. Limited research exists that focuses on Salmonella and Campylobacter contamination in the environment associated with on-farm processing of pasture-raised broilers. The objective of this study was to establish data relative to Salmonella and Campylobacter prevalence and concentration in soil and mortality compost resulting from prior processing waste disposal in the small-scale, on-farm broiler processing environment. Salmonella and Campylobacter concentrations were determined in soil (n = 42), compost (n = 39), and processing wastewater (PWW; n = 46) samples from 4 small broiler farms using a 3-tube most probable number (MPN) method for Salmonella and direct plating method for Campylobacter. Salmonella prevalence and concentration (mean log10 MPN per sample weight or volume) in soil [60%, 0.97 (95% CI: 0.66 to 1.27)], compost [64%, 0.95 (95% CI: 0.66 to 1.24)], and wastewater [48%, 1.29 (95% CI: 0.87 to 1.71)] were not significantly different (P > 0.05). Although Campylobacter prevalence was not significantly different by sample type (64.3, 64.3, and 45.7% in soil, compost, and PWW, respectively), the concentration (mean log10 cfu) of this pathogen was significantly lower (P poultry production waste disposal practices and provides a record of data that may serve as a guide for future improvement of these practices. Further research is needed regarding the small-scale broiler production environment in relation to improving disposal of processing waste for optimum control of human pathogens.

  13. Functional and crystallographic characterization of Salmonella typhimurium Cu,Zn superoxide dismutase coded by the sodCI virulence gene

    NARCIS (Netherlands)

    Pesce, A; Battistoni, A; Stroppolo, ME; Polizio, F; Nardini, M; Kroll, JS; Langford, PR; O'Neill, P; Sette, M; Desideri, A; Bolognesi, M

    2000-01-01

    The functional and three-dimensional structural features of Cu,Zn superoxide dismutase coded by the Salmonella typhimurium sodCI gene, have been characterized. Measurements of the catalytic rate indicate that this enzyme is the most efficient superoxide dismutase analyzed so far, a feature that may

  14. Diversity of antisense and other non-coding RNAs in Archaea revealed by comparative small RNA sequencing in four Pyrobaculum species

    Directory of Open Access Journals (Sweden)

    David L Bernick

    2012-07-01

    Full Text Available A great diversity of small, non-coding RNA molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs in archaea is limited. We employed RNA-seq to identify novel small RNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among four species, we were able to identify conserved RNA genes fitting into known and novel families. Among our findings, we highlight three novel cis-antisense small RNAs encoded opposite to key regulatory (ferric uptake regulator, metabolic (triose-phosphate isomerase, and core transcriptional apparatus genes (transcription factor B. We also found a large increase in the number of conserved C/D box small RNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. Furthermore, the genus-specific nature of these small RNAs indicates they are relatively recent, stable adaptations.

  15. High occurrence and unusual serotype diversity of non-typhoidal Salmonella in non-clinical niches, Angola.

    Science.gov (United States)

    Antunes, P; Campos, J; Mourão, J; Ribeiro, T G; Novais, C; Peixe, L

    2017-04-01

    Non-typhoidal Salmonella is an important burden, particularly in developing countries of the African region. We report for the first time in Angola, a sub-Saharan African country with commercial/travel relationships with Europe, an unexpectedly high occurrence of Salmonella (n = 12/63, 19%) from a high diversity of sources, particularly farm and wild animals. The detection of diverse serotypes (n = 12), involving putative new S. enterica subsp. salamae serotypes, is also of note, reinforcing the need for a comprehensive surveillance in Angola critical to identify animal/food/environmental sources of salmonellosis with impact on animal health, local people, tourists and exported products.

  16. Long non-coding RNAs: Mechanism of action and functional utility

    Directory of Open Access Journals (Sweden)

    Shakil Ahmad Bhat

    2016-10-01

    Full Text Available Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA, small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological and pathological processes. LncRNAs are dysfunctional in a variety of human diseases varying from cancerous to non-cancerous diseases. Characterization of these lncRNA genes and their modes of action may allow their use for diagnosis, monitoring of progression and targeted therapies in various diseases. In this review, we summarize the functional perspectives as well as the mechanism of action of lncRNAs. Keywords: LncRNA, X-chromosome inactivation, Genome imprinting, Transcription regulation, Cancer, Immunity

  17. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells.

    Science.gov (United States)

    Autour, Alexis; C Y Jeng, Sunny; D Cawte, Adam; Abdolahzadeh, Amir; Galli, Angela; Panchapakesan, Shanker S S; Rueda, David; Ryckelynck, Michael; Unrau, Peter J

    2018-02-13

    Despite having many key roles in cellular biology, directly imaging biologically important RNAs has been hindered by a lack of fluorescent tools equivalent to the fluorescent proteins available to study cellular proteins. Ideal RNA labelling systems must preserve biological function, have photophysical properties similar to existing fluorescent proteins, and be compatible with established live and fixed cell protein labelling strategies. Here, we report a microfluidics-based selection of three new high-affinity RNA Mango fluorogenic aptamers. Two of these are as bright or brighter than enhanced GFP when bound to TO1-Biotin. Furthermore, we show that the new Mangos can accurately image the subcellular localization of three small non-coding RNAs (5S, U6, and a box C/D scaRNA) in fixed and live mammalian cells. These new aptamers have many potential applications to study RNA function and dynamics both in vitro and in mammalian cells.

  18. Emerging nalidixic acid and ciprofloxacin resistance in non-typhoidal Salmonella isolated from patients having acute diarrhoeal disease

    International Nuclear Information System (INIS)

    Panhotra, B.R.; Saxena, A.K.; Al-Arabi, Ali M.

    2004-01-01

    Non-typhoidal Salmonella are one of the key etiological agents of diarrhoeal disease. The appearence of multiple drung resistance along with resistance to quinolones in this bacterium poses a serious therapeutic problem. We determined the prevalence of nalidixic acid and ciprofloxacin resistance in non-typhodial Salmonella isolated from faecal samples of patients with acute diarroheal disease attending the outpatient and inpatient department of a hospital in Saudi Arabia during the years 1999 to 2002. Non-typhodial Salmonella were isolated from faecal samples. Antimicrobial susceptibility was tested by the disc diffusion test. MICs to nalidixic acid and ciprofloxacinwere determined by the agar dilution method. During the study period , 524 strains of non-typhoidal Salmonella were isolated. Strains belonging to serogroup C1were the commonest (41.4%) followed by serogroups B and D (15.6% and 14.5%, respectively). Resistance to ampicillin was observed in 22.9% and to trimethoprim/sulphamethoxazole in 18.5%of the strains. Nalidixic acid resistance was encounterd in 9.9% and ciprofloxacin esistance in 2.3% of the strains. Resistance to nalidixic acid significantly increased from 0.1% in 1999 to 5.51% in 2002 ( p=0.0007)and ciprofloxacin resistance increased significantly from 0.1% in 1999 to 0.9% in 2002( p=0.0001). MICs to nalidixic acid and ciprofloxacin were determined among 29 nalidixic acid-resistant strains of non-typhoidal salmonella isolated during 2002. The MIC was >256 ug /ml to nalidixic acid and 8 to 16 ug/ml to ciprofloxacin. The increasing rate of antimicrobial resistance encountered among non-tyophoidal Salmonella necessiate the judicious use of these drugs in humans. Moreover, these findings support the concern that the use of quinolones in animal feed may lead to an increasein resistance and should should be restricted. (author)

  19. The role of Ctk1 kinase in termination of small non-coding RNAs.

    Directory of Open Access Journals (Sweden)

    Tineke L Lenstra

    Full Text Available Transcription termination in Saccharomyces cerevisiae can be performed by at least two distinct pathways and is influenced by the phosphorylation status of the carboxy-terminal domain (CTD of RNA polymerase II (Pol II. Late termination of mRNAs is performed by the CPF/CF complex, the recruitment of which is dependent on CTD-Ser2 phosphorylation (Ser2P. Early termination of shorter cryptic unstable transcripts (CUTs and small nucleolar/nuclear RNAs (sno/snRNAs is performed by the Nrd1-Nab3-Sen1 (NNS complex that binds phosphorylated CTD-Ser5 (Ser5P via the CTD-interacting domain (CID of Nrd1p. In this study, mutants of the different termination pathways were compared by genome-wide expression analysis. Surprisingly, the expression changes observed upon loss of the CTD-Ser2 kinase Ctk1p are more similar to those derived from alterations in the Ser5P-dependent NNS pathway, than from loss of CTD-Ser2P binding factors. Tiling array analysis of ctk1Δ cells reveals readthrough at snoRNAs, at many cryptic unstable transcripts (CUTs and stable uncharacterized transcripts (SUTs, but only at some mRNAs. Despite the suggested predominant role in termination of mRNAs, we observed that a CTK1 deletion or a Pol II CTD mutant lacking all Ser2 positions does not result in a global mRNA termination defect. Rather, termination defects in these strains are widely observed at NNS-dependent genes. These results indicate that Ctk1p and Ser2 CTD phosphorylation have a wide impact in termination of small non-coding RNAs but only affect a subset of mRNA coding genes.

  20. Toward understanding non-coding RNA roles in intracranial aneurysms and subarachnoid hemorrhage

    Directory of Open Access Journals (Sweden)

    Huang Fengzhen

    2017-05-01

    Full Text Available Subarachnoid hemorrhage (SAH is a common and frequently life-threatening cerebrovascular disease, which is mostly related with a ruptured intracranial aneurysm. Its complications include rebleeding, early brain injury, cerebral vasospasm, delayed cerebral ischemia, chronic hydrocephalus, and also non neurological problems. Non-coding RNAs (ncRNAs, comprising of microRNAs (miRNAs, small interfering RNAs (siRNAs and long non-coding RNAs (lncRNAs, play an important role in intracranial aneurysms and SAH. Here, we review the non-coding RNAs expression profile and their related mechanisms in intracranial aneurysms and SAH. Moreover, we suggest that these non-coding RNAs function as novel molecular biomarkers to predict intracranial aneurysms and SAH, and may yield new therapies after SAH in the future.

  1. Salmonella Immunotherapy Improves the Outcome of CHOP Chemotherapy in Non-Hodgkin Lymphoma-Bearing Mice

    Science.gov (United States)

    Bascuas, Thais; Moreno, María; Grille, Sofía; Chabalgoity, José A.

    2018-01-01

    We have previously shown that Salmonella immunotherapy is effective to treat B-cell non-Hodgkin lymphoma (B-NHL) in mice. However, this model involves animals with high tumor burden, whereas in the clinics B-NHL patients are usually treated with chemotherapy (CHOP: cyclophosphamide, doxorubicin, vincristine, and prednisone) as first-line therapy prior to immunotherapy. Recently, we have described a NHL-B preclinical model using CHOP chemotherapy to achieve MRD in immunocompetent animals that closely resemble patients’ conditions. In this work, we assessed the efficacy of Salmonella immunotherapy in B-NHL-bearing mice undergoing chemotherapy. Salmonella administration significantly delayed tumor growth and prolonged survival of chemotherapy-treated NHL-bearing animals. Mice receiving the CHOP–Salmonella combined therapy showed increased numbers of tumor-infiltrating leukocytes and a different profile of cytokines and chemokines expressed in the tumor microenvironment. Further, Salmonella immunotherapy in CHOP-treated animals also enhanced NK cells cytotoxic activity as well as induced systemic lymphoma-specific humoral and cellular responses. Chemotherapy treatment profoundly impacted on the general health status of recipient animals, but those receiving Salmonella showed significantly better overall body condition. Altogether, the results clearly demonstrated that Salmonella immunotherapy could be safely used in individuals under CHOP treatment, resulting in a better prognosis. These results give strong support to consider Salmonella as a neoadjuvant therapy in a clinical setting. PMID:29410666

  2. Non-Protein Coding RNAs

    CERN Document Server

    Walter, Nils G; Batey, Robert T

    2009-01-01

    This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and ot...

  3. A 3' UTR-derived non-coding RNA RibS increases expression of cfa and promotes biofilm formation of Salmonella enterica serovar Typhi.

    Science.gov (United States)

    Zhao, Xin; Liu, Rui; Tang, Hao; Osei-Adjei, George; Xu, Shungao; Zhang, Ying; Huang, Xinxiang

    2018-05-08

    Bacterial non-coding RNAs (ncRNAs) are widely studied and found to play important roles in regulating various cellular processes. Recently, many ncRNAs have been discovered to be transcribed or processed from 3' untranslated regions (3' UTRs). Here we reported a novel 3' UTR-derived ncRNA, RibS, which could influence biofilm formation of Salmonella enterica serovar Typhi (S. Typhi). RibS was confirmed to be a ∼700 nt processed product produced by RNase III-catalyzed cleavage from the 3' UTR of riboflavin synthase subunit alpha mRNA, RibE. Overexpression of RibS increased the expression of the cyclopropane fatty acid synthase gene, cfa, which was located at the antisense strand. Biofilm formation of S. Typhi was enhanced by overexpressing RibS both in the wild type strain and cfa deletion mutant. Deletion of cfa attenuated biofilm formation of S. Typhi, while complementation of cfa partly restored the phenotype. Moreover, overexpressing cfa enhanced the biofilm formation of S. Typhi. In summary, RibS has been identified as a novel ncRNA derived from the 3' UTR of RibE that promotes biofilm formation of S. Typhi, and it appears to do so, at least in part, by increasing the expression of cfa. Copyright © 2018 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  4. Detecting non-coding selective pressure in coding regions

    Directory of Open Access Journals (Sweden)

    Blanchette Mathieu

    2007-02-01

    Full Text Available Abstract Background Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements.

  5. Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection.

    Science.gov (United States)

    Fleming, Damarius S; Miller, Laura C

    2018-04-01

    It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs have emerged as having an important role in the immune system in humans. The study uses transcriptomic read counts to profile the type and quantity of both well and lesser characterized sncRNAs, such as microRNAs and small nucleolar RNAs to identify and quantify the classes of sncRNA expressed in whole blood between healthy and highly pathogenic PRRSV-infected pigs. Our results returned evidence on nine classes of sncRNA, four of which were consistently statistically significantly different based on Fisher's Exact Test, that can be detected and possibly interrogated for their effect on host dysregulation during PRRSV infections. Published by Elsevier Inc.

  6. Mycoplasma non-coding RNA: identification of small RNAs and targets

    Directory of Open Access Journals (Sweden)

    Franciele Maboni Siqueira

    2016-10-01

    Full Text Available Abstract Background Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been identified in the porcine respiratory system. Results A total of 47, 15 and 11 putative sRNAs were predicted in M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively. A comparative genomic analysis revealed the presence of species or lineage specific sRNA candidates. Furthermore, the expression profile of some M. hyopneumoniae sRNAs was determined by a reverse transcription amplification approach, in three different culture conditions. All tested sRNAs were transcribed in at least one condition. A detailed investigation revealed a differential expression profile for two M. hyopneumoniae sRNAs in response to oxidative and heat shock stress conditions, suggesting that their expression is influenced by environmental signals. Moreover, we analyzed sRNA-mRNA hybrids and accessed putative target genes for the novel sRNA candidates. The majority of the sRNAs showed interaction with multiple target genes, some of which could be linked to pathogenesis and cell homeostasis activity. Conclusion This study contributes to our knowledge of Mycoplasma sRNAs and their response to environmental changes. Furthermore, the mRNA target prediction provides a perspective for the characterization and comprehension of the function of the sRNA regulatory mechanisms.

  7. Impact of litter Salmonella status during feed withdrawal on Salmonella recovery from the broiler crop and ceca.

    Science.gov (United States)

    Buhr, R J; Bourassa, D V; Hinton, A; Fairchild, B D; Ritz, C W

    2017-12-01

    Research was conducted to evaluate the impact of litter Salmonella status during feed withdrawal on Salmonella recovery from the crop and ceca following feed withdrawal. In 4 experiments, pens of broilers in separate rooms were challenged with marker strains of either Salmonella Montevideo or Salmonella Heidelberg. Three d post challenge, a 12-hour feed withdrawal was initiated, and one pen of broilers was switched between rooms for each Salmonella serotype. In experiments 3 and 4, non-challenged broilers also were added to the Salmonella challenge pens. The litter of each pen was sampled before and after the feed withdrawal period, the broilers euthanized, and the crop and ceca aseptically removed for Salmonella isolation. Results showed that only the challenge Salmonella serotype was recovered from the litter in challenge pens where broilers were not moved, while both Salmonella serotypes were recovered from the litter of the switched pens. Salmonella was recovered from 56/80 crops and from 66/80 ceca of challenged broilers that remained in the challenge pens. The challenge Salmonella serotype was recovered from 50/80 crops and from 60/80 ceca, and the switched pens' litter Salmonella serotype was recovered from 19/80 crops but not from the ceca in broilers challenged with Salmonella and then switched between pens. For experiments 3 and 4, Salmonella was recovered from 19/40 crops and from only 2/40 ceca from the non-challenged broilers placed into the Salmonella challenge pens. The results from broilers that were switched between Salmonella challenge pens indicate that the recovery of Salmonella from the crop of broilers following feed withdrawal (on Salmonella-contaminated litter) appears to depend mainly on the initial challenge Salmonella (62%) and less on the litter Salmonella (24%) status during the feed withdrawal period. In contrast, only the initial challenge Salmonella was recovered from the ceca (79%) from broilers that remained in challenge pens or

  8. Emerging Roles of Small Epstein-Barr Virus Derived Non-Coding RNAs in Epithelial Malignancy

    Science.gov (United States)

    Lung, Raymond Wai-Ming; Tong, Joanna Hung-Man; To, Ka-Fai

    2013-01-01

    Latent Epstein-Barr virus (EBV) infection is an etiological factor in the progression of several human epithelial malignancies such as nasopharyngeal carcinoma (NPC) and a subset of gastric carcinoma. Reports have shown that EBV produces several viral oncoproteins, yet their pathological roles in carcinogenesis are not fully elucidated. Studies on the recently discovered of EBV-encoded microRNAs (ebv-miRNAs) showed that these small molecules function as post-transcriptional gene regulators and may play a role in the carcinogenesis process. In NPC and EBV positive gastric carcinoma (EBVaGC), 22 viral miRNAs which are located in the long alternative splicing EBV transcripts, named BamH1 A rightward transcripts (BARTs), are abundantly expressed. The importance of several miR-BARTs in carcinogenesis has recently been demonstrated. These novel findings enhance our understanding of the oncogenic properties of EBV and may lead to a more effective design of therapeutic regimens to combat EBV-associated malignancies. This article will review the pathological roles of miR-BARTs in modulating the expression of cancer-related genes in both host and viral genomes. The expression of other small non-coding RNAs in NPC and the expression pattern of miR-BARTs in rare EBV-associated epithelial cancers will also be discussed. PMID:23979421

  9. Seroincidence of non-typhoid Salmonella infections: convenience vs. random community-based sampling.

    Science.gov (United States)

    Emborg, H-D; Simonsen, J; Jørgensen, C S; Harritshøj, L H; Krogfelt, K A; Linneberg, A; Mølbak, K

    2016-01-01

    The incidence of reported infections of non-typhoid Salmonella is affected by biases inherent to passive laboratory surveillance, whereas analysis of blood sera may provide a less biased alternative to estimate the force of Salmonella transmission in humans. We developed a mathematical model that enabled a back-calculation of the annual seroincidence of Salmonella based on measurements of specific antibodies. The aim of the present study was to determine the seroincidence in two convenience samples from 2012 (Danish blood donors, n = 500, and pregnant women, n = 637) and a community-based sample of healthy individuals from 2006 to 2007 (n = 1780). The lowest antibody levels were measured in the samples from the community cohort and the highest in pregnant women. The annual Salmonella seroincidences were 319 infections/1000 pregnant women [90% credibility interval (CrI) 210-441], 182/1000 in blood donors (90% CrI 85-298) and 77/1000 in the community cohort (90% CrI 45-114). Although the differences between study populations decreased when accounting for different age distributions the estimates depend on the study population. It is important to be aware of this issue and define a certain population under surveillance in order to obtain consistent results in an application of serological measures for public health purposes.

  10. Non-typhoidal Salmonella and Campylobacter infections among HIV-positive patients in Denmark

    DEFF Research Database (Denmark)

    Larsen, I.K.; Gradel, Kim Oren; Helms, M.

    2011-01-01

    Non-typhoidal Salmonella (NTS) and Campylobacter are common causes of diarrhoea in human immunodeficiency virus (HIV)-positive patients. To investigate if incidence has changed since the introduction of highly active antiretroviral therapy (HAART), we combined data from The Danish Surveillance Re...... population. Moreover our study suggests that there is an increased incidence of Campylobacter-related illness among homosexual men in the HIV-positive population.......Non-typhoidal Salmonella (NTS) and Campylobacter are common causes of diarrhoea in human immunodeficiency virus (HIV)-positive patients. To investigate if incidence has changed since the introduction of highly active antiretroviral therapy (HAART), we combined data from The Danish Surveillance...... Registry for Enteric Pathogens and The Danish National Hospital Registry. We found that the incidences of NTS- and Campylobacter-related illness among HIV-positive patients in Denmark have declined since the introduction of HAART, although the incidences remained higher compared to the background...

  11. Continuous Non-malleable Codes

    DEFF Research Database (Denmark)

    Faust, Sebastian; Mukherjee, Pratyay; Nielsen, Jesper Buus

    2014-01-01

    or modify it to the encoding of a completely unrelated value. This paper introduces an extension of the standard non-malleability security notion - so-called continuous non-malleability - where we allow the adversary to tamper continuously with an encoding. This is in contrast to the standard notion of non...... is necessary to achieve continuous non-malleability in the split-state model. Moreover, we illustrate that none of the existing constructions satisfies our uniqueness property and hence is not secure in the continuous setting. We construct a split-state code satisfying continuous non-malleability. Our scheme...... is based on the inner product function, collision-resistant hashing and non-interactive zero-knowledge proofs of knowledge and requires an untamperable common reference string. We apply continuous non-malleable codes to protect arbitrary cryptographic primitives against tampering attacks. Previous...

  12. Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells

    Directory of Open Access Journals (Sweden)

    Sarah Inwood

    2018-01-01

    Full Text Available The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK, while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.

  13. Non-binary Entanglement-assisted Stabilizer Quantum Codes

    OpenAIRE

    Riguang, Leng; Zhi, Ma

    2011-01-01

    In this paper, we show how to construct non-binary entanglement-assisted stabilizer quantum codes by using pre-shared entanglement between the sender and receiver. We also give an algorithm to determine the circuit for non-binary entanglement-assisted stabilizer quantum codes and some illustrated examples. The codes we constructed do not require the dual-containing constraint, and many non-binary classical codes, like non-binary LDPC codes, which do not satisfy the condition, can be used to c...

  14. Quantitative Profiling of Peptides from RNAs classified as non-coding

    Science.gov (United States)

    Prabakaran, Sudhakaran; Hemberg, Martin; Chauhan, Ruchi; Winter, Dominic; Tweedie-Cullen, Ry Y.; Dittrich, Christian; Hong, Elizabeth; Gunawardena, Jeremy; Steen, Hanno; Kreiman, Gabriel; Steen, Judith A.

    2014-01-01

    Only a small fraction of the mammalian genome codes for messenger RNAs destined to be translated into proteins, and it is generally assumed that a large portion of transcribed sequences - including introns and several classes of non-coding RNAs (ncRNAs) do not give rise to peptide products. A systematic examination of translation and physiological regulation of ncRNAs has not been conducted. Here, we use computational methods to identify the products of non-canonical translation in mouse neurons by analyzing unannotated transcripts in combination with proteomic data. This study supports the existence of non-canonical translation products from both intragenic and extragenic genomic regions, including peptides derived from anti-sense transcripts and introns. Moreover, the studied novel translation products exhibit temporal regulation similar to that of proteins known to be involved in neuronal activity processes. These observations highlight a potentially large and complex set of biologically regulated translational events from transcripts formerly thought to lack coding potential. PMID:25403355

  15. Contamination of Carcasses and Utensils in Small Swine Slaughterhouses by Salmonella in the Northwestern Region of the State of Rio de Janeiro, Brazil.

    Science.gov (United States)

    Cabral, Claudius Couto; Panzenhagen, Pedro Henrique Nunes; Delgado, Karina Frensel; Silva, Gabriela Rodrigues Alves; Rodrigues, Dália Dos Prazeres; Franco, Robson Maia; Conte-Junior, Carlos Adam

    2017-07-01

    Salmonella is a major foodborne pathogen that constantly threatens food safety in developed countries and underdeveloped countries such as Brazil, where it is responsible for 38% of notified cases of foodborne illness. Swine are one of the main meat-producing species that may asymptomatically carry Salmonella, periodically shedding the bacteria through feces. The state of Rio de Janeiro is not a major producer of swine meat, but small slaughterhouses are operational and produce meat for consumption within the state, although few studies have been conducted in the region. In this context, this study was designed to evaluate Salmonella contamination in carcasses, lymph nodes, feces, utensils, and the environment of three small slaughterhouses in the state of Rio de Janeiro. A total of 344 samples from carcasses, utensils, equipment, water, and the environment were collected from these slaughterhouses in the northwestern region of Rio de Janeiro. Salmonella was isolated from 36 (10.5%) samples: 10 of 48 carcasses, 19 of 96 lymph nodes, 4 of 48 fecal samples, 2 of 6 water samples, and 1 of 6 bleeding knives; 55 isolates were recovered. Serotyping revealed the predominance of Salmonella Typhimurium (20 isolates) followed by Salmonella Abony (10 isolates), Salmonella Give (7 isolates), Salmonella Heidelberg (4 isolates), and Salmonella Infantis (1 isolate). Ten isolates were only partially typeable, with only their O antigen identified, and three isolates had rough, nontypeable colonies. Despite the overall low prevalence of Salmonella in this study, all three slaughterhouses had poor hygienic and sanitary conditions, providing easy routes for carcass and, consequently, meat contamination. Thus, it is imperative to enforce sanitary inspections in these establishments and to apply good manufacture practices to assure the safety of the produced pork.

  16. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ

    Directory of Open Access Journals (Sweden)

    Ohad eGal-Mor

    2014-08-01

    Full Text Available Human infections by the bacterial pathogen Salmonella enterica represent major disease burdens worldwide. This highly ubiquitous species consists of more than 2600 different serovars that can be divided into typhoidal and non-typhoidal Salmonella (NTS serovars. Despite their genetic similarity, these two groups elicit very different diseases and distinct immune responses in humans. Comparative analyses of the genomes of multiple Salmonella serovars have begun to explain the basis of the variation in disease manifestations. Recent advances in modeling both enteric fever and intestinal gastroenteritis in mice will facilitate investigation into both the bacterial- and host-mediated mechanisms involved in salmonelloses. Understanding the genetic and molecular mechanisms responsible for differences in disease outcome will augment our understanding of Salmonella pathogenesis, host immunity, and the molecular basis of host specificity. This review outlines the differences in epidemiology, clinical manifestations, and the human immune response to typhoidal and NTS infections and summarizes the current thinking on why these differences might exist.

  17. Public health investigations of Salmonella Enteritidis in catering raw shell eggs, 2002-2004.

    Science.gov (United States)

    Little, C L; Surman-Lee, S; Greenwood, M; Bolton, F J; Elson, R; Mitchell, R T; Nichols, G N; Sagoo, S K; Threlfall, E J; Ward, L R; Gillespie, I A; O'Brien, S

    2007-06-01

    In response to a dramatic change in the epidemiology of Salmonella Enteritidis in England and Wales thought to be associated with raw shell eggs, the Health Protection Agency initiated public health investigations to establish the incidence of Salmonella contamination and origin of eggs used by catering premises implicated in outbreaks of Salm. Enteritidis. Between October 2002 and November 2004, 16 971 eggs were sampled and Salmonella were recovered from 3.4%. Salmonella was isolated from 5.5% and 6.3% of Spanish and eggs of unknown origin, respectively, used in catering premises linked to outbreaks, a level significantly higher than that (1.1%) found in nonLion Quality UK eggs sampled. The small sample of UK Lion Quality eggs tested (reflecting their lack of use in premises visited) did not contain Salmonella. Several phage types of Salm. Enteritidis other than phage type 4 (PT 4) were identified with nonUK eggs. Eggs from Spain were implicated as a major source of infection. Eggs were contaminated more frequently with Salmonella when shells were dirty and/or cracked, and stored at above 8 degrees C. The use of Spanish eggs by the catering sector has been identified as a consistent significant factor in many of the outbreaks caused by Salm. Enteritidis nonPT4 in England and Wales during 2002-2004. Advice to caterers and hospitals that raw shell eggs should not be used in food that will either not be cooked or only lightly cooked should be reinforced.

  18. Small non-coding RNAs: new insights in modulation of host immune response by intracellular bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Waqas Ahmed

    2016-10-01

    Full Text Available Pathogenic bacteria possess intricate regulatory networks that temporally control the production of virulence factors, and enable the bacteria to survive and proliferate within host cell. Small non-coding RNAs (sRNAs have been identified as important regulators of gene expression in diverse biological contexts. Recent research has shown bacterial sRNAs involved in growth and development, cell proliferation, differentiation, metabolism, cell signaling and immune response through regulating protein–protein interactions or via their ability to base pair with RNA and DNA. In this review, we provide a brief overview of mechanism of action employed by immune-related sRNAs, their known functions in immunity, and how they can be integrated into regulatory circuits that govern virulence, which will facilitates to understand pathogenesis and the development of novel, more effective therapeutic approaches to treat infections caused by intracellular bacterial pathogens.

  19. Non-Saccharomyces yeasts protect against epithelial cell barrier disruption induced by Salmonella enterica subsp. enterica serovar Typhimurium.

    Science.gov (United States)

    Smith, I M; Baker, A; Arneborg, N; Jespersen, L

    2015-11-01

    The human gastrointestinal epithelium makes up the largest barrier separating the body from the external environment. Whereas invasive pathogens cause epithelial barrier disruption, probiotic micro-organisms modulate tight junction regulation and improve epithelial barrier function. In addition, probiotic strains may be able to reduce epithelial barrier disruption caused by pathogenic species. The aim of this study was to explore non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Benchmarking against established probiotic strains, we evaluated the ability of four nonpathogenic yeast species to modulate transepithelial electrical resistance (TER) across a monolayer of differentiated human colonocytes (Caco-2 cells). Further, we assessed yeast modulation of a Salmonella Typhimurium-induced epithelial cell barrier function insult. Our findings demonstrate distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function. While the established probiotic yeast Saccharomyces boulardii increased TER across a Caco-2 monolayer by 30%, Kluyveromyces marxianus exhibited significantly stronger properties of TER enhancement (50% TER increase). In addition, our data demonstrate significant yeast-mediated modulation of Salmonella-induced epithelial cell barrier disruption and identify K. marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion. This study demonstrates distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Further, our data demonstrate significant yeast-mediated modulation of Salmonella Typhimurium-induced epithelial cell barrier disruption and identify Kluyveromyces marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion. This study is the first to demonstrate significant non-Saccharomyces yeast

  20. Granulomatous salmonella osteomyelitis associated with anti-tumor necrosis factor therapy in a non-sickle cell patient: a case report

    Energy Technology Data Exchange (ETDEWEB)

    Gould, Elaine S.; Gilet, Anthony G. [State University of New York at Stony Brook, Department of Radiology, Stony Brook, NY (United States); Vigorita, Vincent J. [SUNY Health Sciences Center Brooklyn, Department of Pathology and Orthopedics, Brooklyn, NY (United States)

    2010-08-15

    Salmonella osteomyelitis is seen most commonly in patients with sickle cell disease and in those with compromised immune systems. We report on the clinical, histological and imaging findings of salmonella osteomyelitis with intraosseous abscess formation occurring in a non-sickle cell patient receiving anti-tumor necrosis factor (TNF) alpha therapy. (orig.)

  1. Granulomatous salmonella osteomyelitis associated with anti-tumor necrosis factor therapy in a non-sickle cell patient: a case report

    International Nuclear Information System (INIS)

    Gould, Elaine S.; Gilet, Anthony G.; Vigorita, Vincent J.

    2010-01-01

    Salmonella osteomyelitis is seen most commonly in patients with sickle cell disease and in those with compromised immune systems. We report on the clinical, histological and imaging findings of salmonella osteomyelitis with intraosseous abscess formation occurring in a non-sickle cell patient receiving anti-tumor necrosis factor (TNF) alpha therapy. (orig.)

  2. Identification of coding and non-coding mutational hotspots in cancer genomes.

    Science.gov (United States)

    Piraino, Scott W; Furney, Simon J

    2017-01-05

    The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from

  3. Epidemiology of Non-Typhoidal Salmonella (NTS in Humans and Animals in the Gambia and Senegal

    Directory of Open Access Journals (Sweden)

    Dione, M.

    2010-01-01

    Full Text Available Non-Typhoidal Salmonella (NTS species are important food-borne pathogens. Although acute gastroenteritis is the most common clinical symptom, complications can occur resulting in bacteraemia with or without focal infections. Food products, especially food of animal origin such as poultry are associated with the transmission to humans. In Africa, NTS are among the most common cause of bloodstream infections in children younger than 5 years. Epidemiological data on NTS are lacking in Africa both for human and animal infections. Therefore, a study providing a better understanding of the factors that lead to the emergence of NTS is a prerequisite for the design of improved intervention strategies to control these pathogens. The aim of this thesis was to study the epidemiology of NTS pathogens in humans and animals in The Gambia and Senegal. Chapter 1 reviews the current status of knowledge on NTS infections in Africa with focus on The Gambia and Senegal. It also provides the background against which these studies were conducted. Chapter 2 describes the prevalence of NTS along the poultry production chain in Casamance, Senegal. Fifty seven randomly selected broiler farms, 42 street restaurants and 285 chicken carcasses were studied. The following farm prevalences were reported: 35.1, 38.6 and 29.8% in chicken faeces, on carcass skin, and in muscles, respectively. NTS were found in chicken meat servings of 14.3% of the 42 street restaurants and in 40.4% of the 285 chicken carcasses examined. The most prevalent serotypes among the eighteen identified were Salmonella Brancaster (57.9%, Salmonella Goelzau (10.7%, Salmonella Kentucky (8.4%, and Salmonella Hadar (7.3%. The following serotypes were for the first time identified in Senegal: Salmonella Bandia, Salmonella Bessi, Salmonella Brunei, Salmonella Hull, Salmonella Istanbul, Salmonella Javiana, Salmonella Magherafelt, Salmonella Molade, Salmonella oxford, Salmonella Poona, Salmonella Rubislaw

  4. RIP-seq of BmAgo2-associated small RNAs reveal various types of small non-coding RNAs in the silkworm, Bombyx mori

    Science.gov (United States)

    2013-01-01

    Background Small non-coding RNAs (ncRNAs) are important regulators of gene expression in eukaryotes. Previously, only microRNAs (miRNAs) and piRNAs have been identified in the silkworm, Bombyx mori. Furthermore, only ncRNAs (50-500nt) of intermediate size have been systematically identified in the silkworm. Results Here, we performed a systematic identification and analysis of small RNAs (18-50nt) associated with the Bombyx mori argonaute2 (BmAgo2) protein. Using RIP-seq, we identified various types of small ncRNAs associated with BmAGO2. These ncRNAs showed a multimodal length distribution, with three peaks at ~20nt, ~27nt and ~33nt, which included tRNA-, transposable element (TE)-, rRNA-, snoRNA- and snRNA-derived small RNAs as well as miRNAs and piRNAs. The tRNA-derived fragments (tRFs) were found at an extremely high abundance and accounted for 69.90% of the BmAgo2-associated small RNAs. Northern blotting confirmed that many tRFs were expressed or up-regulated only in the BmNPV-infected cells, implying that the tRFs play a prominent role by binding to BmAgo2 during BmNPV infection. Additional evidence suggested that there are potential cleavage sites on the D, anti-codon and TψC loops of the tRNAs. TE-derived small RNAs and piRNAs also accounted for a significant proportion of the BmAgo2-associated small RNAs, suggesting that BmAgo2 could be involved in the maintenance of genome stability by suppressing the activities of transposons guided by these small RNAs. Finally, Northern blotting was also used to confirm the Bombyx 5.8 s rRNA-derived small RNAs, demonstrating that various novel small RNAs exist in the silkworm. Conclusions Using an RIP-seq method in combination with Northern blotting, we identified various types of small RNAs associated with the BmAgo2 protein, including tRNA-, TE-, rRNA-, snoRNA- and snRNA-derived small RNAs as well as miRNAs and piRNAs. Our findings provide new clues for future functional studies of the role of small RNAs in insect

  5. Survival of Salmonella Newport in oysters.

    Science.gov (United States)

    Morrison, Christopher M; Armstrong, Alexandra E; Evans, Sanford; Mild, Rita M; Langdon, Christopher J; Joens, Lynn A

    2011-08-02

    Salmonella enterica is the leading cause of laboratory-confirmed foodborne illness in the United States and raw shellfish consumption is a commonly implicated source of gastrointestinal pathogens. A 2005 epidemiological study done in our laboratory by Brands et al., showed that oysters in the United States are contaminated with Salmonella, and in particular, a specific strain of the Newport serovar. This work sought to further investigate the host-microbe interactions between Salmonella Newport and oysters. A procedure was developed to reliably and repeatedly expose oysters to enteric bacteria and quantify the subsequent levels of bacterial survival. The results show that 10 days after an exposure to Salmonella Newport, an average concentration of 3.7 × 10(3)CFU/g remains within the oyster meat, and even after 60 days there still can be more than 10(2)CFU/g remaining. However, the strain of Newport that predominated in the market survey done by Brands et al. does not survive within oysters or the estuarine environment better than any other strains of Salmonella we tested. Using this same methodology, we compared Salmonella Newport's ability to survive within oysters to a non-pathogenic strain of E. coli and found that after 10 days the concentration of Salmonella was 200-times greater than that of E. coli. We also compared those same strains of Salmonella and E. coli in a depuration process to determine if a constant 120 L/h flux of clean seawater could significantly reduce the concentration of bacteria within oysters and found that after 3 days the oysters retained over 10(4)CFU/g of Salmonella while the oysters exposed to the non-pathogenic strain of E. coli contained 100-times less bacteria. Overall, the results of this study demonstrate that any of the clinically relevant serovars of Salmonella can survive within oysters for significant periods of time after just one exposure event. Based on the drastic differences in survivability between Salmonella and a non

  6. Analysis of Non-binary Hybrid LDPC Codes

    OpenAIRE

    Sassatelli, Lucile; Declercq, David

    2008-01-01

    In this paper, we analyse asymptotically a new class of LDPC codes called Non-binary Hybrid LDPC codes, which has been recently introduced. We use density evolution techniques to derive a stability condition for hybrid LDPC codes, and prove their threshold behavior. We study this stability condition to conclude on asymptotic advantages of hybrid LDPC codes compared to their non-hybrid counterparts.

  7. Prevalence and Characterization of Motile Salmonella in Commercial Layer Poultry Farms in Bangladesh

    Science.gov (United States)

    Barua, Himel; Biswas, Paritosh K.; Olsen, Katharina E. P.; Christensen, Jens P.

    2012-01-01

    Salmonella is a globally widespread food-borne pathogen having major impact on public health. All motile serovars of Salmonella enterica of poultry origin are zoonotic, and contaminated meat and raw eggs are an important source to human infections. Information on the prevalence of Salmonella at farm/holding level, and the zoonotic serovars circulating in layer poultry in the South and South-East Asian countries including Bangladesh, where small-scale commercial farms are predominant, is limited. To investigate the prevalence of Salmonella at layer farm level, and to identify the prevalent serovars we conducted a cross-sectional survey by randomly selecting 500 commercial layer poultry farms in Bangladesh. Faecal samples from the selected farms were collected following standard procedure, and examined for the presence of Salmonella using conventional bacteriological procedures. Thirty isolates were randomly selected, from the ninety obtained from the survey, for serotyping and characterized further by plasmid profiling and pulsed-field gel electrophoresis (PFGE). Results of the survey showed that the prevalence of motile Salmonella at layer farm level was 18% (95% confidence interval 15–21%), and Salmonella Kentucky was identified to be the only serovar circulating in the study population. Plasmid analysis of the S. Kentucky and non-serotyped isolates revealed two distinct profiles with a variation of two different sizes (2.7 and 4.8 kb). PFGE of the 30 S. Kentucky and 30 non-serotyped isolates showed that all of them were clonally related because only one genotype and three subtypes were determined based on the variation in two or three bands. This is also the first report on the presence of any specific serovar of Salmonella enterica in poultry in Bangladesh. PMID:22558269

  8. Influence of On-farm pig Salmonella status on Salmonella Shedding at Slaughter.

    Science.gov (United States)

    Casanova-Higes, A; Andrés-Barranco, S; Mainar-Jaime, R C

    2017-08-01

    The risk of Salmonella shedding among pigs at slaughter with regard to their previous on-farm Salmonella status was assessed in a group of pigs from a farm from NE of Spain. A total of 202 pigs that had been serologically monitored monthly during the fattening period and from which mesenteric lymph nodes (MLN) and faecal (SFEC) samples were collected at slaughter for Salmonella isolation were included. A repeated-measures anova was used to assess the relationship between mean OD% values during the fattening period and sampling time and bacteriology on MLN and SFEC. Pigs were also grouped into four groups, that is pigs seronegative during the fattening period and Salmonella negative in MLN (group A; n = 69); pigs seronegative during the fattening period but Salmonella positive in MLN (B; n = 36); pigs seropositive at least once and Salmonella positive in MLN (C; n = 50); and pigs seropositive at least once but Salmonella negative in (D; n = 47). Pigs shedding at slaughter seroconverted much earlier and showed much higher mean OD% values than non-shedders pigs. The proportion of Salmonella shedders in groups A and D was high and similar (26.1% and 29.8%, respectively), but significantly lower than that for groups B and C. The odds of shedding Salmonella for groups B and C were 4.8 (95% CI = 1.5-15.5) and 20.9 (3.7-118) times higher, respectively, when compared to A. It was concluded that a large proportion of Salmonella seronegative pigs may shed Salmonella at slaughter, which would be likely associated to previous exposure with contaminated environments (i.e. transport and lairage). For pigs already infected at farm, the likelihood of shedding Salmonella was much higher and may depend on whether the bacterium has colonized the MLN or not. The odds of shedding Salmonella spp. were always much higher for pigs in which Salmonella was isolated from MLN. © 2016 Blackwell Verlag GmbH.

  9. A single-tube screen for Salmonella and Shigella.

    Science.gov (United States)

    Procop, Gary W; Wallace, Jacqueline D; Tuohy, Marion J; Lasalvia, Margret M; Addison, Rachel M; Reller, L Barth

    2008-08-01

    Salmonella and Shigella species are routinely sought in stool specimens submitted for culture. It is a common practice to screen lactose-negative colonies by using triple sugar iron agar, lysine iron agar, and Christensen urea agar to determine if further identification is necessary. We designed and evaluated a novel combination of media, which are layered in a single tube, for screening isolates suspected to possibly represent Salmonella or Shigella. We tested this media combination with 106 Salmonella, 56 Shigella, and 56 other gram-negative bacilli. All Salmonella and Shigella isolates tested were appropriately characterized as possible Salmonella or Shigella by using an algorithm developed for use with this media combination. Similarly, 53 (95%) of 56 other gram-negative bacilli were appropriately screened as non -Salmonella and non -Shigella isolates. This unique media combination provides the most important biochemical reactions needed to screen for Salmonella and Shigella in a single-tube format, which decreases labor by two thirds (ie, 1 tube is inoculated vs 3).

  10. A carbon nanotube immunosensor for Salmonella

    Science.gov (United States)

    Lerner, Mitchell B.; Goldsmith, Brett R.; McMillon, Ronald; Dailey, Jennifer; Pillai, Shreekumar; Singh, Shree R.; Johnson, A. T. Charlie

    2011-12-01

    Antibody-functionalized carbon nanotube devices have been suggested for use as bacterial detectors for monitoring of food purity in transit from the farm to the kitchen. Here we report progress towards that goal by demonstrating specific detection of Salmonella in complex nutrient broth solutions using nanotube transistors functionalized with covalently-bound anti-Salmonella antibodies. The small size of the active device region makes them compatible with integration in large-scale arrays. We find that the on-state current of the transistor is sensitive specifically to the Salmonella concentration and saturates at low concentration (Salmonella and other bacteria types, with no sign of saturation even at much larger concentrations (108 cfu/ml).

  11. Cellulitis Due to Salmonella infantis.

    Directory of Open Access Journals (Sweden)

    Satish R Patil

    2013-01-01

    Full Text Available Bacteria of the genus Salmonella are highly adapted for the growth in both humans and animals and cause a wide spectrum of disease. The growth of Serotypes S. typhi and S. paratyphi is restricted to human hosts, in whom these organisms cause enteric (typhoid fever. The remaining Serotypes (non typhoidal Salmonella or NTS can colonize the gastrointestinal tracts of the broad range of animals, including mammals, reptiles, birds and insects. The usual clinical presentation of non-typhoidal salmonellae (NTS infection is self limited gastroenteritis; however bacteremia and focal extra intestinal infection may occur. However salmonella localization to the skin presenting as cutaneous ulceration is regarded as a rare event. Rates of morbidity and mortality associated with NTS are highest among the elderly, infants, and immunocompromised individuals, including those with hemoglobinopathies, HIV infection, or infections that cause blockade of the reticuloendothelial system. We isolated S.infantis in 50 years old man with left leg cellulitis. The serotype was confirmed at Central Research Institute, Kasauli.

  12. An expanding universe of the non-coding genome in cancer biology.

    Science.gov (United States)

    Xue, Bin; He, Lin

    2014-06-01

    Neoplastic transformation is caused by accumulation of genetic and epigenetic alterations that ultimately convert normal cells into tumor cells with uncontrolled proliferation and survival, unlimited replicative potential and invasive growth [Hanahan,D. et al. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674]. Although the majority of the cancer studies have focused on the functions of protein-coding genes, emerging evidence has started to reveal the importance of the vast non-coding genome, which constitutes more than 98% of the human genome. A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs, including small ncRNAs and long ncRNAs (lncRNAs), play an important role in cancer development by regulating protein-coding gene expression through diverse mechanisms. In addition to ncRNAs, nearly half of the mammalian genomes consist of transposable elements, particularly retrotransposons. Once depicted as selfish genomic parasites that propagate at the expense of host fitness, retrotransposon elements could also confer regulatory complexity to the host genomes during development and disease. Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor development. Taken together, the functional significance of non-coding genome in tumorigenesis has been previously underestimated, and diverse transcripts derived from the non-coding genome could act as integral functional components of the oncogene and tumor suppressor network. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Salmonellae in avian wildlife in Norway from 1969 to 2000

    DEFF Research Database (Denmark)

    Refsum, T.; Handeland, K.; Baggesen, Dorte Lau

    2002-01-01

    Postmortem records of wild-living birds in Norway with laboratory-confirmed findings of salmonella infection were summarized for the period from 1969 to 2000. Salmonella spp. were isolated from 470 birds belonging to 26 species. The salmonella-positive birds included 441 small passerines, 15 gull...

  14. nRC: non-coding RNA Classifier based on structural features.

    Science.gov (United States)

    Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

    2017-01-01

    Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

  15. Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana.

    Science.gov (United States)

    Hoffmann, Robert D; Palmgren, Michael

    2016-06-13

    Whole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown. Here, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3' untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses. Loss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication.

  16. Seroincidence of non-typhoid Salmonella infections

    DEFF Research Database (Denmark)

    Emborg, H-D; Simonsen, J; Jørgensen, C S

    2016-01-01

    that enabled a back-calculation of the annual seroincidence of Salmonella based on measurements of specific antibodies. The aim of the present study was to determine the seroincidence in two convenience samples from 2012 (Danish blood donors, n = 500, and pregnant women, n = 637) and a community-based sample...... of healthy individuals from 2006 to 2007 (n = 1780). The lowest antibody levels were measured in the samples from the community cohort and the highest in pregnant women. The annual Salmonella seroincidences were 319 infections/1000 pregnant women [90% credibility interval (CrI) 210-441], 182/1000 in blood...

  17. Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs.

    Directory of Open Access Journals (Sweden)

    Chen Xie

    2012-09-01

    Full Text Available Tinkering with pre-existing genes has long been known as a major way to create new genes. Recently, however, motherless protein-coding genes have been found to have emerged de novo from ancestral non-coding DNAs. How these genes originated is not well addressed to date. Here we identified 24 hominoid-specific de novo protein-coding genes with precise origination timing in vertebrate phylogeny. Strand-specific RNA-Seq analyses were performed in five rhesus macaque tissues (liver, prefrontal cortex, skeletal muscle, adipose, and testis, which were then integrated with public transcriptome data from human, chimpanzee, and rhesus macaque. On the basis of comparing the RNA expression profiles in the three species, we found that most of the hominoid-specific de novo protein-coding genes encoded polyadenylated non-coding RNAs in rhesus macaque or chimpanzee with a similar transcript structure and correlated tissue expression profile. According to the rule of parsimony, the majority of these hominoid-specific de novo protein-coding genes appear to have acquired a regulated transcript structure and expression profile before acquiring coding potential. Interestingly, although the expression profile was largely correlated, the coding genes in human often showed higher transcriptional abundance than their non-coding counterparts in rhesus macaque. The major findings we report in this manuscript are robust and insensitive to the parameters used in the identification and analysis of de novo genes. Our results suggest that at least a portion of long non-coding RNAs, especially those with active and regulated transcription, may serve as a birth pool for protein-coding genes, which are then further optimized at the transcriptional level.

  18. Preliminary Transcriptome Analysis of Mature Biofilm and Planktonic Cells of Salmonella Enteritidis Exposure to Acid Stress

    Directory of Open Access Journals (Sweden)

    Kun Jia

    2017-09-01

    Full Text Available Salmonella has emerged as a well-recognized food-borne pathogen, with many strains able to form biofilms and thus cause cross-contamination in food processing environments where acid-based disinfectants are widely encountered. In the present study, RNA sequencing was employed to establish complete transcriptome profiles of Salmonella Enteritidis in the forms of planktonic and biofilm-associated cells cultured in Tryptic Soytone Broth (TSB and acidic TSB (aTSB. The gene expression patterns of S. Enteritidis significantly differed between biofilm-associated and planktonic cells cultivated under the same conditions. The assembled transcriptome of S. Enteritidis in this study contained 5,442 assembled transcripts, including 3,877 differentially expressed genes (DEGs identified in biofilm and planktonic cells. These DEGs were enriched in terms such as regulation of biological process, metabolic process, macromolecular complex, binding and transferase activity, which may play crucial roles in the biofilm formation of S. Enteritidis cultivated in aTSB. Three significant pathways were observed to be enriched under acidic conditions: bacterial chemotaxis, porphyrin-chlorophyll metabolism and sulfur metabolism. In addition, 15 differentially expressed novel non-coding small RNAs (sRNAs were identified, and only one was found to be up-regulated in mature biofilms. This preliminary study of the S. Enteritidis transcriptome serves as a basis for future investigations examining the complex network systems that regulate Salmonella biofilm in acidic environments, which provide information on biofilm formation and acid stress interaction that may facilitate the development of novel disinfection procedures in the food processing industry.

  19. Salmonella

    Science.gov (United States)

    ... Compartir Find out about Salmonella infections linked to Kellogg’s Honey Smacks Cereal Find out about Salmonella infections ... Outbreaks Multistate Outbreak of Salmonella Infections Linked to Kellogg’s Honey Smacks Cereal Multistate Outbreak of Salmonella Adelaide ...

  20. Oral immunisation of laying hens with the live vaccine strains of TAD Salmonella vac E and TAD Salmonella vac T reduces internal egg contamination with Salmonella Enteritidis.

    Science.gov (United States)

    Gantois, Inne; Ducatelle, Richard; Timbermont, Leen; Boyen, Filip; Bohez, Lotte; Haesebrouck, Freddy; Pasmans, Frank; van Immerseel, Filip

    2006-09-11

    Eggs are a major source of human infections with Salmonella. Therefore controlling egg contamination in laying hen flocks is one of the main targets for control programmes. A study was carried out to assess the effect of oral vaccination with TAD Salmonella vac E, TAD Salmonella vac T and with both vaccines TAD Salmonella vac E and TAD Salmonella vac T, on colonization of the reproductive tract and internal egg contamination of laying hens with Salmonella Enteritidis. Three groups of 30 laying hens were vaccinated at 1 day, 6 weeks and 16 weeks of age with either one of the vaccine strains, or a combination of both vaccine strains, while a fourth group was left unvaccinated. At 24 weeks of age, the birds were intravenously challenged with 0.5 ml containing 5 x 10(7)cfu Salmonella Enteritidis PT4 S1400/94. The number of oviducts from which Salmonella was isolated, was significantly lower in the vaccinated than in the non-vaccinated hens at 3 weeks post-challenge. Significantly less egg contents were Salmonella positive in the birds vaccinated with TAD Salmonella vac E or TAD Salmonella vac T (12/105 batches of eggs in both groups) than in the unvaccinated birds (28/105 batches of eggs). Internal egg contamination in the hens vaccinated with both TAD Salmonella vac E and TAD Salmonella vac T was even more reduced, as over the whole experiment, only one batch of eggs was positive. In conclusion, these data indicate that vaccination of laying hens with these live vaccines could be considered as a valuable tool in controlling internal egg contamination.

  1. Salmonella Typhimurium pneumonia in a patient with multiple myeloma.

    Science.gov (United States)

    Khan, Sadia; Kumar, V Anil; Sidharthan, Neeraj; Mehta, Asmita; Backer, Binita; Dinesh, Kavitha R

    2015-04-01

    Pneumonia due to non-typhoidal Salmonella is a rarely reported entity. A fatal case of Salmonella pneumonia is reported here where Salmonella Typhimurium was isolated from the endotracheal aspirate and blood culture. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  2. Annotating pathogenic non-coding variants in genic regions.

    Science.gov (United States)

    Gelfman, Sahar; Wang, Quanli; McSweeney, K Melodi; Ren, Zhong; La Carpia, Francesca; Halvorsen, Matt; Schoch, Kelly; Ratzon, Fanni; Heinzen, Erin L; Boland, Michael J; Petrovski, Slavé; Goldstein, David B

    2017-08-09

    Identifying the underlying causes of disease requires accurate interpretation of genetic variants. Current methods ineffectively capture pathogenic non-coding variants in genic regions, resulting in overlooking synonymous and intronic variants when searching for disease risk. Here we present the Transcript-inferred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-coding variation that causes disease. High TraP scores single out extremely rare variants with lower minor allele frequencies than missense variants. TraP accurately distinguishes known pathogenic and benign variants in synonymous (AUC = 0.88) and intronic (AUC = 0.83) public datasets, dismissing benign variants with exceptionally high specificity. TraP analysis of 843 exomes from epilepsy family trios identifies synonymous variants in known epilepsy genes, thus pinpointing risk factors of disease from non-coding sequence data. TraP outperforms leading methods in identifying non-coding variants that are pathogenic and is therefore a valuable tool for use in gene discovery and the interpretation of personal genomes.While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.

  3. Novel classes of non-coding RNAs and cancer

    Directory of Open Access Journals (Sweden)

    Sana Jiri

    2012-05-01

    Full Text Available Abstract For the many years, the central dogma of molecular biology has been that RNA functions mainly as an informational intermediate between a DNA sequence and its encoded protein. But one of the great surprises of modern biology was the discovery that protein-coding genes represent less than 2% of the total genome sequence, and subsequently the fact that at least 90% of the human genome is actively transcribed. Thus, the human transcriptome was found to be more complex than a collection of protein-coding genes and their splice variants. Although initially argued to be spurious transcriptional noise or accumulated evolutionary debris arising from the early assembly of genes and/or the insertion of mobile genetic elements, recent evidence suggests that the non-coding RNAs (ncRNAs may play major biological roles in cellular development, physiology and pathologies. NcRNAs could be grouped into two major classes based on the transcript size; small ncRNAs and long ncRNAs. Each of these classes can be further divided, whereas novel subclasses are still being discovered and characterized. Although, in the last years, small ncRNAs called microRNAs were studied most frequently with more than ten thousand hits at PubMed database, recently, evidence has begun to accumulate describing the molecular mechanisms by which a wide range of novel RNA species function, providing insight into their functional roles in cellular biology and in human disease. In this review, we summarize newly discovered classes of ncRNAs, and highlight their functioning in cancer biology and potential usage as biomarkers or therapeutic targets.

  4. Research and identification of pathogenic bacteria 'Salmonella and Listeria' in food

    International Nuclear Information System (INIS)

    Harizi Khalil

    2009-01-01

    The sums propose to evaluate the bacterial contamination of certain food taken randomly by two pathogenic bacteria (Salmonella and Listeria) considering the evolution of the diseases of food oignon. For that 78 food samples of different origins were analysed. 2 stocks of the Listeria kind and 3 stocks of the salmonella kind were insulated and identified by biochemical and molecular tests. The pathogenic isolates were identified by coloration gram, test catalase, insulation on specific culture media and Api (20 E for Salmonella and Api listeria. At the end, the PCR were realized to amplify the gene iap which codes for the protein p60 at listeria as well as a sequence clonee randomly specific of Salmonella.

  5. ncRNA-class Web Tool: Non-coding RNA feature extraction and pre-miRNA classification web tool

    KAUST Repository

    Kleftogiannis, Dimitrios A.; Theofilatos, Konstantinos A.; Papadimitriou, Stergios; Tsakalidis, Athanasios K.; Likothanassis, Spiridon D.; Mavroudi, Seferina P.

    2012-01-01

    Until recently, it was commonly accepted that most genetic information is transacted by proteins. Recent evidence suggests that the majority of the genomes of mammals and other complex organisms are in fact transcribed into non-coding RNAs (ncRNAs), many of which are alternatively spliced and/or processed into smaller products. Non coding RNA genes analysis requires the calculation of several sequential, thermodynamical and structural features. Many independent tools have already been developed for the efficient calculation of such features but to the best of our knowledge there does not exist any integrative approach for this task. The most significant amount of existing work is related to the miRNA class of non-coding RNAs. MicroRNAs (miRNAs) are small non-coding RNAs that play a significant role in gene regulation and their prediction is a challenging bioinformatics problem. Non-coding RNA feature extraction and pre-miRNA classification Web Tool (ncRNA-class Web Tool) is a publicly available web tool ( http://150.140.142.24:82/Default.aspx ) which provides a user friendly and efficient environment for the effective calculation of a set of 58 sequential, thermodynamical and structural features of non-coding RNAs, plus a tool for the accurate prediction of miRNAs. © 2012 IFIP International Federation for Information Processing.

  6. The origins and evolutionary history of human non-coding RNA regulatory networks.

    Science.gov (United States)

    Sherafatian, Masih; Mowla, Seyed Javad

    2017-04-01

    The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

  7. The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

    Science.gov (United States)

    Huang, Jingshan; Eilbeck, Karen; Smith, Barry; Blake, Judith A; Dou, Dejing; Huang, Weili; Natale, Darren A; Ruttenberg, Alan; Huan, Jun; Zimmermann, Michael T; Jiang, Guoqian; Lin, Yu; Wu, Bin; Strachan, Harrison J; He, Yongqun; Zhang, Shaojie; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming

    2016-01-01

    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl.

  8. On Coding Non-Contiguous Letter Combinations

    Directory of Open Access Journals (Sweden)

    Frédéric eDandurand

    2011-06-01

    Full Text Available Starting from the hypothesis that printed word identification initially involves the parallel mapping of visual features onto location-specific letter identities, we analyze the type of information that would be involved in optimally mapping this location-specific orthographic code onto a location-invariant lexical code. We assume that some intermediate level of coding exists between individual letters and whole words, and that this involves the representation of letter combinations. We then investigate the nature of this intermediate level of coding given the constraints of optimality. This intermediate level of coding is expected to compress data while retaining as much information as possible about word identity. Information conveyed by letters is a function of how much they constrain word identity and how visible they are. Optimization of this coding is a combination of minimizing resources (using the most compact representations and maximizing information. We show that in a large proportion of cases, non-contiguous letter sequences contain more information than contiguous sequences, while at the same time requiring less precise coding. Moreover, we found that the best predictor of human performance in orthographic priming experiments was within-word ranking of conditional probabilities, rather than average conditional probabilities. We conclude that from an optimality perspective, readers learn to select certain contiguous and non-contiguous letter combinations as information that provides the best cue to word identity.

  9. A comprehensive review of non-enterica subspecies of Salmonella enterica.

    Science.gov (United States)

    Lamas, Alexandre; Miranda, José Manuel; Regal, Patricia; Vázquez, Beatriz; Franco, Carlos Manuel; Cepeda, Alberto

    2018-01-01

    Salmonella is a major foodborne pathogen with a complex nomenclature. This genus is composed of two species, S. enterica and S. bongori. S. enterica is divided into six subspecies. S. enterica subspecies enterica is composed of more than 1500 serotypes with some of great importance, such as S. Typhimurium and S. Enteritidis. S. enterica subsp. enterica is responsible of more than 99% of human salmonellosis and therefore it is widely studied. However, the non-enterica subspecies of S. enterica have been little studied. These subspecies are considered to be related to cold-blooded animals and their pathogenicity is very limited. Phenotype and genotype information generated from different studies of non-enterica subspecies reveal poor ability to invade host cells and the absence or modification of important virulence factors. Also, the great majority of human infections due to non-enterica subspecies are related to a previous depressed immune system. Therefore, we propose to treat these subspecies only as opportunistic pathogens. For establish this premise, the present review evaluated, among other things, the genomic characteristics, prevalence, antimicrobial resistance and reported human cases of the non-enterica subspecies. Copyright © 2017 Elsevier GmbH. All rights reserved.

  10. Discovery of Salmonella Virulence Factors Translocated via Outer Membrane Vesicles to Murine Macrophages.

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hyunjin; Ansong, Charles; Adkins, Joshua N.; Heffron, Fred

    2011-06-01

    We have previously shown that the regulators SpvR, FruR, IHF, PhoP/PhoQ, SsrA/SsrB, SlyA, Hnr, RpoE, SmpB, CsrA, RpoS, Crp, OmpR/EnvZ, and Hfq are essential for Salmonella Typhimurium virulence in mice. Here we use quantitative LC-MS-based proteomics profiling of in-frame deletion mutants of these 14 regulators to identify proteins that are coordinately regulated by these virulence regulators and are thus presumably novel factors contributing to Salmonella pathogenesis. Putative candidate proteins from proteomics analysis were determined, which exhibited similar abundance profiles to those of Salmonella pathogenicity island (SPI)-2 type III secretion system (TTSS) proteins. A subset of 5 proteins including STM0082, STM1548, PdgL, STM1633, and STM3595 was selected for further analysis. All 5 proteins were expressed inside macrophage cells and STM0082 (SrfN) was secreted into host cytoplasm. Furthermore, deletion of STM0082 attenuated virulence in mice when administered intraperitoneally as determined by competitive index. srfN transcription was positively regulated by SsrAB, however, secretion was independent of SPI-2 TTSS as well as SPI-1 TTSS and flagella. Proteins including PagK and STM2585A, which are positively regulated by PhoP/PhoQ, have sec signal peptides as predicted for SrfN and were secreted into macrophage cytoplasm regardless of SPI-2 TTSS. Isolation of outer membrane vesicles (OMVs) revealed the presence of SrfN, PagK, and STM2585A inside vesicle compartments. This result is the first case showing delivery of virulence effectors via OMVs in S. Typhimurium. Moreover, Hfq regulation of SrfN translation suggests that small non-coding RNAs may be responsible for regulating effector protein expression.

  11. Salmonella in wastes produced at commercial poultry farms.

    Science.gov (United States)

    Kraft, D J; Olechowski-Gerhardt, C; Berkowitz, J; Finstein, M S

    1969-11-01

    Composite samples of freshly voided excreta from 91 poultry houses were tested qualitatively for Salmonella; 26 (29%) were positive. The houses were located on 36 farms, 18 of which (50%) yielded one or more positive samples. In a separate, quantitative study, Salmonella densities ranged from less than 1 to over 34,000 per g of excreta (dry weight). High densities were noted in waste from cage houses, but not in waste from floor houses (litter or wire floors). Salmonella-shedding chickens were located in only one small area of the row of cages examined in detail. A total of 15 Salmonella serotypes were identified during the study.

  12. The Non-Coding Regulatory RNA Revolution in Archaea

    Directory of Open Access Journals (Sweden)

    Diego Rivera Gelsinger

    2018-03-01

    Full Text Available Small non-coding RNAs (sRNAs are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting, are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3′ untranslated region (UTR, 5′ UTR, CDS-binding. These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting. While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved and how sRNAs integrate with complex regulatory networks.

  13. The long non-coding RNA HOTAIR indicates a poor prognosis and promotes metastasis in non-small cell lung cancer

    International Nuclear Information System (INIS)

    Liu, Xiang-hua; Liu, Zhi-li; Sun, Ming; Liu, Jing; Wang, Zhao-xia; De, Wei

    2013-01-01

    The identification of cancer-associated long non-coding RNAs and the investigation of their molecular and biological functions are important for understanding the molecular biology and progression of cancer. HOTAIR (HOX transcript antisense intergenic RNA) has been implicated in several cancers; however, its role in non-small cell lung cancer (NSCLC) is unknown. The aim of the present study was to examine the expression pattern of HOTAIR in NSCLC and to evaluate its biological role and clinical significance in tumor progression. Expression of HOTAIR was analyzed in 42 NSCLC tissues and four NSCLC cell lines by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Over-expression and RNA interference (RNAi) approaches were used to investigate the biological functions of HOTAIR. The effect of HOTAIR on proliferation was evaluated by MTT and colony formation assays, and cell migration and invasion were evaluated by transwell assays. Tail vein injection of cells was used to study metastasis in nude mice. Protein levels of HOTAIR targets were determined by western blot analysis. Differences between groups were tested for significance using Student’s t-test (two-tailed). HOTAIR was highly expressed both in NSCLC samples and cell lines compared with corresponding normal counterparts. HOTAIR upregulation was correlated with NSCLC advanced pathological stage and lymph-node metastasis. Moreover, patients with high levels of HOTAIR expression had a relatively poor prognosis. Inhibition of HOTAIR by RNAi decreased the migration and invasion of NSCLC cells in vitro and impeded cell metastasis in vivo. HOXA5 levels were affected by HOTAIR knockdown or over-expression in vitro. Our findings indicate that HOTAIR is significantly up-regulated in NSCLC tissues, and regulates NSCLC cell invasion and metastasis, partially via the down-regulation of HOXA5. Thus, HOTAIR may represent a new marker of poor prognosis and is a potential therapeutic target for NSCLC

  14. Metformin-Induced Changes of the Coding Transcriptome and Non-Coding RNAs in the Livers of Non-Alcoholic Fatty Liver Disease Mice.

    Science.gov (United States)

    Guo, Jun; Zhou, Yuan; Cheng, Yafen; Fang, Weiwei; Hu, Gang; Wei, Jie; Lin, Yajun; Man, Yong; Guo, Lixin; Sun, Mingxiao; Cui, Qinghua; Li, Jian

    2018-01-01

    Recent studies have suggested that changes in non-coding mRNA play a key role in the progression of non-alcoholic fatty liver disease (NAFLD). Metformin is now recommended and effective for the treatment of NAFLD. We hope the current analyses of the non-coding mRNA transcriptome will provide a better presentation of the potential roles of mRNAs and long non-coding RNAs (lncRNAs) that underlie NAFLD and metformin intervention. The present study mainly analysed changes in the coding transcriptome and non-coding RNAs after the application of a five-week metformin intervention. Liver samples from three groups of mice were harvested for transcriptome profiling, which covered mRNA, lncRNA, microRNA (miRNA) and circular RNA (circRNA), using a microarray technique. A systematic alleviation of high-fat diet (HFD)-induced transcriptome alterations by metformin was observed. The metformin treatment largely reversed the correlations with diabetes-related pathways. Our analysis also suggested interaction networks between differentially expressed lncRNAs and known hepatic disease genes and interactions between circRNA and their disease-related miRNA partners. Eight HFD-responsive lncRNAs and three metformin-responsive lncRNAs were noted due to their widespread associations with disease genes. Moreover, seven miRNAs that interacted with multiple differentially expressed circRNAs were highlighted because they were likely to be associated with metabolic or liver diseases. The present study identified novel changes in the coding transcriptome and non-coding RNAs in the livers of NAFLD mice after metformin treatment that might shed light on the underlying mechanism by which metformin impedes the progression of NAFLD. © 2018 The Author(s). Published by S. Karger AG, Basel.

  15. A Comparison of Non-Typhoidal Salmonella from Humans and Food Animals Using Pulsed-Field Gel Electrophoresis and Antimicrobial Susceptibility Patterns

    Science.gov (United States)

    Sandt, Carol H.; Fedorka-Cray, Paula J.; Tewari, Deepanker; Ostroff, Stephen; Joyce, Kevin; M’ikanatha, Nkuchia M.

    2013-01-01

    Salmonellosis is one of the most important foodborne diseases affecting humans. To characterize the relationship between Salmonella causing human infections and their food animal reservoirs, we compared pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility patterns of non-typhoidal Salmonella isolated from ill humans in Pennsylvania and from food animals before retail. Human clinical isolates were received from 2005 through 2011 during routine public health operations in Pennsylvania. Isolates from cattle, chickens, swine and turkeys were recovered during the same period from federally inspected slaughter and processing facilities in the northeastern United States. We found that subtyping Salmonella isolates by PFGE revealed differences in antimicrobial susceptibility patterns and, for human Salmonella, differences in sources and invasiveness that were not evident from serotyping alone. Sixteen of the 20 most common human Salmonella PFGE patterns were identified in Salmonella recovered from food animals. The most common human Salmonella PFGE pattern, Enteritidis pattern JEGX01.0004 (JEGX01.0003ARS), was associated with more cases of invasive salmonellosis than all other patterns. In food animals, this pattern was almost exclusively (99%) found in Salmonella recovered from chickens and was present in poultry meat in every year of the study. Enteritidis pattern JEGX01.0004 (JEGX01.0003ARS) was associated with susceptibility to all antimicrobial agents tested in 94.7% of human and 97.2% of food animal Salmonella isolates. In contrast, multidrug resistance (resistance to three or more classes of antimicrobial agents) was observed in five PFGE patterns. Typhimurium patterns JPXX01.0003 (JPXX01.0003 ARS) and JPXX01.0018 (JPXX01.0002 ARS), considered together, were associated with resistance to five or more classes of antimicrobial agents: ampicillin, chloramphenicol, streptomycin, sulfonamides and tetracycline (ACSSuT), in 92% of human and 80% of food

  16. Non-Binary Protograph-Based LDPC Codes: Analysis,Enumerators and Designs

    OpenAIRE

    Sun, Yizeng

    2013-01-01

    Non-binary LDPC codes can outperform binary LDPC codes using sum-product algorithm with higher computation complexity. Non-binary LDPC codes based on protographs have the advantage of simple hardware architecture. In the first part of this thesis, we will use EXIT chart analysis to compute the thresholds of different protographs over GF(q). Based on threshold computation, some non-binary protograph-based LDPC codes are designed and their frame error rates are compared with binary LDPC codes. ...

  17. Prevalence of Salmonella spp. and Listeria monocytogenes at small-scale spanish factories producing traditional fermented sausages.

    Science.gov (United States)

    Martin, Belen; Garriga, Margarita; Aymerich, Teresa

    2011-05-01

    The manufacturing of fermented sausages is subject to natural contamination processes that can potentially carry foodborne pathogens along the process chain and result in contamination of the final product. The aim of this study was to evaluate the occurrence of Salmonella spp. and Listeria monocytogenes at different sampling points during the manufacturing process of fuet, a type of traditional fermented sausage, at 10 small-scale Spanish factories. The presence of both pathogens was studied in the raw materials (19 casings and 19 meat batters), the final products (19 fermented sausages), and the factory equipment (12 mincing, 12 mixing, and 19 stuffing machines, 19 cutting tables, 11 knives, and 12 cold rooms) by using classical microbiological techniques and real-time PCR. Salmonella was not detected in the equipment analyzed or in the final products, but it was detected in the raw materials (23.7% of samples). L. monocytogenes showed higher incidence than Salmonella and was detected in the equipment (11.8% of samples), the raw materials (28.9%), and the final products (15.8%), confirming its ubiquity throughout the manufacturing process of fermented sausages. Five factories were further investigated to study the changes in the distribution of pathogens in the fuet production process over a period of either 2 or 3 years. There was considerable variation in the incidence of both pathogens at different sampling periods, and there was no relation between seasonal variations or geographic location of the factories.

  18. Non-coding RNAs and heme oxygenase-1 in vaccinia virus infection

    International Nuclear Information System (INIS)

    Meseda, Clement A.; Srinivasan, Kumar; Wise, Jasen; Catalano, Jennifer; Yamada, Kenneth M.; Dhawan, Subhash

    2014-01-01

    Highlights: • Heme oxygenase-1 (HO-1) induction inhibited vaccinia virus infection of macrophages. • Reduced infectivity inversely correlated with increased expression of non-coding RNAs. • The regulation of HO-1 and ncRNAs suggests a novel host defense response against vaccinia virus infection. - Abstract: Small nuclear RNAs (snRNAs) are <200 nucleotide non-coding uridylate-rich RNAs. Although the functions of many snRNAs remain undetermined, a population of snRNAs is produced during the early phase of infection of cells by vaccinia virus. In the present study, we demonstrate a direct correlation between expression of the cytoprotective enzyme heme oxygenase-1 (HO-1), suppression of selective snRNA expression, and inhibition of vaccinia virus infection of macrophages. Hemin induced HO-1 expression, completely reversed virus-induced host snRNA expression, and suppressed vaccinia virus infection. This involvement of specific virus-induced snRNAs and associated gene clusters suggests a novel HO-1-dependent host-defense pathway in poxvirus infection

  19. Reduction of Salmonella in ground chicken using a bacteriophage.

    Science.gov (United States)

    Grant, Ar'Quette; Parveen, Salina; Schwarz, Jurgen; Hashem, Fawzy; Vimini, Bob

    2017-08-01

    This study's goal was to ascertain the effectiveness of a commercially available Salmonella bacteriophage during ground chicken production focusing on: water source, different Salmonella serovars, and time. Salmonella-free boneless, skinless chicken meat was inoculated with 4.0 Log CFU/cm2 of either a cocktail of 3 Salmonella isolates derived from ground chicken (GC) or a cocktail of 3 Salmonella strains not isolated from ground chicken (non-GC). Bacteriophages were spread onto the chicken using sterile tap or filtered water for 30 min or 8 h. Salmonella was recovered using standard plating method. Greater Salmonella reduction was observed when the bacteriophage was diluted in sterile tap water than in sterile filtered water: 0.39 Log CFU/cm2 and 0.23 Log CFU/cm2 reduction after 30 min, respectively (P Salmonella's susceptibility to the bacteriophage, and treatment time. © 2017 Poultry Science Association Inc.

  20. Salmonella Weltevreden in integrated and non-integrated tilapia aquaculture systems in Guangdong, China

    DEFF Research Database (Denmark)

    Li, Kang; Petersen, Gitte; Barco, Lisa

    2017-01-01

    including transmission of faecal zoonotic pathogens and accumulation of antimicrobial and other chemical residues. This study aimed to determine differences in occurrence and characteristics of Salmonella spp. isolated from tilapia-pig and non-integrated aquaculture systems in Guangdong province, China...... method showed a clonal relationship of S. Weltevreden which was supported by similar antimicrobial resistance patterns (sulfamethoxazole and trimethoprim resistance) as well as most isolates harbouring a 147-kb sized plasmid. The common finding of S. Weltevreden in both tilapia production systems...

  1. The Long Non-Coding RNA XIST Controls Non-Small Cell Lung Cancer Proliferation and Invasion by Modulating miR-186-5p

    Directory of Open Access Journals (Sweden)

    Haoyou Wang

    2017-04-01

    Full Text Available Background/Aims: Long non-coding RNAs (lncRNAs are key players in the development and progression of human cancers. The lncRNA XIST (X-inactive specific transcript has been shown to be upregulated in human non-small cell lung cancer (NSCLC; however, its role and molecular mechanisms in NSCLC cell progression remain unclear. Methods: qRT-PCR was conducted to assess the expression of XIST and miR-186. Cell proliferation was detected using MTT assay. Cell invasion and migration were evaluated using transwell assay. Cell cycle distribution and apoptosis rates were analyzed by flow cytometry. Luciferase reporter assay was used to identify the direct regulation of XIST and miR-186. A RNA immunoprecipitation was used to analyze whether XIST was associated with the RNA-induced silencing complex (RISC. Results: We confirmed that XIST was upregulated in NSCLC cell lines and tissues. Functionally, XIST knockdown inhibited cancer cell proliferation and invasion, and induced apoptosis in vitro, and suppressed subcutaneous tumor growth in vivo. Mechanistic investigations revealed a reciprocal repressive interaction between XIST and miR-186-5p. Furthermore, we showed that miR-186-5p has a binding site for XIST. Our data also indicated that XIST and miR-186-5p are likely in the same RNA induced silencing complex. Conclusion: Together, our data revealed that XIST knockdown confers suppressive function in NSCLC and XIST may be a novel therapeutic marker in this disease.

  2. Flavivirus RNAi suppression: decoding non-coding RNA.

    Science.gov (United States)

    Pijlman, Gorben P

    2014-08-01

    Flaviviruses are important human pathogens that are transmitted by invertebrate vectors, mostly mosquitoes and ticks. During replication in their vector, flaviviruses are subject to a potent innate immune response known as antiviral RNA interference (RNAi). This defense mechanism is associated with the production of small interfering (si)RNA that lead to degradation of viral RNA. To what extent flaviviruses would benefit from counteracting antiviral RNAi is subject of debate. Here, the experimental evidence to suggest the existence of flavivirus RNAi suppressors is discussed. I will highlight the putative role of non-coding, subgenomic flavivirus RNA in suppression of RNAi in insect and mammalian cells. Novel insights from ongoing research will reveal how arthropod-borne viruses modulate innate immunity including antiviral RNAi. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Prevalence of antimicrobial resistance of non-typhoidal Salmonella serovars in retail aquaculture products.

    Science.gov (United States)

    Zhang, Jianmin; Yang, Xiaowei; Kuang, Dai; Shi, Xianming; Xiao, Wenjia; Zhang, Jing; Gu, Zhen; Xu, Xuebin; Meng, Jianghong

    2015-10-01

    Aquaculture products can become sources of Salmonella by exposure to contaminated water or through processing practices, thus representing a public health hazard. A study was conducted on Salmonella contamination in aquaculture products sampled from marketplaces and retailers in Shanghai, China. A total of 730 samples (including fish, shellfish, bullfrog, clam, shrimp and others) were obtained from 2006 to 2011. Among them, 217 (29.7%) were positive for Salmonella. Thirty-eight serovars were identified in the 217 Salmonella isolates. The most prevalent were Salmonella Aberdeen (18.4%), S. Wandsworth (12.0%), S. Thompson (9.2%), S. Singapore (5.5%), S. Stanley (4.6%), S. Schwarzengrund (4.6%), S. Hvittingfoss (4.1%) and S. Typhimurium (4.1%). Many resistant isolates were detected, with 69.6% resistant to at least one antimicrobial drug. We observed high resistance to sulfonamides (56.5%), tetracycline (34.1%), streptomycin (28.6%), ampicillin (23.5%) and nalidixic acid (21.2%). Lower levels of resistance were found for gentamicin (3.2%), ciprofloxacin (2.3%), ceftiofur (1.3%), cefotaxime (0.9%), ceftazidime (0.5%) and cefepime (0.5%). A total of 43.3% of the Salmonella isolates were multidrug-resistant and 44 different resistance patterns were found. This study provided data on the prevalence, serovars and antimicrobial resistance of Salmonella from retail aquaculture products in Shanghai, and indicated the need for monitoring programs for microbiologic safety in such projects and for more prudent drug use in aquaculture production in order to reduce the risk of development and spread of antimicrobial resistance. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Salmonella in Wastes Produced at Commercial Poultry Farms1

    Science.gov (United States)

    Kraft, D. J.; Olechowski-Gerhardt, Carolyn; Berkowitz, J.; Finstein, M. S.

    1969-01-01

    Composite samples of freshly voided excreta from 91 poultry houses were tested qualitatively for Salmonella; 26 (29%) were positive. The houses were located on 36 farms, 18 of which (50%) yielded one or more positive samples. In a separate, quantitative study, Salmonella densities ranged from less than 1 to over 34,000 per g of excreta (dry weight). High densities were noted in waste from cage houses, but not in waste from floor houses (litter or wire floors). Salmonella-shedding chickens were located in only one small area of the row of cages examined in detail. A total of 15 Salmonella serotypes were identified during the study. PMID:5370457

  5. Bistability in self-activating genes regulated by non-coding RNAs

    International Nuclear Information System (INIS)

    Miro-Bueno, Jesus

    2015-01-01

    Non-coding RNA molecules are able to regulate gene expression and play an essential role in cells. On the other hand, bistability is an important behaviour of genetic networks. Here, we propose and study an ODE model in order to show how non-coding RNA can produce bistability in a simple way. The model comprises a single gene with positive feedback that is repressed by non-coding RNA molecules. We show how the values of all the reaction rates involved in the model are able to control the transitions between the high and low states. This new model can be interesting to clarify the role of non-coding RNA molecules in genetic networks. As well, these results can be interesting in synthetic biology for developing new genetic memories and biomolecular devices based on non-coding RNAs

  6. Using next generation sequencing to tackle non-typhoidal Salmonella infections

    DEFF Research Database (Denmark)

    Wain, John; Keddy, Karen H.; Hendriksen, Rene S.

    2013-01-01

    The publication of studies using next generation sequencing to analyse large numbers of bacterial isolates from global epidemics is transforming microbiology, epidemiology and public health. The emergence of multidrug resistant Salmonella Typhimurium ST313 is one example. While the epidemiology...... in Africa appears to be human-to-human spread and the association with invasive disease almost absolute, more needs to be done to exclude the possibility of animal reservoirs and to transfer the ability to track all Salmonella infections to the laboratories in the front line. In this mini-review we...

  7. Weight Distribution for Non-binary Cluster LDPC Code Ensemble

    Science.gov (United States)

    Nozaki, Takayuki; Maehara, Masaki; Kasai, Kenta; Sakaniwa, Kohichi

    In this paper, we derive the average weight distributions for the irregular non-binary cluster low-density parity-check (LDPC) code ensembles. Moreover, we give the exponential growth rate of the average weight distribution in the limit of large code length. We show that there exist $(2,d_c)$-regular non-binary cluster LDPC code ensembles whose normalized typical minimum distances are strictly positive.

  8. Short-lived non-coding transcripts (SLiTs): Clues to regulatory long non-coding RNA.

    Science.gov (United States)

    Tani, Hidenori

    2017-03-22

    Whole transcriptome analyses have revealed a large number of novel long non-coding RNAs (lncRNAs). Although the importance of lncRNAs has been documented in previous reports, the biological and physiological functions of lncRNAs remain largely unknown. The role of lncRNAs seems an elusive problem. Here, I propose a clue to the identification of regulatory lncRNAs. The key point is RNA half-life. RNAs with a long half-life (t 1/2 > 4 h) contain a significant proportion of ncRNAs, as well as mRNAs involved in housekeeping functions, whereas RNAs with a short half-life (t 1/2 regulatory ncRNAs and regulatory mRNAs. This novel class of ncRNAs with a short half-life can be categorized as Short-Lived non-coding Transcripts (SLiTs). I consider that SLiTs are likely to be rich in functionally uncharacterized regulatory RNAs. This review describes recent progress in research into SLiTs.

  9. Ludwig′s angina by Salmonella Typhi: A clinical dilemma

    Directory of Open Access Journals (Sweden)

    R K Mahajan

    2015-01-01

    Full Text Available Salmonella Typhi has rarely been associated with focal abscesses; and in literature, there is no evidence of its association with abscesses in the neck spaces. Ability of Salmonella Typhi to invade and localise in the neck spaces not only poses a diagnostic challenge but also underscores the necessity to understand the mechanisms that facilitate Salmonella Typhi to establish infections at sites completely non-traditional to the organism.

  10. Binary Linear-Time Erasure Decoding for Non-Binary LDPC codes

    OpenAIRE

    Savin, Valentin

    2009-01-01

    In this paper, we first introduce the extended binary representation of non-binary codes, which corresponds to a covering graph of the bipartite graph associated with the non-binary code. Then we show that non-binary codewords correspond to binary codewords of the extended representation that further satisfy some simplex-constraint: that is, bits lying over the same symbol-node of the non-binary graph must form a codeword of a simplex code. Applied to the binary erasure channel, this descript...

  11. A Rare Case of Salmonella typhi Meningitis in an Eleven Month Old ...

    African Journals Online (AJOL)

    Non-typhoidal Salmonella are infrequent causes of childhood meningitis. Most reports of Salmonella typhi meningeal infections are confined to neonates. A rare instance of S. typhi in an otherwise healthy eleven month old infant is being reported. Keywords: Salmonella typhi, meningitis, infant.

  12. Characterization of integron mediated antimicrobial resistance in Salmonella isolated from diseased swine

    Science.gov (United States)

    White, David G.; Zhao, Shaohua; McDermott, Patrick F.; Ayers, Sherry; Friedman, Sharon; Sherwood, Julie; Breider-Foley, Missy; Nolan, Lisa K.

    2003-01-01

    Forty-two Salmonella isolates obtained from diseased swine were genetically characterized for the presence of specific antimicrobial resistance mechanisms. Twenty of these isolates were characterized as S. Typhimurium DT104 strains. Pulsed-field gel electrophoresis was used to determine genetic relatedness and revealed 20 distinct genetic patterns among the 42 isolates. However, all DT104 isolates fell within 2 closely related genetic clusters. Other Salmonella isolates were genetically grouped together according to serotype. All DT104 isolates displayed the penta-resistance phenotype to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline. Resistance to sulfamethoxazole, tetracycline, streptomycin, kanamycin, and ampicillin was most common among the non-DT104 Salmonella isolates. All DT104 strains contained 2 chromosomal integrons of 1000 and 1200 base pairs. The DNA sequencing revealed that the 2 integrons contained genes encoding a resistance to streptomycin and ampicillin, respectively. None of the non-DT104 strains showed the same pattern, although several strains possessed integrons of 1000 base pairs or larger. However, the majority of non-DT104 Salmonella strains did not possess any integrons. Two Salmonella isolates displayed tolerance to the organic solvent cyclohexane, indicating the possibility that they are overexpressing chromosomal regulatory genes marA or soxS or the associated multidrug efflux pump, acrAB. This research suggests that integrons contribute to antimicrobial resistance among specific swine Salmonella serotypes; however, they are not as widely disseminated among non-Typhimurium swine Salmonella serotypes as previously thought. PMID:12528827

  13. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella.

    Directory of Open Access Journals (Sweden)

    Marie Touchon

    Full Text Available Prokaryotes thrive in spite of the vast number and diversity of their viruses. This partly results from the evolution of mechanisms to inactivate or silence the action of exogenous DNA. Among these, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR are unique in providing adaptive immunity against elements with high local resemblance to genomes of previously infecting agents. Here, we analyze the CRISPR loci of 51 complete genomes of Escherichia and Salmonella. CRISPR are in two pairs of loci in Escherichia, one single pair in Salmonella, each pair showing a similar turnover rate, repeat sequence and putative linkage to a common set of cas genes. Yet, phylogeny shows that CRISPR and associated cas genes have different evolutionary histories, the latter being frequently exchanged or lost. In our set, one CRISPR pair seems specialized in plasmids often matching genes coding for the replication, conjugation and antirestriction machinery. Strikingly, this pair also matches the cognate cas genes in which case these genes are absent. The unexpectedly high conservation of this anti-CRISPR suggests selection to counteract the invasion of mobile elements containing functional CRISPR/cas systems. There are few spacers in most CRISPR, which rarely match genomes of known phages. Furthermore, we found that strains divergent less than 250 thousand years ago show virtually identical CRISPR. The lack of congruence between cas, CRISPR and the species phylogeny and the slow pace of CRISPR change make CRISPR poor epidemiological markers in enterobacteria. All these observations are at odds with the expectedly abundant and dynamic repertoire of spacers in an immune system aiming at protecting bacteria from phages. Since we observe purifying selection for the maintenance of CRISPR these results suggest that alternative evolutionary roles for CRISPR remain to be uncovered.

  14. Linear-Time Non-Malleable Codes in the Bit-Wise Independent Tampering Model

    DEFF Research Database (Denmark)

    Cramer, Ronald; Damgård, Ivan Bjerre; Döttling, Nico

    Non-malleable codes were introduced by Dziembowski et al. (ICS 2010) as coding schemes that protect a message against tampering attacks. Roughly speaking, a code is non-malleable if decoding an adversarially tampered encoding of a message m produces the original message m or a value m' (eventuall...... non-malleable codes of Agrawal et al. (TCC 2015) and of Cher- aghchi and Guruswami (TCC 2014) and improves the previous result in the bit-wise tampering model: it builds the first non-malleable codes with linear-time complexity and optimal-rate (i.e. rate 1 - o(1)).......Non-malleable codes were introduced by Dziembowski et al. (ICS 2010) as coding schemes that protect a message against tampering attacks. Roughly speaking, a code is non-malleable if decoding an adversarially tampered encoding of a message m produces the original message m or a value m' (eventually...... abort) completely unrelated with m. It is known that non-malleability is possible only for restricted classes of tampering functions. Since their introduction, a long line of works has established feasibility results of non-malleable codes against different families of tampering functions. However...

  15. Non-Coding RNAs in Arabidopsis

    DEFF Research Database (Denmark)

    van Wonterghem, Miranda

    This work evolves around elucidating the mechanisms of micro RNAs (miRNAs) in Arabidopsis thaliana. I identified a new class of nuclear non-coding RNAs derived from protein coding genes. The genes are miRNA targets with extensive gene body methylation. The RNA species are nuclear localized and de...

  16. Pleural Empyema due to Group D Salmonella

    Directory of Open Access Journals (Sweden)

    Jennifer C. Kam

    2012-01-01

    Full Text Available Non-typhi Salmonella normally presents as a bacteremia, enterocolitis, and endovascular infection but rarely manifests as pleuropulmonary disease. We present a case of a 66-year-old female with underlying pulmonary pathology, secondary to an extensive smoking history, who presented with a left-sided pleural effusion. The causative agent was identified as being group D Salmonella. Decortication of the lung was performed and the patient was discharged on antibiotics with resolution of her symptoms. This case helps to support the inclusion of Salmonella group D as a possible etiological agent of infection in the differential causes of exudative pleural effusions.

  17. Associations between the proportion of Salmonella seropositive slaughter pigs and the presence of herd level risk factors for introduction and transmission of Salmonella in 34 Danish organic, outdoor (non-organic) and indoor finishing-pig farms

    DEFF Research Database (Denmark)

    Zheng, D.M.; Bonde, Marianne; Sørensen, Jan Tind

    2007-01-01

    This paper evaluates the association between herd level risk factors for introduction and transmission of Salmonella in farms with three different production systems: organic, outdoor (non-organic) and indoor finishing-pig farms, and the presence of seropositive animals in the herds. Potential risk...... factors for Salmonella in the three pig production systems were identified through a literature review, and management information as well as serological data were collected in 34 pig farms: 11 organic farms, 12 outdoor farms, and 11 indoor farms. There were no general differences in the proportion...

  18. Using molecular techniques for rapid detection of Salmonella ...

    African Journals Online (AJOL)

    PRECIOUS

    2010-02-01

    Feb 1, 2010 ... A total of 152 samples of chicken and chicken products ... detection of Salmonella species in the collected field samples ... that 16 million new cases of typhoid fever occur each ... vative methods for the rapid identification of Salmonella ... saved for the PCR-Non Selective test (PCR-NS) and 1 ml of the.

  19. Salmonella osteomyelitis

    OpenAIRE

    Somsri Wiwanitkit; Viroj Wiwanitkit

    2016-01-01

    Salmonella infection can cause four predominant clinical syndromes: enteric fever, acute gastroenteritis, bacteraemia with or without metastatic infection, and the asymptomatic carrier state. Salmonella as an aetiological agent in osteomyelitis is essentially rare and salmonella osteomyelitis in itself is predominantly seen in patients with haemoglobinopathies such as sickle cell disease or thalassemia. There are very few cases reported in the literature in which salmonella osteomyelitis is s...

  20. Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States

    Energy Technology Data Exchange (ETDEWEB)

    Dolan, Kyle T.; Duguid, Erica M.; He, Chuan (UC)

    2011-11-17

    SlyA is a master virulence regulator that controls the transcription of numerous genes in Salmonella enterica. We present here crystal structures of SlyA by itself and bound to a high-affinity DNA operator sequence in the slyA gene. SlyA interacts with DNA through direct recognition of a guanine base by Arg-65, as well as interactions between conserved Arg-86 and the minor groove and a large network of non-base-specific contacts with the sugar phosphate backbone. Our structures, together with an unpublished structure of SlyA bound to the small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other MarR family proteins, SlyA dissociates from DNA without large conformational changes when bound to this effector. We propose that SlyA and other MarR global regulators rely more on indirect readout of DNA sequence to exert control over many genes, in contrast to proteins (such as OhrR) that recognize a single operator.

  1. Code of practice for safety in laboratory - non ionising radiation

    International Nuclear Information System (INIS)

    Ramli Jaya; Mohd Yusof Mohd Ali; Khoo Boo Huat; Khatijah Hashim

    1995-01-01

    The code identifies the non-ionizing radiation encountered in laboratories and the associated hazards. The code is intended as a laboratory standard reference document for general information on safety requirements relating to the usage of non-ionizing radiations in laboratories. The nonionizing radiations cover in this code, namely, are ultraviolet radiation, visible light, radio-frequency radiation, lasers, sound waves and ultrasonic radiation. (author)

  2. Presence of non-O157 Shiga toxin-producing Escherichia coli, enterotoxigenic E. coli, enteropathogenic E. coli and Salmonella in fresh beetroot (Beta vulgaris L.) juice from public markets in Mexico.

    Science.gov (United States)

    Gómez-Aldapa, Carlos A; Rangel-Vargas, Esmeralda; Bautista-De León, Haydee; Castro-Rosas, Javier

    2014-10-01

    Unpasteurized juice has been associated with foodborne illness outbreaks for many years. Beetroot is a vegetable grown all over the world in temperate areas. In Mexico beetroot is consumed cooked in salads or raw as fresh unpasteurized juices. No data about the microbiological quality or safety of unpasteurized beetroot juices are available. Indicator bacteria, diarrheagenic Escherichia coli pathotypes (DEP) and Salmonella frequencies were determined for fresh unpasteurized beetroot juice from restaurants. One hundred unpasteurized beetroot juice samples were collected from public markets in Pachuca, Mexico. Frequencies in these samples were 100%, 75%, 53%, 9% and 4% of positive samples, for coliform bacteria, fecal coliforms, E. coli, DEP and Salmonella, respectively. Identified DEP included enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC) and non-O157 Shiga toxin-producing E. coli (STEC). Identified Salmonella serotypes included Typhimurium and Enteritidis. This is the first report of microbiological quality and atypical EPEC, ETEC, non-O157 STEC and Salmonella isolation from fresh raw beetroot juice in Mexico. Fresh raw beetroot juice from markets is very probably an important factor contributing to the endemicity of atypical EPEC, ETEC, non-O157 STEC and Salmonella-related gastroenteritis in Mexico. © 2014 Society of Chemical Industry.

  3. Development of non-linear vibration analysis code for CANDU fuelling machine

    International Nuclear Information System (INIS)

    Murakami, Hajime; Hirai, Takeshi; Horikoshi, Kiyomi; Mizukoshi, Kaoru; Takenaka, Yasuo; Suzuki, Norio.

    1988-01-01

    This paper describes the development of a non-linear, dynamic analysis code for the CANDU 600 fuelling machine (F-M), which includes a number of non-linearities such as gap with or without Coulomb friction, special multi-linear spring connections, etc. The capabilities and features of the code and the mathematical treatment for the non-linearities are explained. The modeling and numerical methodology for the non-linearities employed in the code are verified experimentally. Finally, the simulation analyses for the full-scale F-M vibration testing are carried out, and the applicability of the code to such multi-degree of freedom systems as F-M is demonstrated. (author)

  4. Non-Coding Transcript Heterogeneity in Mesothelioma: Insights from Asbestos-Exposed Mice.

    Science.gov (United States)

    Felley-Bosco, Emanuela; Rehrauer, Hubert

    2018-04-11

    Mesothelioma is an aggressive, rapidly fatal cancer and a better understanding of its molecular heterogeneity may help with making more efficient therapeutic strategies. Non-coding RNAs represent a larger part of the transcriptome but their contribution to diseases is not fully understood yet. We used recently obtained RNA-seq data from asbestos-exposed mice and performed data mining of publicly available datasets in order to evaluate how non-coding RNA contribute to mesothelioma heterogeneity. Nine non-coding RNAs are specifically elevated in mesothelioma tumors and contribute to human mesothelioma heterogeneity. Because some of them have known oncogenic properties, this study supports the concept of non-coding RNAs as cancer progenitor genes.

  5. DNA watermarks in non-coding regulatory sequences

    Directory of Open Access Journals (Sweden)

    Pyka Martin

    2009-07-01

    Full Text Available Abstract Background DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli. Findings The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity. Conclusion Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.

  6. Non-Meckel Small Intestine Diverticulitis

    Directory of Open Access Journals (Sweden)

    Shamim Ejaz

    2017-08-01

    Full Text Available Non-Meckel small intestine diverticulitis can have many manifestations and its management is not well-defined. We report 4 unselect cases of small intestine diverticulitis; all patients were seen by the same physician at the Emergency Center at The University of Texas MD Anderson Cancer Center between 1999 and 2014. The median age at diagnosis of these patients was 82 years (range, 76–87 years. All 4 patients presented with acute onset of abdominal pain, and computed tomography scans showed characteristics of small intestine diverticulitis unrelated to cancer. Most of the diverticula were found in the region of the duodenum and jejuno-ileal segments of the small intestine. The patients, even those with peripancreatic inflammation and localized perforation, were treated conservatively. Non-Meckel diverticulitis can be overlooked in the initial diagnosis because of the location of the diverticulosis, the age of the patient, and the rarity of the disease. Because patients with non-Meckel small intestine diverticulitis can present with acute abdominal pain, non-Meckel small intestine diverticulitis should be considered in the differential diagnosis of patients with acute abdominal pain, and computed tomography scans can help identify the condition. Because of the rarity of non-Meckel small intestine diverticulitis, few studies have been published, and the data are inconclusive about how best to approach these patients. Our experience with these 4 elderly patients indicates that non-Meckel small intestine diverticulitis can be treated conservatively, which avoids the potential morbidity and mortality of a surgical approach.

  7. Min-Max decoding for non binary LDPC codes

    OpenAIRE

    Savin, Valentin

    2008-01-01

    Iterative decoding of non-binary LDPC codes is currently performed using either the Sum-Product or the Min-Sum algorithms or slightly different versions of them. In this paper, several low-complexity quasi-optimal iterative algorithms are proposed for decoding non-binary codes. The Min-Max algorithm is one of them and it has the benefit of two possible LLR domain implementations: a standard implementation, whose complexity scales as the square of the Galois field's cardinality and a reduced c...

  8. Salmonella: Salmonellosis

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Hansen, Trine; Maurischat, Sven

    2015-01-01

    Salmonella remains one of the most important zoonotic pathogenic bacteria and is the causative agents of salmonellosis. The aim of this article is to give an overview of Salmonella and salmonellosis, starting by describing the characteristics of the microorganism Salmonella, including biochemical...

  9. SWIMS: a small-angle multiple scattering computer code

    International Nuclear Information System (INIS)

    Sayer, R.O.

    1976-07-01

    SWIMS (Sigmund and WInterbon Multiple Scattering) is a computer code for calculation of the angular dispersion of ion beams that undergo small-angle, incoherent multiple scattering by gaseous or solid media. The code uses the tabulated angular distributions of Sigmund and Winterbon for a Thomas-Fermi screened Coulomb potential. The fraction of the incident beam scattered into a cone defined by the polar angle α is computed as a function of α for reduced thicknesses over the range 0.01 less than or equal to tau less than or equal to 10.0. 1 figure, 2 tables

  10. SPORTS - a simple non-linear thermalhydraulic stability code

    International Nuclear Information System (INIS)

    Chatoorgoon, V.

    1986-01-01

    A simple code, called SPORTS, has been developed for two-phase stability studies. A novel method of solution of the finite difference equations was deviced and incorporated, and many of the approximations that are common in other stability codes are avoided. SPORTS is believed to be accurate and efficient, as small and large time-steps are permitted, and hence suitable for micro-computers. (orig.)

  11. Lung cancer - non-small cell

    Science.gov (United States)

    Cancer - lung - non-small cell; Non-small cell lung cancer; NSCLC; Adenocarcinoma - lung; Squamous cell carcinoma - lung ... Research shows that smoking marijuana may help cancer cells grow. But there is no direct link between ...

  12. The Role of Non-­Coding RNA in Plant Stress

    KAUST Repository

    MacPherson, Cameron R.

    2012-12-01

    Post-transcriptional gene silencing (PTGS) is a powerful mechanism that can be adapted to genetically modify crop plants. PTGS operates in many plant signaling pathways including those mediating stress responses. Given the small number of miRNAs known, research on the characterization of stress-related micro-RNA (miRNA) and their targets could provide the basis for engineering stress tolerant traits in crops. Indeed, several examples of miRNA mediated crop tolerance have been reported. In the research presented here, we aimed to analyze the role of small non-coding RNA (smRNA) pathways involved in plant stress. In particular, we focused on miRNA-mediated PTGS in phosphate (Pi) starvation. The analysis was split into two research projects. First, to identify potential miRNA targets we began by analyzing the response and recovery of coding and long non-coding RNAs (lncRNA) to Pi starvation in shoot and root. The results obtained were the first genome-wide description of the root’s Pi starvation response and recovery. We found that the root\\'s response involved a widely different set of genes than that of the shoot. In the second research project, the results of the first project were correlated with the responses of miRNA and trans-acting small-interfering RNA (tasiRNA) during Pi starvation. Many miRNA circuits have been predicted before, however, tasiRNA circuits are not as well defined. Therefore, we made use of the double-stranded RNA-binding protein 4 (DRB4) smRNA libraries to enhance our prediction of tasiRNAs. Altogether, we provided evidence to support the following miRNA-mRNA pairs that may function in Pi starvation: IPS1:miR399:PHO2; miR399:RS4; miR399:NF-YA10; miR398:CSD1/2; miR2111:TPS11; miR164:NAC6; miR157:TMO7; miR157:PSB28; RPS2:miR169:IPS2; miR397:LAC2; TAS4:PAP1; NR1:PAP1; and Chr3_1967672:TMO7. In general, we found that non-miR399 related circuits were active only during the root’s recovery from Pi starvation. The functional roles of the genes

  13. Functional interrogation of non-coding DNA through CRISPR genome editing.

    Science.gov (United States)

    Canver, Matthew C; Bauer, Daniel E; Orkin, Stuart H

    2017-05-15

    Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Roles of Non-Coding RNA in Sugarcane-Microbe Interaction.

    Science.gov (United States)

    Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Calixto, Edmundo P da R; Motta, Mariana R; Ballesteros, Helkin G F; Peixoto, Barbara; de Lima, Berenice N S; Vieira, Lucas M; Walter, Maria Emilia; de Armas, Elvismary M; Entenza, Júlio O P; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

    2017-12-20

    Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae . Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae , while the siRNAs were repressed in the presence of A. avenae . Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408-a copper-microRNA-was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5'RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

  15. Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

    Science.gov (United States)

    Grativol, Clícia; Motta, Mariana R.; Ballesteros, Helkin G. F.; Peixoto, Barbara; Vieira, Lucas M.; Walter, Maria Emilia; de Armas, Elvismary M.; Entenza, Júlio O. P.; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S.

    2017-01-01

    Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly. PMID:29657296

  16. Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

    Directory of Open Access Journals (Sweden)

    Flávia Thiebaut

    2017-12-01

    Full Text Available Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR. Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

  17. Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.

    Science.gov (United States)

    Papenfort, Kai; Espinosa, Elena; Casadesús, Josep; Vogel, Jörg

    2015-08-25

    Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ(S) and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ(S) and, together, RprA and σ(S) orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.

  18. Retrotransposons and non-protein coding RNAs

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2009-01-01

    does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review...

  19. Pathogenicity, Epidemiology and Virulence Factors of Salmonella species: A Review

    Directory of Open Access Journals (Sweden)

    Tamègnon Victorien DOUGNON

    2017-12-01

    Full Text Available Salmonella infections are major public health problems worldwide. The hereby review aimed to establish an overview on the pathogenicity, epidemiology and virulence factors of Salmonella spp. in the world. A systematic search was conducted online using the keywords ‘Salmonella’, ‘Salmonella spp.’, ‘Salmonella spp. Epidemiology’, ‘virulence factors of Salmonella spp. in the world’, ‘bacteria responsible for the contamination of meat products’, ‘non-typhoid salmonella’. These keywords were entered into databases such as PubMed and Google Scholar using mainly French language. The obtained articles were included based on the reliability of their source, the study area (usually Benin and Africa and the subject. The review revealed that Salmonella spp. is motile Gram-negative rod-shaped bacteria, of the family Enterobacteriaceae, currently counting more than 2,600 serovars. Human contamination occurs through the ingestion of contaminated water and food and can cause gastroenteritis or typhoid fever, which are two serious public health problems. A gene set constituting the pathogenicity islands determines the pathogenesis of Salmonella spp. The diagnosis is based on bacteriological, serological and molecular techniques. Salmonella infections are usually treated using antibiotics; however, emergence of antibiotic resistance in these microorganisms suggests that the anti-salmonella control should explore new sources such as medicinal plants

  20. Swiss Army Pathogen: The Salmonella Entry Toolkit

    Directory of Open Access Journals (Sweden)

    Peter J. Hume

    2017-08-01

    Full Text Available Salmonella causes disease in humans and animals ranging from mild self-limiting gastroenteritis to potentially life-threatening typhoid fever. Salmonellosis remains a considerable cause of morbidity and mortality globally, and hence imposes a huge socio-economic burden worldwide. A key property of all pathogenic Salmonella strains is the ability to invade non-phagocytic host cells. The major determinant of this invasiveness is a Type 3 Secretion System (T3SS, a molecular syringe that injects virulence effector proteins directly into target host cells. These effectors cooperatively manipulate multiple host cell signaling pathways to drive pathogen internalization. Salmonella does not only rely on these injected effectors, but also uses several other T3SS-independent mechanisms to gain entry into host cells. This review summarizes our current understanding of the methods used by Salmonella for cell invasion, with a focus on the host signaling networks that must be coordinately exploited for the pathogen to achieve its goal.

  1. Salmonella enterica serovar Ohio septic arthritis and bone abscess in an immunocompetent patient: a case report

    Directory of Open Access Journals (Sweden)

    Kato Hideaki

    2012-07-01

    Full Text Available Abstract Introduction Non-typhi Salmonella species cause severe extra-intestinal focal infection after occult bacteremia. Although the number of cases of non-typhi salmonellosis is increasing worldwide among patients with immunocompromising conditions such as human immunodeficiency virus infection, infection is uncommon in immunocompetent subjects. We report a case of septic arthritis and bone abscess due to a rare non-typhi Salmonella organism that developed after a prolonged asymptomatic period. Case presentation A 44-year-old Japanese immunocompetent man presented with acute-onset left knee pain and swelling. He had no history of food poisoning, and his most recent travel to an endemic area was 19 years ago. Salmonella enterica serovar Ohio was identified from samples of bone abscess and joint tissue. Arthrotomy and necrotic tissue debridement followed by intravenous ceftriaxone was successful. Conclusions Non-typhi Salmonella species only rarely cause extra-intestinal focal infections in immunocompetent patients. Our case suggests that non-typhi Salmonella species can cause severe focal infections many years after the occult bacteremia associated with food poisoning.

  2. Decoding small surface codes with feedforward neural networks

    Science.gov (United States)

    Varsamopoulos, Savvas; Criger, Ben; Bertels, Koen

    2018-01-01

    Surface codes reach high error thresholds when decoded with known algorithms, but the decoding time will likely exceed the available time budget, especially for near-term implementations. To decrease the decoding time, we reduce the decoding problem to a classification problem that a feedforward neural network can solve. We investigate quantum error correction and fault tolerance at small code distances using neural network-based decoders, demonstrating that the neural network can generalize to inputs that were not provided during training and that they can reach similar or better decoding performance compared to previous algorithms. We conclude by discussing the time required by a feedforward neural network decoder in hardware.

  3. Prevalence and characterization of Salmonella among humans in Ghana

    DEFF Research Database (Denmark)

    Andoh, Linda Aurelia; Ahmed, Shabana; Olsen, John Elmerdahl

    2017-01-01

    Background Non-typhoidal Salmonella (NTS) is a public health problem worldwide and particularly in Africa with high disease burden. This study characterized Salmonella isolates from humans in Ghana to determine serovar distribution, phage types, and antimicrobial resistance. Further, the clonal...... relatedness among isolates was determined. Methods One hundred and thirty-seven Salmonella isolates (111 clinical and 26 public toilet) were characterized using standard serotyping, phage typing, and antimicrobial susceptibility testing methods. The molecular epidemiology of common serovars (Salmonella....... Fifty-eight (n = 58/112; 54.5%) strains were multi-resistant with low resistance to cephalosporins ceftazidime (8.0%), cefotaxime (4.5%), and cefoxitin (2.7%) with synergy to clavulanic acid indicating possible ESBLs. Isolates showed high resistance to trimethoprim (66.1%), tetracycline (61...

  4. Resuscitation of the viable but non-culturable state of Salmonella enterica serovar Oranienburg by recombinant resuscitation-promoting factor derived from Salmonella Typhimurium strain LT2.

    Science.gov (United States)

    Panutdaporn, N; Kawamoto, K; Asakura, H; Makino, S-I

    2006-02-15

    A gene encoding the resuscitation-promoting factor (Rpf) from Salmonella Typhimurium LT2 was cloned and characterized. The amino acid sequence encoded by S. Typhimurium LT2 rpf gene shares 24.2% homology with Micrococcus luteus Rpf, which is secreted by growing cells, and required to resuscitate from viable but non-culturable (VNC) state. The S. Typhimurium LT2 rpf gene is 696 bp long, and shared a conserved segment with Salmonella enterica serovar Oranienburg (99.4%). Recombinant Rpf (rRpf) proteins of S. Typhimurium LT2 after expression in E. coli BL21 harboring the pET15-b plasmid was approximately 25 kDa. Since S. Oranienburg cells are relatively quick to enter the VNC state just after incubating in the presence of 7% NaCl at 37 degrees C for 3 days, we evaluated the biological effect of rRpf by using S. Oranienburg VNC cells. The rRpf not only promoted proliferation but also induced resuscitation of VNC cells to the culturable state in a dose-dependent manner. Therefore, rRpf may be useful for detection of bacterial contaminants present in the VNC form in food samples and the environment.

  5. Sources of Salmonella on broiler carcasses during transportation and processing: modes of contamination and methods of control.

    Science.gov (United States)

    Corry, Janet E L; Allen, V M; Hudson, W R; Breslin, M F; Davies, R H

    2002-01-01

    The prevalence and types of salmonella in broiler chickens during transportation and during slaughter and dressing were studied. This was part of a comprehensive investigation of salmonellas in two UK poultry companies, which aimed to find the origins and mechanisms of salmonella contamination. Salmonellas were isolated using cultural methods. Serovars of Salmonella detected during rearing were usually also found in a small proportion of birds on the day of slaughter and on the carcasses at various points during processing. There was little evidence of salmonellas spreading to large numbers of carcasses during processing. Many serovars found in the feedmills or hatcheries were also detected in the birds during rearing and/or slaughter. Transport crates were contaminated with salmonellas after washing and disinfection. Prevalence of salmonellas fell in the two companies during this survey. A small number of serovars predominated in the processing plants of each company. These serovars originated from the feed mills. Reasons for transport crate contamination were: (1) inadequate cleaning, resulting in residual faecal soiling; (2) disinfectant concentration and temperature of disinfectant too low; (3) contaminated recycled flume water used to soak the crates. Efforts to control salmonella infection in broilers need to concentrate on crate cleaning and disinfection and hygiene in the feed mills.

  6. Survey of Salmonella contamination in chicken layer farms in three Caribbean countries.

    Science.gov (United States)

    Adesiyun, Abiodun; Webb, Lloyd; Musai, Lisa; Louison, Bowen; Joseph, George; Stewart-Johnson, Alva; Samlal, Sannandan; Rodrigo, Shelly

    2014-09-01

    This study was conducted to investigate the demography, management, and production practices on layer chicken farms in Trinidad and Tobago, Grenada, and St. Lucia and the frequency of risk factors for Salmonella infection. The frequency of isolation of Salmonella from the layer farm environment, eggs, feeds, hatchery, and imported day-old chicks was determined using standard methods. Of the eight risk factors (farm size, age group of layers, source of day-old chicks, vaccination, sanitation practices, biosecurity measures, presence of pests, and previous disease outbreaks) for Salmonella infection investigated, farm size was the only risk factor significantly associated (P = 0.031) with the prevalence of Salmonella; 77.8% of large farms were positive for this pathogen compared with 33.3 and 26.1% of medium and small farms, respectively. The overall isolation rate of Salmonella from 35 layer farms was 40.0%. Salmonella was isolated at a significantly higher rate (P hatcheries, and airports in this country were negative. Salmonella Anatum, Salmonella group C, and Salmonella Kentucky were the predominant serotypes in Trinidad and Tobago, Grenada, and St. Lucia, respectively. Although Salmonella infections were found in layer birds sampled, table eggs appear to pose minimal risk to consumers. However, the detection of Salmonella -contaminated farm environments and feeds cannot be ignored. Only 2.9% of the isolates belonged to Salmonella Enteritidis, a finding that may reflect the impact of changes in farm management and poultry production in the region.

  7. Prevalence of Salmonella in poultry processing environments in wet markets in Penang and Perlis, Malaysia

    Directory of Open Access Journals (Sweden)

    Hafiz Nidaullah

    2017-03-01

    Full Text Available Aim: The aim of this study was to determine the prevalence of various Salmonella serotypes in chickens, carcass contact surfaces as well as environmental samples collected from wet markets and small scale processing plant. Materials and Methods: A total of 182 poultry and environmental samples were collected at random on separate occasions from wet markets and small scale processing plant, during the period of October 2014 to July 2015 in Penang and Perlis, Malaysia. The samples were analyzed for the presence of Salmonella using ISO 6579:2002 conventional culture-based method. Presumptive Salmonella colonies were subjected to various biochemical tests (such as triple sugar iron and lysine iron test, serologically confirmed using polyvalent O and H antisera and further serotyped at Public Health Laboratory, Ministry of Health, Perak, Malaysia. Results: Salmonella serotypes were isolated from 161 out of 182 samples (88.46% with 100% prevalence in the whole chicken carcass and chicken cuts - as well as transport crate, cage, drum, knife, chopping board, display table, floor, bench wash water, wash water, and drain water. Salmonella was isolated from 91.67%, 83.33%, and 66.67% of defeathering machines, drain swabs, and apron, respectively. 17 serotypes were isolated in this study with Salmonella Albany (57/161, Salmonella Corvallis (42/161, and Salmonella Brancaster (37/161 being the predominant serovars. Conclusion: The most carcass contact and environmental samples collected along the wet market chicken processing line were consistently contaminated with Salmonella. This indicates that Salmonella has established itself in poultry processing environments by colonizing the surfaces of the equipment and survives in these environments by establishing biofilms. Our results highlight the need of implementing strict hygiene and sanitation standards to reduce the incidence of Salmonella. The prevalence of Salmonella in poultry can be reduced effectively

  8. Prevalence of Salmonella in poultry processing environments in wet markets in Penang and Perlis, Malaysia

    Science.gov (United States)

    Nidaullah, Hafiz; Abirami, Nadarajan; Shamila-Syuhada, Ahamed Kamal; Chuah, Li-Oon; Nurul, Huda; Tan, Teik Pei; Abidin, Farah Wahida Zainal; Rusul, Gulam

    2017-01-01

    Aim: The aim of this study was to determine the prevalence of various Salmonella serotypes in chickens, carcass contact surfaces as well as environmental samples collected from wet markets and small scale processing plant. Materials and Methods: A total of 182 poultry and environmental samples were collected at random on separate occasions from wet markets and small scale processing plant, during the period of October 2014 to July 2015 in Penang and Perlis, Malaysia. The samples were analyzed for the presence of Salmonella using ISO 6579:2002 conventional culture-based method. Presumptive Salmonella colonies were subjected to various biochemical tests (such as triple sugar iron and lysine iron test), serologically confirmed using polyvalent O and H antisera and further serotyped at Public Health Laboratory, Ministry of Health, Perak, Malaysia. Results: Salmonella serotypes were isolated from 161 out of 182 samples (88.46%) with 100% prevalence in the whole chicken carcass and chicken cuts - as well as transport crate, cage, drum, knife, chopping board, display table, floor, bench wash water, wash water, and drain water. Salmonella was isolated from 91.67%, 83.33%, and 66.67% of defeathering machines, drain swabs, and apron, respectively. 17 serotypes were isolated in this study with Salmonella Albany (57/161), Salmonella Corvallis (42/161), and Salmonella Brancaster (37/161) being the predominant serovars. Conclusion: The most carcass contact and environmental samples collected along the wet market chicken processing line were consistently contaminated with Salmonella. This indicates that Salmonella has established itself in poultry processing environments by colonizing the surfaces of the equipment and survives in these environments by establishing biofilms. Our results highlight the need of implementing strict hygiene and sanitation standards to reduce the incidence of Salmonella. The prevalence of Salmonella in poultry can be reduced effectively by identifying

  9. Prevalence of Salmonella in poultry processing environments in wet markets in Penang and Perlis, Malaysia.

    Science.gov (United States)

    Nidaullah, Hafiz; Abirami, Nadarajan; Shamila-Syuhada, Ahamed Kamal; Chuah, Li-Oon; Nurul, Huda; Tan, Teik Pei; Abidin, Farah Wahida Zainal; Rusul, Gulam

    2017-03-01

    The aim of this study was to determine the prevalence of various Salmonella serotypes in chickens, carcass contact surfaces as well as environmental samples collected from wet markets and small scale processing plant. A total of 182 poultry and environmental samples were collected at random on separate occasions from wet markets and small scale processing plant, during the period of October 2014 to July 2015 in Penang and Perlis, Malaysia. The samples were analyzed for the presence of Salmonella using ISO 6579:2002 conventional culture-based method. Presumptive Salmonella colonies were subjected to various biochemical tests (such as triple sugar iron and lysine iron test), serologically confirmed using polyvalent O and H antisera and further serotyped at Public Health Laboratory, Ministry of Health, Perak, Malaysia. Salmonella serotypes were isolated from 161 out of 182 samples (88.46%) with 100% prevalence in the whole chicken carcass and chicken cuts - as well as transport crate, cage, drum, knife, chopping board, display table, floor, bench wash water, wash water, and drain water. Salmonella was isolated from 91.67%, 83.33%, and 66.67% of defeathering machines, drain swabs, and apron, respectively. 17 serotypes were isolated in this study with Salmonella Albany (57/161), Salmonella Corvallis (42/161), and Salmonella Brancaster (37/161) being the predominant serovars. The most carcass contact and environmental samples collected along the wet market chicken processing line were consistently contaminated with Salmonella . This indicates that Salmonella has established itself in poultry processing environments by colonizing the surfaces of the equipment and survives in these environments by establishing biofilms. Our results highlight the need of implementing strict hygiene and sanitation standards to reduce the incidence of Salmonella . The prevalence of Salmonella in poultry can be reduced effectively by identifying and eliminating the sources and contamination

  10. Simulation of small break loss of coolant accident using relap 5/ MOD 2 computer code

    International Nuclear Information System (INIS)

    Megahed, M.M.

    1992-01-01

    An assessment of relap 5 / MOD 2/Cycle 36.05 best estimate computer code capabilities in predicting the thermohydraulic response of a PWR following a small break loss of coolant accident is presented. The experimental data base for the evaluation is the results of Test S-N H-3 performed in the semi scale MOD-2 c Test facility which modeled a 0.5% small break loss of coolant accident with an accompanying failure of the high pressure injection emergency core cooling system. A conclusion was reached that the code is capable of making small break loss of coolant accident calculations efficiently. However, some of the small break loss of coolant accident related phenomena were not properly predicted by the code, suggesting a need for code improvement.9 fig., 3 tab

  11. Long non-coding RNA expression profiling of mouse testis during postnatal development.

    Directory of Open Access Journals (Sweden)

    Jin Sun

    Full Text Available Mammalian testis development and spermatogenesis play critical roles in male fertility and continuation of a species. Previous research into the molecular mechanisms of testis development and spermatogenesis has largely focused on the role of protein-coding genes and small non-coding RNAs, such as microRNAs and piRNAs. Recently, it has become apparent that large numbers of long (>200 nt non-coding RNAs (lncRNAs are transcribed from mammalian genomes and that lncRNAs perform important regulatory functions in various developmental processes. However, the expression of lncRNAs and their biological functions in post-natal testis development remain unknown. In this study, we employed microarray technology to examine lncRNA expression profiles of neonatal (6-day-old and adult (8-week-old mouse testes. We found that 8,265 lncRNAs were expressed above background levels during post-natal testis development, of which 3,025 were differentially expressed. Candidate lncRNAs were identified for further characterization by an integrated examination of genomic context, gene ontology (GO enrichment of their associated protein-coding genes, promoter analysis for epigenetic modification, and evolutionary conservation of elements. Many lncRNAs overlapped or were adjacent to key transcription factors and other genes involved in spermatogenesis, such as Ovol1, Ovol2, Lhx1, Sox3, Sox9, Plzf, c-Kit, Wt1, Sycp2, Prm1 and Prm2. Most differentially expressed lncRNAs exhibited epigenetic modification marks similar to protein-coding genes and tend to be expressed in a tissue-specific manner. In addition, the majority of differentially expressed lncRNAs harbored evolutionary conserved elements. Taken together, our findings represent the first systematic investigation of lncRNA expression in the mammalian testis and provide a solid foundation for further research into the molecular mechanisms of lncRNAs function in mammalian testis development and spermatogenesis.

  12. Third-Generation Cephalosporin-Resistant Non-Typhoidal Salmonella Isolated from Human Feces in Japan.

    Science.gov (United States)

    Saito, Satomi; Koori, Yoshio; Ohsaki, Yusuke; Osaka, Shunsuke; Oana, Kozue; Nagano, Yukiko; Arakawa, Yoshichika; Nagano, Noriyuki

    2017-05-24

    β-lactamase genes were detected and characterized from 10 non-typhoidal Salmonella (NTS) clinical isolates resistant to third-generation cephalosporins collected between 2012 and 2014 in Japan. Five strains showed cefotaxime minimum inhibitory concentration (MIC) ≥ 64 μg/ml and positive clavulanic acid inhibition results. The bla CTX-M-2 was detected in 3 strains (serotypes Stanley and Muenchen), whereas bla TEM-52 (serotype Manhattan) and bla SHV-12 (serotype Infantis) were each found in 1 strain. bla CMY-2 was detected in the remaining 5 strains (serotypes Infantis, Rissen, Newport, and Saintpaul) with cefotaxime MICs of 4-32 μg/ml and positive cloxacillin- and 3-aminophenylboronic acid- based inhibition tests. ISEcp1 was located upstream of the bla CMY-2 in 4 strains and of the bla CTX-M-2 in 1 strain. Incompatibility (Inc)A/C, IncP, and IncI1 plasmids were present in the strains harboring bla CMY-2 , which were detected predominantly in this study. Acquisition of resistance to third-generation cephalosporins by invasive NTS may limit therapeutic options for severe systemic infections and causing serious public health problems. Though such resistant clinical isolates are still rare in Salmonella species in Japan, our findings reveal the presence of cephem-resistant NTS in food handlers, thus emphasizing the necessity of more systematic nationwide investigations.

  13. Non-coding RNA in Deinococcus radiodurans

    International Nuclear Information System (INIS)

    Chen Zhongzhong; Wang Liangyan; Lin Jun; Tian Bing; Hua Yuejin

    2006-01-01

    Researches on DNA damage and repair pathways of Deinococcus radiodurans show its extreme resistance to ionizing radiation, ultraviolet radiation and reactive oxygen species. Non-coding (ncRNA) RNAs are involved in a variety of processes such as transcriptional regulations, RNA processing and modification, mRNA translation, protein transportation and stability. The conserved secondary structures of intergenic regions of Deinococcus radiodurans R1 were predicted using Stochastic Context Free Grammar (SCFG) scan strategy. Results showed that 28 ncRNA families were present in the non-coding regions of the genome of Deinococcus radiodurans R1. Among these families, IRE is the largest family, followed by Histone3, tRNA, SECIS. DicF, ctRNA-pGA1 and tmRNA are one discovered in bacteria. Results from the comparison with other organisms showed that these ncRNA can be applied to the study of biological function of Deinococcus radiodurans and supply reference for the further study of DNA damage and repair mechanisms of this bacterium. (authors)

  14. Salmonella fecal shedding and immune responses are dose- and serotype- dependent in pigs.

    Directory of Open Access Journals (Sweden)

    Renata Ivanek

    Full Text Available Despite the public health importance of Salmonella infection in pigs, little is known about the associated dynamics of fecal shedding and immunity. In this study, we investigated the transitions of pigs through the states of Salmonella fecal shedding and immune response post-Salmonella inoculation as affected by the challenge dose and serotype. Continuous-time multistate Markov models were developed using published experimental data. The model for shedding had four transient states, of which two were shedding (continuous and intermittent shedding and two non-shedding (latency and intermittent non-shedding, and one absorbing state representing permanent cessation of shedding. The immune response model had two transient states representing responses below and above the seroconversion level. The effects of two doses [low (0.65×10(6 CFU/pig and high (0.65×10(9 CFU/pig] and four serotypes (Salmonella Yoruba, Salmonella Cubana, Salmonella Typhimurium, and Salmonella Derby on the models' transition intensities were evaluated using a proportional intensities model. Results indicated statistically significant effects of the challenge dose and serotype on the dynamics of shedding and immune response. The time spent in the specific states was also estimated. Continuous shedding was on average 10-26 days longer, while intermittent non-shedding was 2-4 days shorter, in pigs challenged with the high compared to low dose. Interestingly, among pigs challenged with the high dose, the continuous and intermittent shedding states were on average up to 10-17 and 3-4 days longer, respectively, in pigs infected with S. Cubana compared to the other three serotypes. Pigs challenged with the high dose of S. Typhimurium or S. Derby seroconverted on average up to 8-11 days faster compared to the low dose. These findings highlight that Salmonella fecal shedding and immune response following Salmonella challenge are dose- and serotype-dependent and that the detection of

  15. Inhibitory Effects of Several Essential Oils towards Salmonella typhimurium, Salmonella paratyphi A and Salmonella paratyphi B

    Directory of Open Access Journals (Sweden)

    S.F. Mazhar

    2014-09-01

    Full Text Available Plant essential oils are natural products extracted from plants and because of their antimicrobial properties can be used as natural additives in foods. They are also useful for decontamination of food-borne pathogens and can be a safe additive in foods. The antimicrobial activities of essential oils belonging to Saturiea hortensis, Thymus vulgaris, Mentha polegium, Cuminum cyminum, Lavandula officinalis and Mentha viridis L. (spearmint were investigated at different concentrations (0.1, 0.3, 0.5, 1, 2, 5 and 10%v/v against Salmonella typhimurium, Salmonella paratyphi A and Salmonella paratyphi B by using the agar well diffusion method. Essential oils showed inhibitory effect on Salmonella spp. in the agar well diffusion assay. In addition, the capability of essential oils for decontamination of minced row beef, ground beef, minced raw chicken and minced raw fish inoculated with Salmonella spp. at 0.1 and 0.5%v/v were assessed. Reduction of the Salmonella spp. population was observed following the inoculation of the cultures with 0.1 and 0.5%v/v essential oils.

  16. Non-coding RNAs in the Ovarian Follicle

    Directory of Open Access Journals (Sweden)

    Rosalia Battaglia

    2017-05-01

    Full Text Available The mammalian ovarian follicle is the complex reproductive unit comprising germ cell, somatic cells (Cumulus and Granulosa cells, and follicular fluid (FF: paracrine communication among the different cell types through FF ensures the development of a mature oocyte ready for fertilization. This paper is focused on non-coding RNAs in ovarian follicles and their predicted role in the pathways involved in oocyte growth and maturation. We determined the expression profiles of microRNAs in human oocytes and FF by high-throughput analysis and identified 267 microRNAs in FF and 176 in oocytes. Most of these were FF microRNAs, while 9 were oocyte specific. By bioinformatic analysis, independently performed on FF and oocyte microRNAs, we identified the most significant Biological Processes and the pathways regulated by their validated targets. We found many pathways shared between the two compartments and some specific for oocyte microRNAs. Moreover, we found 41 long non-coding RNAs able to interact with oocyte microRNAs and potentially involved in the regulation of folliculogenesis. These data are important in basic reproductive research and could also be useful for clinical applications. In fact, the characterization of non-coding RNAs in ovarian follicles could improve reproductive disease diagnosis, provide biomarkers of oocyte quality in Assisted Reproductive Treatment, and allow the development of therapies for infertility disorders.

  17. Decoding the function of nuclear long non-coding RNAs.

    Science.gov (United States)

    Chen, Ling-Ling; Carmichael, Gordon G

    2010-06-01

    Long non-coding RNAs (lncRNAs) are mRNA-like, non-protein-coding RNAs that are pervasively transcribed throughout eukaryotic genomes. Rather than silently accumulating in the nucleus, many of these are now known or suspected to play important roles in nuclear architecture or in the regulation of gene expression. In this review, we highlight some recent progress in how lncRNAs regulate these important nuclear processes at the molecular level. Copyright 2010 Elsevier Ltd. All rights reserved.

  18. A comparison of cecal colonization of Salmonella enterica serotype Typhimurium in white leghorn chicks and Salmonella-resistant mice

    Directory of Open Access Journals (Sweden)

    Bogomolnaya Lydia M

    2008-10-01

    Full Text Available Abstract Background Salmonellosis is one of the most important bacterial food borne illnesses worldwide. A major source of infection for humans is consumption of chicken or egg products that have been contaminated with Salmonella enterica serotype Typhimurium, however our knowledge regarding colonization and persistence factors in the chicken is small. Results We compared intestinal and systemic colonization of 1-week-old White Leghorn chicks and Salmonella-resistant CBA/J mice during infection with Salmonella enterica serotype Typhimurium ATCC14028, one of the most commonly studied isolates. We also studied the distribution of wild type serotype Typhimurium ATCC14028 and an isogenic invA mutant during competitive infection in the cecum of 1-week-old White Leghorn chicks and 8-week-old CBA/J mice. We found that although the systemic levels of serotype Typhimurium in both infected animal models are low, infected mice have significant splenomegaly beginning at 15 days post infection. In the intestinal tract itself, the cecal contents are the major site for recovery of serotype Typhimurium in the cecum of 1-week-old chicks and Salmonella-resistant mice. Additionally we show that only a small minority of Salmonellae are intracellular in the cecal epithelium of both infected animal models, and while SPI-1 is important for successful infection in the murine model, it is important for association with the cecal epithelium of 1-week-old chicks. Finally, we show that in chicks infected with serotype Typhimurium at 1 week of age, the level of fecal shedding of this organism does not reflect the level of cecal colonization as it does in murine models. Conclusion In our study, we highlight important differences in systemic and intestinal colonization levels between chick and murine serotype Typhimurium infections, and provide evidence that suggests that the role of SPI-1 may not be the same during colonization of both animal models.

  19. Tumor-targeting Salmonella typhimurium A1-R Inhibits Osteosarcoma Angiogenesis in the In Vivo Gelfoam® Assay Visualized by Color-coded Imaging.

    Science.gov (United States)

    Kiyuna, Tasuku; Tome, Yasunori; Uehara, Fuminari; Murakami, Takashi; Zhang, Yong; Zhao, Ming; Kanaya, Fuminori; Hoffman, Robert M

    2018-01-01

    We previously developed a color-coded imaging model that can quantify the length of nascent blood vessels using Gelfoam® implanted in nestin-driven green fluorescent protein (ND-GFP) nude mice. In this model, nascent blood vessels selectively express GFP. We also previously showed that osteosarcoma cells promote angiogenesis in this assay. We have also previously demonstrated the tumor-targeting bacteria Salmonella typhimurium A1-R (S. typhimurium A1-R) can inhibit or regress all tested tumor types in mouse models. The aim of the present study was to determine if S. typhimurium A1-R could inhibit osteosarcoma angiogenesis in the in vivo Gelfoam® color-coded imaging assay. Gelfoam® was implanted subcutaneously in ND-GFP nude mice. Skin flaps were made 7 days after implantation and 143B-RFP human osteosarcoma cells expressing red fluorescent protein (RFP) were injected into the implanted Gelfoam. After establishment of tumors in the Gelfoam®, control-group mice were treated with phosphate buffered saline via tail-vein injection (iv) and the experimental group was treated with S. typhimurium A1-R iv Skin flaps were made at day 7, 14, 21, and 28 after implantation of the Gelfoam® to allow imaging of vascularization in the Gelfoam® using a variable-magnification small-animal imaging system and confocal fluorescence microscopy. Nascent blood vessels expressing ND-GFP extended into the Gelfoam® over time in both groups. However, the extent of nascent blood-vessel growth was significantly inhibited by S. typhimurium A1-R treatment by day 28. The present results indicate S. typhimurium A1-R has potential for anti-angiogenic targeted therapy of osteosarcoma. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  20. Prevalence, serotype diversity, and antimicrobial resistance of Salmonella in imported shipments of spice offered for entry to the United States, FY2007-FY2009.

    Science.gov (United States)

    Van Doren, Jane M; Kleinmeier, Daria; Hammack, Thomas S; Westerman, Ann

    2013-06-01

    In response to increased concerns about spice safety, the U.S. FDA initiated research to characterize the prevalence of Salmonella in imported spices. Shipments of imported spices offered for entry to the United Sates were sampled during the fiscal years 2007-2009. The mean shipment prevalence for Salmonella was 0.066 (95% CI 0.057-0.076). A wide diversity of Salmonella serotypes was isolated from spices; no single serotype constituted more than 7% of the isolates. A small percentage of spice shipments were contaminated with antimicrobial-resistant Salmonella strains (8.3%). Trends in shipment prevalence for Salmonella associated with spice properties, extent of processing, and export country, were examined. A larger proportion of shipments of spices derived from fruit/seeds or leaves of plants were contaminated than those derived from the bark/flower of spice plants. Salmonella prevalence was larger for shipments of ground/cracked capsicum and coriander than for shipments of their whole spice counterparts. No difference in prevalence was observed between shipments of spice blends and non-blended spices. Some shipments reported to have been subjected to a pathogen reduction treatment prior to being offered for U.S. entry were found contaminated. Statistical differences in Salmonella shipment prevalence were also identified on the basis of export country. Published by Elsevier Ltd.

  1. Seasonal stability of Cladophora-associated Salmonella in Lake Michigan watersheds

    Science.gov (United States)

    Byappanahalli, M.N.; Sawdey, R.; Ishii, S.; Shively, D.A.; Ferguson, J.A.; Whitman, R.L.; Sadowsky, M.J.

    2009-01-01

    The bacterial pathogens Shigella, Salmonella, Campylobacter, and shiga toxin-producing E. coli (STEC) were recently found to be associated with Cladophora growing in southern Lake Michigan. Preliminary results indicated that the Salmonella strains associated with Cladophora were genetically identical to each other. However, because of the small sample size (n = 37 isolates) and a lack of information on spatial-temporal relationships, the nature of the association between Cladophora and Salmonella remained speculative. In this study, we investigated the population structure and genetic relatedness of a large number of Cladophora-borne Salmonella isolates from Lake Michigan (n = 133), as well as those isolated from stream and lake water (n = 31), aquatic plants (n = 8), and beach sands and sediments (n = 8) from adjacent watersheds. Salmonella isolates were collected during 2005-2007 between May and August from Lake Michigan beachsheds in Wisconsin, Illinois, and Indiana. The genetic relatedness of Salmonella isolates was examined by using the horizontal, fluorophore-enhanced rep-PCR (HFERP) DNA fingerprinting technique. While the Salmonella isolates associated with Cladophora exhibited a high degree of genetic relatedness (???92% similarity), the isolates were not all genetically identical. Spatial and temporal relationships were evident in the populations examined, with tight clustering of the isolates both by year and location. These findings suggest that the relationship between Salmonella and Cladophora is likely casual and is related to input sources (e.g. wastewater, runoff, birds) and the predominant Salmonella genotype surviving in the environment during a given season. Our studies indicate that Cladophora is likely an important reservoir for Salmonella and other enteric bacterial pathogens in Lake Michigan beachsheds, which in turn may influence nearshore water quality. ?? 2008 Elsevier Ltd.

  2. Seasonal stability of Cladophora-associated Salmonella in Lake Michigan watersheds.

    Science.gov (United States)

    Byappanahalli, Muruleedhara N; Sawdey, Richard; Ishii, Satoshi; Shively, Dawn A; Ferguson, John A; Whitman, Richard L; Sadowsky, Michael J

    2009-02-01

    The bacterial pathogens Shigella, Salmonella, Campylobacter, and shiga toxin-producing E. coli (STEC) were recently found to be associated with Cladophora growing in southern Lake Michigan. Preliminary results indicated that the Salmonella strains associated with Cladophora were genetically identical to each other. However, because of the small sample size (n=37 isolates) and a lack of information on spatial-temporal relationships, the nature of the association between Cladophora and Salmonella remained speculative. In this study, we investigated the population structure and genetic relatedness of a large number of Cladophora-borne Salmonella isolates from Lake Michigan (n=133), as well as those isolated from stream and lake water (n=31), aquatic plants (n=8), and beach sands and sediments (n=8) from adjacent watersheds. Salmonella isolates were collected during 2005-2007 between May and August from Lake Michigan beachsheds in Wisconsin, Illinois, and Indiana. The genetic relatedness of Salmonella isolates was examined by using the horizontal, fluorophore-enhanced rep-PCR (HFERP) DNA fingerprinting technique. While the Salmonella isolates associated with Cladophora exhibited a high degree of genetic relatedness (>or=92% similarity), the isolates were not all genetically identical. Spatial and temporal relationships were evident in the populations examined, with tight clustering of the isolates both by year and location. These findings suggest that the relationship between Salmonella and Cladophora is likely casual and is related to input sources (e.g. wastewater, runoff, birds) and the predominant Salmonella genotype surviving in the environment during a given season. Our studies indicate that Cladophora is likely an important reservoir for Salmonella and other enteric bacterial pathogens in Lake Michigan beachsheds, which in turn may influence nearshore water quality.

  3. Linear-time non-malleable codes in the bit-wise independent tampering model

    NARCIS (Netherlands)

    R.J.F. Cramer (Ronald); I.B. Damgård (Ivan); N.M. Döttling (Nico); I. Giacomelli (Irene); C. Xing (Chaoping)

    2017-01-01

    textabstractNon-malleable codes were introduced by Dziembowski et al. (ICS 2010) as coding schemes that protect a message against tampering attacks. Roughly speaking, a code is non-malleable if decoding an adversarially tampered encoding of a message m produces the original message m or a value m′

  4. Molecular characterization of Salmonella isolates by REP-PCR and RAPD analysis.

    Science.gov (United States)

    Albufera, U; Bhugaloo-Vial, P; Issack, M I; Jaufeerally-Fakim, Y

    2009-05-01

    Eighteen Salmonella isolates from both human and food (non-human) sources (fish, meat, and poultry) were characterized using conventional culture methods, biochemical, serological, and molecular analyses. REP-PCR and RAPD produced DNA profiles for differentiation purposes. Enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindronic (REP) and BOXAIR primers were selected for REP-PCR and two arbitrary primers, namely OPP-16 and OPS-11 were used for RAPD to generate DNA fingerprints from the Salmonella isolates. REP-PCR method showed greater discriminatory power in differentiating closely related strains of the related strains of Salmonella and produced more complex banding patterns as compared with RAPD. A dendogram was constructed with both sets of profiles using SPSS Version 13.0 computer software and showed that most human isolates were separately clustered from the non-human isolates. Two of the human isolates were closely related to some of the non-human isolates. A good correlation was also observed between the serogrouping of the O antigen and the molecular profiles obtained from REP-PCR and RAPD data of the Salmonella isolates. The results of a principal coordinate analysis (PCA) corresponded to the clustering in the dendrogram.

  5. Cyclic and constacyclic codes over a non-chain ring

    Directory of Open Access Journals (Sweden)

    Ayşegül Bayram

    2014-09-01

    Full Text Available In this study, we consider linear and especially cyclic codes over the non-chain ring $Z_{p}[v]/\\langle v^{p}-v\\rangle$ where $p$ is a prime. This is a generalization of the case $p=3.$ Further, in this work the structure of constacyclic codes are studied as well. This study takes advantage mainly from a Gray map which preserves the distance between codes over this ring and $p$-ary codes and moreover this map enlightens the structure of these codes. Furthermore, a MacWilliams type identity is presented together with some illustrative examples.

  6. Non-coding, mRNA-like RNAs database Y2K.

    Science.gov (United States)

    Erdmann, V A; Szymanski, M; Hochberg, A; Groot, N; Barciszewski, J

    2000-01-01

    In last few years much data has accumulated on various non-translatable RNA transcripts that are synthesised in different cells. They are lacking in protein coding capacity and it seems that they work mainly or exclusively at the RNA level. All known non-coding RNA transcripts are collected in the database: http://www. man.poznan.pl/5SData/ncRNA/index.html

  7. Decoding the Emerging Patterns Exhibited in Non-coding RNAs Characteristic of Lung Cancer with Regard to their Clinical Significance.

    Science.gov (United States)

    Sonea, Laura; Buse, Mihail; Gulei, Diana; Onaciu, Anca; Simon, Ioan; Braicu, Cornelia; Berindan-Neagoe, Ioana

    2018-05-01

    Lung cancer continues to be the leading topic concerning global mortality rate caused by can-cer; it needs to be further investigated to reduce these dramatic unfavorable statistic data. Non-coding RNAs (ncRNAs) have been shown to be important cellular regulatory factors and the alteration of their expression levels has become correlated to extensive number of pathologies. Specifically, their expres-sion profiles are correlated with development and progression of lung cancer, generating great interest for further investigation. This review focuses on the complex role of non-coding RNAs, namely miR-NAs, piwi-interacting RNAs, small nucleolar RNAs, long non-coding RNAs and circular RNAs in the process of developing novel biomarkers for diagnostic and prognostic factors that can then be utilized for personalized therapies toward this devastating disease. To support the concept of personalized medi-cine, we will focus on the roles of miRNAs in lung cancer tumorigenesis, their use as diagnostic and prognostic biomarkers and their application for patient therapy.

  8. Salmonella meningitis and septicaemia in an non-immunocompromised adult, associated with a cluster of Salmonella Enteritidis PT 14b, Ireland, November 2009.

    LENUS (Irish Health Repository)

    OhAiseadha, C O

    2010-01-01

    We report a fatal case of meningitis caused by Salmonella Enteritidis phage type 14b in a middle-aged man who had no history or findings to suggest he was immunocompromised. To our knowledge, this is the first reported case of Salmonella meningitis in an adult in Ireland, and the first case of meningitis in an adult caused by phage type 14b. This case was associated with a nationwide cluster of salmonellosis which is still under investigation at the time of writing.

  9. Eleventh CRL-Salmonella interlaboratory comparison study on typing of Salmonella spp.

    NARCIS (Netherlands)

    Berk PA; Maas HME; de Pinna E; Mooijman KA; MGB

    2006-01-01

    Het elfde ringonderzoek voor de typering van Salmonella werd in maart 2006 georganiseerd door het Communautair Referentie Laboratorium voor Salmonella (CRL-Salmonella, Bilthoven, Nederland) in samenwerking met de Health Protection Agency (HPA, Londen, Verenigd Koninkrijk). 26 Nationale Referentie

  10. Tenth CRL-Salmonella interlaboratory comparison study on typing of Salmonella spp.

    NARCIS (Netherlands)

    Korver H; Maas HME; Ward LR; Mevius DJ; Mooijman KA; MGB

    2006-01-01

    Het tiende ringonderzoek voor de typering van Salmonella werd in maart 2005 georganiseerd door het Communautair Referentie Laboratorium voor Salmonella (CRL-Salmonella, Bilthoven, Nederland) in samenwerking met de Health Protection Agency (HPA, Londen, Verenigd Koninkrijk) en het Centraal Instituut

  11. A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

    Science.gov (United States)

    Zhang, Ai-bing; Feng, Jie; Ward, Robert D; Wan, Ping; Gao, Qiang; Wu, Jun; Zhao, Wei-zhong

    2012-01-01

    Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37%) for 1094 brown algae queries, both using ITS barcodes.

  12. A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

    Directory of Open Access Journals (Sweden)

    Ai-bing Zhang

    Full Text Available Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish and two representing non-coding ITS barcodes (rust fungi and brown algae. Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ and Maximum likelihood (ML methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40% for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37% for 1094 brown algae queries, both using ITS barcodes.

  13. Immunity to intestinal pathogens: lessons learned from Salmonella

    Science.gov (United States)

    McSorley, Stephen J.

    2014-01-01

    Summary Salmonella are a common source of food or water-borne infection and cause a wide range of clinical disease in human and animal hosts. Salmonella are relatively easy to culture and manipulate in a laboratory setting, and the infection of laboratory animals induces robust innate and adaptive immune responses. Thus, immunologists have frequently turned to Salmonella infection models to expand understanding of immunity to intestinal pathogens. In this review, I summarize current knowledge of innate and adaptive immunity to Salmonella and highlight features of this response that have emerged from recent studies. These include the heterogeneity of the antigen-specific T-cell response to intestinal infection, the prominence of microbial mechanisms to impede T and B-cell responses, and the contribution of non-cognate pathways for elicitation of T-cell effector functions. Together, these different issues challenge an overly simplistic view of host-pathogen interaction during mucosal infection but also allow deeper insight into the real-world dynamic of protective immunity to intestinal pathogens. PMID:24942689

  14. Non-Saccharomyces yeasts protect against epithelial cell barrier disruption induced by Salmonella enterica subsp. enterica serovar Typhimurium

    DEFF Research Database (Denmark)

    Smith, Ida Mosbech; Baker, A; Arneborg, Nils

    2015-01-01

    distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function. While the established probiotic yeast Saccharomyces boulardii increased TER across a Caco-2 monolayer by 30%, Kluyveromyces marxianus exhibited significantly stronger properties of TER enhancement (50% TER increase....... In addition, probiotic strains may be able to reduce epithelial barrier disruption caused by pathogenic species. The aim of this study was to explore non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Benchmarking against established probiotic strains, we evaluated the ability......). In addition, our data demonstrate significant yeast-mediated modulation of Salmonella-induced epithelial cell barrier disruption and identify K. marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion. SIGNIFICANCE AND IMPACT...

  15. SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

    Science.gov (United States)

    Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

    2016-06-15

    Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available

  16. Epidemiological studies on Salmonella in a certain area ("Walcheren project"). I. The presence of Salmonella in man, pigs, insects, seagulls and in foods and effluents.

    Science.gov (United States)

    Edel, W; van Schothorst, M; Kampelmacher, E H

    1976-08-01

    During a certain period various materials (pigs, foods, insects, seagull droppings, chopping-block scrapings from butcher's shops, effluents of sewage treatment plants and stools of patients) were examined for the presence of Salmonella at the same time in a relatively small area (Walcheren). Certain types of Salmonella (S. typhi murium type II 505, S. panama, S. infantis and S. brandenburg) were frequently isolated from almost all materials examined. This may indicate the existence of Salmonella contamination cycles: one may think of the cycle: slaughter animal (infected from the environment and/or by meal) - meat - consumer - patient or healthy carrier - effluent and surface water - insects, birds and rodents - slaughter animal or meat and possibly other foods - consumer.

  17. A PCR-based strategy for simple and rapid identification of rough presumptive Salmonella isolates

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey; Baggesen, Dorte Lau; Porting, P.H.

    1999-01-01

    The purpose of the present study was to investigate the application of ready-to-go Salmonella PCR tests, based on dry chemistry, for final identification of rough presumptive Salmonella isolates. The results were compared with two different biotyping methods performed at two different laboratories......, which did not result in any DNA band. A total of 32 out of the 36 rough presumptive isolates were positive in the PCR. All but one isolate were also identified as Salmonella by the two biochemical methods. All 80 Salmonella strains were also tested in the two multiplex serogroup tests based on PCR beads....... The sensitivity of the BAX Salmonella PCR test was assessed by testing a total of 80 Salmonella isolates, covering most serogroups, which correctly identified all the Salmonella strains by resulting in one 800-bp band in the sample tubes. The specificity of the PCR was assessed using 20 non-Salmonella strains...

  18. A novel Salmonella serovar isolated from Peregrine Falcon (Falco peregrinus nestlings in Sweden: Salmonella enterica enterica serovar Pajala (Salmonella Pajala

    Directory of Open Access Journals (Sweden)

    Jorge Hernández

    2012-08-01

    Full Text Available A novel Salmonella serovar was isolated from Peregrine falcon (Falco peregrinus nestlings in northern Sweden in 2006. Three isolates of the same clone was retrieved from three falcon siblings and characterized as Salmonella enterica sub-species enterica: O-phase 13, 23:-: e, n, z 15 and the H-phase was not present. We propose the geographical name Salmonella enterica, sub-species enterica serovar Pajala to this novel Salmonella.

  19. PARN and TOE1 Constitute a 3′ End Maturation Module for Nuclear Non-coding RNAs

    Directory of Open Access Journals (Sweden)

    Ahyeon Son

    2018-04-01

    Full Text Available Summary: Poly(A-specific ribonuclease (PARN and target of EGR1 protein 1 (TOE1 are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A tails. Rather, they promote the maturation of nuclear small non-coding RNAs (ncRNAs. PARN and TOE1 act redundantly on some ncRNAs, most prominently small Cajal body-specific RNAs (scaRNAs. scaRNAs are strongly downregulated when PARN and TOE1 are compromised together, leading to defects in small nuclear RNA (snRNA pseudouridylation. They also function redundantly in the biogenesis of telomerase RNA component (TERC, which shares sequence motifs found in H/ACA box scaRNAs. Our findings extend the knowledge of nuclear ncRNA biogenesis, and they provide insights into the pathology of PARN/TOE1-associated genetic disorders whose therapeutic treatments are currently unavailable. : By analyzing the 3′ termini of transcriptome, Son et al. reveal the targets of PARN and TOE1, two nuclear deadenylases with disease associations. Both deadenylases are involved in nuclear small non-coding RNA maturation, but not in mRNA deadenylation. Their combined activity is particularly important for biogenesis of scaRNAs and TERC. Keywords: PARN, TOE1, CAF1Z, deadenylase, 3′ end maturation, adenylation, deadenylation, scaRNA, TERC

  20. Extracellular vesicle associated long non-coding RNAs functionally enhance cell viability

    Directory of Open Access Journals (Sweden)

    Chris Hewson

    2016-10-01

    Full Text Available Cells communicate with one another to create microenvironments and share resources. One avenue by which cells communicate is through the action of exosomes. Exosomes are extracellular vesicles that are released by one cell and taken up by neighbouring cells. But how exosomes instigate communication between cells has remained largely unknown. We present evidence here that particular long non-coding RNA molecules are preferentially packaged into exosomes. We also find that a specific class of these exosome associated non-coding RNAs functionally modulate cell viability by direct interactions with l-lactate dehydrogenase B (LDHB, high-mobility group protein 17 (HMG-17, and CSF2RB, proteins involved in metabolism, nucleosomal architecture and cell signalling respectively. Knowledge of this endogenous cell to cell pathway, those proteins interacting with exosome associated non-coding transcripts and their interacting domains, could lead to a better understanding of not only cell to cell interactions but also the development of exosome targeted approaches in patient specific cell-based therapies. Keywords: Non-coding RNA, Extracellular RNA, Exosomes, Retroelement, Pseudogene

  1. Determination of gamma radiation dose for destruction of Salmonella spp. in chicken flesh.; Determinacao da dose de radiacao gama para a destruicao de Salmonella spp. em carne de frango

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Andreia Ferreira dos

    1997-07-01

    The aim of this study was to determinate: 1) the radio sensibility of Salmonella typhimurium ATCC 14028 in soy trypticase broth; 2) the radio sensibility of Salmonella typhimurium ATCC 14028 in chicken thigh and; 3) to recommend a radiation dose which can be non hazardous for human consumption

  2. Immunology, epidemiology and mathematical modelling towards a better understanding of invasive non-typhoidal Salmonella disease and rational vaccination approaches.

    Science.gov (United States)

    Mastroeni, Pietro; Rossi, Omar

    2016-12-01

    Invasive non-typhoidal Salmonella (iNTS) infections cause a high burden of lethal sepsis in young children and HIV patients, often associated with malaria, anaemia, malnutrition and sickle-cell disease. Vaccines against iNTS are urgently needed but none are licensed yet. Areas covered: This review illustrates how immunology, epidemiology and within-host pathogen behaviour affect invasive Salmonella infections and highlights how this knowledge can assist the improvement and choice of vaccines. Expert Commentary: Control of iNTS disease requires approaches that reduce transmission and improve diagnosis and treatment. These are often difficult to implement due to the fragile ecology and economies in endemic countries. Vaccines will be key tools in the fight against iNTS disease. To optimise vaccine design, we need to better define protective antigens and mechanisms of resistance to disease in susceptible populations even in those individuals where innate immunity may be impaired by widespread comorbidities.

  3. Towards the development of a DNA-sequence based approach to serotyping of Salmonella enterica

    Directory of Open Access Journals (Sweden)

    Logan Julie MJ

    2004-08-01

    Full Text Available Abstract Background The fliC and fljB genes in Salmonella code for the phase 1 (H1 and phase 2 (H2 flagellin respectively, the rfb cluster encodes the majority of enzymes for polysaccharide (O antigen biosynthesis, together they determine the antigenic profile by which Salmonella are identified. Sequencing and characterisation of fliC was performed in the development of a molecular serotyping technique. Results FliC sequencing of 106 strains revealed two groups; the g-complex included those exhibiting "g" or "m,t" antigenic factors, and the non-g strains which formed a second more diverse group. Variation in fliC was characterised and sero-specific motifs identified. Furthermore, it was possible to identify differences in certain H antigens that are not detected by traditional serotyping. A rapid short sequencing assay was developed to target serotype-specific sequence motifs in fliC. The assay was evaluated for identification of H1 antigens with a panel of 55 strains. Conclusion FliC sequences were obtained for more than 100 strains comprising 29 different H1 alleles. Unique pyrosequencing profiles corresponding to the H1 component of the serotype were generated reproducibly for the 23 alleles represented in the evaluation panel. Short read sequence assays can now be used to identify fliC alleles in approximately 97% of the 50 medically most important Salmonella in England and Wales. Capability for high throughput testing and automation give these assays considerable advantages over traditional methods.

  4. Assessment of Salmonella spp. and Escherichia coli O157:H7 growth on lettuce exposed to isothermal and non-isothermal conditions.

    Science.gov (United States)

    de Oliveira Elias, Susana; Noronha, Tiago Baptista; Tondo, Eduardo Cesar

    2018-06-01

    This study aimed to assess the growth of Salmonella and Escherichia coli O157:H7 on lettuce exposed to isothermal and non-isothermal conditions. Pathogens were inoculated on lettuce separately and stored under isothermal condition at 5 °C, 10 °C, 25 °C, 37 °C for both bacteria, at 40 °C for Salmonella and 42 °C for E. coli O157:H7. Growth curves were built by fitting the data to the Baranyi's DMFit, generating R 2 values greater than 0.92 for primary models. Secondary models were fitted with Ratkowsky equations, generating R 2 values higher than 0.91 and RMSE lower than 0.1. Experimental data showed that both bacteria could grow at all temperatures. Also, the growth of both pathogens under non-isothermal conditions was studied simulating temperatures found from harvest to supermarkets in Brazil. Models were analysed by R 2 , RMSE, bias factor (Bf) and accuracy factor (Af). Salmonella and E. coli O157:H7 were able to grow in this temperature profile and the models could predict the behavior of these microorganisms on lettuce under isothermal and non-isothermal conditions. Based on the results, a negligible growth time (ς) was proposed to provide the time which lettuce could be exposed to a specific temperature and do not present an expressive growth of bacteria. The ς was developed based on Baranyi's primary model equation and on growth potential concept. ς is the value of lag phase added of the time necessary to population grow 0.5 log CFU/g. The ς of lettuce exposed to 37 °C was 1.3 h, while at 5 °C was 3.3 days. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. BIRTH: a beam deposition code for non-circular tokamak plasmas

    International Nuclear Information System (INIS)

    Otsuka, Michio; Nagami, Masayuki; Matsuda, Toshiaki

    1982-09-01

    A new beam deposition code has been developed which is capable of calculating fast ion deposition profiles including the orbit correction. The code incorporates any injection geometry and a non-circular cross section plasma with a variable elongation and an outward shift of the magnetic flux surface. Typical cpu time on a DEC-10 computer is 10 - 20 seconds and 5 - 10 seconds with and without the orbit correction, respectively. This is shorter by an order of magnitude than that of other codes, e.g., Monte Carlo codes. The power deposition profile calculated by this code is in good agreement with that calculated by a Monte Carlo code. (author)

  6. Molecular Epidemiology of Nontyphoidal Salmonella in Poultry and Poultry Products in India: Implications for Human Health

    OpenAIRE

    Saravanan, Sellappan; Purushothaman, Venketaraman; Murthy, Thippichettypalayam Ramasamy Gopala Krishna; Sukumar, Kuppannan; Srinivasan, Palani; Gowthaman, Vasudevan; Balusamy, Mohan; Atterbury, Robert; Kuchipudi, Suresh V.

    2015-01-01

    Human infections with non-typhoidal Salmonella (NTS) serovars are increasingly becoming a threat to human health globally. While all motile Salmonellae have zoonotic potential, Salmonella Enteritidis and Salmonella Typhimurium are most commonly associated with human disease, for which poultry are a major source. Despite the increasing number of human NTS infections, the epidemiology of NTS in poultry in India has not been fully understood. Hence, as a first step, we carried out epidemiologica...

  7. Effects of selected non-digestible dietary carbohydrates on the composition of the large intestinal microbiota and susceptibility to salmonella infections

    DEFF Research Database (Denmark)

    Petersen, Anne

    The mammalian intestinal tract is a complex ecosystem colonised by a high and diverse number of commensal bacterial. Bacteria colonising the intestinal tract have a profound impact on host health e.g. by acting as a barrier against colonisation by pathogens and by contributing to digestion...... of complex food components. In this regard there is a considerable interest in dietary components that can modulate the gut microbiota and potentially improve gut health. Some gut bacteria, known as probiotics, are belived to improve gut health upond ingestion, whereas non-digestible (ND) dietary...... of the gut microbiota or by stimulating the immune response. Salmonella is a genus of Gram-negative bacteria that are a major cause of food-borne illness globally. Several studies with probiotics have demonstrated protective effects against murine Salmonella infections, while studies with prebiotics have...

  8. Control of Salmonella enterica serovar Enteritidis in laying hens by inactivated Salmonella Enteritidis vaccines "Controle de Salmonella enterica sorovar Enteritidis em poedeiras comerciais com a utilização de vacinas inativadas"

    Directory of Open Access Journals (Sweden)

    Oliveiro Caetano de Freitas Neto

    2008-06-01

    Full Text Available Salmonella Enteritidis is one of the agents that is responsible for outbreaks of human foodborne salmonellosis caused by Salmonella Enteritidis and is generally associated with the consumption of poultry products. Inactivated Salmonella Enteritidis cell vaccine is one of the available methods to control Salmonella Enteritidis in breeders and laying hens, however results in terms of efficacy vary. This vaccine has never been tested in Brazil, therefore, the present work was carried out to assess three commercial inactivated Salmonella Enteritidis vaccines allowed in Brazil. Four hundred white light variety commercial laying hens were obtained at one-day-of age. At eight weeks old, the birds were divided into four groups with one hundred animals each. Birds from three groups (V1, V2 and V3 received different intramuscular vaccines, followed by a booster dose at 16 weeks of age. Birds from another group (CG were not vaccinated. When the laying hens were 20, 25 and 31 weeks old, 13 from each group were transferred to another room and were challenged by inoculating 2 mL neat culture of Salmonella Enteritidis. On the second day after each challenge, the caecal contents, spleen, liver and ovary of three birds from each group were analyzed for the presence of Salmonella Enteritidis. Twice a week a cloacal swab of each bird was taken and all eggs laid were examined for the presence of Salmonella Enteritidis. After four consecutive negative cloacal swabs in all the groups, the birds were sacrificed so as to examine the liver, caecal contents and ovaries. Overall, the inactivated vaccine used in group V3 reduced Salmonella Enteritidis in the feces and eggs. A very small amount of Salmonella was found in the spleen, liver, ovary and caeca of the birds in the four groups during the whole experiment. In general, inactivated Salmonella Enteritidis vaccines was able to decrease the presence of Salmonella Enteritidis in the birds and in the eggs as well

  9. Combinatorial Control of mRNA Fates by RNA-Binding Proteins and Non-Coding RNAs

    Directory of Open Access Journals (Sweden)

    Valentina Iadevaia

    2015-09-01

    Full Text Available Post-transcriptional control of gene expression is mediated by RNA-binding proteins (RBPs and small non-coding RNAs (e.g., microRNAs that bind to distinct elements in their mRNA targets. Here, we review recent examples describing the synergistic and/or antagonistic effects mediated by RBPs and miRNAs to determine the localisation, stability and translation of mRNAs in mammalian cells. From these studies, it is becoming increasingly apparent that dynamic rearrangements of RNA-protein complexes could have profound implications in human cancer, in synaptic plasticity, and in cellular differentiation.

  10. Isolation and identification of Salmonella spp. in environmental water by molecular technology in Taiwan

    Science.gov (United States)

    Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Shen, Tsung Yu; Kao, Po Min; Shen, Shu Min; Chen, Jung Sheng

    2013-04-01

    Salmonella spp. is one of the most important causal agents of waterborne diseases. The taxonomy of Salmonella is very complicated and its genus comprises more than 2,500 serotypes. The detection of Salmonella in environmental water samples by routines culture methods using selective media and characterization of suspicious colonies based on biochemical tests and serological assay are generally time consuming. To overcome this drawback, it is desirable to use effective method which provides a higher discrimination and more rapid identification about Salmonella in environmental water. The aim of this study is to investigate the occurrence of Salmonella using molecular technology and to identify the serovars of Salmonella isolates from 70 environmental water samples in Taiwan. The analytical procedures include membrane filtration, non-selective pre-enrichment, selective enrichment of Salmonella. After that, we isolated Salmonella strains by selective culture plates. Both selective enrichment and culture plates were detected by Polymerase Chain Reaction (PCR). Finally, the serovars of Salmonella were confirmed by using biochemical tests and serological assay. In this study, 15 water samples (21.4%) were identified as Salmonella by PCR. The positive water samples will further identify their serotypes by culture method. The presence of Salmonella in environmental water indicates the possibility of waterborne transmission in drinking watershed. Consequently, the authorities need to provide sufficient source protection and to maintain the system for disease prevention. Keywords: Salmonella spp., serological assay, PCR

  11. Survival of Salmonella spp. and fecal indicator bacteria in Vietnamese biogas digesters receiving pig slurry.

    Science.gov (United States)

    Huong, Luu Quynh; Forslund, Anita; Madsen, Henry; Dalsgaard, Anders

    2014-09-01

    Small-scale biogas digesters are widely promoted worldwide as a sustainable technology to manage livestock manure. In Vietnam, pig slurry is commonly applied to biogas digesters for production of gas for electricity and cooking with the effluent being used to fertilize field crops, vegetables and fish ponds. Slurry may contain a variety of zoonotic pathogens, e.g. Salmonella spp., which are able to cause disease in humans either through direct contact with slurry or by fecal contamination of water and foods. The objective of this study was to evaluate the survival of Salmonella spp. and the fecal indicator bacteria, enterococci, E. coli, and spores of Clostridium perfringens in biogas digesters operated by small-scale Vietnamese pig farmers. The serovar and antimicrobial susceptibility of the Salmonella spp. isolated were also established. The study was conducted in 12 farms (6 farms with and 6 farms without toilet connected) located in Hanam province, Vietnam. Sampling of pig slurry and biogas effluent was done during two seasons. Results showed that the concentration of enterococci, E. coli, and Clostridium perfringens spores was overall reduced by only 1-2 log10-units in the biogas digesters when comparing raw slurry and biogas effluent. Salmonella spp. was found in both raw slurry and biogas effluent. A total of 19 Salmonella serovars were identified, with the main serovars being Salmonella Typhimurium (55/138), Salmonella enterica serovar 4,[5],12:i:- (19/138), Salmonella Weltevreden (9/138) and Salmonella Rissen (9/138). The Salmonella serovars showed similar antimicrobial resistance patterns to those previously reported from Vietnam. When promoting biogas, farmers should be made aware that effluent should only be used as fertilizer for crops not consumed raw and that indiscriminate discharge of effluent are likely to contaminate water recipients, e.g. drinking water sources, with pathogens. Relevant authorities should promote safe animal manure management

  12. Analysis code for medium and small rupture accidents in ATR. LOTRAC/HEATUP

    International Nuclear Information System (INIS)

    1997-08-01

    In the evaluation of thermo-hydraulic and fuel temperature transient changes in the events which are classified in medium and small rupture accidents of reactor coolant loss that is the safety evaluation event of the ATR, the analysis code for synthetic thermo-hydraulic transient change at the time of medium and small ruptures LOTRAC and the detailed analysis code for fuel temperature HEATUP are used, respectively. By using the LOTAC, the thermo-hydraulic behavior of reactor cooling facility and the temperature behavior of fuel at the time of blow-down are analyzed, and also the characteristics of changing reactor thermal output is analyzed, considering the functioning characteristics of emergency core cooling system. Based on the data of thermo-hydraulic behavior obtained by the LOTRAC, the time of beginning the turn-around of fuel cladding tube temperature obtained by the data of ECCS pouring characteristics, the heat transfer rate after the turn-around and so on, the detailed temperature change of fuel elements is analyzed by the HEATUP, and the highest temperature and the amount of oxidation of fuel cladding tubes are determined. The LOTRAC code, the HEATUP code, various analysis models, and rupture simulation experiment are reported. (K.I.)

  13. Determination of gamma radiation dose for destruction of Salmonella spp. in chicken flesh

    International Nuclear Information System (INIS)

    Santos, Andreia Ferreira dos

    1997-01-01

    The aim of this study was to determinate: 1) the radio sensibility of Salmonella typhimurium ATCC 14028 in soy trypticase broth; 2) the radio sensibility of Salmonella typhimurium ATCC 14028 in chicken thigh and; 3) to recommend a radiation dose which can be non hazardous for human consumption

  14. Lactobacillus bulgaricus, Lactobacillus rhamnosus and Lactobacillus paracasei Attenuate Salmonella Enteritidis, Salmonella Heidelberg and Salmonella Typhimurium Colonization and Virulence Gene Expression In Vitro.

    Science.gov (United States)

    Muyyarikkandy, Muhammed Shafeekh; Amalaradjou, Mary Anne

    2017-11-09

    Salmonella Enteritidis (SE), Salmonella Typhimurium (ST), and Salmonella Heidelberg (SH) have been responsible for numerous outbreaks associated with the consumption of poultry meat and eggs. Salmonella colonization in chicken is characterized by initial attachment to the cecal epithelial cells (CEC) followed by dissemination to the liver, spleen, and oviduct. Since cecal colonization is critical to Salmonella transmission along the food chain continuum, reducing this intestinal association could potentially decrease poultry meat and egg contamination. Hence, this study investigated the efficacy of Lactobacillus delbreuckii sub species bulgaricus (NRRL B548; LD), Lactobacillus paracasei (DUP-13076; LP), and Lactobacillus rhamnosus (NRRL B442; LR) in reducing SE, ST, and SH colonization in CEC and survival in chicken macrophages. Additionally, their effect on expression of Salmonella virulence genes essential for cecal colonization and survival in macrophages was evaluated. All three probiotics significantly reduced Salmonella adhesion and invasion in CEC and survival in chicken macrophages ( p < 0.05). Further, the probiotic treatment led to a significant reduction in Salmonella virulence gene expression ( p < 0.05). Results of the study indicate that LD, LP, and LR could potentially be used to control SE, ST, and SH colonization in chicken. However, these observations warrant further in vivo validation.

  15. Lactobacillus bulgaricus, Lactobacillus rhamnosus and Lactobacillus paracasei Attenuate Salmonella Enteritidis, Salmonella Heidelberg and Salmonella Typhimurium Colonization and Virulence Gene Expression In Vitro

    Directory of Open Access Journals (Sweden)

    Muhammed Shafeekh Muyyarikkandy

    2017-11-01

    Full Text Available Salmonella Enteritidis (SE, Salmonella Typhimurium (ST, and Salmonella Heidelberg (SH have been responsible for numerous outbreaks associated with the consumption of poultry meat and eggs. Salmonella colonization in chicken is characterized by initial attachment to the cecal epithelial cells (CEC followed by dissemination to the liver, spleen, and oviduct. Since cecal colonization is critical to Salmonella transmission along the food chain continuum, reducing this intestinal association could potentially decrease poultry meat and egg contamination. Hence, this study investigated the efficacy of Lactobacillus delbreuckii sub species bulgaricus (NRRL B548; LD, Lactobacillus paracasei (DUP-13076; LP, and Lactobacillus rhamnosus (NRRL B442; LR in reducing SE, ST, and SH colonization in CEC and survival in chicken macrophages. Additionally, their effect on expression of Salmonella virulence genes essential for cecal colonization and survival in macrophages was evaluated. All three probiotics significantly reduced Salmonella adhesion and invasion in CEC and survival in chicken macrophages (p < 0.05. Further, the probiotic treatment led to a significant reduction in Salmonella virulence gene expression (p < 0.05. Results of the study indicate that LD, LP, and LR could potentially be used to control SE, ST, and SH colonization in chicken. However, these observations warrant further in vivo validation.

  16. Non-small-bowel abnormalities identified during small bowel capsule endoscopy

    NARCIS (Netherlands)

    Hoedemakers, Reinier; Westerhof, Jessie; Weersma, Rinse K.; Koornstra, Jan J.

    2014-01-01

    AIM: To investigate the incidence of non-small-bowel abnormalities in patients referred for small bowel capsule endoscopy, this single center study was performed. METHODS: Small bowel capsule endoscopy is an accepted technique to investigate obscure gastrointestinal bleeding. This is defined as

  17. At the intersection of non-coding transcription, DNA repair, chromatin structure, and cellular senescence

    Directory of Open Access Journals (Sweden)

    Ryosuke eOhsawa

    2013-07-01

    Full Text Available It is well accepted that non-coding RNAs play a critical role in regulating gene expression. Recent paradigm-setting studies are now revealing that non-coding RNAs, other than microRNAs, also play intriguing roles in the maintenance of chromatin structure, in the DNA damage response, and in adult human stem cell aging. In this review, we will discuss the complex inter-dependent relationships among non-coding RNA transcription, maintenance of genomic stability, chromatin structure and adult stem cell senescence. DNA damage-induced non-coding RNAs transcribed in the vicinity of the DNA break regulate recruitment of the DNA damage machinery and DNA repair efficiency. We will discuss the correlation between non-coding RNAs and DNA damage repair efficiency and the potential role of changing chromatin structures around double-strand break sites. On the other hand, induction of non-coding RNA transcription from the repetitive Alu elements occurs during human stem cell aging and hinders efficient DNA repair causing entry into senescence. We will discuss how this fine balance between transcription and genomic instability may be regulated by the dramatic changes to chromatin structure that accompany cellular senescence.

  18. Comparing human-Salmonella with plant-Salmonella protein-protein interaction predictions

    Directory of Open Access Journals (Sweden)

    Sylvia eSchleker

    2015-01-01

    Full Text Available Salmonellosis is the most frequent food-borne disease world-wide and can be transmitted to humans by a variety of routes, especially via animal and plant products. Salmonella bacteria are believed to use not only animal and human but also plant hosts despite their evolutionary distance. This raises the question if Salmonella employs similar mechanisms in infection of these diverse hosts. Given that most of our understanding comes from its interaction with human hosts, we investigate here to what degree knowledge of Salmonella-human interactions can be transferred to the Salmonella-plant system. Reviewed are recent publications on analysis and prediction of Salmonella-host interactomes. Putative protein-protein interactions (PPIs between Salmonella and its human and Arabidopsis hosts were retrieved utilizing purely interolog-based approaches in which predictions were inferred based on available sequence and domain information of known PPIs, and machine learning approaches that integrate a larger set of useful information from different sources. Transfer learning is an especially suitable machine learning technique to predict plant host targets from the knowledge of human host targets. A comparison of the prediction results with transcriptomic data shows a clear overlap between the host proteins predicted to be targeted by PPIs and their gene ontology enrichment in both host species and regulation of gene expression. In particular, the cellular processes Salmonella interferes with in plants and humans are catabolic processes. The details of how these processes are targeted, however, are quite different between the two organisms, as expected based on their evolutionary and habitat differences. Possible implications of this observation on evolution of host-pathogen communication are discussed.

  19. Salmonella testing of pooled pre-enrichment broth cultures for screening multiple food samples.

    Science.gov (United States)

    Price, W R; Olsen, R A; Hunter, J E

    1972-04-01

    A method has been described for testing multiple food samples for Salmonella without loss in sensitivity. The method pools multiple pre-enrichment broth cultures into single enrichment broths. The subsequent stages of the Salmonella analysis are not altered. The method was found applicable to several dry food materials including nonfat dry milk, dried egg albumin, cocoa, cottonseed flour, wheat flour, and shredded coconut. As many as 25 pre-enrichment broth cultures were pooled without apparent loss in the sensitivity of Salmonella detection as compared to individual sample analysis. The procedure offers a simple, yet effective, way to increase sample capacity in the Salmonella testing of foods, particularly where a large proportion of samples ordinarily is negative. It also permits small portions of pre-enrichment broth cultures to be retained for subsequent individual analysis if positive tests are found. Salmonella testing of pooled pre-enrichment broths provides increased consumer protection for a given amount of analytical effort as compared to individual sample analysis.

  20. Aerodynamic shape optimization of non-straight small wind turbine blades

    International Nuclear Information System (INIS)

    Shen, Xin; Yang, Hong; Chen, Jinge; Zhu, Xiaocheng; Du, Zhaohui

    2016-01-01

    Graphical abstract: Small wind turbine blades with 3D stacking lines (sweep and bend) have been considered and analyzed with an optimization code based on the lifting surface method. The results indicated that the power capture and the rotor thrust can be improved with these more complex geometries. The starting behavior of the small wind turbines can be improved by the optimization of the blade chord and twist angle distribution. - Highlights: • The small wind turbine blade was optimized with non-straight shape. • Lifting surface method with free wake was used for aerodyanmic performace evaluation. • The non-straight shape can be used to increase energy production and decrease the thrust. • The energy production should be sacrificed in order to increase the starting behavior. - Abstract: Small wind turbines usually operate in sub-optimal wind conditions in order to satisfy the demand where it is needed. The aerodynamic performance of small horizontal axis wind turbines highly depends on the geometry. In the present study, the geometry of wind turbine blades are optimized not only in terms of the distribution of the chord and twist angle but also with 3-dimensional stacking line. As the blade with 3-dimensional stacking line is given sweep in the plan of rotation and dihedral in the plan containing the blade and rotor axis, the common used blade element momentum method can no longer provide accurate aerodynamic performance solution. A lifting surface method with free wake model is used as the aerodynamic model in the present work. The annual energy production and the starting performance are selected as optimization objective. The starting performance is evaluated based on blade element method. The optimization of the geometry of the non-straight wind turbine blades is carried out by using a micro-genetic algorithm. Results show that the wind turbine blades with properly designed 3-dimensional stacking line can increase the annual energy production and have

  1. Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

    Science.gov (United States)

    Jarquin, Robin; Hanning, Irene; Ahn, Soohyoun; Ricke, Steven C.

    2009-01-01

    Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR) assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered. PMID:22346699

  2. Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

    Directory of Open Access Journals (Sweden)

    Steven C. Ricke

    2009-07-01

    Full Text Available Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered.

  3. On the classification of long non-coding RNAs

    KAUST Repository

    Ma, Lina; Bajic, Vladimir B.; Zhang, Zhang

    2013-01-01

    Long non-coding RNAs (lncRNAs) have been found to perform various functions in a wide variety of important biological processes. To make easier interpretation of lncRNA functionality and conduct deep mining on these transcribed sequences

  4. A Perspective on Invasive Salmonella Disease in Africa.

    Science.gov (United States)

    Crump, John A; Heyderman, Robert S

    2015-11-01

    Salmonella enterica is a leading cause of community-acquired bloodstream infection in Africa. The contribution of typhoidal and nontyphoidal Salmonella serovars to invasive disease varies considerably in place and time, even within the same country. Nonetheless, many African countries are now thought to experience typhoid fever incidence >100 per 100,000 per year with approximately 1% of patients dying. Invasive nontyphoidal Salmonella (iNTS) disease was estimated to cause 3.4 million illnesses and 681 316 deaths in 2010, with the most disease in Africa. Antimicrobial drug resistance is a growing problem in S. enterica that threatens to further compromise patient outcomes. Reservoirs for nontyphoidal Salmonella and the predominant routes of transmission for typhoidal and nontyphoidal Salmonella are not well understood in Africa, hampering the design of evidence-based, non-vaccine- and vaccine-based prevention measures. It is difficult to distinguish clinically invasive Salmonella disease from febrile illnesses caused by other pathogens. Blood cultures are the mainstay of laboratory diagnosis, but lack sensitivity due to the low magnitude of bacteremia, do not produce results at point of care, and are not widely available in Africa. Serologic approaches to diagnosis remain inaccurate, and nucleic acid amplification tests are also compromised by low concentrations of bacteria. High-throughput whole-genome sequencing, together with a range of novel analytic pipelines, has provided new insights into the complex pattern of epidemiology, pathogenesis, and host adaptation. Concerted efforts are therefore needed to apply these new tools in the context of high-quality field surveillance to improve diagnosis, patient management, control, and prevention of invasive Salmonella infections in Africa. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Salmonella risk to consumers via pork is related to the Salmonella prevalence in pig feed.

    Science.gov (United States)

    Rönnqvist, M; Välttilä, V; Ranta, J; Tuominen, P

    2018-05-01

    Pigs are an important source of human infections with Salmonella, one of the most common causes of sporadic gastrointestinal infections and foodborne outbreaks in the European region. Feed has been estimated to be a significant source of Salmonella in piggeries in countries of a low Salmonella prevalence. To estimate Salmonella risk to consumers via the pork production chain, including feed production, a quantitative risk assessment model was constructed. The Salmonella prevalence in feeds and in animals was estimated to be generally low in Finland, but the relative importance of feed as a source of Salmonella in pigs was estimated as potentially high. Discontinuation of the present strict Salmonella control could increase the risk of Salmonella in slaughter pigs and consequent infections in consumers. The increased use of low risk and controlled feed ingredients could result in a consistently lower residual contamination in pigs and help the tracing and control of the sources of infections. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. 78 FR 42526 - Salmonella

    Science.gov (United States)

    2013-07-16

    ...] Salmonella Contamination of Dry Dog Food; Withdrawal of Compliance Policy Guide AGENCY: Food and Drug... the withdrawal of the compliance policy guide (CPG) entitled ``Sec. 690.700 Salmonella Contamination... entitled ``Sec. 690.700 Salmonella Contamination of Dry Dog Food (CPG 690.700)'' on October 1, 1980. CPG...

  7. Junk DNA and the long non-coding RNA twist in cancer genetics

    NARCIS (Netherlands)

    H. Ling (Hui); K. Vincent; M. Pichler; R. Fodde (Riccardo); I. Berindan-Neagoe (Ioana); F.J. Slack (Frank); G.A. Calin (George)

    2015-01-01

    textabstractThe central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs

  8. Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays

    Directory of Open Access Journals (Sweden)

    Patenge Nadja

    2012-10-01

    Full Text Available Abstract Background Small non-coding RNAs (sRNAs have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria to identify sRNA regulators. Many sRNAs are well characterized, including their target mRNAs and mode of action. In comparison, little is known about sRNAs in Gram-positive pathogens. In this study, we identified novel sRNAs in the exclusively human pathogen Streptococcus pyogenes M49 (Group A Streptococcus, GAS M49, employing a whole genome intergenic tiling array approach. GAS is an important pathogen that causes diseases ranging from mild superficial infections of the skin and mucous membranes of the naso-pharynx, to severe toxic and invasive diseases. Results We identified 55 putative sRNAs in GAS M49 that were expressed during growth. Of these, 42 were novel. Some of the newly-identified sRNAs belonged to one of the common non-coding RNA families described in the Rfam database. Comparison of the results of our screen with the outcome of two recently published bioinformatics tools showed a low level of overlap between putative sRNA genes. Previously, 40 potential sRNAs have been reported to be expressed in a GAS M1T1 serotype, as detected by a whole genome intergenic tiling array approach. Our screen detected 12 putative sRNA genes that were expressed in both strains. Twenty sRNA candidates appeared to be regulated in a medium-dependent fashion, while eight sRNA genes were regulated throughout growth in chemically defined medium. Expression of candidate genes was verified by reverse transcriptase-qPCR. For a subset of sRNAs, the transcriptional start was determined by 5′ rapid amplification of cDNA ends-PCR (RACE-PCR analysis. Conclusions In accord with the results of previous studies, we found little overlap between different screening methods, which underlines the fact that a comprehensive analysis of s

  9. Highly conserved non-coding sequences are associated with vertebrate development.

    Directory of Open Access Journals (Sweden)

    Adam Woolfe

    2005-01-01

    Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

  10. Sensitivitas Salmonella Sp. Penyebab Demam Tifoid Terhadap Beberapa Antibiotik di Rumah Sakit Immanuel Bandung

    Directory of Open Access Journals (Sweden)

    Yanti Mulyana

    2009-09-01

    Full Text Available Typhoid fever is an enteric fever caused by Salmonella sp. especially Salmonella typhi and Salmonella paratyphi. Various antibiotics used for therapy beside chloramphenicol as drug of choice. Non rational use of antibiotics may result increasing of resistence in bacteria. The aim of the research is to know the sensitivity of Salmonella typhi and Salmonella paratyphi to some antibiotics. The purpose is to gather information about antibiotics which are still effective for typhoid fever and enteric therapy. Salmonella typhi and Salmonella paratyphi strain from positive cultures diagnose typhoid fever patients at Immanuel Hospital Bandung during 2004-2007. The method of resistance is Kirby Bauer's disk diffusion assay with NCCLS standard. The disk antibiotics used are amoxicillin, amoxicillinclavulanic acid, chloramphenicol, ciprofloxacin, ceftriaxone, trimethoprim, and trimethoprim-sulfamethoxazole. The result showed penicillin group, amoxicillin and amoxicillin-clavulanic acid had 96.3–99.68% sensitive against Salmonella sp. Sensitivity of chloramphenicol as drug of choice of typhoid fever still 99.05%. Since the sensitivity less than 100%, it means there was about 8% resistence. Thats why eventhough this data can be used as empiric therapy, the writer suggest to do sensitivity test to Salmonella sp. that caused typhoid to get rationally dan effective treatment. From the result, it's concluded that Salmonella typhi and Salmonella paratyphi are still sensitive to all that antibiotics.

  11. Design of ACM system based on non-greedy punctured LDPC codes

    Science.gov (United States)

    Lu, Zijun; Jiang, Zihong; Zhou, Lin; He, Yucheng

    2017-08-01

    In this paper, an adaptive coded modulation (ACM) scheme based on rate-compatible LDPC (RC-LDPC) codes was designed. The RC-LDPC codes were constructed by a non-greedy puncturing method which showed good performance in high code rate region. Moreover, the incremental redundancy scheme of LDPC-based ACM system over AWGN channel was proposed. By this scheme, code rates vary from 2/3 to 5/6 and the complication of the ACM system is lowered. Simulations show that more and more obvious coding gain can be obtained by the proposed ACM system with higher throughput.

  12. Salmonella biofilms

    NARCIS (Netherlands)

    Castelijn, G.A.A.

    2013-01-01

    Biofilm formation by Salmonellaspp. is a problem in the food industry, since biofilms may act as a persistent source of product contamination. Therefore the aim of this study was to obtain more insight in the processes involved and the factors contributing to Salmonellabiofilm

  13. Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi.

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    Christina Bronowski

    2013-11-01

    Full Text Available Invasive Non-typhoidal Salmonella (iNTS are an important cause of bacteraemia in children and HIV-infected adults in sub-Saharan Africa. Previous research has shown that iNTS strains exhibit a pattern of gene loss that resembles that of host adapted serovars such as Salmonella Typhi and Paratyphi A. Salmonella enterica serovar Bovismorbificans was a common serovar in Malawi between 1997 and 2004.We sequenced the genomes of 14 Malawian bacteraemia and four veterinary isolates from the UK, to identify genomic variations and signs of host adaptation in the Malawian strains.Whole genome phylogeny of invasive and veterinary S. Bovismorbificans isolates showed that the isolates are highly related, belonging to the most common international S. Bovismorbificans Sequence Type, ST142, in contrast to the findings for S. Typhimurium, where a distinct Sequence Type, ST313, is associated with invasive disease in sub-Saharan Africa. Although genome degradation through pseudogene formation was observed in ST142 isolates, there were no clear overlaps with the patterns of gene loss seen in iNTS ST313 isolates previously described from Malawi, and no clear distinction between S. Bovismorbificans isolates from Malawi and the UK. The only defining differences between S. Bovismorbificans bacteraemia and veterinary isolates were prophage-related regions and the carriage of a S. Bovismorbificans virulence plasmid (pVIRBov.iNTS S. Bovismorbificans isolates, unlike iNTS S. Typhiumrium isolates, are only distinguished from those circulating elsewhere by differences in the mobile genome. It is likely that these strains have entered a susceptible population and are able to take advantage of this niche. There are tentative signs of convergent evolution to a more human adapted iNTS variant. Considering its importance in causing disease in this region, S. Bovismorbificans may be at the beginning of this process, providing a reference against which to compare changes that may

  14. Genomics of Salmonella Species

    Science.gov (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  15. Effects of siRNA Silencing of TUG1 and LCAL6 Long Non-coding RNAs on Patient-derived Xenograft of Non-small Cell Lung Cancer.

    Science.gov (United States)

    Fang, Tian; Huang, Hairong; Li, Xiaoyou; Liao, Jing; Yang, Zhijian; Hoffman, Robert M; Cheng, X I; Liang, Lei; Hu, Wenjuan; Yun, Shifeng

    2018-01-01

    The aim of the present study was to establish a patient-derived xenograft (PDX) mouse model of non-small cell lung cancer (NSCLC) and investigate the anti-tumor efficacy of silencing of TUG1 and LCAL6 long non-coding RNA in the PDX model. PDXs were established by subcutaneously implanting NSCLC surgical tumor fragments into immunodeficient mice. PDX characterization was performed by histopathological, immunohistochemical and real-time polymerase chain reaction (RT-PCR) analyses for NSCLC subtype-specific markers and expression of LCAL6 and TUG1. Anti-tumor efficacy of siRNA silencing of TUG1 and LCAL6 was also investigated in the PDX model. The effect of TUG1 and LCAL6 silencing on protein expression of proliferation marker Ki67 and HOX-gene family HOXB7 in the tumors was assessed by immunohistochemical staining and Western blotting. Establishment of NSCLC PDX models resulted in 9 of 26 cases (34.6%). Lung squamous cell carcinomas (SCC) had a higher engraftment rate (58.3%) than lung adenocarcinomas (ADC) (18.2%) (pTUG1. The tumor volume and weight were significantly reduced in the TUG1-silenced group as compared to the control group (p0.05). Expression of both TUG1and LCAL6 was reduced by siRNA treatment. Expression of Ki67 and HOXB7 was significantly suppressed in both the TUG1- and LCAL6-silenced groups compared to the control group (pTUG1-silenced group showed more reduced Ki67 expression than the LCAL6-silenced group (pTUG1 and LCAL6. Silencing of TUG1 inhibited both tumor growth and expression of the proliferation marker Ki67 and HOX-gene family HOXB7 in the PDX model of NSCLC. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  16. Use of Attenuated but Metabolically Competent Salmonella as a Probiotic To Prevent or Treat Salmonella Infection

    Science.gov (United States)

    Sabag-Daigle, Anice; Blunk, Henry M.; Gonzalez, Juan F.; Steidley, Brandi L.; Boyaka, Prosper N.

    2016-01-01

    Salmonella enterica is among the most burdensome of foodborne disease agents. There are over 2,600 serovars that cause a range of disease manifestations ranging from enterocolitis to typhoid fever. While there are two vaccines in use in humans to protect against typhoid fever, there are none that prevent enterocolitis. If vaccines preventing enterocolitis were to be developed, they would likely protect against only one or a few serovars. In this report, we tested the hypothesis that probiotic organisms could compete for the preferred nutrient sources of Salmonella and thus prevent or treat infection. To this end, we added the fra locus, which encodes a utilization pathway for the Salmonella-specific nutrient source fructose-asparagine (F-Asn), to the probiotic bacterium Escherichia coli Nissle 1917 (Nissle) to increase its ability to compete with Salmonella in mouse models. We also tested a metabolically competent, but avirulent, Salmonella enterica serovar Typhimurium mutant for its ability to compete with wild-type Salmonella. The modified Nissle strain became more virulent and less able to protect against Salmonella in some instances. On the other hand, the modified Salmonella strain was safe and effective in preventing infection with wild-type Salmonella. While we tested for efficacy only against Salmonella Typhimurium, the modified Salmonella strain may be able to compete metabolically with most, if not all, Salmonella serovars, representing a novel approach to control of this pathogen. PMID:27185789

  17. Brucella lipopolysaccharide reinforced Salmonella delivering Brucella immunogens protects mice against virulent challenge.

    Science.gov (United States)

    Lalsiamthara, Jonathan; Lee, John Hwa

    2017-06-01

    Intracellular pathogen Salmonella exhibits natural infection broadly analogous to Brucella, this phenomenon makes Salmonella a pragmatic choice for an anti-Brucella vaccine delivery platform. In this study we developed and formulated a combination of four attenuated Salmonella Typhimurium live vector strains delivering heterologous Brucella antigens (rBs), namely lumazine synthase, proline racemase subunit A, lipoprotein outer membrane protein-19, and Cu-Zn superoxide dismutase. With an aim to develop a cross-protecting vaccine, Brucella pan-species conserved rBs were selected. The present study compared the efficacy of smooth and rough variants of Salmonella delivery vector and also evaluated the inclusion of purified Brucella lipopolysaccharide (LPS) in the formulation. Immunization of SPF-BALB/c mice with the vaccine combinations significantly (P≤0.05) reduced splenic wild-type Brucella abortus 544 colonization as compared to non-immunized mice as well as Salmonella only immunized mice. Increased induction of Brucella specific-IgG, sIgA production, and antigen-specific splenocyte proliferative responses were observed in the mice immunized with the formulations as compared to naïve or vector only immunized mice. Modulatory effects of rB and LPS on production of interleukin (IL)-4, IL-12, and interferon-γ were detected in splenocytes of mice immunized with the formulation. Rough Salmonella variant in combination with LPS could further enhance the efficacy of the delivery when applied intraperitoneally. Taken together, it is compelling that Brucella LPS-augmented Salmonella vector delivering immunogenic Brucella proteins may be more suitable than the current non-ideal live Brucella abortus vaccine. The vaccine system also provides a basis for the development of cross-protecting vaccine capable of preventing multispecies brucellosis. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. The isolation of salmonellas from British pork sausages and sausage meat.

    Science.gov (United States)

    Roberts, D; Boag, K; Hall, M L; Shipp, C R

    1975-10-01

    Between 1969 and 1974, 1467 packets (3309 samples) of pork sausages and sausage meat produced by two large and two medium sized manufacturers and several local butchers were examined for the presence of salmonellas. Of these, 435 packets (786 samples) were found to contain salmonellas, but there was a wide variation in the isolation rates according to the producer. The salmonella incidence in samples from several small and two medium sized producers was low (0-11%) while the results from the two large producers investigated showed a striking difference, the rate of salmonella contamination in the product of one was low (about 2%) and in that of the other consistently high (40-60%). A comparison of liquid enrichment media, incubation temperatures and selective agar media was also carried out to determine the most efficient combination for the isolation of salmonellas from minced meat products. The results showed that (a) incubation of enrichment cultures at 43 degrees C. yielded a consistently greater number of salmonella isolations that at 37 degrees C., regardless of plating medium, (b) tetrathionate broth A (Rolfe) was superior to selenite broth as en enrichment medium at both 37 and 43 degrees C. and (c) brilliant green agar gave better results than deoxycholate citrate sucrose agar and bismuth sulphite agar as a selective medium.

  19. u-Constacyclic codes over F_p+u{F}_p and their applications of constructing new non-binary quantum codes

    Science.gov (United States)

    Gao, Jian; Wang, Yongkang

    2018-01-01

    Structural properties of u-constacyclic codes over the ring F_p+u{F}_p are given, where p is an odd prime and u^2=1. Under a special Gray map from F_p+u{F}_p to F_p^2, some new non-binary quantum codes are obtained by this class of constacyclic codes.

  20. Integration of a complex regulatory cascade involving the SirA/BarA and Csr global regulatory systems that controls expression of the Salmonella SPI-1 and SPI-2 virulence regulons through HilD.

    Science.gov (United States)

    Martínez, Luary C; Yakhnin, Helen; Camacho, Martha I; Georgellis, Dimitris; Babitzke, Paul; Puente, José L; Bustamante, Víctor H

    2011-06-01

    Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2) play key roles in the pathogenesis of Salmonella enterica. Previously, we showed that when Salmonella grows in Luria-Bertani medium, HilD, encoded in SPI-1, first induces the expression of hilA, located in SPI-1, and subsequently of the ssrAB operon, located in SPI-2. These genes code for HilA and the SsrA/B two-component system, the positive regulators of the SPI-1 and SPI-2 regulons respectively. In this study, we demonstrate that CsrA, a global regulatory RNA binding protein, post-transcriptionally regulates hilD expression by directly binding near the Shine-Dalgarno and translation initiation codon sequences of the hilD mRNA, preventing its translation and leading to its accelerated turnover. Negative regulation is counteracted by the global SirA/BarA two-component system, which directly activates the expression of CsrB and CsrC, two non-coding regulatory RNAs that sequester CsrA, thereby preventing it from binding to its target mRNAs. Our results illustrate the integration of global and specific regulators into a multifactorial regulatory cascade controlling the expression of virulence genes acquired by horizontal transfer events. © 2011 Blackwell Publishing Ltd.

  1. Long non-coding RNA expression profile in cervical cancer tissues

    Science.gov (United States)

    Zhu, Hua; Chen, Xiangjian; Hu, Yan; Shi, Zhengzheng; Zhou, Qing; Zheng, Jingjie; Wang, Yifeng

    2017-01-01

    Cervical cancer (CC), one of the most common types of cancer of the female population, presents an enormous challenge in diagnosis and treatment. Long non-coding (lnc)RNAs, non-coding (nc)RNAs with length >200 nucleotides, have been identified to be associated with multiple types of cancer, including CC. This class of nc transcripts serves an important role in tumor suppression and oncogenic signaling pathways. In the present study, the microarray method was used to obtain the expression profile of lncRNAs and protein-coding mRNAs and to compare the expression of lncRNAs between CC tissues and corresponding adjacent non-cancerous tissues in order to screen potential lncRNAs for associations with CC. Overall, 3356 lncRNAs with significantly different expression pattern in CC tissues compared with adjacent non-cancerous tissues were identified, while 1,857 of them were upregulated. These differentially expressed lncRNAs were additionally classified into 5 subgroups. Reverse transcription quantitative polymerase chain reactions were performed to validate the expression pattern of 5 random selected lncRNAs, and 2lncRNAs were identified to have significantly different expression in CC samples compared with adjacent non-cancerous tissues. This finding suggests that those lncRNAs with different expression may serve important roles in the development of CC, and the expression data may provide information for additional study on the involvement of lncRNAs in CC. PMID:28789353

  2. Production of recombinant flagellin to develop ELISA-based detection of Salmonella Enteritidis

    Directory of Open Access Journals (Sweden)

    Seyed Ali Mirhosseini

    Full Text Available ABSTRACT Food-borne diseases, caused by the pathogenic bacteria, are highly prevalent in the world. Salmonella is one of the most important bacterial genera responsible for this. Salmonella Enteritidis (SE is one of the non-typhoid Salmonellae that can be transmitted to human from poultry products, water, and contaminated food. In recent years, new and rapid detection methods such as enzyme-linked immunosorbent assay (ELISA and polymerase chain reaction (PCR have been developed. In this study, recombinant FliC (rFliC was produced to be used as an antigen. The immunization was conducted in mice with the purified recombinant FliC (rFliC. The mice were subcutaneously immunized with rFliC and elicited significant rFliC specific serum IgG antibodies. An indirect ELISA system was established for the detection of Salmonella Enteritidis. Our results confirmed that the recombinant flagellin can be one of the excellent indicators for the detection of Salmonella Enteritidis.

  3. Non-Coding RNAs in Saliva: Emerging Biomarkers for Molecular Diagnostics

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    Blanca Majem

    2015-04-01

    Full Text Available Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, which are extensively supplied by blood. Therefore, molecules such as proteins, DNA, RNA, etc., present in plasma could be also present in saliva. Many studies have reported that saliva body fluid can be useful for discriminating several oral diseases, but also systemic diseases including cancer. Most of these studies revealed messenger RNA (mRNA and proteomic biomarker signatures rather than specific non-coding RNA (ncRNA profiles. NcRNAs are emerging as new regulators of diverse biological functions, playing an important role in oncogenesis and tumor progression. Indeed, the small size of these molecules makes them very stable in different body fluids and not as susceptible as mRNAs to degradation by ribonucleases (RNases. Therefore, the development of a non-invasive salivary test, based on ncRNAs profiles, could have a significant applicability to clinical practice, not only by reducing the cost of the health system, but also by benefitting the patient. Here, we summarize the current status and clinical implications of the ncRNAs present in human saliva as a source of biological information.

  4. Prevalence of Salmonella in Australian reptiles.

    Science.gov (United States)

    Scheelings, T Franciscus; Lightfoot, Dianne; Holz, Peter

    2011-01-01

    From January 2007 until June 2008, 504 reptiles of four families and 57 species were examined for Salmonella by using cloacal or intestinal swabs. Salmonella was identified in 139 (28%) of the 504 animals tested. Of the 504 reptiles examined, 210 were captive and 294 were wild. Ninety-eight (47%) of the captive reptiles were shedding Salmonella at the time of sampling. In contrast, only 41 (14%) of the wild reptiles were shedding Salmonella. The higher prevalence of Salmonella in captive reptiles was statistically significant (Preptiles in Australia are not natural carriers of Salmonella and that diet and captivity may influence Salmonella excretion in other species.

  5. lac repressor is an antivirulence factor of Salmonella enterica: its role in the evolution of virulence in Salmonella.

    Directory of Open Access Journals (Sweden)

    Sandeepa M Eswarappa

    Full Text Available The genus Salmonella includes many pathogens of great medical and veterinary importance. Bacteria belonging to this genus are very closely related to those belonging to the genus Escherichia. lacZYA operon and lacI are present in Escherichia coli, but not in Salmonella enterica. It has been proposed that Salmonella has lost lacZYA operon and lacI during evolution. In this study, we have investigated the physiological and evolutionary significance of the absence of lacI in Salmonella enterica. Using murine model of typhoid fever, we show that the expression of LacI causes a remarkable reduction in the virulence of Salmonella enterica. LacI also suppresses the ability of Salmonella enterica to proliferate inside murine macrophages. Microarray analysis revealed that LacI interferes with the expression of virulence genes of Salmonella pathogenicity island 2. This effect was confirmed by RT-PCR and Western blot analysis. Interestingly, we found that SBG0326 of Salmonella bongori is homologous to lacI of Escherichia coli. Salmonella bongori is the only other species of the genus Salmonella and it lacks the virulence genes of Salmonella pathogenicity island 2. Overall, our results demonstrate that LacI is an antivirulence factor of Salmonella enterica and suggest that absence of lacI has facilitated the acquisition of virulence genes of Salmonella pathogenicity island 2 in Salmonella enterica making it a successful systemic pathogen.

  6. Prevalence of Trichomonas, Salmonella, and Listeria in Wild Birds from Southeast Texas.

    Science.gov (United States)

    Brobey, Britni; Kucknoor, Ashwini; Armacost, Jim

    2017-09-01

    Infectious diseases can be a major threat to wildlife populations, especially in human-modified habitats, but infection rates in populations of wild animals are often poorly studied. Trichomonas, Salmonella, and Listeria are all pathogens known to infect birds, but their infection rates in wild bird populations are not well documented. This study documents infection rates of the three pathogens in wild bird populations inhabiting a suburban to rural gradient in Southeast Texas. Various species of wild birds were sampled at five sites in Southeastern Texas representing rural (Birds were captured in mist nets and samples were taken from the oral cavity, crop, and vent to detect the presence of pathogens. Samples were screened for Trichomonas by examining wet mounts under a light microscope, whereas samples were screened for Salmonella and Listeria by examining colonies grown on agar plates. Pathogens detected during the initial screening were further confirmed by PCR and DNA sequencing. Infection rates for Trichomonas, Salmonella, and Listeria were 9%, 17%, and 5%, respectively. The distributions of infection rates across habitats (i.e., rural, exurban, rural) did not differ significantly from the expected null distributions for any of the three pathogens; however, the data suggested some interesting patterns that should be confirmed with a larger dataset. Infection rates for Trichomonas and Salmonella were highest at the suburban sites, whereas the infection rate for Listeria was highest at the rural site. Feeder birds were more likely to be infected by all three pathogens than non-feeder birds. Small sample sizes prevent definitive conclusions regarding variation in infection rates along the suburban to rural gradient, but the results suggest that pathogens followed the predicted patterns. For many of the bird species sampled, this study presents the first report of infection rates by these three pathogens in wild populations.

  7. Non-typhoidal Salmonella serotypes, antimicrobial resistance and co-infection with parasites among patients with diarrhea and other gastrointestinal complaints in Addis Ababa, Ethiopia.

    Science.gov (United States)

    Eguale, Tadesse; Gebreyes, Wondwossen A; Asrat, Daniel; Alemayehu, Haile; Gunn, John S; Engidawork, Ephrem

    2015-11-04

    Non-typhoidal Salmonella (NTS) is an important public health problem worldwide. Consumption of animal-derived food products and direct and/or indirect contact with animals are the major routes of acquiring infection with NTS. Published information, particularly on the serotype distribution of NTS among human patients with gastroenteritis and associated risk factors, is scarce in Ethiopia. This study investigated the prevalence, risk factors, serotype distribution and antimicrobial susceptibility of Salmonella species among diarrheic out-patients attending health centers in Addis Ababa and patients with various gastrointestinal complaints at Tikur Anbessa Specialized Hospital (TASH). Stool samples were cultured for Salmonella species according to the WHO Global Foodborne Infections Network laboratory protocol. Salmonella serotyping was conducted using slide agglutination and microplate agglutination techniques. Antibiotic susceptibility testing was performed using the disk diffusion method according to Clinical and Laboratory Standards Institute guidelines. A total of 59 (6.2 %) stool samples, out of 957 were culture positive for Salmonella species. Fifty-five (7.2 %) of 765 diarrheic patients from health centers and 4 (2.1 %) of 192 patients from TASH were culture positive for Salmonella species. Multivariable logistic regression analysis after adjusting for all other variables revealed statistically significant association of Salmonella infection with consumption of raw vegetables (OR = 1.91, 95 % CI = 1.29-2.83, χ(2) = 4.74, p = 0.025) and symptom of watery diarrhea (OR = 3.3, 95 % CI = 1.23-8.88, χ(2) = 10.54, p = 0.005). Eleven serotypes were detected, and the most prominent were S. Typhimurium (37.3 %), S. Virchow (34 %), and S. Kottbus (10.2 %). Other serotypes were S. Miami, S. Kentucky, S. Newport, S. Enteritidis, S. Braenderup, S. Saintpaul, S. Concord and S. V:ROUGH-O. Resistance to three or more antimicrobials was detected in 27 (40.3 %) of the

  8. Evaluation of Shape and Textural Features from CT as Prognostic Biomarkers in Non-small Cell Lung Cancer.

    Science.gov (United States)

    Bianconi, Francesco; Fravolini, Mario Luca; Bello-Cerezo, Raquel; Minestrini, Matteo; Scialpi, Michele; Palumbo, Barbara

    2018-04-01

    We retrospectively investigated the prognostic potential (correlation with overall survival) of 9 shape and 21 textural features from non-contrast-enhanced computed tomography (CT) in patients with non-small-cell lung cancer. We considered a public dataset of 203 individuals with inoperable, histologically- or cytologically-confirmed NSCLC. Three-dimensional shape and textural features from CT were computed using proprietary code and their prognostic potential evaluated through four different statistical protocols. Volume and grey-level run length matrix (GLRLM) run length non-uniformity were the only two features to pass all four protocols. Both features correlated negatively with overall survival. The results also showed a strong dependence on the evaluation protocol used. Tumour volume and GLRLM run-length non-uniformity from CT were the best predictor of survival in patients with non-small-cell lung cancer. We did not find enough evidence to claim a relationship with survival for the other features. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  9. Interaction between Salmonella typhimurium and phagocytic cells in pigs - Phagocytosis, oxidative burst and killing in polymorphonuclear leukocytes and monocytes

    DEFF Research Database (Denmark)

    Riber, Ulla; Lind, Peter

    1999-01-01

    Interactions between Salmonella typhimurium and peripheral blood leucocytes from healthy, Salmonella-free pigs were investigated in vitro. Both granulocytes and monocytes phagocytized FITC-labelled heat-killed Salmonella bacteria as shown by flow cytometry. Phagocytosis in whole blood and isolated...... with the exhaustion of oxidative burst in non-adherent monocytes were performed by prestimulation with PMA, heat-killed Salmonella or buffer. Prestimulation with PMA led to a strong reduction in oxidative burst induced by living opsonized Salmonella bacteria, whereas prestimulation with heat-killed bacteria gave rise...

  10. An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.

    Directory of Open Access Journals (Sweden)

    Ru Huang

    Full Text Available Imprinted macro non-protein-coding (nc RNAs are cis-repressor transcripts that silence multiple genes in at least three imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome. Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80-118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than 8 kb show a gradual loss of sequencing tags towards the 3' end. Comparisons to published RNA-Seq datasets show that the strategy presented here is more efficient in detecting known functional imprinted macro ncRNAs and also indicate that standardization of RNA preparation protocols would increase the comparability of the transcriptome between different RNA-Seq datasets.

  11. Cloning and over expression of non-coding RNA rprA in E.coli and its resistance to Kanamycin without osmotic shock.

    Science.gov (United States)

    Sahni, Azita; Hajjari, Mohammadreza; Raheb, Jamshid; Foroughmand, Ali Mohammad; Asgari, Morteza

    2017-01-01

    Recent reports have indicated that small RNAs have key roles in the response of the E.coli to stress and also in the regulating of virulence factors. It seems that some small non-coding RNAs are involved in multidrug resistance. Previous studies have indicated that rprA can increase the tolerance to Kanamycin in RcsB-deficient Escherichia coli K-12 following osmotic shock. The current study aims to clone and over-express the non-coding RNA rprA in E.coli and investigate its effect on the bacterial resistance to Kanamycin without any osmotic shock. For this purpose, rprA gene was amplified by the PCR and then cloned into the PET-28a (+) vector. The recombinant plasmid was transformed into wild type E.coli BL21 (DE3). The over expression was induced by IPTG and confirmed by qRT-PCR. The resistance to the kanamycin was then measured in different times by spectrophotometry. The statistical analysis showed that the rprA can increase the resistance to Kanamycin in Ecoli K12. The interaction between rprA and rpoS was reviewed and analyzed by in silico methods. The results showed that the bacteria with over-expressed rprA were more resistant to Kanamycin. The present study is an important step to prove the role of non-coding RNA rprA in bacterial resistance. The data can be the basis for future works and can also help to develop and deliver next-generation antibiotics.

  12. Broad-range (pan) Salmonella and Salmonella serotype typhi-specific real-time PCR assays: potential tools for the clinical microbiologist.

    Science.gov (United States)

    Farrell, John J; Doyle, Laura J; Addison, Rachel M; Reller, L Barth; Hall, Geraldine S; Procop, Gary W

    2005-03-01

    We describe broad-range salmonellae (ie, Salmonella) and Salmonella serotype Typhi-specific LightCycler (Roche Diagnostics, Indianapolis, IN) real-time polymerase chain reaction assays. We validated these with a battery of 280 bacteria, 108 of which were salmonellae representing 20 serotypes. In addition, 298 isolates from 170 clinical specimens that were suspected to possibly represent Salmonella were tested with the pan- Salmonella assay. Finally, the pan-Salmonella assay also was used to test DNA extracts from 101 archived, frozen stool specimens, 55 of which were culture-positive for salmonellae. Both assays were 100% sensitive and specific when cultured isolates of the battery were tested. The pan- Salmonella assay also characterized correctly all salmonellae on the primary isolation agar and was 96% sensitive (53/55) and 96% specific (49/51) when nucleic acid extracts from direct stool specimens were tested. These assays represent potential tools the clinical microbiologist could use to screen suspect isolates or stool specimens for Salmonella.

  13. Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes

    Directory of Open Access Journals (Sweden)

    Maggi Giorgio P

    2008-06-01

    Full Text Available Abstract Background The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between conserved coding and non-coding sequences. This discrimination is often based (thus dependent on the availability of annotated proteins. Results In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of conserved sequences and accurate assessment of their coding potential. By detecting clusters of coding conserved sequences the system is also suitable to accurately identify potential gene loci. Following this analysis we created a collection of human-mouse conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST sequences but not corresponding to as yet annotated genes. Conclusion Here we present a new system which allows comprehensive comparison of genomes to detect conserved coding and non-coding sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.

  14. Completeness and timeliness of Salmonella notifications in Ireland in 2008: a cross sectional study

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    Cormican Martin

    2010-09-01

    Full Text Available Abstract Background In Ireland, salmonellosis is the second most common cause of bacterial gastroenteritis. A new electronic system for reporting (Computerised Infectious Disease Reporting - CIDR of Salmonella cases was established in 2004. It collates clinical (and/or laboratory data on confirmed and probable Salmonella cases. The authors studied the completeness and the timeliness of Salmonella notifications in 2008. Methods This analysis was based upon laboratory confirmed cases of salmonella gastroenteritis. Using data contained in CIDR, we examined completeness for certain non-mandatory fields (country of infection, date of onset of illness, organism, outcome, patient type, and ethnicity. We matched the CIDR data with the dataset provided by the national Salmonella reference laboratory (NSRL to which all Salmonella spp. isolates are referred for definitive typing. We calculated the main median time intervals in the flow of events of the notification process. Results In total, 416 laboratory confirmed Salmonella cases were captured by the national surveillance system and the NSRL and were included in the analysis. Completeness of non mandatory fields varied considerably. Organism was the most complete field (98.8%, ethnicity the least (11%. The median time interval between sample collection (first contact of the patient with the healthcare professional to the first notification to the regional Department of Public Health (either a clinical or a laboratory notification was 6 days (Interquartile 4-7 days. The median total identification time interval, time between sample collections to availability of serotyping and phage-typing results on the system was 25 days (Interquartile 19-32 days. Timeliness varied with respect to Salmonella species. Clinical notifications occurred more rapidly than laboratory notifications. Conclusions Further feedback and education should be given to health care professionals to improve completeness of reporting of

  15. Completeness and timeliness of Salmonella notifications in Ireland in 2008: a cross sectional study

    LENUS (Irish Health Repository)

    Nicolay, Nathalie

    2010-09-22

    Abstract Background In Ireland, salmonellosis is the second most common cause of bacterial gastroenteritis. A new electronic system for reporting (Computerised Infectious Disease Reporting - CIDR) of Salmonella cases was established in 2004. It collates clinical (and\\/or laboratory) data on confirmed and probable Salmonella cases. The authors studied the completeness and the timeliness of Salmonella notifications in 2008. Methods This analysis was based upon laboratory confirmed cases of salmonella gastroenteritis. Using data contained in CIDR, we examined completeness for certain non-mandatory fields (country of infection, date of onset of illness, organism, outcome, patient type, and ethnicity). We matched the CIDR data with the dataset provided by the national Salmonella reference laboratory (NSRL) to which all Salmonella spp. isolates are referred for definitive typing. We calculated the main median time intervals in the flow of events of the notification process. Results In total, 416 laboratory confirmed Salmonella cases were captured by the national surveillance system and the NSRL and were included in the analysis. Completeness of non mandatory fields varied considerably. Organism was the most complete field (98.8%), ethnicity the least (11%). The median time interval between sample collection (first contact of the patient with the healthcare professional) to the first notification to the regional Department of Public Health (either a clinical or a laboratory notification) was 6 days (Interquartile 4-7 days). The median total identification time interval, time between sample collections to availability of serotyping and phage-typing results on the system was 25 days (Interquartile 19-32 days). Timeliness varied with respect to Salmonella species. Clinical notifications occurred more rapidly than laboratory notifications. Conclusions Further feedback and education should be given to health care professionals to improve completeness of reporting of non

  16. TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements.

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    Kamila Maliszewska-Olejniczak

    2015-07-01

    Full Text Available Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline nucleus, while the old somatic nucleus degenerates. In the ciliate Paramecium tetraurelia, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs. Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in P. tetraurelia genome. Using RNA interference, we showed that TFIIS4, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon TFIIS4 RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in Paramecium

  17. Food poisoning due to Salmonella Enteritidis--a case report.

    Science.gov (United States)

    Ogata, Mamoru; Ago, Kazutoshi; Ago, Mihoko; Nakashima, Hiroshi; Hayashi, Takahito

    2009-04-01

    A male in his early seventies complained of abdominal pain and diarrhea at 7h after ingesting a small piece of gratin from a box lunch prepared by a caterer. He was admitted to a hospital, but died 37 h later. Dozens of people who had eaten the same box lunch also complained of diarrhea. All of them recovered after medical treatment. A later investigation demonstrated Salmonella Enteritidis (SE) in the gratin from the box lunch. An autopsy revealed very severe typhloenteritis with edema and submucosal hemorrhage. The digestive tract contained fluid contents without foodstuffs. Bacteriological examination revealed SE in the contents of the lower ileum and large intestine. Based on these findings, we concluded that the cause of death was food poisoning due to SE. In this case, ingesting only a small piece of contaminated food caused fatal food poisoning due to SE. These results emphasize the importance of prevention against food poisoning due to Salmonella, particularly SE.

  18. AOAC Official MethodSM Matrix Extension Validation Study of Assurance GDSTM for the Detection of Salmonella in Selected Spices.

    Science.gov (United States)

    Feldsine, Philip; Kaur, Mandeep; Shah, Khyati; Immerman, Amy; Jucker, Markus; Lienau, Andrew

    2015-01-01

    Assurance GDSTM for Salmonella Tq has been validated according to the AOAC INTERNATIONAL Methods Committee Guidelines for Validation of Microbiological Methods for Food and Environmental Surfaces for the detection of selected foods and environmental surfaces (Official Method of AnalysisSM 2009.03, Performance Tested MethodSM No. 050602). The method also completed AFNOR validation (following the ISO 16140 standard) compared to the reference method EN ISO 6579. For AFNOR, GDS was given a scope covering all human food, animal feed stuff, and environmental surfaces (Certificate No. TRA02/12-01/09). Results showed that Assurance GDS for Salmonella (GDS) has high sensitivity and is equivalent to the reference culture methods for the detection of motile and non-motile Salmonella. As part of the aforementioned validations, inclusivity and exclusivity studies, stability, and ruggedness studies were also conducted. Assurance GDS has 100% inclusivity and exclusivity among the 100 Salmonella serovars and 35 non-Salmonella organisms analyzed. To add to the scope of the Assurance GDS for Salmonella method, a matrix extension study was conducted, following the AOAC guidelines, to validate the application of the method for selected spices, specifically curry powder, cumin powder, and chili powder, for the detection of Salmonella.

  19. P53-regulated long non-coding RNA TUG1 affects cell proliferation in human non-small cell lung cancer, partly through epigenetically regulating HOXB7 expression.

    Science.gov (United States)

    Zhang, E-b; Yin, D-d; Sun, M; Kong, R; Liu, X-h; You, L-h; Han, L; Xia, R; Wang, K-m; Yang, J-s; De, W; Shu, Y-q; Wang, Z-x

    2014-05-22

    Recently, a novel class of transcripts, long non-coding RNAs (lncRNAs), is being identified at a rapid pace. These RNAs have critical roles in diverse biological processes, including tumorigenesis. Here we report that taurine-upregulated gene 1 (TUG1), a 7.1-kb lncRNA, recruiting and binding to polycomb repressive complex 2 (PRC2), is generally downregulated in non-small cell lung carcinoma (NSCLC) tissues. In a cohort of 192 NSCLC patients, the lower expression of TUG1 was associated with a higher TNM stage and tumor size, as well as poorer overall survival (PTUG1 expression serves as an independent predictor for overall survival (PTUG1 expression was induced by p53, and luciferase and chromatin immunoprecipitation (ChIP) assays confirmed that TUG1 was a direct transcriptional target of p53. TUG1 knockdown significantly promoted the proliferation in vitro and in vivo. Moreover, the lncRNA-mediated regulation of the expression of HOX genes in tumorigenesis and development has been recently receiving increased attention. Interestingly, inhibition of TUG1 could upregulate homeobox B7 (HOXB7) expression; ChIP assays demonstrated that the promoter of HOXB7 locus was bound by EZH2 (enhancer of zeste homolog 2), a key component of PRC2, and was H3K27 trimethylated. This TUG1-mediated growth regulation is in part due to specific modulation of HOXB7, thus participating in AKT and MAPK pathways. Together, these results suggest that p53-regulated TUG1 is a growth regulator, which acts in part through control of HOXB7. The p53/TUG1/PRC2/HOXB7 interaction might serve as targets for NSCLC diagnosis and therapy.

  20. Enterobacteriaceae and Salmonella recovered from non-sanitized and sanitized broiler hatching eggs

    Science.gov (United States)

    Sanitizing hatching eggs may reduce the chances that a flock will become colonized with Salmonella and reduce the numbers of other microorganisms, such as Enterobacteriaceae, that can depress hatchability. An experiment was conducted to determine if a quaternary-biguanide sanitizer applied as foam ...

  1. RsmV a small non-coding regulatory RNA in Pseudomonas aeruginosa that sequesters RsmA and RsmF from target mRNAs.

    Science.gov (United States)

    Janssen, Kayley H; Diaz, Manisha R; Gode, Cindy J; Wolfgang, Matthew C; Yahr, Timothy L

    2018-06-04

    The Gram-negative opportunistic pathogen Pseudomonas aeruginosa has distinct genetic programs that favor either acute or chronic virulence gene expression. Acute virulence is associated with twitching and swimming motility, expression of a type III secretion system (T3SS), and the absence of alginate, Psl, or Pel polysaccharide production. Traits associated with chronic infection include growth as a biofilm, reduced motility, and expression of a type VI secretion system (T6SS). The Rsm post-transcriptional regulatory system plays important roles in the inverse control of phenotypes associated with acute and chronic virulence. RsmA and RsmF are RNA-binding proteins that interact with target mRNAs to control gene expression at the post-transcriptional level. Previous work found that RsmA activity is controlled by at least three small, non-coding regulatory RNAs (RsmW, RsmY, and RsmZ). In this study, we took an in-silico approach to identify additional sRNAs that might function in the sequestration of RsmA and/or RsmF and identified RsmV, a 192 nt transcript with four predicted RsmA/RsmF consensus binding sites. RsmV is capable of sequestering RsmA and RsmF in vivo to activate translation of tssA1 , a component of the T6SS, and to inhibit T3SS gene expression. Each of the predicted RsmA/RsmF consensus binding sites contribute to RsmV activity. Electrophoretic mobility shifts assays show that RsmF binds RsmV with >10-fold higher affinity than RsmY and RsmZ. Gene expression studies revealed that the temporal expression pattern of RsmV differs from RsmW, RsmY, and RsmZ. These findings suggest that each sRNA may play distinct roles in controlling RsmA and RsmF activity. IMPORTANCE The CsrA/RsmA family of RNA-binding proteins play important roles in post-transcriptional control of gene expression. The activity of CsrA/RsmA proteins is controlled by small non-coding RNAs that function as decoys to sequester CsrA/RsmA from target mRNAs. Pseudomonas aeruginosa has two Csr

  2. Long Non-Coding RNA in Cancer

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    Damjan Glavač

    2013-02-01

    Full Text Available Long non-coding RNAs (lncRNAs are pervasively transcribed in the genome and are emerging as new players in tumorigenesis due to their various functions in transcriptional, posttranscriptional and epigenetic mechanisms of gene regulation. LncRNAs are deregulated in a number of cancers, demonstrating both oncogenic and tumor suppressive roles, thus suggesting their aberrant expression may be a substantial contributor in cancer development. In this review, we will summarize their emerging role in human cancer and discuss their perspectives in diagnostics as potential biomarkers.

  3. Molecular epidemiology of fluoroquinolone resistant Salmonella in Africa: A systematic review and meta-analysis.

    Science.gov (United States)

    Tadesse, Getachew; Tessema, Tesfaye S; Beyene, Getenet; Aseffa, Abraham

    2018-01-01

    Wide-ranging evidence on the occurrence of fluoroquinolone (FQ) resistance genetic determinants in African Salmonella strains is not available. The main objectives of this study were to assess the heterogeneity, estimate pooled proportions and describe the preponderance of FQ-resistance determinants in typhoidal and non-typhoidal Salmonella (NTS) isolates of Africa. Genetic and phenotypic data on 6103 Salmonella isolates were considered. Meta- and frequency analyses were performed depending on the number of studies by category, number of isolates and risks of bias. A random effects model was used to assess heterogeneity and estimate pooled proportions. Relative and cumulative frequencies were calculated to describe the overall preponderance of FQ-resistance determinants in quinolone resistant isolates. The pooled proportion of gyrA mutants (Salmonella enterica serovar Typhi, Salmonella enterica serovar Typhimurium, and Salmonella enterica serovar Enteritidis) was estimated at 5.7% (95% Confidence interval (CI) = 2.6, 9.8; Tau squared (T2) = 0.1105), and was higher in S. Typhi than in S. Typhimurium (odds ratio (OR) = 3.3, 95%CI = 2, 5.7). The proportions of each of gyrB and parC mutants, and strains with Plasmid Mediated Quinolone Resistance genes (qnrA, qnrB and qnrS) were low (≤ 0.3%). Overall, 23 mutant serotypes were identified, and most strains had mutations at codons encoding Ser83 and Asp87 of gyrA (82%, 95%CI = 78, 86). Mutations at gyrA appear to account for ciprofloxacin non-susceptibility in most clinical Salmonella strains in Africa. The estimates could be harnessed to develop a mismatch-amplification mutation-assay for the detection of FQ-resistant strains in Africa.

  4. Independent bottlenecks characterize colonization of systemic compartments and gut lymphoid tissue by salmonella.

    Science.gov (United States)

    Lim, Chee Han; Voedisch, Sabrina; Wahl, Benjamin; Rouf, Syed Fazle; Geffers, Robert; Rhen, Mikael; Pabst, Oliver

    2014-07-01

    Vaccination represents an important instrument to control typhoid fever in humans and protects mice from lethal infection with mouse pathogenic serovars of Salmonella species. Mixed infections with tagged Salmonella can be used in combination with probabilistic models to describe the dynamics of the infection process. Here we used mixed oral infections with tagged Salmonella strains to identify bottlenecks in the infection process in naïve and vaccinated mice. We established a next generation sequencing based method to characterize the composition of tagged Salmonella strains which offers a fast and reliable method to characterise the composition of genome-tagged Salmonella strains. We show that initial colonization of Salmonella was distinguished by a non-Darwinian selection of few bacteria setting up the infection independently in gut associated lymphoid tissue and systemic compartments. Colonization of Peyer's patches fuels the sustained spread of bacteria into mesenteric lymph nodes via dendritic cells. In contrast, infection of liver and spleen originated from an independent pool of bacteria. Vaccination only moderately reduced invasion of Peyer's patches but potently uncoupled bacterial populations present in different systemic compartments. Our data indicate that vaccination differentially skews the capacity of Salmonella to colonize systemic and gut immune compartments and provide a framework for the further dissection of infection dynamics.

  5. Independent bottlenecks characterize colonization of systemic compartments and gut lymphoid tissue by salmonella.

    Directory of Open Access Journals (Sweden)

    Chee Han Lim

    2014-07-01

    Full Text Available Vaccination represents an important instrument to control typhoid fever in humans and protects mice from lethal infection with mouse pathogenic serovars of Salmonella species. Mixed infections with tagged Salmonella can be used in combination with probabilistic models to describe the dynamics of the infection process. Here we used mixed oral infections with tagged Salmonella strains to identify bottlenecks in the infection process in naïve and vaccinated mice. We established a next generation sequencing based method to characterize the composition of tagged Salmonella strains which offers a fast and reliable method to characterise the composition of genome-tagged Salmonella strains. We show that initial colonization of Salmonella was distinguished by a non-Darwinian selection of few bacteria setting up the infection independently in gut associated lymphoid tissue and systemic compartments. Colonization of Peyer's patches fuels the sustained spread of bacteria into mesenteric lymph nodes via dendritic cells. In contrast, infection of liver and spleen originated from an independent pool of bacteria. Vaccination only moderately reduced invasion of Peyer's patches but potently uncoupled bacterial populations present in different systemic compartments. Our data indicate that vaccination differentially skews the capacity of Salmonella to colonize systemic and gut immune compartments and provide a framework for the further dissection of infection dynamics.

  6. A Case for Dynamic Reverse-code Generation to Debug Non-deterministic Programs

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    Jooyong Yi

    2013-09-01

    Full Text Available Backtracking (i.e., reverse execution helps the user of a debugger to naturally think backwards along the execution path of a program, and thinking backwards makes it easy to locate the origin of a bug. So far backtracking has been implemented mostly by state saving or by checkpointing. These implementations, however, inherently do not scale. Meanwhile, a more recent backtracking method based on reverse-code generation seems promising because executing reverse code can restore the previous states of a program without state saving. In the literature, there can be found two methods that generate reverse code: (a static reverse-code generation that pre-generates reverse code through static analysis before starting a debugging session, and (b dynamic reverse-code generation that generates reverse code by applying dynamic analysis on the fly during a debugging session. In particular, we espoused the latter one in our previous work to accommodate non-determinism of a program caused by e.g., multi-threading. To demonstrate the usefulness of our dynamic reverse-code generation, this article presents a case study of various backtracking methods including ours. We compare the memory usage of various backtracking methods in a simple but nontrivial example, a bounded-buffer program. In the case of non-deterministic programs such as this bounded-buffer program, our dynamic reverse-code generation outperforms the existing backtracking methods in terms of memory efficiency.

  7. Identification of Novel Long Non-coding and Circular RNAs in Human Papillomavirus-Mediated Cervical Cancer

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    Hongbo Wang

    2017-09-01

    Full Text Available Cervical cancer is the third most common cancer worldwide and the fourth leading cause of cancer-associated mortality in women. Accumulating evidence indicates that long non-coding RNAs (lncRNAs and circular RNAs (circRNAs may play key roles in the carcinogenesis of different cancers; however, little is known about the mechanisms of lncRNAs and circRNAs in the progression and metastasis of cervical cancer. In this study, we explored the expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs in HPV16 (human papillomavirus genotype 16 mediated cervical squamous cell carcinoma and matched adjacent non-tumor (ATN tissues from three patients with high-throughput RNA sequencing (RNA-seq. In total, we identified 19 lncRNAs, 99 circRNAs, 28 miRNAs, and 304 mRNAs that were commonly differentially expressed (DE in different patients. Among the non-coding RNAs, 3 lncRNAs and 44 circRNAs are novel to our knowledge. Functional enrichment analysis showed that DE lncRNAs, miRNAs, and mRNAs were enriched in pathways crucial to cancer as well as other gene ontology (GO terms. Furthermore, the co-expression network and function prediction suggested that all 19 DE lncRNAs could play different roles in the carcinogenesis and development of cervical cancer. The competing endogenous RNA (ceRNA network based on DE coding and non-coding RNAs showed that each miRNA targeted a number of lncRNAs and circRNAs. The link between part of the miRNAs in the network and cervical cancer has been validated in previous studies, and these miRNAs targeted the majority of the novel non-coding RNAs, thus suggesting that these novel non-coding RNAs may be involved in cervical cancer. Taken together, our study shows that DE non-coding RNAs could be further developed as diagnostic and therapeutic biomarkers of cervical cancer. The complex ceRNA network also lays the foundation for future research of the roles of coding and non-coding RNAs in cervical cancer.

  8. Identification of Novel Long Non-coding and Circular RNAs in Human Papillomavirus-Mediated Cervical Cancer

    Science.gov (United States)

    Wang, Hongbo; Zhao, Yingchao; Chen, Mingyue; Cui, Jie

    2017-01-01

    Cervical cancer is the third most common cancer worldwide and the fourth leading cause of cancer-associated mortality in women. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) may play key roles in the carcinogenesis of different cancers; however, little is known about the mechanisms of lncRNAs and circRNAs in the progression and metastasis of cervical cancer. In this study, we explored the expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs in HPV16 (human papillomavirus genotype 16) mediated cervical squamous cell carcinoma and matched adjacent non-tumor (ATN) tissues from three patients with high-throughput RNA sequencing (RNA-seq). In total, we identified 19 lncRNAs, 99 circRNAs, 28 miRNAs, and 304 mRNAs that were commonly differentially expressed (DE) in different patients. Among the non-coding RNAs, 3 lncRNAs and 44 circRNAs are novel to our knowledge. Functional enrichment analysis showed that DE lncRNAs, miRNAs, and mRNAs were enriched in pathways crucial to cancer as well as other gene ontology (GO) terms. Furthermore, the co-expression network and function prediction suggested that all 19 DE lncRNAs could play different roles in the carcinogenesis and development of cervical cancer. The competing endogenous RNA (ceRNA) network based on DE coding and non-coding RNAs showed that each miRNA targeted a number of lncRNAs and circRNAs. The link between part of the miRNAs in the network and cervical cancer has been validated in previous studies, and these miRNAs targeted the majority of the novel non-coding RNAs, thus suggesting that these novel non-coding RNAs may be involved in cervical cancer. Taken together, our study shows that DE non-coding RNAs could be further developed as diagnostic and therapeutic biomarkers of cervical cancer. The complex ceRNA network also lays the foundation for future research of the roles of coding and non-coding RNAs in cervical cancer. PMID:28970820

  9. Estradiol-Induced Transcriptional Regulation of Long Non-Coding RNA, HOTAIR.

    Science.gov (United States)

    Bhan, Arunoday; Mandal, Subhrangsu S

    2016-01-01

    HOTAIR (HOX antisense intergenic RNA) is a 2.2 kb long non-coding RNA (lncRNA), transcribed from the antisense strand of homeobox C (HOXC) gene locus in chromosome 12. HOTAIR acts as a scaffolding lncRNA. It interacts and guides various chromatin-modifying complexes such as PRC2 (polycomb-repressive complex 2) and LSD1 (lysine-specific demethylase 1) to the target gene promoters leading to their gene silencing. Various studies have demonstrated that HOTAIR overexpression is associated with breast cancer. Recent studies from our laboratory demonstrate that HOTAIR is required for viability of breast cancer cells and is transcriptionally regulated by estradiol (E2) in vitro and in vivo. This chapter describes protocols for analysis of the HOTAIR promoter, cloning, transfection and dual luciferase assays, knockdown of protein synthesis by antisense oligonucleotides, and chromatin immunoprecipitation (ChIP) assay. These protocols are useful for studying the estrogen-mediated transcriptional regulation of lncRNA HOTAIR, as well as other protein coding genes and non-coding RNAs.

  10. Unravelling the Long Non-Coding RNA Profile of Undifferentiated Large Cell Lung Carcinoma.

    Science.gov (United States)

    Shukla, Sudhanshu

    2018-02-05

    Undifferentiated large cell lung carcinoma (LCLC) accounts for 2.9-9% of total lung cancers. Recently, RNA-seq based studies have revealed major genomic aberrations in LCLC. In this study, we aim to identify long non-coding RNAs (LncRNAs) expression pattern specific to LCLC. The RNA-seq profile of LCLC and other non-small cell lung carcinoma (NSCLC) was downloaded from Gene Expression Omnibus (GEO) and analyzed. Using 10 LCLC samples, we found that 18% of all the annotated LncRNAs are expressed in LCLC samples. Among 1794 expressed LncRNAs, 11 were overexpressed and 14 were downregulated in LCLC compared to normal samples. Based on receiver operating characteristic (ROC) analysis, we showed that the top five differentially expressed LncRNAs were able to differentiate between LCLC and normal samples with high sensitivity and specificity. Guilt by association analysis using genes correlating with differentially expressed LncRNAs identified several cancer-associated pathways, suggesting the role of these deregulated LncRNA in LCLC biology. We also identified the LncRNA differentially expressed in LCLC compared to lung squamous carcinoma (LUSC) and Lung-adenocarcinoma (LUAD). We found that LCLC sample showed more deregulated LncRNA in LUSC than LUAD. Interestingly, LCLC had more downregulated LncRNA compared to LUAD and LUSC. Our study provides novel insight into LncRNA deregulation in LCLC. This study also finds tools to diagnose LCLC and differentiate LCLC with other Non-Small Cell Lung Cancer.

  11. Reproducibility of microbial mutagenicity assays. I. Tests with Salmonella typhimurium and Escherichia coli using a standardized protocol

    International Nuclear Information System (INIS)

    Dunkel, V.C.; Zeiger, E.; Brusick, D.; McCoy, E.; McGregor, D.; Mortelmans, K.; Rosenkranz, H.S.; Simmon, V.F.

    1984-01-01

    The Salmonella/microsome test developed by Ames and his coworkers has been widely used in the evaluation of chemicals for genotoxic potential. Although the value of this assay is well recognized, there have been no comprehensive studies on the interlaboratory reproducibility of the method using a standardized protocol. A program was therefore initiated to compare the results obtained in four laboratories from testing a series of coded mutagens and nonmutagens using a standardized protocol. Additional objectives of this study were to compare male Fisher 344 rat, B6C3F1 mouse, and Syrian hamster liver S-9 preparations for the activation of chemicals; to compare Aroclor 1254-induced liver S-9 from all three species with the corresponding non-induced liver S-9's; and to compare the response of Escherichia coli WP-2 uvrA with the Salmonella typhimurium tester strains recommended by Ames. Since a primary use of in vitro microbial mutagenesis tests is the identification of potential carcinogens by their mutagenicity, the authors decided to compare the animal species and strains used by the National Cancer Institute/National Toxicology Program (NCI/NTP) for animal carcinogenicity studies

  12. The Role of the spv Genes in Salmonella Pathogenesis

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    Donald G. Guiney

    2011-06-01

    Full Text Available Salmonella strains cause three main types of diseases in people: gastroenteritis, enteric (typhoid fever, and non-typhoid extra-intestinal disease with bacteremia. Genetic analysis indicates that each clinical syndrome requires distinct sets of virulence genes, and Salmonella isolates differ in their constellation of virulence traits. The spv locus is strongly associated with strains that cause non-typhoid bacteremia, but are not present in typhoid strains. The spv region contains three genes required for the virulence phenotype in mice: the positive transcriptional regulator spvR and two structural genes spvB and spvC. SpvB and SpvC are translocated into the host cell by the SPI-2 type-three secretion system. SpvB prevents actin polymerization by ADP-ribosylation of actin monomers, while SpvC has phosphothreonine lyase activity and has been shown to inhibit MAP kinase signaling. The exact mechanisms by which SpvB and SpvC act in concert to enhance virulence are still unclear. SpvB exhibits a cytotoxic effect on host cells and is required for delayed cell death by apoptosis following intracellular infection. Strains isolated from systemic infections of immune compromised patients, particularly HIV patients, usually carry the spv locus, strongly suggesting that CD4 T cells are required to control disease due to Salmonella that are spv positive. This association is not seen with typhoid fever, indicating that the pathogenesis and immunology of typhoid have fundamental differences from the syndrome of non-typhoid bacteremia.

  13. Advanced GF(32) nonbinary LDPC coded modulation with non-uniform 9-QAM outperforming star 8-QAM.

    Science.gov (United States)

    Liu, Tao; Lin, Changyu; Djordjevic, Ivan B

    2016-06-27

    In this paper, we first describe a 9-symbol non-uniform signaling scheme based on Huffman code, in which different symbols are transmitted with different probabilities. By using the Huffman procedure, prefix code is designed to approach the optimal performance. Then, we introduce an algorithm to determine the optimal signal constellation sets for our proposed non-uniform scheme with the criterion of maximizing constellation figure of merit (CFM). The proposed nonuniform polarization multiplexed signaling 9-QAM scheme has the same spectral efficiency as the conventional 8-QAM. Additionally, we propose a specially designed GF(32) nonbinary quasi-cyclic LDPC code for the coded modulation system based on the 9-QAM non-uniform scheme. Further, we study the efficiency of our proposed non-uniform 9-QAM, combined with nonbinary LDPC coding, and demonstrate by Monte Carlo simulation that the proposed GF(23) nonbinary LDPC coded 9-QAM scheme outperforms nonbinary LDPC coded uniform 8-QAM by at least 0.8dB.

  14. Modelling transfer of Salmonella Typhimurium DT104 during simulation of grinding of pork.

    Science.gov (United States)

    Møller, C O A; Nauta, M J; Christensen, B B; Dalgaard, P; Hansen, T B

    2012-01-01

    The aim of this study was to develop a model to predict cross-contamination of Salmonella during grinding of pork. Transfer rates of Salmonella were measured in three experiments, where between 10 and 20 kg meat was ground into 200-g portions. In each experiment, five pork slices of about 200 g per slice were inoculated with 8-9 log-units of Salmonella Typhimurium DT104 and used for building up the contamination in the grinder. Subsequently, Salmonella-free slices were ground and collected as samples of c. 200 g minced pork. Throughout the process, representative samples were quantitatively analysed for Salmonella. A model suggested by Nauta et al. (2005) predicting cross-contamination of Campylobacter in poultry processing and two modified versions of this model were tested. The present study observed a tailing phenomenon of transfer of Salmonella during a small-scale grinding process. It was, therefore, hypothesized that transfer occurred from two environmental matrices inside the grinder and a model was developed. The developed model satisfactorily predicted the observed concentrations of Salmonella during its cross-contamination in the grinding of up to 110 pork slices. The proposed model provides an important tool to examine the effect of cross-contamination in quantitative microbial risk assessments and might also be applied to various other food processes where cross-contamination is involved. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

  15. Evolution of Salmonella enterica virulence via point mutations in the fimbrial adhesin.

    Directory of Open Access Journals (Sweden)

    Dagmara I Kisiela

    Full Text Available Whereas the majority of pathogenic Salmonella serovars are capable of infecting many different animal species, typically producing a self-limited gastroenteritis, serovars with narrow host-specificity exhibit increased virulence and their infections frequently result in fatal systemic diseases. In our study, a genetic and functional analysis of the mannose-specific type 1 fimbrial adhesin FimH from a variety of serovars of Salmonella enterica revealed that specific mutant variants of FimH are common in host-adapted (systemically invasive serovars. We have found that while the low-binding shear-dependent phenotype of the adhesin is preserved in broad host-range (usually systemically non-invasive Salmonella, the majority of host-adapted serovars express FimH variants with one of two alternative phenotypes: a significantly increased binding to mannose (as in S. Typhi, S. Paratyphi C, S. Dublin and some isolates of S. Choleraesuis, or complete loss of the mannose-binding activity (as in S. Paratyphi B, S. Choleraesuis and S. Gallinarum. The functional diversification of FimH in host-adapted Salmonella results from recently acquired structural mutations. Many of the mutations are of a convergent nature indicative of strong positive selection. The high-binding phenotype of FimH that leads to increased bacterial adhesiveness to and invasiveness of epithelial cells and macrophages usually precedes acquisition of the non-binding phenotype. Collectively these observations suggest that activation or inactivation of mannose-specific adhesive properties in different systemically invasive serovars of Salmonella reflects their dynamic trajectories of adaptation to a life style in specific hosts. In conclusion, our study demonstrates that point mutations are the target of positive selection and, in addition to horizontal gene transfer and genome degradation events, can contribute to the differential pathoadaptive evolution of Salmonella.

  16. Recent Trends in Salmonella Outbreaks and Emerging Technology for Biocontrol of Salmonella Using Phages in Foods: A Review.

    Science.gov (United States)

    Oh, Jun-Hyun; Park, Mi-Kyung

    2017-12-28

    Salmonella is one of the principal causes of foodborne outbreaks. As traditional control methods have shown less efficacy against emerging Salmonella serotypes or antimicrobialresistant Salmonella , new approaches have been attempted. The use of lytic phages for the biocontrol of Salmonella in the food industry has become an attractive method owing to the many advantages offered by the use of phages as biocontrol agents. Phages are natural alternatives to traditional antimicrobial agents; they have proven effective in the control of bacterial pathogens in the food industry, which has led to the development of different phage products. The treatment with specific phages in the food industry can prevent the decay of products and the spread of bacterial diseases, and ultimately promotes safe environments for animal and plant food production, processing, and handling. After an extensive investigation of the current literature, this review focuses predominantly on the efficacy of phages for the successful control of Salmonella spp. in foods. This review also addresses the current knowledge on the pathogenic characteristics of Salmonella , the prevalence of emerging Salmonella outbreaks, the isolation and characterization of Salmonella -specific phages, the effectiveness of Salmonella -specific phages as biocontrol agents, and the prospective use of Salmonella -specific phages in the food industry.

  17. TUG1: a pivotal oncogenic long non-coding RNA of human cancers.

    Science.gov (United States)

    Li, Zheng; Shen, Jianxiong; Chan, Matthew T V; Wu, William Ka Kei

    2016-08-01

    Long non-coding RNAs (lncRNAs) are a group greater than 200 nucleotides in length. An increasing number of studies has shown that lncRNAs play important roles in diverse cellular processes, including proliferation, differentiation, apoptosis, invasion and chromatin remodelling. In this regard, deregulation of lncRNAs has been documented in human cancers. TUG1 is a recently identified oncogenic lncRNA whose aberrant upregulation has been detected in different types of cancer, including B-cell malignancies, oesophageal squamous cell carcinoma, bladder cancer, hepatocellular carcinoma and osteosarcoma. In these malignancies, knock-down of TUG1 has been shown to suppress cell proliferation, invasion and/or colony formation. Interestingly, TUG1 has been found to be downregulated in non-small cell lung carcinoma, indicative of its tissue-specific function in tumourigenesis. Pertinent to clinical practice, TUG1 may act as a prognostic biomarker for tumours. In this review, we summarize current knowledge concerning the role of TUG1 in tumour progression and discuss mechanisms associated with it. © 2016 John Wiley & Sons Ltd.

  18. Python Radiative Transfer Emission code (PyRaTE): non-LTE spectral lines simulations

    Science.gov (United States)

    Tritsis, A.; Yorke, H.; Tassis, K.

    2018-05-01

    We describe PyRaTE, a new, non-local thermodynamic equilibrium (non-LTE) line radiative transfer code developed specifically for post-processing astrochemical simulations. Population densities are estimated using the escape probability method. When computing the escape probability, the optical depth is calculated towards all directions with density, molecular abundance, temperature and velocity variations all taken into account. A very easy-to-use interface, capable of importing data from simulations outputs performed with all major astrophysical codes, is also developed. The code is written in PYTHON using an "embarrassingly parallel" strategy and can handle all geometries and projection angles. We benchmark the code by comparing our results with those from RADEX (van der Tak et al. 2007) and against analytical solutions and present case studies using hydrochemical simulations. The code will be released for public use.

  19. Microarray data re-annotation reveals specific lncRNAs and their potential functions in non-small cell lung cancer subtypes

    OpenAIRE

    Zhou, Dongbo; Xie, Mingxuan; He, Baimei; Gao, Ying; Yu, Qiao; He, Bixiu; Chen, Qiong

    2017-01-01

    Non-small-cell lung cancer (NSCLC) is a leading cause of cancer mortality worldwide. The most common subtypes of NSCLC are adenocarcinoma (AC) and squamous cell carcinoma (SCC). However, the pathophysiological mechanisms contributing to AC and SCC are still largely unknown, especially the roles of long non-coding RNAs (lncRNAs). The present study identified differentially expressed lncRNAs between lung AC and SCC by re-annotation of NSCLC microarray data analysis profiling. The potential func...

  20. Isolation and Determination of Antibiotic Resistance Patterns in Nontyphoid Salmonella spp isolated from chicken

    Directory of Open Access Journals (Sweden)

    Seyyedeh Hoorieh Fallah

    2013-01-01

    Full Text Available Background: Salmonellosis is one of the most common food borne diseases in industrial and developing countries. In recent years, an increase in antimicrobial drug resistance, among non-typhoid Salmonella spp has been observed. Objectives: The aim of this study was to isolate and determine antibiotic resistance pattern in non-typhoid Salmonella spp. Materials and Methods: This descriptive study was done on 100 samples of chickens collected from 196 retail markets and was examined for the presence of Salmonella using standard bacteriological procedures and stereotyping kit. Antimicrobial susceptibility testing was performed by disk diffusion methods according to the National Committee for Clinical Laboratory Standards (CLSI. The data were analyzed by using the SPSS software version 18. Result: Forty- four percent of samples were contaminated with Salmonella infection and 56% didn’t have any contamination. The stereotyping results showed that 34 of 44 isolates of Salmonella belonged to Salmonella infantis (79.5 %, one strain (2.3% of group C and 8 strain (18.2% of group D. However, all these strains were sensitive to Cefotaxime and Ciprofloxacin, and 100% were resistant to Nalidixic acid, Tetracyclin and Sterptomycin. The most common resistance pattern (34.1% was towards six antibiotics, and 6.8% of strains were resistant to at least three antibiotics. Conclusion: High levels of resistance to antibiotics that are used commonly for human and poultry can be a warning for our community health and this information must be used to form important strategies for improvement of infection control.

  1. Antimicrobial residues and resistance against critically important antimicrobials in non-typhoidal Salmonella from meat sold at wet markets and supermarkets in Vietnam.

    OpenAIRE

    Nhung, NT; Van, NTB; Cuong, NV; Duong, TTQ; Nhat, TT; Hang, TTT; Nhi, NTH; Kiet, BT; Hien, VB; Ngoc, PT; Campbell, J; Thwaites, G; Carrique-Mas, J

    2017-01-01

    Excessive antimicrobial usage and deficiencies in hygiene in meat production systems may result in undesirable human health hazards, such as the presence of antimicrobial drug residues and non-typhoidal Salmonella (NTS), including antimicrobial resistant (AMR) NTS. Recently, Vietnam has witnessed the emergence of integrated intensive animal production systems, coexisting with more traditional, locally-sourced wet markets. To date no systematic studies have been carried out to compare health h...

  2. MetastamiRs: Non-Coding MicroRNAs Driving Cancer Invasion and Metastasis

    Directory of Open Access Journals (Sweden)

    Sergio Rodriguez-Cuevas

    2012-01-01

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs of ~22 nucleotides that function as negative regulators of gene expression by either inhibiting translation or inducing deadenylation-dependent degradation of target transcripts. Notably, deregulation of miRNAs expression is associated with the initiation and progression of human cancers where they act as oncogenes or tumor suppressors contributing to tumorigenesis. Abnormal miRNA expression may provide potential diagnostic and prognostic tumor biomarkers and new therapeutic targets in cancer. Recently, several miRNAs have been shown to initiate invasion and metastasis by targeting multiple proteins that are major players in these cellular events, thus they have been denominated as metastamiRs. Here, we present a review of the current knowledge of miRNAs in cancer with a special focus on metastamiRs. In addition we discuss their potential use as novel specific markers for cancer progression.

  3. New paradigms for Salmonella source attribution based on microbial subtyping.

    Science.gov (United States)

    Mughini-Gras, Lapo; Franz, Eelco; van Pelt, Wilfrid

    2018-05-01

    Microbial subtyping is the most common approach for Salmonella source attribution. Typically, attributions are computed using frequency-matching models like the Dutch and Danish models based on phenotyping data (serotyping, phage-typing, and antimicrobial resistance profiling). Herewith, we critically review three major paradigms facing Salmonella source attribution today: (i) the use of genotyping data, particularly Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA), which is replacing traditional Salmonella phenotyping beyond serotyping; (ii) the integration of case-control data into source attribution to improve risk factor identification/characterization; (iii) the investigation of non-food sources, as attributions tend to focus on foods of animal origin only. Population genetics models or simplified MLVA schemes may provide feasible options for source attribution, although there is a strong need to explore novel modelling options as we move towards whole-genome sequencing as the standard. Classical case-control studies are enhanced by incorporating source attribution results, as individuals acquiring salmonellosis from different sources have different associated risk factors. Thus, the more such analyses are performed the better Salmonella epidemiology will be understood. Reparametrizing current models allows for inclusion of sources like reptiles, the study of which improves our understanding of Salmonella epidemiology beyond food to tackle the pathogen in a more holistic way. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Isolation and Evaluation Virulence Factors of Salmonella typhimurium and Salmonella enteritidis in Milk and Dairy Products

    Directory of Open Access Journals (Sweden)

    Shima Shaigan nia

    2014-06-01

    Conclusions: To our best knowledge the present study is the first prevalence report of Salmonella spp., Salmonella enteritidis and Salmonella typhimurium in raw sheep and goat samples in Iran. Consumption of pasteurized milk and dairy products can reduce the risk of salmonellosis.

  5. PREVALENCE OF SALMONELLA IN CAPTIVE REPTILES FROM CROATIA.

    Science.gov (United States)

    Lukac, Maja; Pedersen, Karl; Prukner-Radovcic, Estella

    2015-06-01

    Salmonellosis transmitted by pet reptiles is an increasing public health issue worldwide. The aim of this study was to investigate the prevalence of Salmonella strains from captive reptiles in Croatia. From November 2009 to November 2011 a total of 292 skin, pharyngeal, cloacal, and fecal samples from 200 apparently healthy reptiles were tested for Salmonella excretions by bacteriologic culture and serotyping. These 200 individual reptiles included 31 lizards, 79 chelonians, and 90 snakes belonging to private owners or housed at the Zagreb Zoo, Croatia. Salmonella was detected in a total of 13% of the animals, among them 48.4% lizards, 8.9% snakes, and 3.8% turtles. Representatives of five of the six Salmonella enterica subspecies were identified with the following proportions in the total number of isolates: Salmonella enterica enterica 34.6%, Salmonella enterica houtenae 23.1%, Salmonella enterica arizonae 23.1%, Salmonella enterica diarizonae 15.4%, and Salmonella enterica salamae 3.8%. The 14 different serovars isolated included several rarely occurring serovars such as Salmonella Apapa, Salmonella Halle, Salmonella Kisarawe, and Salmonella Potengi. These findings confirm that the prevalence of Salmonella is considerable in captive reptiles in Croatia, indicating that these animals may harbor serovars not commonly seen in veterinary or human microbiologic practice. This should be addressed in the prevention and diagnostics of human reptile-transmitted infections.

  6. Prevalence, risk factors and antimicrobial resistance of Salmonella diarrhoeal infection among children in Thi-Qar Governorate, Iraq.

    Science.gov (United States)

    Harb, A; O'Dea, M; Hanan, Z K; Abraham, S; Habib, I

    2017-12-01

    We conducted a hospital-based cross-sectional study among children aged Salmonella infection. From 320 diarrhoea cases enrolled between March and August 2016, 33 (10·3%, 95% confidence interval (CI) 8·4-12·4) cases were stool culture-positive for non-typhoidal Salmonella enterica. The most commonly identified serovar was Typhimurium (54%). Multivariable logistic regression analysis indicated that the odds of Salmonella infection in children from households supplied by pipe water was 4·7 (95% CI 1·6-13·9) times higher compared with those supplied with reverse osmosis treated water. Similarly, children from households with domestic animals were found to have a higher odds (OR 10·5; 95% CI 3·8-28·4) of being Salmonella stool culture-positive. The likelihood of Salmonella infection was higher (OR 3·9; 95% CI 1·0-6·4) among children belonging to caregiver with primary vs. tertiary education levels. Lower odds (OR 0·4; 95% CI 0·1-0·9) of Salmonella infection were associated with children exclusively breast fed as compared with those exclusively bottle fed. Salmonella infection was three times lower (95% CI 0·1-0·7) in children belonging to caregiver who reported always washing hands after cleaning children following defecation, vs. those belonging to caregivers who did not wash hands. The antimicrobial resistance profile by disc diffusion revealed that non-susceptibility to tetracycline (78·8%), azithromycin (66·7%) and ciprofloxacin (57·6%) were the most commonly seen, and 84·9% of Salmonella isolates were classified as multi-drug resistant. This is the first study on prevalence and antimicrobial resistance of Salmonella infection among children in this setting. This work provides specific epidemiological data which are crucial to understand and combat paediatric diarrhoea in Iraq.

  7. Bacteriophage SP6 encodes a second tailspike protein that recognizes Salmonella enterica serogroups C2 and C3

    International Nuclear Information System (INIS)

    Gebhart, Dana; Williams, Steven R.; Scholl, Dean

    2017-01-01

    SP6 is a salmonella phage closely related to coliphage K1-5. K1-5 is notable in that it encodes two polysaccharide-degrading tailspike proteins, an endosialidase that allows it to infect E. coli K1, and a lyase that enables it to infect K5 strains. SP6 is similar to K1-5 except that it encodes a P22-like endorhamnosidase tailspike, gp46, allowing it to infect group B Salmonella. We show here that SP6 can also infect Salmonella serogroups C 2 and C 3 and that a mutation in a putative second tailspike, gp47, eliminates this specificity. Gene 47 was fused to the coding region of the N-terminal portion of the Pseudomonas aeruginosa R2 pyocin tail fiber and expressed in trans such that the fusion protein becomes incorporated into pyocin particles. These pyocins, termed AvR2-SP47, killed serogroups C 2 and C 3 Salmonella. We conclude that SP6 encodes two tail proteins providing it a broad host range among Salmonella enterica. - Highlights: • SP6 is a “dual specificity” bacteriophage that encodes two different receptor binding proteins giving it a broad host range. • These receptor binding proteins can be used to re-target the spectrum of R-type bacteriocins to Salmonella enterica. • Both SP6 and the engineered R-type bacteriocins can kill the Salmonella serovars most associated with human disease making them attractive for development as antimicrobial agents.

  8. 9 CFR 113.122 - Salmonella Choleraesuis Bacterin.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Salmonella Choleraesuis Bacterin. 113... REQUIREMENTS Inactivated Bacterial Products § 113.122 Salmonella Choleraesuis Bacterin. Salmonella Choleraesuis Bacterin shall be prepared from a culture of Salmonella choleraesuis which has been inactivated and is...

  9. 9 CFR 113.120 - Salmonella Typhimurium Bacterin.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Salmonella Typhimurium Bacterin. 113... REQUIREMENTS Inactivated Bacterial Products § 113.120 Salmonella Typhimurium Bacterin. Salmonella Typhimurium Bacterin shall be prepared from a culture of Salmonella typhimurium which has been inactivated and is...

  10. Salmonella spp. in raw broiler parts: occurrence, antimicrobial resistance profile and phage typing of the Salmonella Enteritidis isolates Salmonella spp. em cortes de frango: ocorrência, resistência antimicrobiana e fagotipificação dos isolados de Salmonella Enteritidis

    Directory of Open Access Journals (Sweden)

    Aldemir Reginato Ribeiro

    2007-06-01

    Full Text Available The present study was carried out to evaluate the occurrence of Salmonellae in raw broiler parts and to determine the antimicrobial resistance profile of the isolated strains. Twenty-four (39.3% broiler parts samples were positive for Salmonella and twenty-five Salmonella strains were isolated, since two different serovars were detected in one single positive sample. Salmonella Enteritidis was the most prevalent serovar. Among Salmonella Enteritidis isolates, 95.2% belonged to Phage Type 4 (PT4 (20/21 and 4.8% to PT7 (1/21. Twenty-two (88% strains of Salmonella were resistant to at least one antimicrobial agent, generating eight different resistance patterns. The S. Typhimurium (n: 1 and S. Hadar (n: 3 isolates presented multiple resistance. Three S. Enteritidis isolates were susceptible to all antimicrobials tested, two were resistant only to tetracycline. The high prevalence of Salmonella in the broiler parts strenghtens the importance of the use of good manufacturing practices (GMP, and HACCP. The results also emphasize the need for the responsible use of antimicrobials in animal production.Este trabalho foi conduzido para avaliar a ocorrência de Salmonella em cortes de frango e para determinar o perfil de resistência antimicrobiana das cepas isoladas. Vinte e quatro (39,3% cortes de frango foram positivas para Salmonella, tendo sido isoladas vinte e cinco cepas de Salmonella, uma vez que em uma amostra isolaram-se dois sorovares. Salmonella Enteritidis foi o sorovar prevalente. Entre as Salmonella Enteritidis isoladas, 95,2% pertencem ao Fagotipo 4 (PT4 (20/21 e 4,8% ao PT7 (1/21. Vinte e duas (88% cepas de Salmonella foram resistentes a pelo menos um agente antimicrobiano e oito diferentes padrões de resistência foram observados. S. Typhimurium (n:1 e S. Hadar (n: 3, apresentaram múltipla resistência. Três cepas de S. Enteritidis foram sensíveis a todos os antimicrobianos e duas resistentes somente a tetraciclina. A elevada ocorr

  11. Salmonella Infections - Multiple Languages

    Science.gov (United States)

    ... Are Here: Home → Multiple Languages → All Health Topics → Salmonella Infections URL of this page: https://medlineplus.gov/ ... V W XYZ List of All Topics All Salmonella Infections - Multiple Languages To use the sharing features ...

  12. Comprehensive reconstruction andvisualization of non-coding regulatorynetworks in human

    Directory of Open Access Journals (Sweden)

    Vincenzo eBonnici

    2014-12-01

    Full Text Available Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs. Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established online repositories. The interactions involve RNA, DNA, proteins and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command line and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.

  13. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

    DEFF Research Database (Denmark)

    Kröger, Carsten; Dillon, Shane C.; Cameron, Andrew D. S.

    2012-01-01

    More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required......-thirds of these TSSs were associated with σ70 (including phoP, slyA, and invF) from which we identified the −10 and −35 motifs of σ70-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium...

  14. Automated 5 ' nuclease PCR assay for identification of Salmonella enterica

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey; Ahrens, Peter; Rådström, P.

    2000-01-01

    -point fluorescence (FAM) signals for the samples and positive control (TET) signals (relative sensitivity [Delta Rn], >0.6). The diagnostic specificity of the method was assessed using 120 non-Salmonella strains, which all resulted in negative FAM signals (Delta Rn, less than or equal to 0.5). All 100 rough...... Salmonella strains tested resulted in positive FAM and TET signals. In addition, it was found that the complete PCR mixture, predispensed in microwell plates, could be stored for up to 3 months at -20 degrees C, Thus, the diagnostic TaqMan assay developed can be a useful and simple alternative method......A simple and ready-to-go test based on a 5' nuclease (TaqMan) PCR technique was developed for identification of presumptive Salmonella enterica isolates. The results were compared with those of conventional methods. The TaqMan assay was evaluated for its ability to accurately detect 210 S. enterica...

  15. 9 CFR 113.123 - Salmonella Dublin Bacterin.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Salmonella Dublin Bacterin. 113.123... Inactivated Bacterial Products § 113.123 Salmonella Dublin Bacterin. Salmonella Dublin Bacterin shall be prepared from a culture of Salmonella dublin which has been inactivated and is nontoxic. Each serial of...

  16. Evaluation of mice infected to Salmonella Spp in Poultry farms of Tehran Province

    Directory of Open Access Journals (Sweden)

    M Hadadian

    2012-08-01

    Full Text Available In this survey, 290 mice and rats fecal samples from commercial layer and broiler poultry houses were tested for Salmonella sp. presence. All samples were cultured on Selenite F broth media and passaged on SS agar and McConkey agar. The suspected colonies were cultured on Urea and TSI agars to be confirmed as Salmonella sp.. Finally, Salmonella isolates were identified genetically and biochemically by PCR and conventional methods, respectively. Serogrouping and Antibiotic resistance profiling were done for further differentiation of isolates. Twenty eight (9.65% Salmonellas were isolated from (out of 290 samples. Eight (28.6%, seven (25%, four (14.3%, and two (7.2% isolates were located in serogroups C, D, B and E, respectively. Seven isolates (25% belonged to Arizona subspecies and just one non-motile serogroup D Salmonella was isolated. All isolates were sensitive to enrofloxacin, difloxacin, norfloxacin, chloramphenicol and florfenicol, but they were resistant to sulfamethoxazole, trimethoprim and neomycin in decreasing order. In addition to former surveys, this study confirmed the role of mice and rats in spreading of Salmonella spp. in poultry farms. In conclusion it is essential to take appropriate measurements (measures for pest management in poultry houses to approach the prevention of some bacterial infection like  (such as salmonellosis.

  17. Attenuation of 10 MeV electron beam energy to achieve low doses does not affect Salmonella spp. inactivation kinetics

    International Nuclear Information System (INIS)

    Hieke, Anne-Sophie Charlotte; Pillai, Suresh D.

    2015-01-01

    The effect of attenuating the energy of a 10 MeV electron beam on Salmonella inactivation kinetics was investigated. No statistically significant differences were observed between the D 10 values of either Salmonella 4,[5],12:i:- or a Salmonella cocktail (S. 4,[5],12:i:-, Salmonella Heidelberg, Salmonella Newport, Salmonella Typhimurium, Salmonella) when irradiated with either a non-attenuated 10 MeV eBeam or an attenuated 10 MeV eBeam (~2.9±0.22 MeV). The results show that attenuating the energy of a 10 MeV eBeam to achieve low doses does not affect the inactivation kinetics of Salmonella spp. when compared to direct 10 MeV eBeam irradiation. - Highlights: • 10 MeV eBeam energy was attenuated to 2.9±0.22 MeV using HDPE sheets. • Attenuation of eBeam energy does not affect the inactivation kinetics of Salmonella. • Microbial inactivation is independent of eBeam energy in the range of 3–10 MeV

  18. Therapeutic targeting of non-coding RNAs in cancer

    Czech Academy of Sciences Publication Activity Database

    Slabý, O.; Laga, Richard; Sedláček, Ondřej

    2017-01-01

    Roč. 474, č. 24 (2017), s. 4219-4251 ISSN 0264-6021 R&D Projects: GA MŠk(CZ) LQ1604; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 Keywords : non-coding RNA * RNA delivery * polymer carriers Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemical research methods Impact factor: 3.797, year: 2016

  19. Antimicrobial Resistance Profiles and Diversity in Salmonella from Humans and Cattle, 2004-2011.

    Science.gov (United States)

    Afema, J A; Mather, A E; Sischo, W M

    2015-11-01

    Analysis of long-term anti-microbial resistance (AMR) data is useful to understand source and transmission dynamics of AMR. We analysed 5124 human clinical isolates from Washington State Department of Health, 391 cattle clinical isolates from the Washington Animal Disease Diagnostic Laboratory and 1864 non-clinical isolates from foodborne disease research on dairies in the Pacific Northwest. Isolates were assigned profiles based on phenotypic resistance to 11 anti-microbials belonging to eight classes. Salmonella Typhimurium (ST), Salmonella Newport (SN) and Salmonella Montevideo (SM) were the most common serovars in both humans and cattle. Multinomial logistic regression showed ST and SN from cattle had greater probability of resistance to multiple classes of anti-microbials than ST and SN from humans (P resistant ST and SN for people, occurrence of profiles unique to cattle and not observed in temporally related human isolates indicates these profiles are circulating in cattle only. We used various measures to assess AMR diversity, conditional on the weighting of rare versus abundant profiles. AMR profile richness was greater in the common serovars from humans, although both source data sets were dominated by relatively few profiles. The greater profile richness in human Salmonella may be due to greater diversity of sources entering the human population compared to cattle or due to continuous evolution in the human environment. Also, AMR diversity was greater in clinical compared to non-clinical cattle Salmonella, and this could be due to anti-microbial selection pressure in diseased cattle that received treatment. The use of bootstrapping techniques showed that although there were shared profiles between humans and cattle, the expected and observed number of profiles was different, suggesting Salmonella and associated resistance from humans and cattle may not be wholly derived from a common population. © 2014 The Authors. Zoonoses and Public Health Published by

  20. New technologies accelerate the exploration of non-coding RNAs in horticultural plants

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Degao; Mewalal, Ritesh; Hu, Rongbin; Tuskan, Gerald A.; Yang, Xiaohan

    2017-07-05

    Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.

  1. Constacyclic codes over the ring F_q+v{F}_q+v2F_q and their applications of constructing new non-binary quantum codes

    Science.gov (United States)

    Ma, Fanghui; Gao, Jian; Fu, Fang-Wei

    2018-06-01

    Let R={F}_q+v{F}_q+v2{F}_q be a finite non-chain ring, where q is an odd prime power and v^3=v. In this paper, we propose two methods of constructing quantum codes from (α +β v+γ v2)-constacyclic codes over R. The first one is obtained via the Gray map and the Calderbank-Shor-Steane construction from Euclidean dual-containing (α +β v+γ v2)-constacyclic codes over R. The second one is obtained via the Gray map and the Hermitian construction from Hermitian dual-containing (α +β v+γ v2)-constacyclic codes over R. As an application, some new non-binary quantum codes are obtained.

  2. Selected Lactobacillus strains isolated from sugary and milk kefir reduce Salmonella infection of epithelial cells in vitro.

    Science.gov (United States)

    Zavala, L; Golowczyc, M A; van Hoorde, K; Medrano, M; Huys, G; Vandamme, P; Abraham, A G

    2016-09-01

    The isolation of potentially probiotic strains and the subsequent study of their properties are very important steps to gain insight in the health benefits ascribed to sugary and milk kefir. The aim of the present study was to characterise fifteen Lactobacillus strains isolated from these beverages by determining some surface properties and their ability to antagonise enterocyte cell damage after Salmonella infection in vitro. Lactobacillus surface properties were determined by hydrophobicity, autoaggregation, and coaggregation assays with Salmonella. In addition, lactobacilli adhesion to Caco-2/TC-7 cells and the effect on Salmonella invasion were evaluated. Finally, the disassembly of F-actin cytoskeleton on intestinal epithelial cells was assayed in vitro when Salmonella infection was performed in the presence of selected Lactobacillus strains. Ten out of the 15 strains showed a high adhesion capacity to Caco-2/TC-7 cells. Most of the strains were hydrophilic and non-autoaggregating. Strains isolated from sugary kefir were non-coaggregating with Salmonella, while strains Lactobacillus paracasei CIDCA 83120, 83121, 83123, 83124, 8339, 83102 isolated from milk kefir were able to coaggregate after 1 h. L. paracasei CIDCA 8339 and Lactobacillus kefiri CIDCA 83102 were able to diminish Salmonella invasion to the enterocytes. An antagonistic effect on cytoskeleton disruption elicited by the pathogen was also demonstrated. Our results suggest that both strains isolated from milk kefir could be considered as appropriate probiotic candidates.

  3. Test results of Salmonella typing by the NRLs-Salmonella in the Member States of the EU and the EnterNet Laboratories - Collaborative study VI on typing of Salmonella

    NARCIS (Netherlands)

    Korver H; Raes M; Maas HME; Ward LR; Wannet WJB; Henken AM; MGB; LIS

    2002-01-01

    Test resultaten van Salmonella sero- en faagtypering en antimicrobiele gevoeligheidsbepalingen door de Nationale Referentie Laboratoria voor Salmonella in de Lidstaten van de Europese Unie en EnterNet Laboratoria: Ringonderzoek VI (2001) voor Salmonella. Een zesde ringonderzoek betreffende de

  4. Determination of the Thermal Inactivation Kinetics of Listeria monocytogenes, Salmonella enterica, and Escherichia coli O157:H7 and non-O157 in Buffer and a Spinach Homogenate.

    Science.gov (United States)

    Monu, Emefa Angelica; Valladares, Malcond; D'Souza, Doris H; Davidson, P Michael

    2015-08-01

    Produce has been associated with a rising number of foodborne illness outbreaks. While much produce is consumed raw, some is treated with mild heat, such as blanching or cooking. The objectives of this research were to compare the thermal inactivation kinetics of Listeria monocytogenes, Salmonella enterica, Shiga toxin-producing Escherichia coli (STEC) O157:H7, and non-O157 STEC in phosphate-buffered saline (PBS; pH 7.2) and a spinach homogenate and to provide an estimate of the safety of mild heat processes for spinach. Five individual strains of S. enterica, L. monocytogenes, STEC O157:H7, and non-O157 STEC were tested in PBS in 2-ml glass vials, and cocktails of the organisms were tested in blended spinach in vacuum-sealed bags. For Listeria and Salmonella at 56 to 60°C, D-values in PBS ranged from 4.42 ± 0.94 to 0.35 ± 0.03 min and 2.11 ± 0.14 to 0.16 ± 0.03 min, respectively. D-values at 54 to 58°C were 5.18 ± 0.21 to 0.53 ± 0.04 min for STEC O157:H7 and 5.01 ± 0.60 to 0.60 ± 0.13 min for non-O157 STEC. In spinach at 56 to 60°C, Listeria D-values were 11.77 ± 2.18 to 1.22 ± 0.12 min and Salmonella D-values were 3.51 ± 0.06 to 0.47 ± 0.06 min. D-values for STEC O157:H7 and non-O157 STEC were 7.21 ± 0.17 to 1.07 ± 0.11 min and 5.57 ± 0.38 to 0.99 ± 0.07 min, respectively, at 56 to 60°C. In spinach, z-values were 4.07 ± 0.16, 4.59 ± 0.26, 4.80 ± 0.92, and 5.22 ± 0.20°C for Listeria, Salmonella, STEC O157:H7, and non-O157 STEC, respectively. Results indicated that a mild thermal treatment of blended spinach at 70°C for less than 1 min would result in a 6-log reduction of all pathogens tested. These findings may assist the food industry in the design of suitable mild thermal processes to ensure food safety.

  5. Prediction of Salmonella carcass contamination by a comparative quantitative analysis of E. coli and Salmonella during pig slaughter

    DEFF Research Database (Denmark)

    Nauta, Maarten; Barfod, Kristen; Hald, Tine

    2013-01-01

    Salmonella concentrations. It is concluded that the faecal carriage of Salmonella together with the faecal contamination of carcasses, as predicted from E. coli data in the animal faeces and hygiene performance of the slaughterhouse, is not sufficient to explain carcass contamination with Salmonella. Our...... extensive data set showed that other factors than the observed faecal carriage of Salmonella by the individual animals brought to slaughter, play a more important role in the Salmonella carcass contamination of pork.......Faecal contamination of carcasses in the slaughterhouse is generally considered to be the source of Salmonella on pork. In this study the hygiene indicator Escherichia coli is used to quantify faecal contamination of carcasses and it is hypothesized that it can be used to predict the quantitative...

  6. In vitro characterization and in vivo properties of Salmonellae lytic bacteriophages isolated from free-range layers

    Directory of Open Access Journals (Sweden)

    L Fiorentin

    2004-06-01

    Full Text Available Occurrence of food poisoning related to Salmonella-contaminated eggs and chicken meat has been frequent in humans. Salmonella Enteritidis (SE and Salmonella Typhimurium (ST are included among the most important paratyphoid salmonellae associated with chicken meat and eggs. Elimination of Salmonella at the pre-harvest stage can play a significant role in preventing the introduction of this pathogen into the food chain and consequently in the reduction of food poisoning in humans. Bactericidal bacteriophages may provide a natural, nontoxic, feasible and non-expensive component of the multi-factorial approach for a pre-harvest control of Salmonella in poultry. Five bacteriophages lytic for SE PT4 and ST were obtained from 107 samples of feces of free-range layers in Brazil. All bacteriophages were characterized in vitro and in vivo, showing head and tail morphology and dsDNA as nucleic acids. Results of "in vivo" studies suggested that bacteriophages do not remain in Salmonella-free birds longer than one day, whereas they multiply in Salmonella-infected birds for longer periods. Besides, selection for phage-resistant SE PT4 did not seem to occur in the short term. Isolated bacteriophages will be investigated for their potential for pre-harvest biocontrol of SE PT4 in poultry.

  7. Construction of Fixed Rate Non-Binary WOM Codes Based on Integer Programming

    Science.gov (United States)

    Fujino, Yoju; Wadayama, Tadashi

    In this paper, we propose a construction of non-binary WOM (Write-Once-Memory) codes for WOM storages such as flash memories. The WOM codes discussed in this paper are fixed rate WOM codes where messages in a fixed alphabet of size $M$ can be sequentially written in the WOM storage at least $t^*$-times. In this paper, a WOM storage is modeled by a state transition graph. The proposed construction has the following two features. First, it includes a systematic method to determine the encoding regions in the state transition graph. Second, the proposed construction includes a labeling method for states by using integer programming. Several novel WOM codes for $q$ level flash memories with 2 cells are constructed by the proposed construction. They achieve the worst numbers of writes $t^*$ that meet the known upper bound in many cases. In addition, we constructed fixed rate non-binary WOM codes with the capability to reduce ICI (inter cell interference) of flash cells. One of the advantages of the proposed construction is its flexibility. It can be applied to various storage devices, to various dimensions (i.e, number of cells), and various kind of additional constraints.

  8. Impact of desiccation and heat exposure stress on Salmonella tolerance to acidic conditions.

    Science.gov (United States)

    Richardson, Kurt E; Cox, Nelson A; Cosby, Douglas E; Berrang, Mark E

    2018-02-01

    In a recent study, the pH of commonly used Salmonella pre-enrichment media became acidic (pH 4.0 to 5.0) when feed or feed ingredients were incubated for 24 h. Acidic conditions have been reported to injure or kill Salmonella. In this study, cultures of four known feed isolates (S. montevideo, S. senftenberg, S. tennessee, and S. schwarzengrund) and four important processing plant isolates (S. typhimurium, S. enteritidis, S. infantis, and S. heidelberg) were grown on meat and bone meal and later subjected to desiccation and heat exposure to stress the microorganism. The impact of stress on the isolates ability to survive in acidic conditions ranging from pH 4.0 to 7.0 was compared to the non-stressed isolate. Cell injury was determined on xylose lysine tergitol 4 (XLT4) and cell death determined on nutrient agar (NA). When measured by cell death in non-stressed Salmonella, S. typhimurium was the most acid tolerant and S. heidelberg was the most acid sensitive whereas in stressed Salmonella, S. senftenberg was the most acid tolerant and S. tennessee was the most acid sensitive. The pH required to cause cell injury varied among isolates. With some isolates, the pH required for 50% cell death and 50% cell injury was similar. In other isolates, cell injury occurred at a more neutral pH. These findings suggest that the pH of pre-enrichment media may influence the recovery and bias the serotype of Salmonella recovered from feed during pre-enrichment.

  9. Detection and Identification of Salmonella spp. in Surface Water by Molecular Technology in Taiwan

    Science.gov (United States)

    Tseng, S. F.; Hsu, B. M.; Huang, K. H.; Hsiao, H. Y.; Kao, P. M.; Shen, S. M.; Tsai, H. F.; Chen, J. S.

    2012-04-01

    Salmonella spp. is classified to gram-negative bacterium and is one of the most important causal agents of waterborne diseases. The genus of Salmonella comprises more than 2,500 serotypes and its taxonomy is also very complicated. In tradition, the detection of Salmonella in environmental water samples by routines culture methods using selective media and characterization of suspicious colonies based on biochemical tests and serological assay are generally time and labor consuming. To overcome this disadvantage, it is desirable to use effective method which provides a higher discrimination and more rapid identification about Salmonella in environmental water. The aim of this study is to investigate the occurrence of Salmonella using novel procedures of detection method and to identify the serovars of Salmonella isolates from 157 surface water samples in Taiwan. The procedures include membrane filtration, non-selective pre-enrichment, selective enrichment of Salmonella, and then isolation of Salmonella strains by selective culture plates. The selective enrichment and culture plates were both detected by PCR. Finally, we used biochemical tests and serological assay to confirm the serovars of Salmonella and also used Pulsed-field gel electrophoresis (PFGE) to identify their sarovar catagories by the genetic pattern. In this study, 44 water samples (28%) were indentified as Salmonella. The 44 positive water samples by culture method were further identified as S. Agona(1/44), S. Albany (10/44), S. Bareilly (13/44),S. Choleraesuis (2/44),S. Derby (4/44),S. Isangi (3/44),S.Kedougou(3/44),S. Mbandaka(1/44),S.Newport (3/44), S. Oranienburg(1/44), S. Potsdam (1/44),S. Typhimurium (1/44), andS. Weltevreden(1/44) by PFGE. The presence of Salmonella in surface water indicates the possibility of waterborne transmission in drinking watershed if water is not adequately treated. Therefore, the authorities need to have operating systems that currently provide adequate source

  10. Test results of Salmonella typing by the NRLs-Salmonella in the Member States of the EU and the EnterNet Laboratories - Collaborative study VI on typing of Salmonella

    NARCIS (Netherlands)

    Korver H; Raes M; Maas HME; Ward LR; Wannet WJB; Henken AM; PHLS-Colindale/London; MGB; LIS

    2002-01-01

    Test results of Salmonella sero- and phage typing and antimicrobial susceptibility testing by the National Reference Laboratories for Salmonella in the Member States of the European Union and the EnterNet Laboratories: Collaborative study VI (2001) for Salmonella. The sixth collaborative typing

  11. Vaccines against invasive Salmonella disease

    Science.gov (United States)

    MacLennan, Calman A; Martin, Laura B; Micoli, Francesca

    2014-01-01

    Though primarily enteric pathogens, Salmonellae are responsible for a considerable yet under-appreciated global burden of invasive disease. In South and South-East Asia, this manifests as enteric fever caused by serovars Typhi and Paratyphi A. In sub-Saharan Africa, a similar disease burden results from invasive nontyphoidal Salmonellae, principally serovars Typhimurium and Enteritidis. The existing Ty21a live-attenuated and Vi capsular polysaccharide vaccines target S. Typhi and are not effective in young children where the burden of invasive Salmonella disease is highest. After years of lack of investment in new Salmonella vaccines, recent times have seen increased interest in the area led by emerging-market manufacturers, global health vaccine institutes and academic partners. New glycoconjugate vaccines against S. Typhi are becoming available with similar vaccines against other invasive serovars in development. With other new vaccines under investigation, including live-attenuated, protein-based and GMMA vaccines, now is an exciting time for the Salmonella vaccine field. PMID:24804797

  12. Thermal inactivation of eight Salmonella serotypes on dry corn flour.

    OpenAIRE

    VanCauwenberge, J E; Bothast, R J; Kwolek, W F

    1981-01-01

    Dry heat was used to inactivate Salmonella newington, Salmonella typhimurium, Salmonella anatum, Salmonella kentucky, Salmonella cubana, Salmonella seftenberg, Salmonella thompson, and Salmonella tennessee in corn flour at 10 and 15% moisture. The flour was spray inoculated at 10(5) Salmonella cells per g and then stored at 49 degrees C (120 degrees F); viable Salmonella cells were counted on Trypticase (BBL Microbiology Systems) soy agar plates every 30 min for the first 4 h and then at 4-h ...

  13. Incidence of non-typhoidal Salmonella in poultry products in the North West Province, South Africa

    Directory of Open Access Journals (Sweden)

    Roseline Y. Olobatoke

    2015-11-01

    Full Text Available This study was conducted to evaluate the incidence of non-typhoidal Salmonella (NTS serotypes in raw and ready-to-eat (RTE broiler products in the North West Province of South Africa. A total of 120 raw broiler samples, 40 samples of polonies and 20 samples of smoked viennas were obtained from retail points in major cities and towns in the province. Samples were subjected to aerobic plate count and later screened for the presence of NTS using phenotypic and genotypic techniques. The average bacterial count in raw products was 3.1 x 105 cfu/g whereas bacterial contamination of RTE products was 1.8 x 103 cfu/g. The average recovery rate of NTS species from raw broiler products was 12.5% and the serotypes identified were S. typhimurium (46.4%, S. enteritidis (30.9% and S. newport (22.9%. No NTS was recovered from the RTE products. However, S. typhimurium was the predominant serotype in whole carcasses whereas S. enteritidis and S. newport were prevalent in chicken parts. Out of the 160 presumptive NTS isolates screened by polymerase chain reaction (PCR, 140 (87.5% were confirmed for the presence of the Salmonella-specific invA gene. In addition, 115 (82.4% of the confirmed isolates harboured the plasmid spvC gene. Random Amplified Polymorphic DNA (RAPD fingerprinting of isolates using RAPD 1 and RAPD 3 primers, revealed some inter- and intra-serotype genetic diversity among isolates, suggesting varying sources of contamination. The results of this study represent the first report on the incidence and prevalent serotypes of NTS in chicken products in the North West Province of South Africa.

  14. Antimicrobial sensitivity pattern of Salmonella: comparison of isolates from HIV-infected and HIV-uninfected patients.

    Science.gov (United States)

    Wolday, D; Erge, W

    1998-07-01

    A retrospective analysis of all cases of Salmonella infections occurring between 1991 and 1995 was undertaken in order to evaluate the antimicrobial sensitivity pattern of the isolates from both human immunodeficiency virus (HIV) infected and uninfected Ethiopian patients. During the 5-year study period, we identified 147 cases of Salmonella infections. Only in 49 cases was the HIV serostatus known; 22 (44.9%) of the infections were in HIV seronegative patients while 27 (55.9%) were in HIV seropositive patients. The strains were isolated from blood (71.4%), urine (18.4%) and stool (8.2%). Salmonella infection was found to be more frequent (55.15% versus 44.9%) among HIV positive than HIV-negative patients. Moreover, Salmonella isolates recovered from HIV-seropositive patients were significantly resistant to many of the antibiotics tested when compared to the isolates from HIV-seronegative patients. The only chloramphenicol resistant Salmonella typhi occurred in a patient who was seropositive for HIV. According to these results, Ethiopian patients infected with HIV may be at risk of acquiring infections, especially non-typhoidal salmonellas, that are multi-drug resistant (MDR) strains than HIV-uninfected subjects. The emergence of MDR Salmonella infection among HIV-positive patients requires reassessment of chemotherapeutic approaches in this patient population, and warrants continued laboratory surveillance.

  15. Salmonella radicidation of poultry carcasses

    International Nuclear Information System (INIS)

    Mulder, R.W.A.W.

    1982-01-01

    This thesis reports investigations using gamma-radiation to decontaminate poultry carcasses. The application to foods of doses of ionizing radiation sufficient to reduce the number of viable specific non-sporeforming pathogenic microorganisms so that none is detectable in the treated food by any standard method is termed radicidation. The doses used in this study were at such a level that no undesirable or unfavourable side-effects occurred. The effects of these doses were studied on salmonellae and other microorganisms present in, or associated with poultry carcasses and in liquid and on solid culture media as well. Decimal reduction (D 10 ) values were estimated. These represent the dose (kGy) required to achieve a reduction in initial colony count from N 0 to 0.1 N 0 . Together with the estimation of the numbers of Salmonella present per carcass the data were used to predict the effect of an ionizing radiation treatment of poultry. Data on the effect of ionizing radiation on the total microflora of poultry carcasses were also collected. (Auth.)

  16. Spectrum of small mutations in the dystrophin coding region

    Energy Technology Data Exchange (ETDEWEB)

    Prior, T.W.; Bartolo, C.; Pearl, D.K. [Ohio State Univ., Columbus, OH (United States)] [and others

    1995-07-01

    Duchenne and Becker muscular dystrophies (DMD and BMD) are caused by defects in the dystrophin gene. About two-thirds of the affected patients have large deletions or duplications, which occur in the 5` and central portion of the gene. The nondeletion/duplication cases are most likely the result of smaller mutations that cannot be identified by current diagnostic screening strategies. We screened {approximately} 80% of the dystrophin coding sequence for small mutations in 158 patients without deletions or duplications and identified 29 mutations. The study indicates that many of the DMD and the majority of the BMD small mutations lie in noncoding regions of the gene. All of the mutations identified were unique to single patients, and most of the mutations resulted in protein truncation. We did not find a clustering of small mutations similar to the deletion distribution but found > 40% of the small mutations 3` of exon 55. The extent of protein truncation caused by the 3` mutations did not determine the phenotype, since even the exon 76 nonsense mutation resulted in the severe DMD phenotype. Our study confirms that the dystrophin gene is subject to a high rate of mutation in CpG sequences. As a consequence of not finding any hotspots or prevalent small mutations, we conclude that it is presently not possible to perform direct carrier and prenatal diagnostics for many families without deletions or duplications. 71 refs., 2 figs., 2 tabs.

  17. Interactions of Salmonella enterica Serovar Typhimurium and Pectobacterium carotovorum within a Tomato Soft Rot.

    Science.gov (United States)

    George, Andrée S; Cox, Clayton E; Desai, Prerak; Porwollik, Steffen; Chu, Weiping; de Moraes, Marcos H; McClelland, Michael; Brandl, Maria T; Teplitski, Max

    2018-03-01

    Salmonella spp. are remarkably adaptable pathogens, and this adaptability allows these bacteria to thrive in a variety of environments and hosts. The mechanisms with which these pathogens establish within a niche amid the native microbiota remain poorly understood. Here, we aimed to uncover the mechanisms that enable Salmonella enterica serovar Typhimurium strain ATCC 14028 to benefit from the degradation of plant tissue by a soft rot plant pathogen, Pectobacterium carotovorum The hypothesis that in the soft rot, the liberation of starch (not utilized by P. carotovorum ) makes this polymer available to Salmonella spp., thus allowing it to colonize soft rots, was tested first and proven null. To identify the functions involved in Salmonella soft rot colonization, we carried out transposon insertion sequencing coupled with the phenotypic characterization of the mutants. The data indicate that Salmonella spp. experience a metabolic shift in response to the changes in the environment brought on by Pectobacterium spp. and likely coordinated by the csrBC small regulatory RNA. While csrBC and flhD appear to be of importance in the soft rot, the global two-component system encoded by barA sirA (which controls csrBC and flhDC under laboratory conditions) does not appear to be necessary for the observed phenotype. Motility and the synthesis of nucleotides and amino acids play critical roles in the growth of Salmonella spp. in the soft rot. IMPORTANCE Outbreaks of produce-associated illness continue to be a food safety concern. Earlier studies demonstrated that the presence of phytopathogens on produce was a significant risk factor associated with increased Salmonella carriage on fruits and vegetables. Here, we genetically characterize some of the requirements for interactions between Salmonella and phytobacteria that allow Salmonella spp. to establish a niche within an alternate host (tomato). Pathways necessary for nucleotide synthesis, amino acid synthesis, and motility

  18. Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse

    Directory of Open Access Journals (Sweden)

    Lu Lu

    2010-11-01

    Full Text Available Abstract Background Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression in mammalian brain is globally regulated or locally regulated in diverse brain structures, and to study the genomic organisation of brain-expressed sex-biased genes, we performed a large scale gene expression analysis of distinct brain regions in adult male and female mice. Results This study revealed spatial specificity in sex-biased transcription in the mouse brain, and identified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampus and 31 in the eye. Genes located on sex chromosomes were consistently over-represented in all brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealed Y-encoded male-biased transcripts and X-encoded female-biased transcripts known to escape X-inactivation. In addition, we identified novel coding and non-coding X-linked genes with female-biased expression in multiple tissues. Interestingly, the chromosomal positions of all of the female-biased non-coding genes are in close proximity to protein-coding genes that escape X-inactivation. This defines X-chromosome domains each of which contains a coding and a non-coding female-biased gene. Lack of repressive chromatin marks in non-coding transcribed loci supports the possibility that they escape X-inactivation. Moreover, RNA-DNA combined FISH experiments confirmed the biallelic expression of one such novel domain. Conclusion This study demonstrated that the amount of genes with sex-biased expression varies between individual brain regions in mouse. The sex-biased genes identified are localized on many chromosomes. At the same time, sexually dimorphic gene expression that is common to several parts of the brain is mostly restricted to the sex chromosomes. Moreover, the study uncovered

  19. Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli.

    Science.gov (United States)

    Wang, Rui-Sheng; Jin, Guangxu; Zhang, Xiang-Sun; Chen, Luonan

    2009-04-29

    Transcriptional regulation is a fundamental process in biological systems, where transcription factors (TFs) have been revealed to play crucial roles. In recent years, in addition to TFs, an increasing number of non-coding RNAs (ncRNAs) have been shown to mediate post-transcriptional processes and regulate many critical pathways in both prokaryotes and eukaryotes. On the other hand, with more and more high-throughput biological data becoming available, it is possible and imperative to quantitatively study gene regulation in a systematic and detailed manner. Most existing studies for inferring transcriptional regulatory interactions and the activity of TFs ignore the possible post-transcriptional effects of ncRNAs. In this work, we propose a novel framework to infer the activity of regulators including both TFs and ncRNAs by exploring the expression profiles of target genes and (post)transcriptional regulatory relationships. We model the integrated regulatory system by a set of biochemical reactions which lead to a log-bilinear problem. The inference process is achieved by an iterative algorithm, in which two linear programming models are efficiently solved. In contrast to available related studies, the effects of ncRNAs on transcription process are considered in this work, and thus more reasonable and accurate reconstruction can be expected. In addition, the approach is suitable for large-scale problems from the viewpoint of computation. Experiments on two synthesized data sets and a model system of Escherichia coli (E. coli) carbon source transition from glucose to acetate illustrate the effectiveness of our model and algorithm. Our results show that incorporating the post-transcriptional regulation of ncRNAs into system model can mine the hidden effects from the regulation activity of TFs in transcription processes and thus can uncover the biological mechanisms in gene regulation in a more accurate manner. The software for the algorithm in this paper is available

  20. Long Non-coding RNAs in Response to Genotoxic Stress

    Institute of Scientific and Technical Information of China (English)

    Xiaoman Li; Dong Pan; Baoquan Zhao; Burong Hu

    2016-01-01

    Long non-coding RNAs(lncRNAs) are increasingly involved in diverse biological processes.Upon DNA damage,the DNA damage response(DDR) elicits a complex signaling cascade,which includes the induction of lncRNAs.LncRNA-mediated DDR is involved in non-canonical and canonical manners.DNA-damage induced lncRNAs contribute to the regulation of cell cycle,apoptosis,and DNA repair,thereby playing a key role in maintaining genome stability.This review summarizes the emerging role of lncRNAs in DNA damage and repair.

  1. Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus

    Directory of Open Access Journals (Sweden)

    Hakenbeck Regine

    2010-11-01

    Full Text Available Abstract Background Post-transcriptional regulation by small RNAs (sRNAs in bacteria is now recognized as a wide-spread regulatory mechanism modulating a variety of physiological responses including virulence. In Streptococcus pneumoniae, an important human pathogen, the first sRNAs to be described were found in the regulon of the CiaRH two-component regulatory system. Five of these sRNAs were detected and designated csRNAs for cia-dependent small RNAs. CiaRH pleiotropically affects β-lactam resistance, autolysis, virulence, and competence development by yet to be defined molecular mechanisms. Since CiaRH is highly conserved among streptococci, it is of interest to determine if csRNAs are also included in the CiaRH regulon in this group of organisms consisting of commensal as well as pathogenic species. Knowledge on the participation of csRNAs in CiaRH-dependent regulatory events will be the key to define the physiological role of this important control system. Results Genes for csRNAs were predicted in streptococcal genomes and data base entries other than S. pneumoniae by searching for CiaR-activated promoters located in intergenic regions that are followed by a transcriptional terminator. 61 different candidate genes were obtained specifying csRNAs ranging in size from 51 to 202 nt. Comparing these genes among each other revealed 40 different csRNA types. All streptococcal genomes harbored csRNA genes, their numbers varying between two and six. To validate these predictions, S. mitis, S. oralis, and S. sanguinis were subjected to csRNA-specific northern blot analysis. In addition, a csRNA gene from S. thermophilus plasmid pST0 introduced into S. pneumoniae was also tested. Each of the csRNAs was detected on these blots and showed the anticipated sizes. Thus, the method applied here is able to predict csRNAs with high precision. Conclusions The results of this study strongly suggest that genes for small non-coding RNAs, csRNAs, are part of

  2. A Case Report of Salmonella muenchen Enteritis Causing Rhabdomyolysis and Myocarditis in a Previously Healthy 26-Year-Old Man.

    Science.gov (United States)

    Chapple, Will; Martell, Jon; Wilson, Joy S; Matsuura, Don T

    2017-04-01

    This case report examines an unusual presentation of a non-typhoidal Salmonella serovar with limited prevalence in the literature. This is the first case report to associate specifically the Salmonella muenchen serovar with rhabdomyolysis and myocarditis. This case report reviews the diagnostic criteria for myocarditis and explores the diagnostic dilemma of troponin elevation in the setting of rhabdomyolysis. It demonstrates that Salmonella muenchen has the ability to present in a broad range of individuals with complications extending beyond classical gastrointestinal symptoms. This report also concludes that diagnosis of the many possible complications from non-typhoidal Salmonella infections can be difficult due to patient comorbidities, variability in the severity of the illnesses, laboratory test limitations, and imaging limitations. When a patient presents with elevated troponins in the setting of rhabdomyolysis a careful workup should be done to evaluate for ischemic causes, myocarditis, or false elevation secondary to rhabdomyolysis.

  3. Analysis of the baseline survey on the prevalence of Salmonella in holdings with breeding pigs in the EU, 2008

    DEFF Research Database (Denmark)

    Bole-Hribovšek, Vojislava; Chriél, Mariann; Davies, Robert

    Union was 54 and 88, respectively. Salmonella Derby and Salmonella Typhimurium predominated in both types of holdings. Breeding pigs may be an important source of dissemination of Salmonella throughout the pig-production chain. The results of this survey provide valuable information for setting......Salmonella is a major cause of food-borne illness in humans. Farm animals and foods of animal origin are important sources of human Salmonella infections. This European Union-wide Salmonella baseline survey was conducted in 2008 in holdings with breeding pigs. A total of 1,609 holdings housing...... and selling mainly breeding pigs (breeding holdings) and 3,508 holdings housing breeding pigs and selling mainly pigs for fattening or slaughter (production holdings) from 24 European Union Member States and two non-Member States, were randomly selected and included in the survey. In each selected breeding...

  4. Development of a 3D non-linear implicit MHD code

    International Nuclear Information System (INIS)

    Nicolas, T.; Ichiguchi, K.

    2016-06-01

    This paper details the on-going development of a 3D non-linear implicit MHD code, which aims at making possible large scale simulations of the non-linear phase of the interchange mode. The goal of the paper is to explain the rationale behind the choices made along the development, and the technical difficulties encountered. At the present stage, the development of the code has not been completed yet. Most of the discussion is concerned with the first approach, which utilizes cartesian coordinates in the poloidal plane. This approach shows serious difficulties in writing the preconditioner, closely related to the choice of coordinates. A second approach, based on curvilinear coordinates, also faced significant difficulties, which are detailed. The third and last approach explored involves unstructured tetrahedral grids, and indicates the possibility to solve the problem. The issue to domain meshing is addressed. (author)

  5. Prevalence of Salmonella spp., and serovars isolated from captive exotic reptiles in New Zealand.

    Science.gov (United States)

    Kikillus, K H; Gartrell, B D; Motion, E

    2011-07-01

    To investigate the prevalence of Salmonella spp. in captive exotic reptile species in New Zealand, and identify the serovars isolated from this population. Cloacal swabs were obtained from 378 captive exotic reptiles, representing 24 species, residing in 25 collections throughout New Zealand between 2008 and 2009. Samples were cultured for Salmonella spp., and suspected colonies were serotyped by the Institute of Environmental Science and Research (ESR). Forty-three of the 378 (11.4%) reptiles sampled tested positive for Salmonella spp., with 95% CI for the estimated true prevalence being 12-25% in exotic reptiles in this study population. Lizards tested positive for Salmonella spp. more often than chelonians. Agamid lizards tested positive more often than any other family group, with 95% CI for the estimated true prevalence being 56-100%.. Six Salmonella serovars from subspecies I and two from subspecies II were isolated. The serovar most commonly isolated was S. Onderstepoort (30.2%), followed by S. Thompson (20.9%), S. Potsdam (14%), S. Wangata (14%), S. Infantis (11.6%) and S. Eastbourne (2.3%). All of the subspecies I serovars have been previously reported in both reptiles and humans in New Zealand, and include serovars previously associated with disease in humans. This study showed that Salmonella spp. were commonly carried by exotic reptiles in the study population in New Zealand. Several serovars of Salmonella spp. with known pathogenicity to humans were isolated, including S. Infantis, which is one of the most common serovars isolated from both humans and non-human sources in New Zealand. The limitations of this study included the bias engendered by the need for voluntary involvement in the study, and the non-random sampling design. Based on the serovars identified in this and previous studies, it is recommended native and exotic reptiles be segregated within collections, especially when native reptiles may be used for biodiversity restoration

  6. Long Non-Coding RNAs Embedded in the Rb and p53 Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Subramanian, Murugan; Jones, Matthew F.; Lal, Ashish, E-mail: ashish.lal@nih.gov [Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (United States)

    2013-12-04

    In recent years, long non-coding RNAs (lncRNAs) have gained significant attention as a novel class of gene regulators. Although a small number of lncRNAs have been shown to regulate gene expression through diverse mechanisms including transcriptional regulation, mRNA splicing and translation, the physiological function and mechanism of action of the vast majority are not known. Profiling studies in cell lines and tumor samples have suggested a potential role of lncRNAs in cancer. Indeed, distinct lncRNAs have been shown to be embedded in the p53 and Rb networks, two of the major tumor suppressor pathways that control cell cycle progression and survival. Given the fact that inactivation of Rb and p53 is a hallmark of human cancer, in this review we discuss recent evidence on the function of lncRNAs in the Rb and p53 signaling pathways.

  7. Long Non-Coding RNAs Embedded in the Rb and p53 Pathways

    International Nuclear Information System (INIS)

    Subramanian, Murugan; Jones, Matthew F.; Lal, Ashish

    2013-01-01

    In recent years, long non-coding RNAs (lncRNAs) have gained significant attention as a novel class of gene regulators. Although a small number of lncRNAs have been shown to regulate gene expression through diverse mechanisms including transcriptional regulation, mRNA splicing and translation, the physiological function and mechanism of action of the vast majority are not known. Profiling studies in cell lines and tumor samples have suggested a potential role of lncRNAs in cancer. Indeed, distinct lncRNAs have been shown to be embedded in the p53 and Rb networks, two of the major tumor suppressor pathways that control cell cycle progression and survival. Given the fact that inactivation of Rb and p53 is a hallmark of human cancer, in this review we discuss recent evidence on the function of lncRNAs in the Rb and p53 signaling pathways

  8. Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions

    DEFF Research Database (Denmark)

    Lavstsen, Thomas; Salanti, Ali; Jensen, Anja T R

    2003-01-01

    and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence. METHODS: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains. RESULTS: var genes can be sub...

  9. Rapid detection of food-borne Salmonella contamination using IMBs-qPCR method based on pagC gene

    Directory of Open Access Journals (Sweden)

    Jiashun Wang

    Full Text Available Abstract Detection of Salmonella is very important to minimize the food safety risk. In this study, the recombinant PagC protein and PagC antibody were prepared and coupled with immunomagnetic beads (IMBs to capture Salmonella cells from pork and milk samples. And then the SYBR Green qualitative PCR was developed to detect the pathogenic Salmonella. The results showed that the PagC polyclonal antiserum is of good specificity and the capture rate of 0.1 mg IMBs for Salmonella tended to be stable at the range of 70-74% corresponding to the concentrations between 101 and 104 CFU/mL. The method developed demonstrated high specificity for the positive Salmonella samples when compared to non-specific DNA samples, such as Escherichia coli, Staphylococcus aureus, Yersinia enterocolitica, and Yersinia pseudotuberculosis. The limit of detection of this assay was 18 CFU/mL. Detection and quantitative enumeration of Salmonella in samples of pork or milk shows good recoveries of 54.34% and 52.07%. In conclusion, the polyclonal antibody of recombinant PagC protein is effective to capture Salmonella from detected samples. The developed pagC antibody IMBs-qPCR method showed efficiency, sensitivity and specificity for 30 Salmonella detection, enabling detection within 10 h, which is a promising rapid method to detect Salmonella in emergency.

  10. Assessment of Salmonella survival in dry-cured Italian salami.

    Science.gov (United States)

    Bonardi, S; Bruini, I; Bolzoni, L; Cozzolino, P; Pierantoni, M; Brindani, F; Bellotti, P; Renzi, M; Pongolini, S

    2017-12-04

    The inactivation of Salmonella during curing of Italian traditional pork salami was investigated. A total of 150 batches of ground raw meat (GRM) used for salami manufacturing by four producers were tested for Salmonella by real-time PCR followed by ISO 6579 cultural confirmation and MPN enumeration. Salami produced with Salmonella positive GRMs were re-tested at the end of their curing period. Aw, pH and NaCl content were also measured. Detection of Salmonella was performed testing both 25 and 50g of the samples. By Real-Time PCR 37% of the GRMs resulted positive, but cultural detection of Salmonella was obtained in 14% of the samples only. Salmonella enumeration ranged from 31 MPN/g to Salmonella in 100% of all positive samples, vs. 62% of ISO-25g. Salami made of the contaminated GRMs were 29% Salmonella-positive, as most batches of salami produced with Salmonella-positive GRMs resulted negative after regular curing (20-48days). Overall, 13% of salami produced with Salmonella-contaminated GRMs were positive. They belonged to six batches, which turned out negative after prolonged curing ranging between 49 and 86days. Salmonella enumeration in salami ranged from 8.7 MPN/g to Salmonella in cured salami (p value: >0.05). The most common Salmonella serovars in GRMs were Derby (52%), Typhimurium monophasic variant 4, (Barbuti et al., 1993), 12:i:- (19%) and Stanley (10%). Salmonella Derby (56%), London, Branderup, Panama (13%, respectively) and Goldcoast (6%) were most frequent in cured salami. The study showed negative correlation between real-time CT values and cultural confirmation of Salmonella, as well as the importance of sample size for Salmonella detection. Among considered factors with possible effect on the occurrence of Salmonella in salami, statistical analysis revealed a role for aw in salami and for Salmonella load in GRMs, while pH and NaCl content did not significantly affect the probability of finding Salmonella in dry-cured salami in the context of

  11. Autophagy Facilitates Salmonella Replication in HeLa Cells

    Science.gov (United States)

    Yu, Hong B.; Croxen, Matthew A.; Marchiando, Amanda M.; Ferreira, Rosana B. R.; Cadwell, Ken; Foster, Leonard J.; Finlay, B. Brett

    2014-01-01

    ABSTRACT Autophagy is a process whereby a double-membrane structure (autophagosome) engulfs unnecessary cytosolic proteins, organelles, and invading pathogens and delivers them to the lysosome for degradation. We examined the fate of cytosolic Salmonella targeted by autophagy and found that autophagy-targeted Salmonella present in the cytosol of HeLa cells correlates with intracellular bacterial replication. Real-time analyses revealed that a subset of cytosolic Salmonella extensively associates with autophagy components p62 and/or LC3 and replicates quickly, whereas intravacuolar Salmonella shows no or very limited association with p62 or LC3 and replicates much more slowly. Replication of cytosolic Salmonella in HeLa cells is significantly decreased when autophagy components are depleted. Eventually, hyperreplication of cytosolic Salmonella potentiates cell detachment, facilitating the dissemination of Salmonella to neighboring cells. We propose that Salmonella benefits from autophagy for its cytosolic replication in HeLa cells. PMID:24618251

  12. Salmonella er en sjælden årsag til meningitis hos nyfødte

    DEFF Research Database (Denmark)

    Jensen, Lotte; Hoffmann, Thomas; Knudsen, Inge Jenny Dahl

    2013-01-01

    In developed countries, invasive disease caused by non typhoidal Salmonella spp. is rare. Here we present a Danish case of Salmonella enterica serovar Enteritidis (S. Enteritidis) meningitis in an infant who had no underlying diseases. The child had had no known expositions, and the source...... of the infection was never identified. The chance of finding uncommon microorganisms as cause of invasive infections such as meningitis and the choice of initial empiric antimicrobial treatments is discussed....

  13. A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

    Directory of Open Access Journals (Sweden)

    Timothy T Perkins

    2009-07-01

    Full Text Available High-density, strand-specific cDNA sequencing (ssRNA-seq was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi. By mapping sequence data to the entire S. Typhi genome, we analyzed the transcriptome in a strand-specific manner and further defined transcribed regions encoded within prophages, pseudogenes, previously un-annotated, and 3'- or 5'-untranslated regions (UTR. An additional 40 novel candidate non-coding RNAs were identified beyond those previously annotated. Proteomic analysis was combined with transcriptome data to confirm and refine the annotation of a number of hpothetical genes. ssRNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome.

  14. Confinement of Reinforced-Concrete Columns with Non-Code Compliant Confining Reinforcement plus Supplemental Pen-Binder

    Directory of Open Access Journals (Sweden)

    Anang Kristianto

    2012-11-01

    Full Text Available One of the important requirements for earthquake resistant building related to confinement is the use of seismic hooks in the hoop or confining reinforcement of reinforced-concrete column elements. However, installation of a confining reinforcement with a 135-degree hook is not easy. Therefore, in practice, many construction workers apply a confining reinforcement with a 90-degreehook (non-code compliant. Based on research and records of recent earthquakes in Indonesia, the use of a non-code compliant confining reinforcement for concrete columns produces structures with poor seismic performance. This paper presents a study that introduces an additional element that is expected to improve the effectiveness of concrete columns confined with a non-code compliant confining reinforcement. The additional element, named a pen-binder, is used to keep the non-code compliant confining reinforcement in place. The effectiveness of this element under pure axial concentric loading was investigatedcomprehensively.The specimens tested in this study were 18 concrete columns,with a cross-section of 170 mm x 170 mm and a height of 480 mm. The main test variables were the material type of the pen-binder, the angle of the hook, and the confining reinforcement configuration.The test results indicate that adding pen-binders can effectively improve the strength and ductility of the column specimens confined with a non-code compliant confining reinforcement

  15. Organoid and Enteroid Modeling of Salmonella Infection

    Directory of Open Access Journals (Sweden)

    Yuebang Yin

    2018-04-01

    Full Text Available Salmonella are Gram-negative rod-shaped facultative anaerobic bacteria that are comprised of over 2,000 serovars. They cause gastroenteritis (salmonellosis with headache, abdominal pain and diarrhea clinical symptoms. Salmonellosis brings a heavy burden for the public health in both developing and developed countries. Antibiotics are usually effective in treating the infected patients with severe gastroenteritis, although antibiotic resistance is on the rise. Understanding the molecular mechanisms of Salmonella infection is vital to combat the disease. In vitro immortalized 2-D cell lines, ex vivo tissues/organs and several animal models have been successfully utilized to study Salmonella infections. Although these infection models have contributed to uncovering the molecular virulence mechanisms, some intrinsic shortcomings have limited their wider applications. Notably, cell lines only contain a single cell type, which cannot reproduce some of the hallmarks of natural infections. While ex vivo tissues/organs alleviate some of these concerns, they are more difficult to maintain, in particular for long term experiments. In addition, non-human animal models are known to reflect only part of the human disease process. Enteroids and induced intestinal organoids are emerging as effective infection models due to their closeness in mimicking the infected tissues/organs. Induced intestinal organoids are derived from iPSCs and contain mesenchymal cells whereas enteroids are derive from intestinal stem cells and are comprised of epithelial cells only. Both enteroids and induced intestinal organoids mimic the villus and crypt domains comparable to the architectures of the in vivo intestine. We review here that enteroids and induced intestinal organoids are emerging as desired infection models to study bacterial-host interactions of Salmonella.

  16. Investigations of sensitivity to antibiotics of salmonella strain species originating from poultry from different epizootiological areas

    Directory of Open Access Journals (Sweden)

    Stošić Zorica

    2006-01-01

    Full Text Available A total of 1666 samples were examined, of which 512 samples of parenchymatous organs of dead or deliberately sacrtificed animals, 60 samples of non-hatched fertilized eggs, 202 samples of feces, 652 samples of cloacal smears, 221 samples of smears from walls of maintenance objects, incubator stations, and transport vehicles, 19 samples of beddings and shavings. The samples originated from poultry farms and which were taken to a laboratory immediately on sampling and sown the same day. A total of 104 strains of Salmonella were isolated: 94 strains from samples of parenchymatous organs of dead chicks, 1 strain from non-hatched eggs, 3 strains from feces samples, 1 strain from samples of cloacal smears, 4 strains from samples of surface smears of maintenance objects and transport vehicles, and 1 strain from samples of beddings and shavings. Serological typization established the presence of the following serovarieties: Salmonella Enteritidis 79 strains, Salmonella Hartford 17 strains, Salmonella Typohimurium 5 strains, Salmonella Mbandaka 2 strains, and Salmonella Glostrup 1 strain. We examined the sensitivity of Salmonella strains to ampicillin, amoxicillin, gentamycin, streptomycin, neomycin, enrofloxacine, norfloxacine, flumequin, erythromycin, lincospectin, colistin, fluorphenicol, and a combination of sulphamethoxasole and trimethoprim. In S. Enteritidis strains, no resistence was established to colistin, fluorphenicol and sulphamethoxasole+trimethoprim, in fact, the sensitivity to these antibiotics and chemotherapeutics was 100%. Prevalence resitence of 0.96%, in only one strain, was established for enrofloxacine. A high prevalence resistence of 33.6% was established for neomycin, while prevalence resistence of 3.86% was established for the related aminoglycozide antibiotic gentamycin. The highest prevalence resistance in S.Hartford strains was established for erythromycin, 15.38%, and streptomycin, 7.6%. Resistence of S. Tyohimurium was

  17. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus

    DEFF Research Database (Denmark)

    tang, T. H.; Polacek, N.; Zywicki, M.

    2005-01-01

    By generating a specialized cDNA library from the archaeon Sulfolobus solfataricus, we have identified 57 novel small non-coding RNA (ncRNA) candidates and confirmed their expression by Northern blot analysis. The majority was found to belong to one of two classes, either antisense or antisense...... elements by inhibiting expression of the transposase mRNA. Surprisingly, the class of antisense RNAs also contained RNAs complementary to tRNAs or sRNAs (small-nucleolar-like RNAs). For the antisense-box ncRNAs, the majority could be assigned to the class of C/D sRNAs, which specify 2'-O-methylation sites...... on rRNAs or tRNAs. Five C/D sRNAs of this group are predicted to target methylation at six sites in 13 different tRNAs, thus pointing to the widespread role of these sRNA species in tRNA modification in Archaea. Another group of antisense-box RNAs, lacking typical C/D sRNA motifs, was predicted...

  18. Immune-based Therapies for Non-small Cell Lung Cancer.

    Science.gov (United States)

    Rafei, Hind; El-Bahesh, Ehab; Finianos, Antoine; Nassereddine, Samah; Tabbara, Imad

    2017-02-01

    Lung cancer is the leading cause of cancer-related death worldwide. Treatment of non-small cell lung cancer has evolved tremendously over the past decade. Specifically, immune checkpoint inhibitors have become an increasingly interesting target of pharmacological blockade. These immune inhibitors have shown promising results in front-line therapy and after failure of multiple lines, as well as in monotherapy and combination with other therapies. Vaccination in non-small cell lung cancer is also an emerging field of research that holds promising results for the future of immunotherapy in non-small cell lung cancer. This review presents a concise update on the most recent data regarding the role of checkpoint inhibitors as well as vaccination in non-small cell lung cancer. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  19. Study of Salmonella Typhimurium infection in laying hens

    Directory of Open Access Journals (Sweden)

    Kapil eChousalkar

    2016-02-01

    Full Text Available Members of Salmonella enterica are frequently involved in egg and egg product related human food poisoning outbreaks worldwide. In Australia, Salmonella Typhimurium is frequently involved in egg and egg product related foodborne illness and Salmonella Mbandaka has also been found to be a contaminant of the layer farm environment. The ability possessed by Salmonella Enteritidis to colonise reproductive organs and contaminate developing eggs has been well described. However, there are few studies investigating this ability for Salmonella Typhimurium. The hypothesis of this study was that the Salmonella Typhimurium can colonise the gut for a prolonged period of time and that horizontal infection through feces is the main route of egg contamination. At 14 weeks of age hens were orally infected with either S. Typhimurium PT 9 or S. Typhimurium PT 9 and Salmonella Mbandaka. Salmonella shedding in feces and eggs was monitored for 15 weeks post infection. Egg shell surface and internal contents of eggs laid by infected hens were cultured independently for detection of Salmonella spp. The mean Salmonella load in feces ranged from 1.54 to 63.35 and 0.31 to 98.38 most probable number/g (MPN/g in the S. Typhimurium and S. Typhimurium + S. Mbandaka group respectively. No correlation was found between mean fecal Salmonella load and frequency of egg shell contamination. Egg shell contamination was higher in S. Typhimurium + S. Mbandaka infected group (7.2% Typhimurium, 14.1% Mbandaka compared to birds infected with S. Typhimurium (5.66% however, co-infection had no significant impact on egg contamination by S. Typhimurium. Throughout the study Salmonella was not recovered from internal contents of eggs laid by hens. Salmonella was isolated from different segments of oviduct of hens from both the groups, however pathology was not observed on microscopic examination. This study investigated Salmonella shedding for up to 15 weeks p.i which is a longer period of

  20. A comparison of transmission characteristics of Salmonella enterica serovar Enteritidis between pair-housed and group-housed laying hens

    Directory of Open Access Journals (Sweden)

    Thomas Ekelijn

    2011-02-01

    Full Text Available Abstract Human cases of bacterial gastro-enteritis are often caused by the consumption of eggs contaminated with Salmonella species, mainly Salmonella enterica serovar Enteriditis (Salmonella Enteritidis. To reduce human exposure, in several countries worldwide surveillance programmes are implemented to detect colonized layer flocks. The sampling schemes are based on the within-flock prevalence, and, as this changes over time, knowledge of the within-flock dynamics of Salmonella Enteritidis is required. Transmission of Salmonella Enteritidis has been quantified in pairs of layers, but the question is whether the dynamics in pairs is comparable to transmission in large groups, which are more representative for commercial layer flocks. The aim of this study was to compare results of transmission experiments between pairs and groups of laying hens. Experimental groups of either 2 or 200 hens were housed at similar densities, and 1 or 4 hens were inoculated with Salmonella Enteritidis, respectively. Excretion was monitored by regularly testing of fecal samples for the presence of Salmonella Enteritidis. Using mathematical modeling, the group experiments were simulated with transmission parameter estimates from the pairwise experiments. Transmission of the bacteria did not differ significantly between pairs or groups. This finding suggests that the transmission parameter estimates from small-scale experiments might be extrapolated to the field situation.

  1. Culling decisions of dairy farmers during a 3-year Salmonella control study

    DEFF Research Database (Denmark)

    Nielsen, Liza Rosenbaum; Dohoo, I.

    2011-01-01

    Dublin which is the most prevalent and most persistent serotype in the Danish cattle population. A field study in 10 dairy herds with persistent Salmonella infections was carried out over three years to gain experience with control procedures including risk assessment, targeted control actions and test...... animals into risk groups. These risk groups and all individual ELISA-results were communicated to the farmers as colour-coded lists four to six times per year. Farmers were advised to manage the risk of Salmonella transmission from cattle with repeatedly high ELISA results (flagged as “red”) or cows...... if animals with red and yellow flags had higher probability of being slaughtered or sold before first calving than animals without any risk flags. For adult cows a semi-parametric proportional hazard survival model was used to test the effect of number of red and yellow flags on hazards of culling...

  2. Salmonella enterica serovar Typhimurium lacking hfq gene confers protective immunity against murine typhoid.

    Directory of Open Access Journals (Sweden)

    Uday Shankar Allam

    Full Text Available Salmonella enterica is an important enteric pathogen and its various serovars are involved in causing both systemic and intestinal diseases in humans and domestic animals. The emergence of multidrug-resistant strains of Salmonella leading to increased morbidity and mortality has further complicated its management. Live attenuated vaccines have been proven superior over killed or subunit vaccines due to their ability to induce protective immunity. Of the various strategies used for the generation of live attenuated vaccine strains, focus has gradually shifted towards manipulation of virulence regulator genes. Hfq is a RNA chaperon which mediates the binding of small RNAs to the mRNA and assists in post-transcriptional gene regulation in bacteria. In this study, we evaluated the efficacy of the Salmonella Typhimurium Δhfq strain as a candidate for live oral vaccine in murine model of typhoid fever. Salmonella hfq deletion mutant is highly attenuated in cell culture and animal model implying a significant role of Hfq in bacterial virulence. Oral immunization with the Salmonella hfq deletion mutant efficiently protects mice against subsequent oral challenge with virulent strain of Salmonella Typhimurium. Moreover, protection was induced upon both multiple as well as single dose of immunizations. The vaccine strain appears to be safe for use in pregnant mice and the protection is mediated by the increase in the number of CD4(+ T lymphocytes upon vaccination. The levels of serum IgG and secretory-IgA in intestinal washes specific to lipopolysaccharide and outer membrane protein were significantly increased upon vaccination. Furthermore, hfq deletion mutant showed enhanced antigen presentation by dendritic cells compared to the wild type strain. Taken together, the studies in murine immunization model suggest that the Salmonella hfq deletion mutant can be a novel live oral vaccine candidate.

  3. Long Non-Coding RNAs in Metabolic Organs and Energy Homeostasis

    Directory of Open Access Journals (Sweden)

    Maude Giroud

    2017-11-01

    Full Text Available Single cell organisms can surprisingly exceed the number of human protein-coding genes, which are thus not at the origin of the complexity of an organism. In contrast, the relative amount of non-protein-coding sequences increases consistently with organismal complexity. Moreover, the mammalian transcriptome predominantly comprises non-(protein-coding RNAs (ncRNA, of which the long ncRNAs (lncRNAs constitute the most abundant part. lncRNAs are highly species- and tissue-specific with very versatile modes of action in accordance with their binding to a large spectrum of molecules and their diverse localization. lncRNAs are transcriptional regulators adding an additional regulatory layer in biological processes and pathophysiological conditions. Here, we review lncRNAs affecting metabolic organs with a focus on the liver, pancreas, skeletal muscle, cardiac muscle, brain, and adipose organ. In addition, we will discuss the impact of lncRNAs on metabolic diseases such as obesity and diabetes. In contrast to the substantial number of lncRNA loci in the human genome, the functionally characterized lncRNAs are just the tip of the iceberg. So far, our knowledge concerning lncRNAs in energy homeostasis is still in its infancy, meaning that the rest of the iceberg is a treasure chest yet to be discovered.

  4. Comparing validation of four ELISAsystems for detection of Salmonella Derby- and Salmonella Infantis-infected pigs

    OpenAIRE

    Rösler, Uwe; Szabo, Istvan; Matthies, Claudia; Albrecht, Kerstin; Leffler, Kerstin; Scherer, Kathrin; Nöckler, Karsten; Lehmann, Jörg; Methner, Ulrich; Hensel, Andreas

    2018-01-01

    The objective of this study was the comparative evaluation of four indirect Salmonella ELISA tests at study time approved in Germany to detect Salmonella infection in pigs. Three tests are based on a LPS-antigen mix and directed against specific IgG antibodies. The fourth test is based on a purified S. Typhimurium whole-cell lysate antigen and discriminates between Salmonella-specific IgM-, IgA-, and IgG- antibodies. In a longitudinal study, two groups of six weeks old hybrid piglets were ...

  5. Coding chaotic billiards: I-Non-Compact billiards on a negative curvature manifold

    International Nuclear Information System (INIS)

    Giannoni, M.J.; Ullmo, D.

    1989-03-01

    This paper presents a method for coding billiards. The main device is to use a proper surface of section, the bounce mapping, and foliate the reduced phase space into regions associated with a given code. The alphabet is merely the ensemble of the labels of the sides of the billiard. The procedure is applied here to non-compact polygonal billiard defined on a manifold of constant negative curvature, with all vertices at infinity. A simple grammar rule is necessary and sufficient to insure existence and uniqueness of the coding

  6. Prevalence and antibiotic resistance of Salmonella Enteritidis and Salmonella Typhimurium in raw chicken meat at retail markets in Malaysia.

    Science.gov (United States)

    Thung, T Y; Mahyudin, N A; Basri, D F; Wan Mohamed Radzi, C W J; Nakaguchi, Y; Nishibuchi, M; Radu, S

    2016-08-01

    Salmonellosis is one of the major food-borne diseases in many countries. This study was carried out to determine the occurrence of Salmonella spp., Salmonella Enteritidis, and Salmonella Typhimurium in raw chicken meat from wet markets and hypermarkets in Selangor, as well as to determine the antibiotic susceptibility profile of S. Enteritidis and S. Typhimurium. The most probable number (MPN) in combination with multiplex polymerase chain reaction (mPCR) method was used to quantify the Salmonella spp., S. Enteritidis, and S. Typhimurium in the samples. The occurrence of Salmonella spp., S. Enteritidis, and S. Typhimurium in 120 chicken meat samples were 20.80%, 6.70%, and 2.50%, respectively with estimated quantity varying from retail chicken meat could be a source of multiple antimicrobial-resistance Salmonella and may constitute a public health concern in Malaysia. © 2016 Poultry Science Association Inc.

  7. Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Krause, Michael; Josefsen, Mathilde Hartmann

    2009-01-01

    of the published PCR methods for Salmonella have been validated in collaborative studies. This study describes a validation including comparative and collaborative trials, based on the recommendations from the Nordic organization for validation of alternative microbiological methods (NordVal) of a same-day, non....... Partly based on results obtained in this study, the method has obtained NordVal approval for analysis of Salmonella in meat and carcass swabs. The PCR method was transferred to a production laboratory and the performance was compared with the BAX Salmonella test on 39 pork samples artificially...... contaminated with Salmonella. There was no significant difference in the results obtained by the two methods. Conclusion: The real-time PCR method for detection of Salmonella in meat and carcass swabs was validated in comparative and collaborative trials according to NordVal recommendations. The PCR method...

  8. Non-coding RNAs and epigenome: de novo DNA methylation, allelic exclusion and X-inactivation

    Directory of Open Access Journals (Sweden)

    V. A. Halytskiy

    2013-12-01

    Full Text Available Non-coding RNAs are widespread class of cell RNAs. They participate in many important processes in cells – signaling, posttranscriptional silencing, protein biosynthesis, splicing, maintenance of genome stability, telomere lengthening, X-inactivation. Nevertheless, activity of these RNAs is not restricted to posttranscriptional sphere, but cover also processes that change or maintain the epigenetic information. Non-coding RNAs can directly bind to the DNA targets and cause their repression through recruitment of DNA methyltransferases as well as chromatin modifying enzymes. Such events constitute molecular mechanism of the RNA-dependent DNA methylation. It is possible, that the RNA-DNA interaction is universal mechanism triggering DNA methylation de novo. Allelic exclusion can be also based on described mechanism. This phenomenon takes place, when non-coding RNA, which precursor is transcribed from one allele, triggers DNA methylation in all other alleles present in the cell. Note, that miRNA-mediated transcriptional silencing resembles allelic exclusion, because both miRNA gene and genes, which can be targeted by this miRNA, contain elements with the same sequences. It can be assumed that RNA-dependent DNA methylation and allelic exclusion originated with the purpose of counteracting the activity of mobile genetic elements. Probably, thinning and deregulation of the cellular non-coding RNA pattern allows reactivation of silent mobile genetic elements resulting in genome instability that leads to ageing and carcinogenesis. In the course of X-inactivation, DNA methylation and subsequent hete­rochromatinization of X chromosome can be triggered by direct hybridization of 5′-end of large non-coding RNA Xist with DNA targets in remote regions of the X chromosome.

  9. Effect of vaccinating breeder chickens with a killed Salmonella vaccine on Salmonella prevalences and loads in breeder and broiler chicken flocks.

    Science.gov (United States)

    Berghaus, R D; Thayer, S G; Maurer, J J; Hofacre, C L

    2011-05-01

    The objective of this study was to evaluate the effect of vaccination of breeder chickens on Salmonella prevalences and loads in breeder and broiler chicken flocks. Chickens housed on six commercial breeder farms were vaccinated with a killed Salmonella vaccine containing Salmonella Typhimurium, Salmonella Enteritidis, and Salmonella Kentucky. Unvaccinated breeders placed on six additional farms served as controls. Eggs from vaccinated and unvaccinated breeder flocks were kept separately in the hatchery, and the resulting chicks were used to populate 58 commercial broiler flock houses by using a pair-matched design. Vaccinated breeder flocks had significantly higher Salmonella-specific antibody titers than did the unvaccinated breeder flocks, although they did not differ significantly with respect to environmental Salmonella prevalences or loads. Broiler flocks that were the progeny of vaccinated breeders had significantly lower Salmonella prevalences and loads than broiler flocks that were the progeny of unvaccinated breeders. After adjusting for sample type and clustering at the farm level, the odds of detecting Salmonella in samples collected from broiler flocks originating from vaccinated breeders were 62% lower (odds ratio [95% confidence interval] = 0.38 [0.21, 0.68]) than in flocks from unvaccinated breeders. In addition, the mean load of culture-positive samples was lower in broilers from vaccinated breeders by 0.30 log most probable number per sample (95% confidence interval of -0.51, -0.09; P = 0.004), corresponding to a 50% decrease in Salmonella loads. In summary, vaccination of broiler breeder pullets increased humoral immunity in the breeders and reduced Salmonella prevalences and loads in their broiler progeny, but did not significantly decrease Salmonella in the breeder farm environment.

  10. Salmonella-secreted Virulence Factors

    Energy Technology Data Exchange (ETDEWEB)

    Heffron, Fred; Niemann, George; Yoon, Hyunjin; Kidwai, Afshan S.; Brown, Roslyn N.; McDermott, Jason E.; Smith, Richard D.; Adkins, Joshua N.

    2011-05-01

    In this short review we discuss secreted virulence factors of Salmonella, which directly affect Salmonella interaction with its host. Salmonella secretes protein to subvert host defenses but also, as discussed, to reduce virulence thereby permitting the bacteria to persist longer and more successfully disperse. The type III secretion system (TTSS) is the best known and well studied of the mechanisms that enable secretion from the bacterial cytoplasm to the host cell cytoplasm. Other secretion systems include outer membrane vesicles, which are present in all Gram-negative bacteria examined to date, two-partner secretion, and type VI secretion will also be addressed. Excellent reviews of Salmonella secreted effectors have focused on themes such as actin rearrangements, vesicular trafficking, ubiquitination, and the activities of the virulence factors themselves. This short review is based on S. Typhimurium infection of mice because it is a model of typhoid like disease in humans. We have organized effectors in terms of events that happen during the infection cycle and how secreted effectors may be involved.

  11. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences.

    LENUS (Irish Health Repository)

    Ivanov, Ivaylo P

    2011-05-01

    In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5\\' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized--both for increased coding capacity and potentially also for novel regulatory mechanisms--remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5\\' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.

  12. Test results of Salmonella typing by the National Reference Laboratories for Salmonella in the Member States of the European Union and the EnterNet Laboratories - Collaborative study VII on typing of Salmonella

    NARCIS (Netherlands)

    Korver H; Maas HME; Ward LR; Wannet WJB; Henken AM; MGB; LIS

    2003-01-01

    Het Communautair Referentie Laboratorium voor Salmonella (CRL-Salmonella, Bilthoven, Nederland) organiseerde in samenwerking met Public Health Laboratory Services (PHLS), London, Verenigd Koninkrijk een zevende ringonderzoek aangaande de typering van Salmonella. Zeventien Nationale Referentie

  13. Similarities between Salmonella Enteritidis isolated from humans and captive wild animals in South Africa.

    Science.gov (United States)

    Smith, Anthony M; Ismail, Husna; Henton, Maryke M; Keddy, Karen H

    2014-12-15

    Salmonella is well recognized as an aetiological agent of gastrointestinal and diarrhoeal disease. Salmonella enterica serotype Enteritidis (Salmonella Enteritidis) is one of the commonest serotypes associated with foodborne illness. In South Africa, we compared Salmonella Enteritidis strains isolated from humans with gastroenteritis and strains isolated from captive wild animals, between June 2011 and July 2012. Bacteria were phenotypically characterized using standard microbiological techniques. Genotypic relatedness of isolates was investigated by pulsed-field gel electrophoresis (PFGE) analysis. a diversity of 27 PFGE patterns amongst 196 human non-invasive isolates was shown; two PFGE patterns predominated and accounted for 74% of all human isolates. Human isolates showed a 12% prevalence rate for nalidixic acid resistance. Animal isolates from 5 different sources were investigated. With the exception of an isolate from a ground hornbill, all animal isolates (jaguar, crocodile, lion and poultry) showed PFGE pattern matches to a human isolate. Animal isolates showed susceptibility to all antimicrobial agents tested, with the exception of nalidixic acid resistance in isolates from the lion and poultry source. Our data showed similarities between Salmonella Enteritidis strains isolated from humans and captive wild animals, suggesting a probable common source for strains from humans and animals.

  14. The Salmonella enterica Pan-genome

    DEFF Research Database (Denmark)

    Jacobsen, Annika; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2011-01-01

    Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22......, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst...... there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection...

  15. Salmonella Control Programs in Denmark

    DEFF Research Database (Denmark)

    Wegener, Henrik Caspar; Hald, Tine; Wong, Danilo Lo Fo

    2003-01-01

    We describe Salmonella control programs of broiler chickens, layer hens, and pigs in Denmark. Major reductions in the incidence of foodborne human salmonellosis have occurred by integrated control of farms and food processing plants. Disease control has been achieved by monitoring the herds...... and flocks, eliminating infected animals, and diversifying animals (animals and products are processed differently depending on Salmonella status) and animal food products according to the determined risk. In 2001, the Danish society saved U.S.$25.5 million by controlling Salmonella. The total annual...... Salmonella control costs in year 2001 were U.S.$14.1 million (U.S.$0.075/kg of pork and U.S.$0.02/kg of broiler or egg). These costs are paid almost exclusively by the industry. The control principles described are applicable to most industrialized countries with modern intensive farming systems....

  16. Interaction of Saccharomyces boulardii with Salmonella enterica serovar Typhimurium protects mice and modifies T84 cell response to the infection.

    Directory of Open Access Journals (Sweden)

    Flaviano S Martins

    Full Text Available BACKGROUND: Salmonella pathogenesis engages host cells in two-way biochemical interactions: phagocytosis of bacteria by recruitment of cellular small GTP-binding proteins induced by the bacteria, and by triggering a pro-inflammatory response through activation of MAPKs and nuclear translocation of NF-kappaB. Worldwide interest in the use of functional foods containing probiotic bacteria for health promotion and disease prevention has increased significantly. Saccharomyces boulardii is a non-pathogenic yeast used as a probiotic in infectious diarrhea. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we reported that S. boulardii (Sb protected mice from Salmonella enterica serovar Typhimurium (ST-induced death and prevented bacterial translocation to the liver. At a molecular level, using T84 human colorectal cancer cells, we demonstrate that incubation with Sb before infection totally abolished Salmonella invasion. This correlates with a decrease of activation of Rac1. Sb preserved T84 barrier function and decreased ST-induced IL-8 synthesis. This anti-inflammatory effect was correlated with an inhibitory effect of Sb on ST-induced activation of the MAPKs ERK1/2, p38 and JNK as well as on activation of NF-kappaB. Electron and confocal microscopy experiments showed an adhesion of bacteria to yeast cells, which could represent one of the mechanisms by which Sb exerts its protective effects. CONCLUSIONS: Sb shows modulating effects on permeability, inflammation, and signal transduction pathway in T84 cells infected by ST and an in vivo protective effect against ST infection. The present results also demonstrate that Sb modifies invasive properties of Salmonella.

  17. Interaction of Saccharomyces boulardii with Salmonella enterica Serovar Typhimurium Protects Mice and Modifies T84 Cell Response to the Infection

    Science.gov (United States)

    Martins, Flaviano S.; Dalmasso, Guillaume; Arantes, Rosa M. E.; Doye, Anne; Lemichez, Emmanuel; Lagadec, Patricia; Imbert, Veronique; Peyron, Jean-François; Rampal, Patrick; Nicoli, Jacques R.; Czerucka, Dorota

    2010-01-01

    Background Salmonella pathogenesis engages host cells in two-way biochemical interactions: phagocytosis of bacteria by recruitment of cellular small GTP-binding proteins induced by the bacteria, and by triggering a pro-inflammatory response through activation of MAPKs and nuclear translocation of NF-κB. Worldwide interest in the use of functional foods containing probiotic bacteria for health promotion and disease prevention has increased significantly. Saccharomyces boulardii is a non-pathogenic yeast used as a probiotic in infectious diarrhea. Methodology/Principal Findings In this study, we reported that S. boulardii (Sb) protected mice from Salmonella enterica serovar Typhimurium (ST)-induced death and prevented bacterial translocation to the liver. At a molecular level, using T84 human colorectal cancer cells, we demonstrate that incubation with Sb before infection totally abolished Salmonella invasion. This correlates with a decrease of activation of Rac1. Sb preserved T84 barrier function and decreased ST-induced IL-8 synthesis. This anti-inflammatory effect was correlated with an inhibitory effect of Sb on ST-induced activation of the MAPKs ERK1/2, p38 and JNK as well as on activation of NF-κB. Electron and confocal microscopy experiments showed an adhesion of bacteria to yeast cells, which could represent one of the mechanisms by which Sb exerts its protective effects. Conclusions Sb shows modulating effects on permeability, inflammation, and signal transduction pathway in T84 cells infected by ST and an in vivo protective effect against ST infection. The present results also demonstrate that Sb modifies invasive properties of Salmonella. PMID:20111723

  18. Rapid detection of salmonella using SERS with silver nano-substrate

    Science.gov (United States)

    Sundaram, J.; Park, B.; Hinton, A., Jr.; Windham, W. R.; Yoon, S. C.; Lawrence, K. C.

    2011-06-01

    Surface Enhanced Raman Scattering (SERS) can detect the pathogen in rapid and accurate. In SERS weak Raman scattering signals are enhanced by many orders of magnitude. In this study silver metal with biopolymer was used. Silver encapsulated biopolymer polyvinyl alcohol nano-colloid was prepared and deposited on stainless steel plate. This was used as metal substrate for SERS. Salmonella typhimurium a common food pathogen was selected for this study. Salmonella typhimurium bacteria cells were prepared in different concentrations in cfu/mL. Small amount of these cells were loaded on the metal substrate individually, scanned and spectra were recorded using confocal Raman microscope. The cells were exposed to laser diode at 785 nm excitation and object 50x was used to focus the laser light on the sample. Raman shifts were obtained from 400 to 2400 cm-1. Multivariate data analysis was carried to predict the concentration of unknown sample using its spectra. Concentration prediction gave an R2 of 0.93 and standard error of prediction of 0.21. The results showed that it could be possible to find out the Salmonella cells present in a low concentration in food samples using SERS.

  19. Erlotinib in previously treated non-small-cell lung cancer

    International Nuclear Information System (INIS)

    Smrdel, U.; Kovac, V.

    2006-01-01

    Background. Erlotinib is a novel biological anti-tumour agent in the treatment of advanced non small cell lung cancer. It represents the molecularly-targeted therapy which has been studied extensively. Case report. We present a case of a patient who suffered from advanced non-small-cell lung cancer. After the progress of disease following a prior chemotherapy he was treated with erlotinib with remarkable effect which was shown at chest x ray and symptoms were quite reduced. Conclusions. In selected patients with advanced non-small-cell lung cancer Erlotinib improves survival and symptom control as it results in presented case. (author)

  20. Flow cytometry for rapid detection of Salmonella spp. in seed sprouts

    Directory of Open Access Journals (Sweden)

    Bledar Bisha

    2014-12-01

    Full Text Available Seed sprouts (alfalfa, mung bean, radish, etc. have been implicated in several recent national and international outbreaks of salmonellosis. Conditions used for sprouting are also conducive to the growth of Salmonella. As a result, this pathogen can quickly grow to very high cell densities during sprouting without any detectable organoleptic impact. Seed sprouts typically also support heavy growth (~108 CFU g−1 of a heterogeneous microbiota consisting of various bacterial, yeast, and mold species, often dominated by non-pathogenic members of the family Enterobacteriaceae. This heavy background may present challenges to the detection of Salmonella, especially if this pathogen is present in relatively low numbers. We combined DNA-based fluorescence in situ hybridization (FISH with flow cytometry (FCM for the rapid molecular detection of Salmonella enterica ser. Typhimurium in artificially contaminated alfalfa and other seed sprouts. Components of the assay included a set of cooperatively binding probes, a chemical blocking treatment intended to reduce non-specific background, and sample concentration via tangential flow filtration (TFF. We were able to detect S. Typhimurium in sprout wash at levels as low as 103 CFU ml−1 sprout wash (104 CFU g−1 sprouts against high microbial backgrounds (~108 CFU g−1 sprouts. Hybridization times were typically 30 min, with additional washing, but we ultimately found that S. Typhimurium could be readily detected using hybridization times as short as 2 min, without a wash step. These results clearly demonstrate the potential of combined DNA-FISH and FCM for rapid detection of Salmonella in this challenging food matrix and provide industry with a useful tool for compliance with sprout production standards proposed in the Food Safety Modernization Act (FSMA.

  1. Factors Associated with Non-typhoidal Salmonella Bacteremia versus Typhoidal Salmonella Bacteremia in Patients Presenting for Care in an Urban Diarrheal Disease Hospital in Bangladesh.

    Directory of Open Access Journals (Sweden)

    K M Shahunja

    Full Text Available Non-typhoidal Salmonella (NTS and Salmonella enterica serovar Typhi bacteremia are the causes of significant morbidity and mortality worldwide. There is a paucity of data regarding NTS bacteremia in South Asia, a region with a high incidence of typhoidal bacteremia. We sought to determine clinical predictors and outcomes associated with NTS bacteremia compared with typhoidal bacteremia.We performed a retrospective age-matched case-control study of patients admitted to the Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh, between February 2009 and March 2013. We compared demographic, clinical, microbiological, and outcome variables of NTS bacteremic patients with age-matched S. Typhi bacteremic patients, and a separate comparison of patients with NTS bacteremia and patients with NTS gastroenteritis.Of 20 patients with NTS bacteremia, 5 died (25% case fatality, compared to none of 60 age-matched cases of S. Typhi bacteremia. In univariate analysis, we found that compared with S. Typhi bacteremia, cases of NTS bacteremia had more severe acute malnutrition (SAM in children under five years of age, less often presented with a duration of fever ≥ 5 days, and were more likely to have co-morbidities on admission such as pneumonia and clinical signs of sepsis (p<0.05 in all cases. In multivariable logistic regression, SAM, clinical sepsis, and pneumonia were independent risk factors for NTS bacteremia compared with S. Typhi bacteremia (p<0.05 in all cases. Notably, we found marked differences in antibiotic susceptibilities, including NTS strains resistant to antibiotics commonly used for empiric therapy of patients suspected to have typhoid fever.Diarrheal patients with NTS bacteremia more often presented with co-morbidities and had a higher case fatality rate compared to those with typhoidal bacteremia. Clinicians in regions where both typhoid and NTS bacteremia are prevalent need to be vigilant about the

  2. Facial Expression Recognition via Non-Negative Least-Squares Sparse Coding

    Directory of Open Access Journals (Sweden)

    Ying Chen

    2014-05-01

    Full Text Available Sparse coding is an active research subject in signal processing, computer vision, and pattern recognition. A novel method of facial expression recognition via non-negative least squares (NNLS sparse coding is presented in this paper. The NNLS sparse coding is used to form a facial expression classifier. To testify the performance of the presented method, local binary patterns (LBP and the raw pixels are extracted for facial feature representation. Facial expression recognition experiments are conducted on the Japanese Female Facial Expression (JAFFE database. Compared with other widely used methods such as linear support vector machines (SVM, sparse representation-based classifier (SRC, nearest subspace classifier (NSC, K-nearest neighbor (KNN and radial basis function neural networks (RBFNN, the experiment results indicate that the presented NNLS method performs better than other used methods on facial expression recognition tasks.

  3. Salmonella contamination: a significant challenge to the global marketing of animal food products.

    Science.gov (United States)

    L Plym, Forshell; Wierup, M

    2006-08-01

    Salmonellosis is the most common food-borne bacterial disease in the world. Salmonella is a significant pathogen for food-producing animals and these animals are the primary source of salmonellosis. It is estimated that herd prevalence varies between 0% and 90%, depending on the animal species and region. The pathogen is spread by trade in animals and non-heated animal food products. The emergence of strains that are resistant to antimicrobials, often as a result of antimicrobial usage in animals, is a public health hazard of great concern. It is increasingly accepted that the prevalence of Salmonella in animal production must be decreased and, in the European Union, plans to achieve this are currently being implemented. In this paper, the authors propose various risk mitigation strategies. Successful control must focus on a range of preventive actions because there is no simple 'silver bullet' solution to reduce Salmonella contamination. The authors conclude that the key to controlling Salmonella is to follow the general rules that have been successfully applied to other infectious diseases.

  4. nocoRNAc: Characterization of non-coding RNAs in prokaryotes

    Directory of Open Access Journals (Sweden)

    Nieselt Kay

    2011-01-01

    Full Text Available Abstract Background The interest in non-coding RNAs (ncRNAs constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved. This led to the discovery of numerous ncRNA genes across many species. However, for most organisms the non-coding transcriptome still remains unexplored to a great extent. Various experimental techniques for the identification of ncRNA transcripts are available, but as these methods are costly and time-consuming, there is a need for computational methods that allow the detection of functional RNAs in complete genomes in order to suggest elements for further experiments. Several programs for the genome-wide prediction of functional RNAs have been developed but most of them predict a genomic locus with no indication whether the element is transcribed or not. Results We present NOCORNAc, a program for the genome-wide prediction of ncRNA transcripts in bacteria. NOCORNAc incorporates various procedures for the detection of transcriptional features which are then integrated with functional ncRNA loci to determine the transcript coordinates. We applied RNAz and NOCORNAc to the genome of Streptomyces coelicolor and detected more than 800 putative ncRNA transcripts most of them located antisense to protein-coding regions. Using a custom design microarray we profiled the expression of about 400 of these elements and found more than 300 to be transcribed, 38 of them are predicted novel ncRNA genes in intergenic regions. The expression patterns of many ncRNAs are similarly complex as those of the protein-coding genes, in particular many antisense ncRNAs show a high expression correlation with their protein-coding partner. Conclusions We have developed NOCORNAc, a framework that facilitates the automated characterization of functional ncRNAs. NOCORNAc increases the confidence of predicted ncRNA loci, especially if they contain transcribed ncRNAs. NOCORNAc is not restricted to

  5. Phenotypic and molecular characterization of Salmonella serotypes ...

    African Journals Online (AJOL)

    The presence of Salmonella and human pathogens in unpasteurized milk remains a public health hazard. The study reported the phenotypic and molecular characterization of Salmonella serotypes in cow raw milk, cheese and traditional yoghurt marketed for man's consumption in Nigeria. Isolation of Salmonella was done ...

  6. Developmental programming of long non-coding RNAs during postnatal liver maturation in mice.

    Directory of Open Access Journals (Sweden)

    Lai Peng

    Full Text Available The liver is a vital organ with critical functions in metabolism, protein synthesis, and immune defense. Most of the liver functions are not mature at birth and many changes happen during postnatal liver development. However, it is unclear what changes occur in liver after birth, at what developmental stages they occur, and how the developmental processes are regulated. Long non-coding RNAs (lncRNAs are involved in organ development and cell differentiation. Here, we analyzed the transcriptome of lncRNAs in mouse liver from perinatal (day -2 to adult (day 60 by RNA-Sequencing, with an attempt to understand the role of lncRNAs in liver maturation. We found around 15,000 genes expressed, including about 2,000 lncRNAs. Most lncRNAs were expressed at a lower level than coding RNAs. Both coding RNAs and lncRNAs displayed three major ontogenic patterns: enriched at neonatal, adolescent, or adult stages. Neighboring coding and non-coding RNAs showed the trend to exhibit highly correlated ontogenic expression patterns. Gene ontology (GO analysis revealed that some lncRNAs enriched at neonatal ages have their neighbor protein coding genes also enriched at neonatal ages and associated with cell proliferation, immune activation related processes, tissue organization pathways, and hematopoiesis; other lncRNAs enriched at adolescent ages have their neighbor protein coding genes associated with different metabolic processes. These data reveal significant functional transition during postnatal liver development and imply the potential importance of lncRNAs in liver maturation.

  7. Non-coding RNA networks in cancer.

    Science.gov (United States)

    Anastasiadou, Eleni; Jacob, Leni S; Slack, Frank J

    2018-01-01

    Thousands of unique non-coding RNA (ncRNA) sequences exist within cells. Work from the past decade has altered our perception of ncRNAs from 'junk' transcriptional products to functional regulatory molecules that mediate cellular processes including chromatin remodelling, transcription, post-transcriptional modifications and signal transduction. The networks in which ncRNAs engage can influence numerous molecular targets to drive specific cell biological responses and fates. Consequently, ncRNAs act as key regulators of physiological programmes in developmental and disease contexts. Particularly relevant in cancer, ncRNAs have been identified as oncogenic drivers and tumour suppressors in every major cancer type. Thus, a deeper understanding of the complex networks of interactions that ncRNAs coordinate would provide a unique opportunity to design better therapeutic interventions.

  8. Bacteriophage SP6 encodes a second tailspike protein that recognizes Salmonella enterica serogroups C{sub 2} and C{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Gebhart, Dana; Williams, Steven R.; Scholl, Dean, E-mail: dean@avidbiotics.com

    2017-07-15

    SP6 is a salmonella phage closely related to coliphage K1-5. K1-5 is notable in that it encodes two polysaccharide-degrading tailspike proteins, an endosialidase that allows it to infect E. coli K1, and a lyase that enables it to infect K5 strains. SP6 is similar to K1-5 except that it encodes a P22-like endorhamnosidase tailspike, gp46, allowing it to infect group B Salmonella. We show here that SP6 can also infect Salmonella serogroups C{sub 2} and C{sub 3} and that a mutation in a putative second tailspike, gp47, eliminates this specificity. Gene 47 was fused to the coding region of the N-terminal portion of the Pseudomonas aeruginosa R2 pyocin tail fiber and expressed in trans such that the fusion protein becomes incorporated into pyocin particles. These pyocins, termed AvR2-SP47, killed serogroups C{sub 2} and C{sub 3}Salmonella. We conclude that SP6 encodes two tail proteins providing it a broad host range among Salmonella enterica. - Highlights: • SP6 is a “dual specificity” bacteriophage that encodes two different receptor binding proteins giving it a broad host range. • These receptor binding proteins can be used to re-target the spectrum of R-type bacteriocins to Salmonella enterica. • Both SP6 and the engineered R-type bacteriocins can kill the Salmonella serovars most associated with human disease making them attractive for development as antimicrobial agents.

  9. Tentative Colistin Epidemiological Cut-Off Value for Salmonella spp

    DEFF Research Database (Denmark)

    Agersø, Yvonne; Torpdahl, Mia; Zachariasen, Camilla

    2012-01-01

    . Interestingly, Salmonella Dublin and Salmonella Enteritidis belong to the same O-group (O:1, 9,12), suggesting that surface lipopolysaccharides (LPS) of the cell (O-antigen) play a role in colistin susceptibility. The epidemiological cut-off value of >2 mg/L for colistin suggested by European Committee...... on Antimicrobial Susceptibility Testing (EUCAST) is placed inside the distribution for both Salmonella Dublin and Salmonella Enteritidis. All tested Salmonella Dublin isolates, regardless of MIC colistin value, had identical pmrA and pmrB sequences. Missense mutations were found only in pmrA in one Salmonella...

  10. Development of 3D CFD code based on structured non-orthogonal grids

    International Nuclear Information System (INIS)

    Vaidya, Abhijeet Mohan; Maheshwari, Naresh Kumar; Rama Rao, A.

    2016-01-01

    Most of the nuclear industry problems involve complex geometries. Solution of flow and heat transfer over complex geometries is a very important requirement for designing new reactor systems. Hence development of a general purpose three dimensional (3D) CFD code is undertaken. For handling complex shape of computational domain, implementation on structured non-orthogonal coordinates is being done. The code is validated by comparing its results for 3D inclined lid driven cavity at different inclination angles and Reynolds numbers with OpenFOAM results. This paper contains formulation and validation of the new code developed. (author)

  11. Prognostic value of long non-coding RNA MALAT1 in cancer patients.

    Science.gov (United States)

    Wu, Yihua; Lu, Wei; Xu, Jinming; Shi, Yu; Zhang, Honghe; Xia, Dajing

    2016-01-01

    Metastasis associated in lung adenocarcinoma transcript 1 (MALAT1) was identified to be the first long non-coding RNA as a biomarker of independent prognostic value for early stage non-small cell lung cancer patient survival. In recent years, the association between upregulated tissue MALAT1 level and incidence of various cancers including bladder cancer, colorectal cancer, and renal cancer has been widely discussed. The aim of our present study was to assess the potential prognostic value of MALAT1 in various human cancers. PubMed, Embase, Ovid, and Cochrane Library databases were systematically searched, and eligible studies evaluating the prognostic value of MALAT1 in various cancers were included. Finally, 11 studies encompassing 1216 participants reporting with sufficient data were enrolled in the current meta-analysis. The pooled hazard ratio (HR) was 2.05 (95 % confidence interval (CI) 1.64-2.55, p < 0.01) for overall survival (OS) and 2.66 (95 % CI 1.86-3.80, p < 0.01) for disease-free survival (DFS). In conclusion, high tissue MALAT1 level was associated with an inferior clinical outcome in various cancers, suggesting that MALAT1 might serve as a potential prognostic biomarker for various cancers.

  12. An Electrochemical DNA Biosensor for the Detection of Salmonella Using Polymeric Films and Electrochemical Labels

    Science.gov (United States)

    Diaz Serrano, Madeline

    Waterborne and foodborne diseases are one of the principal public health problems worldwide. Microorganisms are the major agents of foodborne illness: pathogens such as Salmonella, Campylobacter jejuni and Escherichia coli, and parasites such as cryptosporidium. The most popular methods to detect Salmonella are based on culture and colony counting methods, ELISA, Gel electrophoresis and the polymerase chain reaction. Conventional detection methods are laborious and time-consuming, allowing for portions of the food to be distributed, marketed, sold and eaten before the analysis is done and the problem even detected. By these reasons, the rapid, easy and portable detection of foodborne organisms will facilitate the disease treatment. Our particular interest is to develop a nucleic acid biosensor (NAB) for the detection of pathogenic microorganisms in food and water samples. In this research, we report on the development of a NAB prototype using a polymer modified electrode surface together with sequences of different lengths for the OmpC gene from Salmonella as probes and Ferrocene-labeled target (Fc-ssDNA), Ferrocene-labeled tri(ethylene glycol) (Fc-PEG) and Ruthenium-Ferrocene (Ru-Fe) bimetallic complex as an electrochemical labels. We have optimized several PS films and anchored nucleic acid sequences with different lengths at gold and carbon surfaces. Non contact mode AFM and XPS were used to monitor each step of the NAB preparation, from polymer modification to oligos hybridization (conventional design). The hybridization reaction was followed electrochemically using a Fc-ssDNA and Fc-PEG in solution taking advantage of the morphological changes generated upon hybridization. We observed a small current at the potential for the Fe oxidation without signal amplification at +296 mV vs. Ag/AgCl for the Fc-ssDNA strategy and a small current at +524 mV for the Fc-PEG strategy. The immobilization, hybridization and signal amplification of Biotin- OmpC Salmonella genes

  13. Analysis of interactions of Salmonella type three secretion mutants with 3-D intestinal epithelial cells.

    Directory of Open Access Journals (Sweden)

    Andrea L Radtke

    Full Text Available The prevailing paradigm of Salmonella enteropathogenesis based on monolayers asserts that Salmonella pathogenicity island-1 Type Three Secretion System (SPI-1 T3SS is required for bacterial invasion into intestinal epithelium. However, little is known about the role of SPI-1 in mediating gastrointestinal disease in humans. Recently, SPI-1 deficient nontyphoidal Salmonella strains were isolated from infected humans and animals, indicating that SPI-1 is not required to cause enteropathogenesis and demonstrating the need for more in vivo-like models. Here, we utilized a previously characterized 3-D organotypic model of human intestinal epithelium to elucidate the role of all characterized Salmonella enterica T3SSs. Similar to in vivo reports, the Salmonella SPI-1 T3SS was not required to invade 3-D intestinal cells. Additionally, Salmonella strains carrying single (SPI-1 or SPI-2, double (SPI-1/2 and complete T3SS knockout (SPI-1/SPI-2: flhDC also invaded 3-D intestinal cells to wildtype levels. Invasion of wildtype and TTSS mutants was a Salmonella active process, whereas non-invasive bacterial strains, bacterial size beads, and heat-killed Salmonella did not invade 3-D cells. Wildtype and T3SS mutants did not preferentially target different cell types identified within the 3-D intestinal aggregates, including M-cells/M-like cells, enterocytes, or Paneth cells. Moreover, each T3SS was necessary for substantial intracellular bacterial replication within 3-D cells. Collectively, these results indicate that T3SSs are dispensable for Salmonella invasion into highly differentiated 3-D models of human intestinal epithelial cells, but are required for intracellular bacterial growth, paralleling in vivo infection observations and demonstrating the utility of these models in predicting in vivo-like pathogenic mechanisms.

  14. Computational Approaches Reveal New Insights into Regulation and Function of Non; coding RNAs and their Targets

    KAUST Repository

    Alam, Tanvir

    2016-01-01

    Regulation and function of protein-coding genes are increasingly well-understood, but no comparable evidence exists for non-coding RNA (ncRNA) genes, which appear to be more numerous than protein-coding genes. We developed a novel machine

  15. A novel secretion pathway of Salmonella enterica acts as an antivirulence modulator during salmonellosis.

    Directory of Open Access Journals (Sweden)

    Ohad Gal-Mor

    2008-04-01

    Full Text Available Salmonella spp. are Gram-negative enteropathogenic bacteria that infect a variety of vertebrate hosts. Like any other living organism, protein secretion is a fundamental process essential for various aspects of Salmonella biology. Herein we report the identification and characterization of a horizontally acquired, autonomous and previously unreported secretion pathway. In Salmonella enterica serovar Typhimurium, this novel secretion pathway is encoded by STM1669 and STM1668, designated zirT and zirS, respectively. We show that ZirT is localized to the bacterial outer membrane, expected to adopt a compact beta-barrel conformation, and functions as a translocator for ZirS. ZirS is an exoprotein, which is secreted into the extracellular environment in a ZirT-dependent manner. The ZirTS secretion pathway was found to share several important features with two-partner secretion (TPS systems and members of the intimin/invasin family of adhesions. We show that zirTS expression is affected by zinc; and that in vivo, induction of zirT occurs distinctively in Salmonella colonizing the small intestine, but not in systemic sites. Additionally, strong expression of zirT takes place in Salmonella shed in fecal pellets during acute and persistent infections of mice. Inactivation of ZirTS results in a hypervirulence phenotype of Salmonella during oral infection of mice. Cumulatively, these results indicate that the ZirTS pathway plays a unique role as an antivirulence modulator during systemic disease and is involved in fine-tuning a host-pathogen balance during salmonellosis.

  16. Salmonella serotype distribution in the Dutch broiler supply chain.

    Science.gov (United States)

    van Asselt, E D; Thissen, J T N M; van der Fels-Klerx, H J

    2009-12-01

    Salmonella serotype distribution can give insight in contamination routes and persistence along a production chain. Therefore, it is important to determine not only Salmonella prevalence but also to specify the serotypes involved at the different stages of the supply chain. For this purpose, data from a national monitoring program in the Netherlands were used to estimate the serotype distribution and to determine whether this distribution differs for the available sampling points in the broiler supply chain. Data covered the period from 2002 to 2005, all slaughterhouses (n = 22), and the following 6 sampling points: departure from hatchery, arrival at the farm, departure from the farm, arrival at the slaughterhouse, departure from the slaughterhouse, and end of processing. Furthermore, retail data for 2005 were used for comparison with slaughterhouse data. The following serotypes were followed throughout the chain: Salmonella Enteritidis, Salmonella Typhimurium, Salmonella Paratyphi B var. Java (Salmonella Java), Salmonella Infantis, Salmonella Virchow, and Salmonella Mbandaka. Results showed that serotype distribution varied significantly throughout the supply chain (P supply chain up to the retail phase.

  17. Development of non-orthogonal and 2-dimensional numerical code TFC2D-BFC for fluid flow

    International Nuclear Information System (INIS)

    Park, Ju Yeop; In, Wang Kee; Chun, Tae Hyun; Oh, Dong Seok

    2000-09-01

    The development of algorithm for three dimensional non-orthogonal coordinate system has been made. The algorithm adopts a non-staggered grid system, Cartesian velocity components for independent variables of momentum equations and a SIMPLER algorithm for a pressure correction equation. Except the pressure correction method, the selected grid system and the selected independent variables for momentum equations have been widely used in a commercial code. It is well known that the SIMPLER is superior to the SIMPLE algorithm in the view of convergence rate. Using this algorithm, a two dimensional non-orthogonal numerical code has been completed. The code adopts a structured single square block in a computational domain with a uniform mesh interval. Consequently, any solid body existing in a flow field can be implemented in the numerical code through a blocked-off method which was devised by Patankar

  18. Evaluation of temporary non-code repairs in safety class 3 piping systems

    International Nuclear Information System (INIS)

    Godha, P.C.; Kupinski, M.; Azevedo, N.F.

    1996-01-01

    Temporary non-ASME Code repairs in safety class 3 pipe and piping components are permissible during plant operation in accordance with Nuclear Regulatory Commission Generic Letter 90-05. However, regulatory acceptance of such repairs requires the licensee to undertake several timely actions. Consistent with the requirements of GL 90-05, this paper presents an overview of the detailed evaluation and relief request process. The technical criteria encompasses both ductile and brittle piping materials. It also lists appropriate evaluation methods that a utility engineer can select to perform a structural integrity assessment for design basis loading conditions to support the use of temporary non-Code repair for degraded piping components. Most use of temporary non-code repairs at a nuclear generating station is in the service water system which is an essential safety related system providing the ultimate heat sink for various plant systems. Depending on the plant siting, the service water system may use fresh water or salt water as the cooling medium. Various degradation mechanisms including general corrosion, erosion/corrosion, pitting, microbiological corrosion, galvanic corrosion, under-deposit corrosion or a combination thereof continually challenge the pressure boundary structural integrity. A good source for description of corrosion degradation in cooling water systems is provided in a cited reference

  19. Presence of Campylobacter and Salmonella in sand from bathing beaches.

    Science.gov (United States)

    Bolton, F J; Surman, S B; Martin, K; Wareing, D R; Humphrey, T J

    1999-02-01

    The purpose of this study was to determine the presence of thermophilic Campylobacter spp. and Salmonella spp. in sand from non-EEC standard and EEC standard designated beaches in different locations in the UK and to assess if potentially pathogenic strains were present. Campylobacter spp. were detected in 82/182 (45%) of sand samples and Salmonella spp. in 10/182 (6%). Campylobacter spp. were isolated from 46/92 (50%) of samples from non-EEC standard beaches and 36/90 (40%) from EEC standard beaches. The prevalence of Campylobacter spp. was greater in wet sand from both types of beaches but, surprisingly, more than 30% of samples from dry sand also contained these organisms. The major pathogenic species C. jejuni and C. coli were more prevalent in sand from non-EEC standard beaches. In contrast, C. lari and urease positive thermophilic campylobacters, which are associated with seagulls and other migratory birds, were more prevalent in sand from EEC standard beaches. Campylobacter isolates were further characterized by biotyping and serotyping, which confirmed that strains known to be of types associated with human infections were frequently found in sand on bathing beaches.

  20. Inferring source attribution from a multiyear multisource data set of Salmonella in Minnesota.

    Science.gov (United States)

    Ahlstrom, C; Muellner, P; Spencer, S E F; Hong, S; Saupe, A; Rovira, A; Hedberg, C; Perez, A; Muellner, U; Alvarez, J

    2017-12-01

    Salmonella enterica is a global health concern because of its widespread association with foodborne illness. Bayesian models have been developed to attribute the burden of human salmonellosis to specific sources with the ultimate objective of prioritizing intervention strategies. Important considerations of source attribution models include the evaluation of the quality of input data, assessment of whether attribution results logically reflect the data trends and identification of patterns within the data that might explain the detailed contribution of different sources to the disease burden. Here, more than 12,000 non-typhoidal Salmonella isolates from human, bovine, porcine, chicken and turkey sources that originated in Minnesota were analysed. A modified Bayesian source attribution model (available in a dedicated R package), accounting for non-sampled sources of infection, attributed 4,672 human cases to sources assessed here. Most (60%) cases were attributed to chicken, although there was a spike in cases attributed to a non-sampled source in the second half of the study period. Molecular epidemiological analysis methods were used to supplement risk modelling, and a visual attribution application was developed to facilitate data exploration and comprehension of the large multiyear data set assessed here. A large amount of within-source diversity and low similarity between sources was observed, and visual exploration of data provided clues into variations driving the attribution modelling results. Results from this pillared approach provided first attribution estimates for Salmonella in Minnesota and offer an understanding of current data gaps as well as key pathogen population features, such as serotype frequency, similarity and diversity across the sources. Results here will be used to inform policy and management strategies ultimately intended to prevent and control Salmonella infection in the state. © 2017 Blackwell Verlag GmbH.

  1. pH-, Lactic acid-, and non-lactic acid-dependent activities of probiotic Lactobacilli against Salmonella enterica Serovar Typhimurium.

    Science.gov (United States)

    Fayol-Messaoudi, Domitille; Berger, Cédric N; Coconnier-Polter, Marie-Hélène; Liévin-Le Moal, Vanessa; Servin, Alain L

    2005-10-01

    The mechanism(s) underlying the antibacterial activity of probiotic Lactobacillus strains appears to be multifactorial and includes lowering of the pH and the production of lactic acid and of antibacterial compounds, including bacteriocins and nonbacteriocin, non-lactic acid molecules. Addition of Dulbecco's modified Eagle's minimum essential medium to the incubating medium delays the killing activity of lactic acid. We found that the probiotic strains Lactobacillus johnsonii La1, Lactobacillus rhamnosus GG, Lactobacillus casei Shirota YIT9029, L. casei DN-114 001, and L. rhamnosus GR1 induced a dramatic decrease in the viability of Salmonella enterica serovar Typhimurium SL1344 mainly attributable to non-lactic acid molecule(s) present in the cell-free culture supernatant (CFCS). These molecules were more active against serovar Typhimurium SL1344 in the exponential growth phase than in the stationary growth phase. We also showed that the production of the non-lactic acid substance(s) responsible for the killing activity was dependent on growth temperature and that both unstable and stable substances with killing activity were present in the CFCSs. We found that the complete inhibition of serovar Typhimurium SL1344 growth results from a pH-lowering effect.

  2. Cloud Computing for Complex Performance Codes.

    Energy Technology Data Exchange (ETDEWEB)

    Appel, Gordon John [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hadgu, Teklu [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Klein, Brandon Thorin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Miner, John Gifford [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-02-01

    This report describes the use of cloud computing services for running complex public domain performance assessment problems. The work consisted of two phases: Phase 1 was to demonstrate complex codes, on several differently configured servers, could run and compute trivial small scale problems in a commercial cloud infrastructure. Phase 2 focused on proving non-trivial large scale problems could be computed in the commercial cloud environment. The cloud computing effort was successfully applied using codes of interest to the geohydrology and nuclear waste disposal modeling community.

  3. Detection of Salmonella Carriers in Sheep and Goat Flocks of Bushehr and Lorestan Provinces, Iran

    Directory of Open Access Journals (Sweden)

    Hossein Esmaeili

    2017-01-01

    Full Text Available Background:    Salmonellosis is an infectious and a food-borne disease of humans and animals. The initial source of the infection is the intestinal tracts of birds and other animals. Apparently healthy animals can become subclinical carriers and persistently shed Salmonella in their feces which can act as a reservoir for the pathogen. The aim of this study is to detect the carriers of Salmonella among apparently healthy sheep and goat flocks of Bushehr and Lorestan provinces, Iran.Methods:    A total of 389 fecal samples were aseptically collected from the rectum of apparently healthy sheep and goat flocks of Bushehr and Lorestan provinces. Bacteriological culture was conducted using selenite cystine, Rappaport–Vassiliadis, brilliant green and xylose lysine deoxycholate agar. Suspected colonies were inoculated in to TSI, peptone water, Simmon’s Citrate, Urea medium and MRVP. Sero-groups were detected by antisera.              Results:    Two samples from 189 samples (1.05% were positive for Salmonella in Bushehr province. Salmonella abortusovis and Salmonella typhimurium were detected following serotyping. No Salmonella carriers were detected in Lorestan province.Conclusion:    As the rate of carriers of Salmonella was low, the risk of food-borne salmonellosis due to consumption of small ruminant's meat is low, especially in the condition of well cooked meat. Since S. abortusovis was detected, strategies of prevention and control of abortion due to this agent must be taken to reduce the economic losses. Moreover, the presence of S. typhimurium is a hazard to public health and people who have close contact to sheep and goats.

  4. Decoding the non-coding RNAs in Alzheimer's disease.

    Science.gov (United States)

    Schonrock, Nicole; Götz, Jürgen

    2012-11-01

    Non-coding RNAs (ncRNAs) are integral components of biological networks with fundamental roles in regulating gene expression. They can integrate sequence information from the DNA code, epigenetic regulation and functions of multimeric protein complexes to potentially determine the epigenetic status and transcriptional network in any given cell. Humans potentially contain more ncRNAs than any other species, especially in the brain, where they may well play a significant role in human development and cognitive ability. This review discusses their emerging role in Alzheimer's disease (AD), a human pathological condition characterized by the progressive impairment of cognitive functions. We discuss the complexity of the ncRNA world and how this is reflected in the regulation of the amyloid precursor protein and Tau, two proteins with central functions in AD. By understanding this intricate regulatory network, there is hope for a better understanding of disease mechanisms and ultimately developing diagnostic and therapeutic tools.

  5. Involvement of a putative intercellular signal-recognizing G protein-coupled receptor in the engulfment of Salmonella by the protozoan Tetrahymena

    Directory of Open Access Journals (Sweden)

    P.N. Agbedanu

    2013-07-01

    Full Text Available In an effort to investigate the molecular basis of protozoa engulfment-mediated hypervirulence of Salmonella in cattle, we evaluated protozoan G protein-coupled receptors (GPCRs as transducers of Salmonella engulfment by the model protozoan Tetrahymena. Our laboratory previously demonstrated that non-pathogenic protozoa (including Tetrahymena engulf Salmonella and then exacerbate its virulence in cattle, but the mechanistic details of the phenomenon are not fully understood. GPCRs were investigated since these receptors facilitate phagocytosis of particulates by Tetrahymena, and a GPCR apparently modulates bacterial engulfment for the pathogenic protozoan Entamoeba histolytica. A database search identified three putative Tetrahymena GPCRs, based on sequence homologies and predicted transmembrane domains, that were the focus of this study. Salmonella engulfment by Tetrahymena was assessed in the presence of suramin, a non-specific GPCR inhibitor. Salmonella engulfment was also assessed in Tetrahymena in which expression of putative GPCRs was knocked-down using RNAi. A candidate GPCR was then expressed in a heterologous yeast expression system for further characterization. Our results revealed that Tetrahymena were less efficient at engulfing Salmonella in the presence of suramin. Engulfment was reduced concordantly with a reduction in the density of protozoa. RNAi-based studies revealed that knock-down of one the Tetrahymena GPCRs caused diminished engulfment of Salmonella. Tetrahymena lysates activated this receptor in the heterologous expression system. These data demonstrate that the Tetrahymena receptor is a putative GPCR that facilitates bacterial engulfment by Tetrahymena. Activation of the putative GPCR seemed to be related to protozoan cell density, suggesting that its cognate ligand is an intercellular signaling molecule.

  6. Breast abscess due to Salmonella Typhimurium in a patient with rheumatoid arthritis: a case report.

    Science.gov (United States)

    Baran, Irmak; Aksu, Neriman; Aksoy, Altan

    2016-07-22

    This is the first report of breast abscess due to Salmonella enterica serotype Typhimurium. Staphylococcus aureus is known as the most common cause of breast abscess. Salmonella spp. may occasionally form localized abscesses after dissemination to various organ systems following a bacteraemia. But breast abscess related to Salmonella spp is a very rare complication. A 43-year-old female patient referred to our hospital with a lump, fever and mild pain in her breast. The patient was not pregnant or lactating at that time. She had a history of rheumatoid arthritis for 5 years and was under immunosuppressive therapy. Ultrasonography of the breast revealed an abscess. The abscess was drained and sent for culture to medical microbiology laboratory. The microorganism was identified as Salmonella enterica serotype Typhimurium and found to be sensitive to all antibiotics tested. The patient was cured after surgical debridement and antibiotic therapy. The abscess did not recur again. This case is presented to draw attention to non-typhoidal Salmonella as rare causes of breast abscess and submission of specimens to the microbiology laboratory for accurate diagnosis and treatment especially in patients with underlying immunosuppressive diseases.

  7. Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

    KAUST Repository

    Alam, Tanvir

    2014-10-02

    Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.

  8. Rapid radiometric method for detection of Salmonella in foods

    International Nuclear Information System (INIS)

    Stewart, B.J.; Eyles, M.J.; Murrell, W.G.

    1980-01-01

    A radiometric method for the detection of Salmonella in foods has been developed which is based on Salmonella poly H agglutinating serum preventing Salmonella from producing 14CO2 from [14C] dulcitol. The method will detect the presence or absence of Salmonella in a product within 30 h compared to 4 to 5 days by routine culture methods. The method has been evaluated against a routine culture method using 58 samples of food. The overall agreement was 91%. Five samples negative for Salmonella by the routine method were positive by the radiometric method. These may have been false positives. However, the routine method may have failed to detect Salmonella due to the presence of large numbers of lactose-fermenting bacteria which hindered isolation of Salmonella colonies on the selective agar plates

  9. Buffer capacity of food components influences the acid tolerance response in Salmonella Typhimurium during simulated gastric passage

    DEFF Research Database (Denmark)

    Aabo, Søren; Buschhardt, Tasja; Hansen, Tina Beck

    2014-01-01

    Food composition, buffer capacity, and fat and protein content have been shown to effect the gastric acid survival of pathogens (Waterman & Small 1998). In this study, simple food-model substances with different buffer capacities were investigated for their ability to support survival of stationary...... Heart Infusion Broth having a higher buffer capacity. We suggest this to be associated with a varying ability of Salmonella Typhimurium to mount a stationary phase acid tolerance response (ATR) depending on the buffer capacity of the food vehicle....... phase Salmonella Typhimurium during simulated gastric acid passage. We used a computer-controlled fermentor to employ pH changes in synthetic gastric fluid, mimicking the dynamic pH during gastric passage. In order to minimise variation, Salmonella enterica serovar Typhimurium was contained in dialysis...

  10. Salmonella capture using orbiting magnetic microbeads

    Science.gov (United States)

    Owen, Drew; Ballard, Matthew; Mills, Zachary; Hanasoge, Srinivas; Hesketh, Peter; Alexeev, Alexander

    2014-11-01

    Using three-dimensional simulations and experiments, we examine capture of salmonella from a complex fluid sample flowing through a microfluidic channel. Capture is performed using orbiting magnetic microbeads, which can easily be extracted from the system for analysis after salmonella capture. Numerical simulations are used to model the dynamics of the system, which consists of a microchannel filled with a viscous fluid, model salmonella, magnetic microbeads and a series of angled parallel ridges lining the top of the microchannel. Simulations provide a statistical measure of the ability of the system to capture target salmonella. Our modeling findings guide the design of a lab-on-a-chip experimental device to be used for the detection of salmonella from complex food samples, allowing for the detection of the bacteria at the food source and preventing the consumption of contaminated food. Such a device can be used as a generic platform for the detection of a variety of biomaterials from complex fluids. This work is supported by a grant from the United States Department of Agriculture.

  11. A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species.

    Science.gov (United States)

    Radhika, M; Saugata, Majumder; Murali, H S; Batra, H V

    2014-01-01

    Salmonella enterica and Shigella species are commonly associated with food and water borne infections leading to gastrointestinal diseases. The present work was undertaken to develop a sensitive and reliable PCR based detection system for simultaneous detection of Salmonella enterica and Shigella at species level. For this the conserved regions of specific genes namely ipaH1, ipaH, wbgZ, wzy and invA were targeted for detection of Shigella genus, S. flexneri, S. sonnei, S. boydii and Salmonella enterica respectively along with an internal amplification control (IAC). The results showed that twenty Salmonella and eleven Shigella spp., were accurately identified by the assay without showing non-specificity against closely related other Enterobacteriaceae organisms and also against other pathogens. Further evaluation of multiplex PCR was undertaken on 50 natural samples of chicken, eggs and poultry litter and results compared with conventional culture isolation and identification procedure. The multiplex PCR identified the presence of Salmonella and Shigella strains with a short pre-enrichment step of 5 h in peptone water and the same samples were processed by conventional procedures for comparison. Therefore, this reported multiplex PCR can serve as an alternative to the tedious time-consuming procedure of culture and identification in food safety laboratories.

  12. Culture- and molecular-based detection of swine-adapted Salmonella shed by avian scavengers.

    Science.gov (United States)

    Blanco, Guillermo; Díaz de Tuesta, Juan A

    2018-04-13

    Salmonella can play an important role as a disease agent in wildlife, which can then act as carriers and reservoirs of sanitary importance at the livestock-human interface. Transmission from livestock to avian scavengers can occur when these species consume contaminated carcasses and meat remains in supplementary feeding stations and rubbish dumps. We compared the performance of PCR-based detection with conventional culture-based methods to detect Salmonella in the faeces of red kites (Milvus milvus) and griffon vultures (Gyps fulvus) in central Spain. The occurrence of culturable Salmonella was intermediate in red kites (1.9%, n=52) and high in griffon vultures (26.3%, n=99). These proportions were clearly higher with PCR-based detection (13.5% and 40.4%, respectively). Confirmation cultures failed to grow Salmonella in all faecal samples positive by the molecular assay but negative by the initial conventional culture in both scavenger species, indicating the occurrence of false (non-culturable) positives by PCR-based detection. This suggests that the molecular assay is highly sensitive to detecting viable Salmonella in cultures, but also partial genomes and dead or unviable bacteria from past infections or contamination. Thus, the actual occurrence of Salmonella in a particular sampling time period can be underestimated when using only culture detection. The serovars found in the scavenger faeces were among the most frequently isolated in pigs from Spain and other EU countries, especially those generally recognized as swine-adapted monophasic variants of S. Typhimurium. Because the studied species obtain much of their food from pig carcasses, this livestock may be the primary source of Salmonella via direct ingestion of infected carcasses and indirectly via contamination due to the unsanitary conditions found in supplementary feeding stations established for scavenger conservation. Combining culture- and molecular-based detection is encouraged to understand the

  13. Bacteriological detection of Salmonella in the presence of competitive micro-organisms (A collaborative study amongst the National Reference Laboratories for Salmonella)

    NARCIS (Netherlands)

    Voogt N; Veld PH in ' t; Nagelkerke N; Henken AM; MGB

    1997-01-01

    Het Communautair Referentie Laboratorium voor Salmonella heeft een tweede bacteriologisch ringonderzoek georganiseerd met deelname van de Nationale Referentie Laboratoria voor Salmonella. Het belangrijkste doel van dit onderzoek was verschillen tussen de NRLs in de resultaten van Salmonella

  14. Non-Coding RNAs: Multi-Tasking Molecules in the Cell

    Directory of Open Access Journals (Sweden)

    Anita Quintal Gomes

    2013-07-01

    Full Text Available In the last years it has become increasingly clear that the mammalian transcriptome is highly complex and includes a large number of small non-coding RNAs (sncRNAs and long noncoding RNAs (lncRNAs. Here we review the biogenesis pathways of the three classes of sncRNAs, namely short interfering RNAs (siRNAs, microRNAs (miRNAs and PIWI-interacting RNAs (piRNAs. These ncRNAs have been extensively studied and are involved in pathways leading to specific gene silencing and the protection of genomes against virus and transposons, for example. Also, lncRNAs have emerged as pivotal molecules for the transcriptional and post-transcriptional regulation of gene expression which is supported by their tissue-specific expression patterns, subcellular distribution, and developmental regulation. Therefore, we also focus our attention on their role in differentiation and development. SncRNAs and lncRNAs play critical roles in defining DNA methylation patterns, as well as chromatin remodeling thus having a substantial effect in epigenetics. The identification of some overlaps in their biogenesis pathways and functional roles raises the hypothesis that these molecules play concerted functions in vivo, creating complex regulatory networks where cooperation with regulatory proteins is necessary. We also highlighted the implications of biogenesis and gene expression deregulation of sncRNAs and lncRNAs in human diseases like cancer.

  15. Survival of Salmonella during Drying of Fresh Ginger Root (Zingiber officinale) and Storage of Ground Ginger.

    Science.gov (United States)

    Gradl, Dana R; Sun, Lingxiang; Larkin, Emily L; Chirtel, Stuart J; Keller, Susanne E

    2015-11-01

    The survival of Salmonella on fresh ginger root (Zingiber officinale) during drying was examined using both a laboratory oven at 51 and 60°C with two different fan settings and a small commercially available food dehydrator. The survival of Salmonella in ground ginger stored at 25 and 37°C at 33% (low) and 97% (high) relative humidity (RH) was also examined. To inoculate ginger, a four-serovar cocktail of Salmonella was collected by harvesting agar lawn cells. For drying experiments, ginger slices (1 ± 0.5 mm thickness) were surface inoculated at a starting level of approximately 9 log CFU/g. Higher temperature (60°C) coupled with a slow fan speed (nonstringent condition) to promote a slower reduction in the water activity (aw) of the ginger resulted in a 3- to 4-log reduction in Salmonella populations in the first 4 to 6 h with an additional 2- to 3-log reduction by 24 h. Higher temperature with a higher fan speed (stringent condition) resulted in significantly less destruction of Salmonella throughout the 24-h period (P ginger. During storage at 97% RH, the maximum aw values were 0.85 at 25°C and 0.87 at 37°C; Salmonella was no longer detected after 25 and 5 days of storage, respectively, under these conditions. At 33% RH, the aw stabilized to approximately 0.35 at 25°C and 0.31 at 37°C. Salmonella levels remained relatively constant throughout the 365-day and 170-day storage periods for the respective temperatures. These results indicate a relationship between temperature and aw and the survival of Salmonella during both drying and storage of ginger.

  16. Sources of salmonellae in an uninfected commercially-processed broiler flock.

    Science.gov (United States)

    Rigby, C E; Pettit, J R; Baker, M F; Bentley, A H; Salomons, M O; Lior, H

    1980-07-01

    Cultural monitoring was used to study the incidence and sources of salmonellae in a 4160 bird broiler flock during the growing period, transport and processing in a commercial plant. No salmonellae were isolated from any of 132 litter samples of 189 chickens cultured during the seven-week growing period, even though nest litter samples from four of the eight parent flocks yielded salmonellae and Salmonella worthington was isolated from the meat meal component of the grower ration. On arrival at the plant, 2/23 birds sampled carried S. infantis on their feathers, although intestinal cultures failed to yield salmonellae. Three of 18 processed carcasses samples yielded salmonellae (S. infantis, S. heidelberg, S. typhimurium var copenhagen). The most likely source of these salmonellae was the plastic transport crates, since 15/107 sampled before the birds were loaded yielded salmonellae (S. infantis, S. typhimurium). The crate washer at the plant did not reduce the incidence of Salmonella-contaminated crates, since 16/116 sampled after washing yielded salmonellae (S. infantis, S. typhimurium, S. heidelberg, S. schwarzengrund, S. albany).

  17. Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes.

    Science.gov (United States)

    Peng, Hui; Lan, Chaowang; Liu, Yuansheng; Liu, Tao; Blumenstein, Michael; Li, Jinyan

    2017-10-03

    Disease-related protein-coding genes have been widely studied, but disease-related non-coding genes remain largely unknown. This work introduces a new vector to represent diseases, and applies the newly vectorized data for a positive-unlabeled learning algorithm to predict and rank disease-related long non-coding RNA (lncRNA) genes. This novel vector representation for diseases consists of two sub-vectors, one is composed of 45 elements, characterizing the information entropies of the disease genes distribution over 45 chromosome substructures. This idea is supported by our observation that some substructures (e.g., the chromosome 6 p-arm) are highly preferred by disease-related protein coding genes, while some (e.g., the 21 p-arm) are not favored at all. The second sub-vector is 30-dimensional, characterizing the distribution of disease gene enriched KEGG pathways in comparison with our manually created pathway groups. The second sub-vector complements with the first one to differentiate between various diseases. Our prediction method outperforms the state-of-the-art methods on benchmark datasets for prioritizing disease related lncRNA genes. The method also works well when only the sequence information of an lncRNA gene is known, or even when a given disease has no currently recognized long non-coding genes.

  18. Characterization of Four Novel Bacteriophages Isolated from British Columbia for Control of Non-typhoidal Salmonella in Vitro and on Sprouting Alfalfa Seeds

    Directory of Open Access Journals (Sweden)

    Karen Fong

    2017-11-01

    Full Text Available Alfalfa sprouts have been linked to numerous North American outbreaks of Salmonella in recent years. Conventionally, treatments involving chlorine, heat, and irradiation are used for alfalfa seed sanitation. However, such treatments may be highly variable in their efficacy for pathogen control and/or detrimental to sprout quality, therefore negatively perceived by consumers advocating for natural alternatives. The usage of bacteriophages for pathogen control in sprouts has been previously explored, although with conflicting and inconsistent results. Lytic phages, viral predators of bacteria, represent an attractive approach as they provide several advantages compared to conventional treatments, such as their high specificity for bacterial targets and their ubiquity in nature. In this study, four Salmonella phages were isolated from British Columbia, Canada and characterized with respect to host range, burst size, latent period, and environmental stability to assess their potential to control Salmonella. Phage isolate SI1 showed the greatest host range, highest burst size and shortest latent period, greatest stability across all pH and temperatures and was the most effective in control of S. Enteritidis in vitro. Therefore, SI1 was chosen for treatment of sprouting alfalfa seeds artificially contaminated with S. Enteritidis with a multiplicity of infection (MOI of ∼110 PFU/CFU. A significant (p < 0.05 reduction of 38.3 ± 3.0% of viable Salmonella cells was observed following two h of phage treatment. On days two to six of the sprouting process, reductions of Salmonella were also observed, but were not significant compared to the control (p > 0.05. It was further demonstrated that the sprout yield was not significantly (p > 0.05 affected by phage treatment. These results highlight the potential of phages recovered from the British Columbia environment for use as biocontrol agents against Salmonella, although differing efficacies in vitro was

  19. Survival of Salmonella during baking of peanut butter cookies.

    Science.gov (United States)

    Lathrop, Amanda A; Taylor, Tiffany; Schnepf, James

    2014-04-01

    Peanuts and peanut-based products have been the source of recent Salmonella outbreaks worldwide. Because peanut butter is commonly used as an ingredient in baked goods, such as cookies, the potential risk of Salmonella remaining in these products after baking needs to be assessed. This research examines the potential hazard of Salmonella in peanut butter cookies when it is introduced via the peanut-derived ingredient. The survival of Salmonella during the baking of peanut butter cookies was determined. Commercial, creamy-style peanut butter was artificially inoculated with a five-strain Salmonella cocktail at a target concentration of 10(8) CFU/g. The inoculated peanut butter was then used to prepare peanut butter cookie dough following a standard recipe. Cookies were baked at 350 °F (177 °C) and were sampled after 10, 11, 12, 13, 14, and 15 min. Temperature profiles of the oven and cookies were monitored during baking. The water activity and pH of the inoculated and uninoculated peanut butter, raw dough, and baked cookies were measured. Immediately after baking, cookies were cooled, and the survival of Salmonella was determined by direct plating or enrichment. After baking cookies for 10 min, the minimum reduction of Salmonella observed was 4.8 log. In cookies baked for 13 and 14 min, Salmonella was only detectable by enrichment reflecting a Salmonella reduction in the range of 5.2 to 6.2 log. Cookies baked for 15 min had no detectable Salmonella. Results of this study showed that proper baking will reduce Salmonella in peanut butter cookies by 5 log or more.

  20. The emerging role of non-coding RNAs in drug addiction

    Directory of Open Access Journals (Sweden)

    Gregory Charles Sartor

    2012-06-01

    Full Text Available Prolonged drug use causes long-lasting neuroadaptations in reward-related brain areas that contribute to addiction. Despite significant amount of research dedicated to understanding the underlying mechanisms of addiction, the molecular underpinnings remain unclear. At the same time, much of the pervasive transcription that encompasses the human genome occurs in the nervous system and contributes to its heterogeneity and complexity. Recent evidence suggests that non-coding RNAs (ncRNAs play an important and dynamic role in transcriptional regulation, epigenetic signaling, stress response, and plasticity in the nervous system. Dysregulation of ncRNAs are thought to contribute to many, and perhaps all, neurological disorders, including addiction. Here, we review recent insights in the functional relevance of ncRNAs, including both microRNAs (miRNAs and long non-coding RNAs (lncRNAs, and then illustrate specific examples of ncRNA regulation in the context of drug addiction. We conclude that ncRNAs are importantly involved in the persistent neuroadaptations associated with addiction-related behaviors, and that therapies that target specific ncRNAs may represent new avenues for the treatment of drug addiction.

  1. The roles of non-coding RNAs in cardiac regenerative medicine

    Directory of Open Access Journals (Sweden)

    Oi Kuan Choong

    2017-06-01

    Full Text Available The emergence of non-coding RNAs (ncRNAs has challenged the central dogma of molecular biology that dictates that the decryption of genetic information starts from transcription of DNA to RNA, with subsequent translation into a protein. Large numbers of ncRNAs with biological significance have now been identified, suggesting that ncRNAs are important in their own right and their roles extend far beyond what was originally envisaged. ncRNAs do not only regulate gene expression, but are also involved in chromatin architecture and structural conformation. Several studies have pointed out that ncRNAs participate in heart disease; however, the functions of ncRNAs still remain unclear. ncRNAs are involved in cellular fate, differentiation, proliferation and tissue regeneration, hinting at their potential therapeutic applications. Here, we review the current understanding of both the biological functions and molecular mechanisms of ncRNAs in heart disease and describe some of the ncRNAs that have potential heart regeneration effects. Keywords: Non-coding RNAs, Cardiac regeneration, Cardiac fate, Proliferation, Differentiation, Reprograming

  2. Improvements to Busquet's Non LTE algorithm in NRL's Hydro code

    Science.gov (United States)

    Klapisch, M.; Colombant, D.

    1996-11-01

    Implementation of the Non LTE model RADIOM (M. Busquet, Phys. Fluids B, 5, 4191 (1993)) in NRL's RAD2D Hydro code in conservative form was reported previously(M. Klapisch et al., Bull. Am. Phys. Soc., 40, 1806 (1995)).While the results were satisfactory, the algorithm was slow and not always converging. We describe here modifications that address the latter two shortcomings. This method is quicker and more stable than the original. It also gives information about the validity of the fitting. It turns out that the number and distribution of groups in the multigroup diffusion opacity tables - a basis for the computation of radiation effects in the ionization balance in RADIOM- has a large influence on the robustness of the algorithm. These modifications give insight about the algorithm, and allow to check that the obtained average charge state is the true average. In addition, code optimization resulted in greatly reduced computing time: The ratio of Non LTE to LTE computing times being now between 1.5 and 2.

  3. Verification of codes used for the nuclear safety assessment of the small space heterogeneous reactors with zirconium hydride moderator

    International Nuclear Information System (INIS)

    Glushkov, E.S.; Gomin, E.A.; Kompaniets, G.V.

    1994-01-01

    Computer codes used for assessment of nuclear safety for space NPP are compared taking as an example small-sized heterogeneous reactor with zirconium hydride moderator of the Topaz-2 facility. The code verifications are made for five different variants

  4. Conservation of Salmonella infection mechanisms in plants and animals.

    Directory of Open Access Journals (Sweden)

    Adam Schikora

    Full Text Available Salmonella virulence in animals depends on effectors injected by Type III Secretion Systems (T3SSs. In this report we demonstrate that Salmonella mutants that are unable to deliver effectors are also compromised in infection of Arabidopsis thaliana plants. Transcriptome analysis revealed that in contrast to wild type bacteria, T3SS mutants of Salmonella are compromised in suppressing highly conserved Arabidopsis genes that play a prominent role during Salmonella infection of animals. We also found that Salmonella originating from infected plants are equally virulent for human cells and mice. These results indicate a high degree of conservation in the defense and infection mechanism of animal and plant hosts during Salmonella infection.

  5. Modification of Salmonella Typhimurium motility by the probiotic yeast strain Saccharomyces boulardii.

    Directory of Open Access Journals (Sweden)

    Rodolphe Pontier-Bres

    Full Text Available BACKGROUND: Motility is an important component of Salmonella enterica serovar Typhimurium (ST pathogenesis allowing the bacteria to move into appropriate niches, across the mucus layer and invade the intestinal epithelium. In vitro, flagellum-associated motility is closely related to the invasive properties of ST. The probiotic yeast Saccharomyces boulardii BIOCODEX (S.b-B is widely prescribed for the prophylaxis and treatment of diarrheal diseases caused by bacteria or antibiotics. In case of Salmonella infection, S.b-B has been shown to decrease ST invasion of T84 colon cell line. The present study was designed to investigate the impact of S.b-B on ST motility. METHODOLOGY/PRINCIPAL FINDINGS: Experiments were performed on human colonic T84 cells infected by the Salmonella strain 1344 alone or in the presence of S.b-B. The motility of Salmonella was recorded by time-lapse video microscopy. Next, a manual tracking was performed to analyze bacteria dynamics (MTrackJ plugin, NIH image J software. This revealed that the speed of bacterial movement was modified in the presence of S.b-B. The median curvilinear velocity (CLV of Salmonella incubated alone with T84 decreased from 43.3 µm/sec to 31.2 µm/sec in the presence of S.b-B. Measurement of track linearity (TL showed similar trends: S.b-B decreased by 15% the number of bacteria with linear tract (LT and increased by 22% the number of bacteria with rotator tract (RT. Correlation between ST motility and invasion was further established by studying a non-motile flagella-deficient ST strain. Indeed this strain that moved with a CLV of 0.5 µm/sec, presented a majority of RT and a significant decrease in invasion properties. Importantly, we show that S.b-B modified the motility of the pathogenic strain SL1344 and significantly decreased invasion of T84 cells by this strain. CONCLUSIONS: This study reveals that S.b-B modifies Salmonella's motility and trajectory which may account for the modification

  6. Validation of a Salmonella loop-mediated isothermal amplification assay in animal food.

    Science.gov (United States)

    Domesle, Kelly J; Yang, Qianru; Hammack, Thomas S; Ge, Beilei

    2018-01-02

    Loop-mediated isothermal amplification (LAMP) has emerged as a promising alternative to PCR for pathogen detection in food testing and clinical diagnostics. This study aimed to validate a Salmonella LAMP method run on both turbidimetry (LAMP I) and fluorescence (LAMP II) platforms in representative animal food commodities. The U.S. Food and Drug Administration (FDA)'s culture-based Bacteriological Analytical Manual (BAM) method was used as the reference method and a real-time quantitative PCR (qPCR) assay was also performed. The method comparison study followed the FDA's microbiological methods validation guidelines, which align well with those from the AOAC International and ISO. Both LAMP assays were 100% specific among 300 strains (247 Salmonella of 185 serovars and 53 non-Salmonella) tested. The detection limits ranged from 1.3 to 28 cells for six Salmonella strains of various serovars. Six commodities consisting of four animal feed items (cattle feed, chicken feed, horse feed, and swine feed) and two pet food items (dry cat food and dry dog food) all yielded satisfactory results. Compared to the BAM method, the relative levels of detection (RLODs) for LAMP I ranged from 0.317 to 1 with a combined value of 0.610, while those for LAMP II ranged from 0.394 to 1.152 with a combined value of 0.783, which all fell within the acceptability limit (2.5) for an unpaired study. This also suggests that LAMP was more sensitive than the BAM method at detecting low-level Salmonella contamination in animal food and results were available 3days sooner. The performance of LAMP on both platforms was comparable to that of qPCR but notably faster, particularly LAMP II. Given the importance of Salmonella in animal food safety, the LAMP assays validated in this study holds great promise as a rapid, reliable, and robust method for routine screening of Salmonella in these commodities. Published by Elsevier B.V.

  7. Modification of Salmonella Typhimurium Motility by the Probiotic Yeast Strain Saccharomyces boulardii

    Science.gov (United States)

    Pontier-Bres, Rodolphe; Prodon, François; Munro, Patrick; Rampal, Patrick; Lemichez, Emmanuel; Peyron, Jean François; Czerucka, Dorota

    2012-01-01

    Background Motility is an important component of Salmonella enterica serovar Typhimurium (ST) pathogenesis allowing the bacteria to move into appropriate niches, across the mucus layer and invade the intestinal epithelium. In vitro, flagellum-associated motility is closely related to the invasive properties of ST. The probiotic yeast Saccharomyces boulardii BIOCODEX (S.b-B) is widely prescribed for the prophylaxis and treatment of diarrheal diseases caused by bacteria or antibiotics. In case of Salmonella infection, S.b-B has been shown to decrease ST invasion of T84 colon cell line. The present study was designed to investigate the impact of S.b-B on ST motility. Methodology/Principal Findings Experiments were performed on human colonic T84 cells infected by the Salmonella strain 1344 alone or in the presence of S.b-B. The motility of Salmonella was recorded by time-lapse video microscopy. Next, a manual tracking was performed to analyze bacteria dynamics (MTrackJ plugin, NIH image J software). This revealed that the speed of bacterial movement was modified in the presence of S.b-B. The median curvilinear velocity (CLV) of Salmonella incubated alone with T84 decreased from 43.3 µm/sec to 31.2 µm/sec in the presence of S.b-B. Measurement of track linearity (TL) showed similar trends: S.b-B decreased by 15% the number of bacteria with linear tract (LT) and increased by 22% the number of bacteria with rotator tract (RT). Correlation between ST motility and invasion was further established by studying a non-motile flagella-deficient ST strain. Indeed this strain that moved with a CLV of 0.5 µm/sec, presented a majority of RT and a significant decrease in invasion properties. Importantly, we show that S.b-B modified the motility of the pathogenic strain SL1344 and significantly decreased invasion of T84 cells by this strain. Conclusions This study reveals that S.b-B modifies Salmonella's motility and trajectory which may account for the modification of Salmonella

  8. Wind Noise Reduction using Non-negative Sparse Coding

    DEFF Research Database (Denmark)

    Schmidt, Mikkel N.; Larsen, Jan; Hsiao, Fu-Tien

    2007-01-01

    We introduce a new speaker independent method for reducing wind noise in single-channel recordings of noisy speech. The method is based on non-negative sparse coding and relies on a wind noise dictionary which is estimated from an isolated noise recording. We estimate the parameters of the model ...... and discuss their sensitivity. We then compare the algorithm with the classical spectral subtraction method and the Qualcomm-ICSI-OGI noise reduction method. We optimize the sound quality in terms of signal-to-noise ratio and provide results on a noisy speech recognition task....

  9. Molecular study on some antibiotic resistant genes in Salmonella spp. isolates

    Science.gov (United States)

    Nabi, Ari Q.

    2017-09-01

    Studying the genes related with antimicrobial resistance in Salmonella spp. is a crucial step toward a correct and faster treatment of infections caused by the pathogen. In this work Integron mediated antibiotic resistant gene IntI1 (Class I Integrase IntI1) and some plasmid mediated antibiotic resistance genes (Qnr) were scanned among the isolated non-Typhoid Salmonellae strains with known resistance to some important antimicrobial drugs using Sybr Green real time PCR. The aim of the study was to correlate the multiple antibiotics and antimicrobial resistance of Salmonella spp. with the presence of integrase (IntI1) gene and plasmid mediated quinolone resistant genes. Results revealed the presence of Class I Integrase gene in 76% of the isolates with confirmed multiple antibiotic resistances. Moreover, about 32% of the multiple antibiotic resistant serotypes showed a positive R-PCR for plasmid mediated qnrA gene encoding for nalidixic acid and ciprofloxacin resistance. No positive results could be revealed form R-PCRs targeting qnrB or qnrS. In light of these results we can conclude that the presence of at least one of the qnr genes and/or the presence of Integrase Class I gene were responsible for the multiple antibiotic resistance to for nalidixic acid and ciprofloxacin from the studied Salmonella spp. and further studies required to identify the genes related with multiple antibiotic resistance of the pathogen.

  10. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.

    Science.gov (United States)

    Kress, W John; Erickson, David L

    2007-06-06

    A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

  11. Incidence of Salmonella contamination in broiler chickens in Saskatchewan.

    Science.gov (United States)

    Bhargava, K K; O'Neil, J B; Prior, M G; Dunkelgod, K E

    1983-01-01

    The incidence of Salmonella contamination in ten Saskatchewan broiler flocks varying in size from 6 200 to 14 000 was investigated from February, 1977 to April, 1979. Prior to the initial chick placement, brooding equipment, feed, water and fresh litter samples were found to be free of Salmonellae. Samples obtained from the clean and disinfected processing plant equipment before the commencement of daily operation were negative except the isolation for Salmonella anatum from the fingers of the defeathering machine in flock 4. There was no evidence of Salmonella contamination in flocks 5, 6, 8 and 10. The incidence of Salmonella was lower when cloacal swabs were taken from day old chicks fasted for 48 hours than for the same groups of chicks when carcasses were blended in nutrient broth (flocks 7 and 9). The blending of such chicks appears to be a more critical test. The serotypes isolated from eviscerated birds were the same as those isolated from used litter samples. Salmonella saintpaul was isolated from a water sample at 53 days in flock 1 and the same serotype was recovered from the intestinal contents and skin of eviscerated birds. Salmonella typhimurium was recovered from the eviscerated birds and neck samples in flock 3. In flock 4, S. saintpaul and S. anatum were isolated from 13% of the eviscerated birds sampled. Salmonella thompson, Salmonella agona and Salmonella heidelberg were recovered from 61%, 5% and 1%, respectively, of the processed carcasses sampled in flock 7.

  12. Risks Involved in the Use of Enrofloxacin for Salmonella Enteritidis or Salmonella Heidelberg in Commercial Poultry.

    Science.gov (United States)

    Morales-Barrera, Eduardo; Calhoun, Nicole; Lobato-Tapia, Jose L; Lucca, Vivian; Prado-Rebolledo, Omar; Hernandez-Velasco, Xochitl; Merino-Guzman, Ruben; Petrone-García, Victor M; Latorre, Juan D; Mahaffey, Brittany D; Teague, Kyle D; Graham, Lucas E; Wolfenden, Amanda D; Baxter, Mikayla F A; Hargis, Billy M; Tellez, Guillermo

    2016-01-01

    The objectives of the present study were to evaluate the risks involved in the use of Enrofloxacin for Salmonella Enteritidis (SE) or Salmonella Heidelberg (SH) in commercial poultry and determine the effects of a probiotic as an antibiotic alternative. Two experiments were conducted to evaluate the risks involved in the use of Enrofloxacin for SE or SH in commercial poultry. Experiment 1 consisted of two trials. In each trial, chickens were assigned to one of three groups; control + SE challenged; Enrofloxacin 25 mg/kg + SE; and Enrofloxacin 50 mg/kg + SE. Chickens received Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, all groups received fresh water without any treatment. All chickens were orally gavaged with 10(7) cfu/chick of SE at 7 days of age and euthanized on 8 days of age. In Experiment 2, turkey poults were assigned to one of the three groups; control + SH; probiotic + SH; and Enrofloxacin 50 mg/kg + SH. Poults received probiotic or Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, poults received fresh water without any treatment. Poults were orally gavaged with 10(7) cfu/poult of SH at 7 days of age. Poults were weighed and humanely killed 24 h post-SH challenge to evaluate serum concentration of fluorescein isothiocyanate-dextran to evaluate intestinal permeability, metagenomics, and SH infection. In both trials of Experiment 1, chickens treated with Enrofloxacin were more susceptible to SE organ invasion and intestinal colonization when compared with control non-treated chickens (P Enrofloxacin showed an increase in body weight, however, this group also showed an increase in SH susceptibility, intestinal permeability, and lower proportion of Firmicutes and Bacteroidetes, but with control group had the highest proportion of Proteobacteria. By contrast, poults that received the probiotic had the highest proportion of Firmicutes and Bacteroidetes, but lowest

  13. Salmonella serovar spectrum associated with reptiles in Poland

    Directory of Open Access Journals (Sweden)

    Tomasz Piasecki

    2014-01-01

    Full Text Available This study aimed to evaluate the incidence of Salmonella isolates from a wide variety of reptiles in Poland. A total of 374 faecal samples from chelonians, lizards and snakes were collected between 2009 and 2012. The nested, two-step PCR and multiplex PCR were performed to access the incidence and to characterize Salmonella isolates. Salmonella strains were found in 122 of 374 samples (32.6%. Among the different reptilian species, Salmonella strains were found in 58 samples from lizards (38.9%, 31 samples from snakes (28.7% and 33 samples from chelonians (28.2%. Of the total of 122 strains, 72 belonged to the species Salmonella enterica subsp. enterica, 20 to the species S. enterica subs. salamae or S. enterica subs. houtanae. The incidence of S. enterica subs. diarizonae and S. enterica subs. indica was low, constituting less than 3.5% of the examined population. The findings show that reptiles can be considered as a reservoir for Salmonella and hence could pose a zoonotic hazard. In addition, multiplex PCR assay is a rapid, specific and easy-to-perform method and might be applied for rapid screening of large numbers of Salmonella samples.

  14. Salmonella Typhimurium infection in the porcine intestine

    DEFF Research Database (Denmark)

    Schauser, Kirsten; Olsen, John Elmerdahl; Larsson, Lars-Inge

    2005-01-01

    The normal intestinal epithelium is renewed with a turnover rate of 3-5 days. During Salmonella infection increased cell loss is observed, possibly as a result of programmed cell death (PCD). We have, therefore, studied the effects of Salmonella Typhimurium infection on three elements involved...... in scattered epithelial cells and the number of positive cells increased with increasing times of exposure to Salmonella (P

  15. Overexpression of MicA induces production of OmpC-enriched outer membrane vesicles that protect against Salmonella challenge.

    Science.gov (United States)

    Choi, Hyun-Il; Kim, Moonjeong; Jeon, Jinseong; Han, Jin Kwan; Kim, Kwang-Sun

    2017-08-26

    Outer membrane vesicles (OMVs) derived from bacteria are promising candidates for subunit vaccines. Stresses that modulate the composition of outer membrane proteins (OMPs) are important for OMV synthesis. Small RNAs (sRNAs) expressed in response to stress regulate OMPs, although the mechanism underlying sRNA-mediated OMV biogenesis and its utility for developing vaccine platforms remains to be elucidated. Here, we characterized the role of a sRNA, MicA, which regulates OmpA, a major OMP involved in both production of OMVs and reactive immunity against Salmonella challenge. A Salmonella strain overexpressing MicA generated more OMVs than a control strain. In addition, OmpC was the major component of MicA-derived OMV proteins. MicA-derived OMVs induced Th1- and Th17-type immune responses in vitro and reduced Salmonella-mediated lethality in a mouse model. Thus, OmpA-regulatory sRNA-derived OMVs may facilitate production of Salmonella-protective vaccines. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Occurrence and antimicrobial resistance of Salmonella spp. isolated from food other than meat in Poland

    Directory of Open Access Journals (Sweden)

    Łukasz Mąka

    2015-09-01

    Full Text Available Introduction and objectives. Antimicrobial resistance of pathogenic bacteria can result in therapy failure, increased hospitalization, and increased risk of death. In Poland, [i]Salmonella[/i] spp. is a major bacterial agent of food poisoning. The majority of studies on antimicrobial resistance in [i]Salmonella[/i] spp. isolates from food have focused on meat products as the source of this pathogen. In comparison, this study examines the antimicrobial susceptibility of [i]Salmonella[/i] spp. isolated from retail food products other than meat in Poland. Materials and Methods. A collection of 122 [i]Salmonella[/i] spp. isolates were isolated in Poland in 2008–2012 from foods other than meat: confectionery products, eggs, fruits, vegetables, spices and others. The resistance of these isolates to 19 antimicrobial agents was tested using the disc diffusion method. Results. [i]Salmonella[/i] Enteritidis was the most frequently identified serotype (84.4% of all tested isolates. In total, 42.6% of the [i]Salmonella[/i] spp. isolates were resistant to antibiotics. The highest frequencies of resistance were observed in isolates from 2009 (60.0% and 2012 (59.5%. Antibiotic resistance was most prevalent among [i]Salmonella[/i] spp. isolated from egg-containing food samples (68.0%. Resistance to nalidixic acid was most common and was observed in 35.2% of all tested isolates. The isolates were less frequently resistant to sulphonamides (6.6%, ampicillin (4.9%, amoxicillin/clavulanic acid (2.5% and to streptomycin, cefoxitin, gentamicin and tetracycline (1.6%. Only one isolate showed resistance to chloramphenicol. Four isolates displayed multiresistance. Conclusions. Although, the level of resistance and multiresistance of [i]Salmonella[/i] spp. isolates from non-meat foods was lower than in those from meat products, the presence of these resistant bacteria poses a real threat to the health of consumers.

  17. Applications of microscopy in Salmonella research.

    Science.gov (United States)

    Malt, Layla M; Perrett, Charlotte A; Humphrey, Suzanne; Jepson, Mark A

    2015-01-01

    Salmonella enterica is a Gram-negative enteropathogen that can cause localized infections, typically resulting in gastroenteritis, or systemic infection, e.g., typhoid fever, in humans and many other animals. Understanding the mechanisms by which Salmonella induces disease has been the focus of intensive research. This has revealed that Salmonella invasion requires dynamic cross-talk between the microbe and host cells, in which bacterial adherence rapidly leads to a complex sequence of cellular responses initiated by proteins translocated into the host cell by a type 3 secretion system. Once these Salmonella-induced responses have resulted in bacterial invasion, proteins translocated by a second type 3 secretion system initiate further modulation of cellular activities to enable survival and replication of the invading pathogen. Elucidation of the complex and highly dynamic pathogen-host interactions ultimately requires analysis at the level of single cells and single infection events. To achieve this goal, researchers have applied a diverse range of microscopy techniques to analyze Salmonella infection in models ranging from whole animal to isolated cells and simple eukaryotic organisms. For example, electron microscopy and high-resolution light microscopy techniques such as confocal microscopy can reveal the precise location of Salmonella and its relationship to cellular components. Widefield light microscopy is a simpler approach with which to study the interaction of bacteria with host cells and often has advantages for live cell imaging, enabling detailed analysis of the dynamics of infection and cellular responses. Here we review the use of imaging techniques in Salmonella research and compare the capabilities of different classes of microscope to address specific types of research question. We also provide protocols and notes on some microscopy techniques used routinely in our own research.

  18. Simultaneous oral administration of Salmonella Infantis and S. Typhimurium in chicks.

    Science.gov (United States)

    Murakami, Koichi; Maeda-Mitani, Eriko; Onozuka, Daisuke; Noda, Tamie; Sera, Nobuyuki; Kimura, Hirokazu; Fujimoto, Shuji; Murakami, Satoshi

    2017-01-01

    To confirm the hypothesis that Salmonella enterica subspecies enterica serovar ( S. ) Infantis has higher basic reproductive rates in chicks compared with other Salmonella serovars, 1-day-old specific-pathogen-free chicks ( n  = 8) were challenged simultaneously with S. Infantis and S. Typhimurium per os . Challenged chicks (Group A) were then housed with non-infected chicks (Group B, n  = 4) for 6 days (from 2 to 8 days of age). Group B birds were then housed with other non-infected birds (Group C, n  = 4), which were then transferred to cages containing a further group of untreated chicks (Group D, n  = 2). A control group consisting of four non-infected chicks was used for comparison. All chickens were humanely sacrificed at 18 days of age, and Salmonella from bowel and liver samples were enumerated. Both serovars were isolated from all groups except the control group. S. Typhimurium was isolated at a greater frequency than S. Infantis from the bowel samples of chicks from Groups B, C and D, while no differences in colonisation rates were observed between the two serovars in liver samples from Groups B, C and D. S. Typhimurium, but not S. Infantis, was immunohistochemically detected in the lamina propria of the cecum and rectum in five birds of Group A. Despite the competitive administration, neither of the two serovars completely excluded the other, and no differences were observed in basic reproductive rates between the two serovars. These findings, together with data from previous studies, suggest that the initial quantitative domination of S. Infantis in chicken flocks may explain why this serovar is predominant in broiler chickens.

  19. Epidemiological studies on salmonella in a certain area ("Walcheren project") III. The presence of salmonella in man, insects, seagulls and in foods, chopping-block scrapings from butcher's shops, effluent of sewage treatment plants and drains of butcher's shops.

    Science.gov (United States)

    Edel, W; van Schothorst, M; van Leusden, F M; Kampelmacher, E H

    1978-12-01

    For a period of three months in a relatively small area (Walcheren), various materials (meat and meat products, insects, seagull droppings, chopping-block scrapings from butcher's shops, effluent of sewage treatment plants, drains from butcher's shops and stools of patients) were examined again for the presence of Salmonella as a continuation of previous investigations. As had been the case in previous studies, S. typhimurium (27.5%), S. panama (22.2%) and S. brandenburg (9.2%) were the three most frequently isolated serotypes. The three most frequently isolated phage types of S. typhimurium were II 505 (62.1%) II 502 (5.3%) and I 650 (4.2%). The serotypes and phage types were present in almost all the materials examined which again emphasizes the fact that there are contamination cycles of Salmonella. These studies show that the route of contamination divides in the butcher's shops. Salmonella organisms carried with the meat from the slaughter-house find their way into the drains on the one hand, and through meat and meat products, to the consumer on the other. Moreover, the high degree of contamination of effluent is not in accordance with the small number of cases of salmonellosis in man.

  20. A method of non-contact reading code based on computer vision

    Science.gov (United States)

    Zhang, Chunsen; Zong, Xiaoyu; Guo, Bingxuan

    2018-03-01

    With the purpose of guarantee the computer information exchange security between internal and external network (trusted network and un-trusted network), A non-contact Reading code method based on machine vision has been proposed. Which is different from the existing network physical isolation method. By using the computer monitors, camera and other equipment. Deal with the information which will be on exchanged, Include image coding ,Generate the standard image , Display and get the actual image , Calculate homography matrix, Image distort correction and decoding in calibration, To achieve the computer information security, Non-contact, One-way transmission between the internal and external network , The effectiveness of the proposed method is verified by experiments on real computer text data, The speed of data transfer can be achieved 24kb/s. The experiment shows that this algorithm has the characteristics of high security, fast velocity and less loss of information. Which can meet the daily needs of the confidentiality department to update the data effectively and reliably, Solved the difficulty of computer information exchange between Secret network and non-secret network, With distinctive originality, practicability, and practical research value.

  1. Comprehensive Reconstruction and Visualization of Non-Coding Regulatory Networks in Human

    Science.gov (United States)

    Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

    2014-01-01

    Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape. PMID:25540777

  2. Comprehensive reconstruction and visualization of non-coding regulatory networks in human.

    Science.gov (United States)

    Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

    2014-01-01

    Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.

  3. The Genome sequences of four non-human/non-clinical Salmonella enterica serovar Kentucky ST198 isolates recovered between 1972 and 1973

    Science.gov (United States)

    Salmonella Kentucky is a polyphyletic member of S. enterica subclade A1 with multiple sequence types that often colonize the same hosts but in different frequencies on different continents. To evaluate the genomic features involved in S. Kentucky host specificity we sequenced the genomes of four iso...

  4. A role for the non-canonical Wnt-ß-Catenin and TGF-ß signaling pathways in the induction of tolerance during the establishment of a Salmonella enterica serovar Enteritidis persistent cecal infection in chickens

    Science.gov (United States)

    Non-typhoidal Salmonella enterica induce an early pro-inflammatory response in chickens. However, the response is short-lived, asymptomatic of disease, resulting in a persistent colonization of the ceca, and fecal shedding of bacteria. The underlying mechanisms that control this persistent infecti...

  5. Non-Coding RNAs in Castration-Resistant Prostate Cancer: Regulation of Androgen Receptor Signaling and Cancer Metabolism.

    Science.gov (United States)

    Shih, Jing-Wen; Wang, Ling-Yu; Hung, Chiu-Lien; Kung, Hsing-Jien; Hsieh, Chia-Ling

    2015-12-04

    Hormone-refractory prostate cancer frequently relapses from therapy and inevitably progresses to a bone-metastatic status with no cure. Understanding of the molecular mechanisms conferring resistance to androgen deprivation therapy has the potential to lead to the discovery of novel therapeutic targets for type of prostate cancer with poor prognosis. Progression to castration-resistant prostate cancer (CRPC) is characterized by aberrant androgen receptor (AR) expression and persistent AR signaling activity. Alterations in metabolic activity regulated by oncogenic pathways, such as c-Myc, were found to promote prostate cancer growth during the development of CRPC. Non-coding RNAs represent a diverse family of regulatory transcripts that drive tumorigenesis of prostate cancer and various other cancers by their hyperactivity or diminished function. A number of studies have examined differentially expressed non-coding RNAs in each stage of prostate cancer. Herein, we highlight the emerging impacts of microRNAs and long non-coding RNAs linked to reactivation of the AR signaling axis and reprogramming of the cellular metabolism in prostate cancer. The translational implications of non-coding RNA research for developing new biomarkers and therapeutic strategies for CRPC are also discussed.

  6. Reorganization of the Endosomal System in Salmonella-Infected Cells: The Ultrastructure of Salmonella-Induced Tubular Compartments

    Science.gov (United States)

    Krieger, Viktoria; Liebl, David; Zhang, Yuying; Rajashekar, Roopa; Chlanda, Petr; Giesker, Katrin; Chikkaballi, Deepak; Hensel, Michael

    2014-01-01

    During the intracellular life of Salmonella enterica, a unique membrane-bound compartment termed Salmonella-containing vacuole, or SCV, is formed. By means of translocated effector proteins, intracellular Salmonella also induce the formation of extensive, highly dynamic membrane tubules termed Salmonella-induced filaments or SIF. Here we report the first detailed ultrastructural analyses of the SCV and SIF by electron microscopy (EM), EM tomography and live cell correlative light and electron microscopy (CLEM). We found that a subset of SIF is composed of double membranes that enclose portions of host cell cytosol and cytoskeletal filaments within its inner lumen. Despite some morphological similarities, we found that the formation of SIF double membranes is independent from autophagy and requires the function of the effector proteins SseF and SseG. The lumen of SIF network is accessible to various types of endocytosed material and our CLEM analysis of double membrane SIF demonstrated that fluid phase markers accumulate only between the inner and outer membrane of these structures, a space continual with endosomal lumen. Our work reveals how manipulation of the endosomal membrane system by an intracellular pathogen results in a unique tubular membrane compartmentalization of the host cell, generating a shielded niche permissive for intracellular proliferation of Salmonella. PMID:25254663

  7. Salmonella spp. on chicken carcasses in processing plants in Poland.

    Science.gov (United States)

    Mikołajczyk, Anita; Radkowski, Mieczysław

    2002-09-01

    Chickens at selected points in the slaughter process and after slaughter on the dressing line in poultry plants were sampled and analyzed for Salmonella. These chickens came from the northeast part of Poland. The examinations were carried out in quarters I, II, III, and IV of 1999. All the birds were determined to be healthy by a veterinary inspection. Swab samples were taken from the cloaca after stunning and from the skin surface and body cavity of the whole bird after evisceration, after rinsing at the final rinse station but before chilling in the spin-chiller, and after cooling in the continuous cooling plant at the end of the production day. In 1999, 400 whole chickens were examined. The percentage of these 400 chickens from which Salmonella spp. were isolated was relatively high (23.75%; Salmonella-positive results were observed in 95 cases). Salmonella spp. were found after stunning in 6% of the chickens (6 of 100 samples), after evisceration in 24% (24 of 100), before cooling in 52% (52 of 100), and after cooling in 13% (13 of 100). These results show that Salmonella spp. were found more often at some processing points than at others. The lowest Salmonella spp. contamination rate (6%) for slaughter birds was found after stunning, and the highest contamination rate was found before chilling (52%). The serological types of Salmonella spp. isolated from whole chickens were Salmonella Enteritidis, Salmonella Typhimurium, Salmonella Saintpaul, Salmonella Agona, and Salmonella Infantis. The results of these investigations indicate that Salmonella Enteritidis is the dominant serological type in infections of slaughter chickens, as it is in many countries.

  8. 9 CFR 113.30 - Detection of Salmonella contamination.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Detection of Salmonella contamination... REQUIREMENTS Standard Procedures § 113.30 Detection of Salmonella contamination. The test for detection of Salmonella contamination provided in this section shall be conducted when such a test is prescribed in an...

  9. Characterization of a multidrug resistant Salmonella enterica give ...

    African Journals Online (AJOL)

    Salmonella enterica Give is one of the serotypes that have been incriminated in Salmonella infections; sometimes associated with hospitalization and mortalities in humans and animals in some parts of the world. In this work, we characterized one Salmonella Give isolated from cloaca swab of an Agama agama lizard ...

  10. Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.

    Science.gov (United States)

    Gussow, Ayal B; Copeland, Brett R; Dhindsa, Ryan S; Wang, Quanli; Petrovski, Slavé; Majoros, William H; Allen, Andrew S; Goldstein, David B

    2017-01-01

    There is broad agreement that genetic mutations occurring outside of the protein-coding regions play a key role in human disease. Despite this consensus, we are not yet capable of discerning which portions of non-coding sequence are important in the context of human disease. Here, we present Orion, an approach that detects regions of the non-coding genome that are depleted of variation, suggesting that the regions are intolerant of mutations and subject to purifying selection in the human lineage. We show that Orion is highly correlated with known intolerant regions as well as regions that harbor putatively pathogenic variation. This approach provides a mechanism to identify pathogenic variation in the human non-coding genome and will have immediate utility in the diagnostic interpretation of patient genomes and in large case control studies using whole-genome sequences.

  11. Evaluation of 3M molecular detection assay (MDA) Salmonella for the detection of Salmonella in selected foods: collaborative study.

    Science.gov (United States)

    Bird, Patrick; Fisher, Kiel; Boyle, Megan; Huffman, Travis; Benzinger, M Joseph; Bedinghaus, Paige; Flannery, Jonathan; Crowley, Erin; Agin, James; Goins, David; Benesh, DeAnn; David, John

    2013-01-01

    The 3M Molecular Detection Assay (MDA) Salmonella is used with the 3M Molecular Detection System for the detection of Salmonella spp. in food, food-related, and environmental samples after enrichment. The assay utilizes loop-mediated isothermal amplification to rapidly amplify Salmonella target DNA with high specificity and sensitivity, combined with bioluminescence to detect the amplification. The 3M MDA Salmonella method was compared using an unpaired study design in a multilaboratory collaborative study to the U.S. Department of Agriculture/Food Safety and Inspection Service-Microbiology Laboratory Guidebook (USDA/FSIS-MLG 4.05), Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg and Catfish Products for raw ground beef and the U.S. Food and Drug Administration/Bacteriological Analytical Manual (FDA/BAM) Chapter 5 Salmonella reference method for wet dog food following the current AOAC guidelines. A total of 20 laboratories participated. For the 3M MDA Salmonella method, raw ground beef was analyzed using 25 g test portions, and wet dog food was analyzed using 375 g test portions. For the reference methods, 25 g test portions of each matrix were analyzed. Each matrix was artificially contaminated with Salmonella at three inoculation levels: an uninoculated control level (0 CFU/test portion), a low inoculum level (0.2-2 CFU/test portion), and a high inoculum level (2-5 CFU/test portion). In this study, 1512 unpaired replicate samples were analyzed. Statistical analysis was conducted according to the probability of detection (POD). For the low-level raw ground beef test portions, the following dLPOD (difference between the POD of the reference and candidate method) values with 95% confidence intervals were obtained: -0.01 (-0.14, +0.12). For the low-level wet dog food test portions, the following dLPOD with 95% confidence intervals were obtained: -0.04 (-0.16, +0.09). No significant differences were observed in the number of positive

  12. Investigations of multiresistance to antibiotics and chemotherapeutics and extended spectrum beta: Lactamase effect (ESBL test in strains E.coli and salmonella originating from domestic animals

    Directory of Open Access Journals (Sweden)

    Mišić Dušan

    2006-01-01

    Full Text Available The presence of multiresistance to the effects of antibiotics and chemotherapeutics and extended spectrum beta-lactamase were examined in 45 strains of E. coli and 35 strains of Salmonella. The strains of E. coli originated from several species of domestic animals: dogs, cats, poultry, and cattle, and 30 strains of Salmonella originated from poultry, 4 strains from cattle, and 1 strain from swine. The presence of the following serovarieties was established using serological examinations: Salmonella Enteritidis 17 strains, Salmonella Gallinarum 1 strain, Salmonella Hartford 5 strains, Salmonella Anatum 1 strain, Salmonella Typhimurium 4 strains, Salmonella Agona 1 strain, Salmonella Infantis 1 strain, Salmonella Thompson var. Berlin 1 strain, Salmonella Tennessee 1 strain, Salmonella Senftenberg 1 strain, Salmonella Glostrup 1 strain, and Salmonella Hadar 1 strain. In the examinations of the listed strains we used antibiogram discs of ampicillin, amoxicillin with clavulanic acid, cephalexin, cephtriaxon, cephotaxim, cephtazidime, aztreonam, gentamycin, chloramphenicol, tetracycline, cyprofloxacine, and a combination of sulphamethoxasole and trimethoprim. The lowest prevalence of multiresistance in E. Coli strains to 3 or more antibiotics was established in dogs 20%, and the highest in 60% strains originating from swine. In 62.88% strains of Salmonella we established sensitivity to all applied antibiotics. Resistance was also established in a small number of the examined strains to ampicillin (11 strains, to tetracycline (5 strains, to amoxicillin with clavulanic acid (5 strains, to sulphamethoxasole with trimethoprim (5 strains, to gentamycin (3 strains, and to cloramphenicol (1 strain. Of all the examined strains of Salmonella, 6 strains originating from poultry exhibited multiresistence. The presence of extended spectrum beta-lactamase effects examined using the ESBL test, was not established in strains of E. coli and Salmonella strains.

  13. Interactions of Salmonella with animals and plants.

    Science.gov (United States)

    Wiedemann, Agnès; Virlogeux-Payant, Isabelle; Chaussé, Anne-Marie; Schikora, Adam; Velge, Philippe

    2014-01-01

    Salmonella enterica species are Gram-negative bacteria, which are responsible for a wide range of food- and water-borne diseases in both humans and animals, thereby posing a major threat to public health. Recently, there has been an increasing number of reports, linking Salmonella contaminated raw vegetables and fruits with food poisoning. Many studies have shown that an essential feature of the pathogenicity of Salmonella is its capacity to cross a number of barriers requiring invasion of a large variety of cells and that the extent of internalization may be influenced by numerous factors. However, it is poorly understood how Salmonella successfully infects hosts as diversified as animals or plants. The aim of this review is to describe the different stages required for Salmonella interaction with its hosts: (i) attachment to host surfaces; (ii) entry processes; (iii) multiplication; (iv) suppression of host defense mechanisms; and to point out similarities and differences between animal and plant infections.

  14. Interactions of Salmonella with animals and plants

    Directory of Open Access Journals (Sweden)

    Agnès eWiedemann

    2015-01-01

    Full Text Available Salmonella enterica species is a Gram negative bacterium, which is responsible for a wide range of food- and water-borne diseases in both humans and animals, thereby posing a major threat to public health. Recently, there has been an increasing number of reports, linking Salmonella contaminated raw vegetables and fruit with food poisoning. Many studies have shown that an essential feature of the pathogenicity of Salmonella is its capacity to cross a number of barriers requiring invasion of a large variety of cells and that the extent of internalization may be influenced by numerous factors. However, it is poorly understood how Salmonella successfully infects hosts as diversified as animals or plants. The aim of this review is to describe the different stages required for Salmonella interaction with its hosts: (i attachment to host surfaces; (ii entry processes; (iii, multiplication; (iv suppression of host defence mechanisms ; and to point out similarities and differences between animal and plant infections.

  15. Interactions of Salmonella with animals and plants

    Science.gov (United States)

    Wiedemann, Agnès; Virlogeux-Payant, Isabelle; Chaussé, Anne-Marie; Schikora, Adam; Velge, Philippe

    2015-01-01

    Salmonella enterica species are Gram-negative bacteria, which are responsible for a wide range of food- and water-borne diseases in both humans and animals, thereby posing a major threat to public health. Recently, there has been an increasing number of reports, linking Salmonella contaminated raw vegetables and fruits with food poisoning. Many studies have shown that an essential feature of the pathogenicity of Salmonella is its capacity to cross a number of barriers requiring invasion of a large variety of cells and that the extent of internalization may be influenced by numerous factors. However, it is poorly understood how Salmonella successfully infects hosts as diversified as animals or plants. The aim of this review is to describe the different stages required for Salmonella interaction with its hosts: (i) attachment to host surfaces; (ii) entry processes; (iii) multiplication; (iv) suppression of host defense mechanisms; and to point out similarities and differences between animal and plant infections. PMID:25653644

  16. Salmonella in beef and produce from honduras.

    Science.gov (United States)

    Maradiaga, Martha; Miller, Mark F; Thompson, Leslie; Pond, Ansen; Gragg, Sara E; Echeverry, Alejandro; Garcia, Lyda G; Loneragan, Guy H; Brashears, Mindy M

    2015-03-01

    Salmonella continues to cause a considerable number of foodborne illnesses worldwide. The sources of outbreaks include contaminated meat and produce. The purpose of this study was to establish an initial investigation of the burden of Salmonella in produce and beef from Honduras by sampling retail markets and abattoirs. Retail produce samples (cantaloupes, cilantro, cucumbers, leafy greens, peppers, and tomatoes; n = 573) were purchased in three major cities of Honduras, and retail whole-muscle beef (n = 555) samples were also purchased in four major cities. Additionally, both hide and beef carcass (n = 141) samples were collected from two Honduran abattoirs. Whole-muscle beef samples were obtained using a sponge hydrated with buffered peptone water, and 10 ml of the buffered peptone water rinsate of each produce sample was collected with a dry sponge and placed in a bag to be transported back to the United States. Salmonella was detected using a commercially available, closeplatform PCR system, and positive samples were subjected to culture on selective media to obtain isolates. Overall, the prevalence of Salmonella-positive samples, based on PCR detection in Honduras (n = 555) retail beef was 10.1% (95% confidence interval = 7.8, 12.9), whereas 7.8% (n = 141) of beef carcass and hides samples were positive in both beef plants. The overall Salmonella prevalence for all produce samples (n = 573) collected was 2.1% (95% confidence interval = 1.2, 3.6). The most common serotypes identified in Honduras were Salmonella Typhimurium followed by Derby. These results provide an indication of Salmonella contamination of beef and produce in Honduras. Developing a Salmonella baseline for Latin America through an initial investigation like the one presented here contributes to a broader global understanding of the potential exposure through food, thus providing insight into the needs for control strategies.

  17. Amoxicillin / Clavulanic Acid and Cefotaxime Resistance in Salmonella Minnesota and Salmonella Heidelberg from Broiler Chickens

    Directory of Open Access Journals (Sweden)

    Rodrigues IBBE

    2017-10-01

    Full Text Available This study investigated the resistance of various Salmonella strains to beta-lactam antibiotics. Salmonella Minnesota (36 strains and Salmonella Heidelberg (24 strains were isolated from broiler chickens and carcasses by the Disk Diffusion Test and resistance genes blaCTX-M-8, blaACC-1 and blaCMY-2 were detected by PCR. Of the 60 strains tested, 80% were resistant to at least one antibiotic. Specifically, 66.7% were resistant to amoxicillin/clavulanic acid and 75% were resistant to cefotaxime. Among the amoxicillin/clavulanic acid resistant strains, the blaCMY-2 gene was detected in 40%, blaACC-1 in 37.5% and blaCTX-M-8 in 7.5%. Among the cefotaxime resistant strains, we detected the genes blaCTX-M-8 in 13.3%, blaACC-1 in 33.3%, and blaCMY-2 in 31.1%. The presence of cefotaxime- and amoxicillin/clavulanic acid-resistant Salmonella in poultry, and the prevalence of extended spectrum betalactamases and AmpC-betalactamases in these strains are of huge concern to public health and economy.

  18. Salmonella enterica Induces And Subverts The Plant Immune System

    Directory of Open Access Journals (Sweden)

    Ana Victoria Garcia

    2014-04-01

    Full Text Available Infections with Salmonella enterica belong to the most prominent causes of food poisoning and infected fruits and vegetables represent important vectors for salmonellosis. Whereas it was shown that plants raise defense responses against Salmonella, these bacteria persist and proliferate in various plant tissues. Recent reports shed light into the molecular interaction between plants and Salmonella, highlighting the defense pathways induced and the means used by the bacteria to escape the plant immune system and accomplish colonization. It was recently shown that plants detect Salmonella pathogen-associated molecular patterns (PAMPs, such as the flagellin peptide flg22, and activate hallmarks of the defense program known as PAMP-triggered immunity (PTI. Interestingly, certain Salmonella strains carry mutations in the flg22 domain triggering PTI, suggesting that a strategy of Salmonella is to escape plant detection by mutating PAMP motifs. Another strategy may rely on the type III secretion system (T3SS as T3SS mutants were found to induce stronger plant defense responses than wild type bacteria. Although Salmonella effector delivery into plant cells has not been shown, expression of Salmonella effectors in plant tissues shows that these bacteria also possess powerful means to manipulate the plant immune system. Altogether, the data gathered suggest that Salmonella triggers PTI in plants and evolved strategies to avoid or subvert plant immunity.

  19. Salmonella enterica induces and subverts the plant immune system

    KAUST Repository

    García, Ana V.

    2014-04-04

    Infections with Salmonella enterica belong to the most prominent causes of food poisoning and infected fruits and vegetables represent important vectors for salmonellosis. Although it was shown that plants raise defense responses against Salmonella, these bacteria persist and proliferate in various plant tissues. Recent reports shed light into the molecular interaction between plants and Salmonella, highlighting the defense pathways induced and the means used by the bacteria to escape the plant immune system and accomplish colonization. It was recently shown that plants detect Salmonella pathogen-associated molecular patterns (PAMPs), such as the flagellin peptide flg22, and activate hallmarks of the defense program known as PAMP-triggered immunity (PTI). Interestingly, certain Salmonella strains carry mutations in the flg22 domain triggering PTI, suggesting that a strategy of Salmonella is to escape plant detection by mutating PAMP motifs. Another strategy may rely on the type III secretion system (T3SS) as T3SS mutants were found to induce stronger plant defense responses than wild type bacteria. Although Salmonella effector delivery into plant cells has not been shown, expression of Salmonella effectors in plant tissues shows that these bacteria also possess powerful means to manipulate the plant immune system. Altogether, these data suggest that Salmonella triggers PTI in plants and evolved strategies to avoid or subvert plant immunity. 2014 Garca and Hirt.

  20. Salmonella Yoruba infection in white-tufted-ear marmoset (Callithrix jacchus

    Directory of Open Access Journals (Sweden)

    Terezinha Knöbl

    2011-08-01

    Full Text Available The aim of this study was to describe a fatal salmonellosis case in a non-human female primate (Callithrix jacchus, found in the illegal pet trade in Brazil. The marmoset was sent to the quarantine section of the Guarulhos City Zoo and died in the sequence of an episode of profuse diarrhea. Necropsy findings included mucous enteritis, and liver enlargement and necrosis. Feces and liver fragments were collected for bacteriological tests, which indicated the presence of Salmonella sp.; it was subsequently characterized as pertaining to the Yoruba serotype. The susceptibility profile demonstrated resistance to tetracycline only. The strain was positive for genes that encoded the virulence factors investigated (invA, sefC, pefA and spvC. The results indicated the risk of introduction of Salmonella pathogenic serotypes in primates in captivity.

  1. Multiple antimicrobial resistance of Escherichia coli and Salmonella ...

    African Journals Online (AJOL)

    Presumptive isolates were subjected to antimicrobial susceptibility testing using 13 panels of antibiotics for both E. coli and Salmonella spp. Results showed that the overall isolation rate of Salmonella spp. was 12 (11.4%), broiler chickens had higher isolation rate 9 (12.0%) of Salmonella than local chickens. However, the ...

  2. Analysis of a small PWR core with the PARCS/Helios and PARCS/Serpent code systems

    International Nuclear Information System (INIS)

    Baiocco, G.; Petruzzi, A.; Bznuni, S.; Kozlowski, T.

    2017-01-01

    Highlights: • The consistency between Helios and Serpent few-group cross sections is shown. • The PARCS model is validated against a Monte Carlo 3D model. • The fission and capture rates are compared. • The influence of the spacer grids on the axial power distribution is shown. - Abstract: Lattice physics codes are primarily used to generate cross-section data for nodal codes. In this work the methodology of homogenized constant generation was applied to a small Pressurized Water Reactor (PWR) core, using the deterministic code Helios and the Monte Carlo code Serpent. Subsequently, a 3D analysis of the PWR core was performed with the nodal diffusion code PARCS using the two-group cross section data sets generated by Helios and Serpent. Moreover, a full 3D model of the PWR core was developed using Serpent in order to obtain a reference solution. Several parameters, such as k eff , axial and radial power, fission and capture rates were compared and found to be in good agreement.

  3. Antimicrobial resistance, class 1 integrons, and genomic island 1 in Salmonella isolates from Vietnam.

    Directory of Open Access Journals (Sweden)

    An T T Vo

    Full Text Available BACKGROUND: The objective was to investigate the phenotypic and genotypic resistance and the horizontal transfer of resistance determinants from Salmonella isolates from humans and animals in Vietnam. METHODOLOGY/PRINCIPAL FINDINGS: The susceptibility of 297 epidemiologically unrelated non-typhoid Salmonella isolates was investigated by disk diffusion assay. The isolates were screened for the presence of class 1 integrons and Salmonella genomic island 1 by PCR. The potential for the transfer of resistance determinants was investigated by conjugation experiments. Resistance to gentamicin, kanamycin, chloramphenicol, streptomycin, trimethoprim, ampicillin, nalidixic acid, sulphonamides, and tetracycline was found in 13 to 50% of the isolates. Nine distinct integron types were detected in 28% of the isolates belonging to 11 Salmonella serovars including S. Tallahassee. Gene cassettes identified were aadA1, aadA2, aadA5, bla(PSE-1, bla(OXA-30, dfrA1, dfrA12, dfrA17, and sat, as well as open reading frames with unknown functions. Most integrons were located on conjugative plasmids, which can transfer their antimicrobial resistance determinants to Escherichia coli or Salmonella Enteritidis, or with Salmonella Genomic Island 1 or its variants. The resistance gene cluster in serovar Emek identified by PCR mapping and nucleotide sequencing contained SGI1-J3 which is integrated in SGI1 at another position than the majority of SGI1. This is the second report on the insertion of SGI1 at this position. High-level resistance to fluoroquinolones was found in 3 multiresistant S. Typhimurium isolates and was associated with mutations in the gyrA gene leading to the amino acid changes Ser83Phe and Asp87Asn. CONCLUSIONS: Resistance was common among Vietnamese Salmonella isolates from different sources. Legislation to enforce a more prudent use of antibiotics in both human and veterinary medicine should be implemented by the authorities in Vietnam.

  4. Diversity of Salmonella isolates from central Florida surface waters.

    Science.gov (United States)

    McEgan, Rachel; Chandler, Jeffrey C; Goodridge, Lawrence D; Danyluk, Michelle D

    2014-11-01

    Identification of Salmonella serotypes is important for understanding the environmental diversity of the genus Salmonella. This study evaluates the diversity of Salmonella isolates recovered from 165 of 202 Central Florida surface water samples and investigates whether the serotype of the environmental Salmonella isolates can be predicted by a previously published multiplex PCR assay (S. Kim, J. G. Frye, J. Hu, P. J. Fedorka-Cray, R. Gautom, and D. S. Boyle, J. Clin. Microbiol. 44:3608-3615, 2006, http://dx.doi.org/10.1128/JCM.00701-06). Multiplex PCR was performed on 562 Salmonella isolates (as many as 36 isolates per water sample) to predict serotypes. Kauffmann-White serogrouping was used to confirm multiplex PCR pattern groupings before isolates were serotyped, analyzed by pulsed-field gel electrophoresis, and assayed for antimicrobial susceptibility. In 41.2% of the Salmonella-positive water samples, all Salmonella isolates had identical multiplex PCR patterns; in the remaining 58.8%, two or more multiplex PCR patterns were identified. Within each sample, isolates with matching multiplex PCR patterns had matching serogroups. The multiplex patterns of 495 isolates (88.1%) did not match any previously reported pattern. The remaining 68 isolates matched reported patterns but did not match the serotypes for those patterns. The use of the multiplex PCR allowed the number of isolates requiring further analysis to be reduced to 223. Thirty-three Salmonella enterica serotypes were identified; the most frequent included serotypes Muenchen, Rubislaw, Anatum, Gaminara, and IV_50:z4,z23:-. A majority (141/223) of Salmonella isolates clustered into one genotypic group. Salmonella isolates in Central Florida surface waters are serotypically, genotypically, and phenotypically (in terms of antimicrobial susceptibility) diverse. While isolates could be grouped as different or potentially the same using multiplex PCR, the multiplex PCR pattern did not predict the Salmonella

  5. Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes

    Directory of Open Access Journals (Sweden)

    Mondal U

    2008-01-01

    Full Text Available Purpose: To anlyse codon usage patterns of five complete genomes of Salmonella , predict highly expressed genes, examine horizontally transferred pathogenicity-related genes to detect their presence in the strains, and scrutinize the nature of highly expressed genes to infer upon their lifestyle. Methods: Protein coding genes, ribosomal protein genes, and pathogenicity-related genes were analysed with Codon W and CAI (codon adaptation index Calculator. Results: Translational efficiency plays a role in codon usage variation in Salmonella genes. Low bias was noticed in most of the genes. GC3 (guanine cytosine at third position composition does not influence codon usage variation in the genes of these Salmonella strains. Among the cluster of orthologous groups (COGs, translation, ribosomal structure biogenesis [J], and energy production and conversion [C] contained the highest number of potentially highly expressed (PHX genes. Correspondence analysis reveals the conserved nature of the genes. Highly expressed genes were detected. Conclusions: Selection for translational efficiency is the major source of variation of codon usage in the genes of Salmonella . Evolution of pathogenicity-related genes as a unit suggests their ability to infect and exist as a pathogen. Presence of a lot of PHX genes in the information and storage-processing category of COGs indicated their lifestyle and revealed that they were not subjected to genome reduction.

  6. The occurrence of Salmonella spp. in duck eggs on sale at retail or from catering in England.

    Science.gov (United States)

    Owen, M; Jorgensen, F; Willis, C; McLauchlin, J; Elviss, N; Aird, H; Fox, A; Kaye, M; Lane, C; de Pinna, E

    2016-11-01

    Since 2010, human salmonellosis outbreaks in the UK have been detected as associated with the consumption of duck eggs. Little data are available on the rate of occurrence of Salmonella in duck eggs. The aim of this study was to investigate the occurrence of Salmonella spp. in duck eggs on sale and from catering in England during 2011, particularly those from small-scale production. All samples were collected independently of human salmonellosis outbreak investigations. Composite samples of 6-10 eggs (shells and contents were examined separately) were examined for the presence of Salmonella spp. using the ISO 6579:2002 method. Salmonella spp. was recovered from two of 145 samples (1·4%). In one sample, Salmonella Typhimurium DT 8 was isolated from the shells while Salm. Typhimurium DT 8 and Salm. Typhimurium DT30 were isolated from the contents. Salmonella Typhimurium DT8 was isolated from the egg shells only in the second contaminated sample. This study provides baseline data for risk assessors, regulators and the food industry and may be helpful in communicating risks associated with the consumption of this product as well as evaluating risk management options to control food safety including vaccination of ducks. Human salmonellosis outbreaks in England and Northern Ireland due to Salmonella enterica serovar Typhimurium definitive phage type (DT) 8 have been identified as associated with the consumption of duck eggs since 2010. This study has shown that Salmonella spp. was detected in 1·4% of ducks egg samples providing baseline data for risk assessors, regulators and the food industry. This may be helpful in communicating risks associated with the consumption of this product as well as evaluating risk management options to control food safety including vaccination of ducks. © 2016 Crown copyright. Letters in Applied Microbiology © 2016 The Society for Applied Microbiology.

  7. Web-based surveillance and global Salmonella distribution, 2000-2002

    DEFF Research Database (Denmark)

    Galanis, E.; Wong, Danilo Lo Fo; Patrick, M.E.

    2006-01-01

    Salmonellae are a common cause of foodborne disease worldwide. The World Health Organization (WHO) supports international foodborne disease surveillance through WHO Global Salm-Surv and other activities. WHO Global Salm-Surv members annually report the 15 most frequently isolated Salmonella...... serotypes to a Web-based country databank. We describe the global distribution of reported Salmonella serotypes from human and nonhuman sources from 2000 to 2002. Among human isolates, Salmonella enterica serovar Enteritidis was the most common serotype, accounting for 65% of all isolates. Among nonhuman...... professionals to explore hypotheses related to the sources and distribution of salmonellae worldwide....

  8. Inactivation of Salmonellae in Frozen Catfish by Gamma Irradiation

    International Nuclear Information System (INIS)

    Nouchpramoon, Kovit; Amsiri, Jarurat

    2003-06-01

    The effect of gamma irradiation on salmonellae viability in frozen catfish was investigated using fresh cut of catfish artificially contaminated with stationary phase cells of salmonellae, frozen at-18 οC and irradiated with does ranging from 0.0 to 2.4 kGy. The D 10 values for ten serovars of salmonellae ranged from 0.47 to 0.77 kGy. Salmonella Enteritidis was the most resistant serovars found in frozen catfish. Dosage at 2.5 kGy would be sufficient to kill 10 3 . 2 Salmonella Enteritidis that may occasionally present in frozen catfish

  9. Effects of transparent exopolymer particles and suspended particles on the survival of Salmonella enterica serovar Typhimurium in seawater.

    Science.gov (United States)

    Davidson, Marion C F; Berardi, Terra; Aguilar, Beatriz; Byrne, Barbara A; Shapiro, Karen

    2015-03-01

    The bacterium Salmonella enterica can infect marine mammals and has been increasingly implicated in seafood-borne disease outbreaks in humans. Despite the risk this zoonotic agent poses to animals and people, little is known regarding the environmental factors that affect its persistence in the sea. The goal of this study was to evaluate the impact of two constituents on the survival of Salmonella in the marine environment: transparent exopolymer particles (TEP) and suspended particles. A decay experiment was conducted by spiking Salmonella into bottles containing seawater, seawater with alginic acid as a source of TEP, filtered seawater or filtered seawater with alginic acid. Survival of Salmonella was monitored using culture followed by enrichment assays to evaluate if the bacteria entered a viable but non-cultivable (VBNC) state. Salmonella cell counts dropped significantly faster (P ≤ 0.05) in the unfiltered seawater samples with and without TEP. The slowest decay occurred in filtered seawater containing alginic acid, with VBNC Salmonella persisting for 17 months. These findings suggest that TEP may favor Salmonella survival while suspended particles facilitate its decay. Insight on the survival of allochthonous, zoonotic pathogens in seawater can guide monitoring, management and policy decisions relevant to wildlife and human public health. © FEMS 2015. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Presentation of life-threatening invasive nontyphoidal Salmonella disease in Malawian children: A prospective observational study.

    Science.gov (United States)

    MacLennan, Calman A; Msefula, Chisomo L; Gondwe, Esther N; Gilchrist, James J; Pensulo, Paul; Mandala, Wilson L; Mwimaniwa, Grace; Banda, Meraby; Kenny, Julia; Wilson, Lorna K; Phiri, Amos; MacLennan, Jenny M; Molyneux, Elizabeth M; Molyneux, Malcolm E; Graham, Stephen M

    2017-12-01

    Nontyphoidal Salmonellae commonly cause invasive disease in African children that is often fatal. The clinical diagnosis of these infections is hampered by the absence of a clear clinical syndrome. Drug resistance means that empirical antibiotic therapy is often ineffective and currently no vaccine is available. The study objective was to identify risk factors for mortality among children presenting to hospital with invasive Salmonella disease in Africa. We conducted a prospective study enrolling consecutive children with microbiologically-confirmed invasive Salmonella disease admitted to Queen Elizabeth Central Hospital, Blantyre, in 2006. Data on clinical presentation, co-morbidities and outcome were used to identify children at risk of inpatient mortality through logistic-regression modeling. Over one calendar year, 263 consecutive children presented with invasive Salmonella disease. Median age was 16 months (range 0-15 years) and 52/256 children (20%; 95%CI 15-25%) died. Nontyphoidal serovars caused 248/263 (94%) of cases. 211/259 (81%) of isolates were multi-drug resistant. 251/263 children presented with bacteremia, 6 with meningitis and 6 with both. Respiratory symptoms were present in 184/240 (77%; 95%CI 71-82%), 123/240 (51%; 95%CI 45-58%) had gastrointestinal symptoms and 101/240 (42%; 95%CI 36-49%) had an overlapping clinical syndrome. Presentation at Salmonella disease in Malawi is characterized by high mortality and prevalence of multi-drug resistant isolates, along with non-specific presentation. Young infants, children with dyspnea and HIV-infected children bear a disproportionate burden of the Salmonella-associated mortality in Malawi. Strategies to improve prevention, diagnosis and management of invasive Salmonella disease should be targeted at these children.

  11. Changes in the Coding and Non-coding Transcriptome and DNA Methylome that Define the Schwann Cell Repair Phenotype after Nerve Injury.

    Science.gov (United States)

    Arthur-Farraj, Peter J; Morgan, Claire C; Adamowicz, Martyna; Gomez-Sanchez, Jose A; Fazal, Shaline V; Beucher, Anthony; Razzaghi, Bonnie; Mirsky, Rhona; Jessen, Kristjan R; Aitman, Timothy J

    2017-09-12

    Repair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34. Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Severity of infection and seasonal variation of non-typhoid Salmonelle occurence in humans

    DEFF Research Database (Denmark)

    Gradel, K.O.; Dethlefsen, Claus; Schønheyder, H.C.

    2007-01-01

    Non-typhoid Salmonella infections may present as severe gastroenteritis necessitatinghospitalization and some patients become septic with bacteraemia. We hypothesized that theseasonal variation of non-typhoid Salmonella occurrence in humans diminishes with increasedseverity of infection. We...... examined the seasonal variation of non-typhoid Salmonella infections inthree patient groups with differing severity of infection: outpatients treated for gastroenteritis(n=1490); in-patients treated for gastroenteritis (n=492); and in-patients treated for bacteraemia(n=113). The study was population......-based and included all non-typhoid Salmonella patients ina Danish county from 1994 to 2003. A periodic regression model was used to compute thepeak-to-trough ratio for the three patient groups. The peak-to-trough ratios were 4·3 [95%confidence interval (CI) 3·6–5.0] for outpatients with gastroenteritis, 3·2 (95% CI...

  13. Transcriptomic analysis of Salmonella desiccation resistance.

    Science.gov (United States)

    Li, Haiping; Bhaskara, Anuhya; Megalis, Christina; Tortorello, Mary Lou

    2012-12-01

    The survival of Salmonella in low moisture foods and processing environments remains a great challenge for the food industry and public health. To explore the mechanisms of Salmonella desiccation resistance, we studied the transcriptomic responses in Salmonella Tennessee (Tennessee), using Salmonella Typhimurium LT2 (LT2), a strain weakly resistant to desiccation, as a reference strain. In response to 2 h of air-drying at 11% equilibrated relative humidity, approximately one-fourth of the open reading frames (ORFs) in the Tennessee genome and one-fifth in LT2 were differentially expressed (>2-fold). Among all differentially expressed functional groups (>5-fold) in both strains, the expression fold change associated with fatty acid metabolism was the highest, and constituted 51% and 35% of the total expression fold change in Tennessee and LT2, respectively. Tennessee showed greater changes in expression of genes associated with stress response and envelope modification than LT2, while showing lesser changes in protein biosynthesis expression. Expression of flagella genes was significantly more inhibited in stationary phase cells of Tennessee than LT2 both before and after desiccation. The accumulation of the osmolyte trehalose was significantly induced by desiccation in Tennessee, but no increase was detectable in LT2, which is consistent with the expression patterns of the entire trehalose biosynthesis and degradation pathways in both strains. Results from this study present a global view of the dynamic desiccation responses in Salmonella, which will guide future research efforts to control Salmonella in low moisture environments.

  14. Salmonella Typhimurium transcription profiles in space flight

    Data.gov (United States)

    National Aeronautics and Space Administration — Salmonella transcription profiles were obtained from samples flown on space shuttle mission STS-115 and compared to profiles from Salmonella grown under identical...

  15. Numerical exploration of non-axisymmetric divertor closure in the small angle slot (SAS) divertor at DIII-D

    Science.gov (United States)

    Frerichs, H.; Schmitz, O.; Covele, B.; Feng, Y.; Guo, H. Y.; Hill, D.

    2018-05-01

    Numerical simulations of toroidal asymmetries in a tightly baffled small angle slot (SAS) divertor on the DIII-D tokamak show that toroidal asymmetries in divertor closure result in (non-axisymmetric) local onset of detachment within a density window of 10-15% on top of the nominal threshold separatrix density. The SAS divertor is explored at DIII-D for improving access to cold, dissipative/detached divertor conditions. The narrow width of the slot divertor coupled with a small magnetic field line-to-target angle facilitates the buildup of neutral density, thereby increasing radiative and neutrals-related (atoms and molecules) losses in the divertor. Small changes in the strike point location can be expected to have a large impact on divertor conditions. The combination of misaligned slot structure and non-axisymmetric perturbations to the magnetic field configuration causes the strike point to move along the divertor target plate, possibly leaving the divertor slot at some locations. The latter extreme case essentially introduces an opening in the divertor slot from where recycling neutrals can easily escape, and thereby degrade the performance of the slot divertor. Such a strike point dislocation is approximated by a finite gap in the divertor baffle for which 3D edge plasma and neutral gas simulations are performed with the EMC3-EIRENE code.

  16. antimicrobial susceptibility pattern of Salmonella species

    African Journals Online (AJOL)

    user

    ABSTRACT. Treatment of enteric fever is increasingly becoming very challenging due to the increasing wave of antibiotic resistance. This study is a review of the contemporary antimicrobial susceptibility pattern of. Salmonella species. The antimicrobial susceptibility pattern of Salmonella species to a wide range of.

  17. EURL-Salmonella 8th interlaboratory comparison study Food 2016 : Detection of Salmonella in minced chicken meat

    NARCIS (Netherlands)

    Kuijpers AFA; Mooijman KA; VDL; Z&O

    2018-01-01

    In 2016, it was shown that all 34 National Reference Laboratories (NRLs), 30 of which are located in the European Union, were able to detect high and low levels of Salmonella in minced chicken meat. Three NRLs reported Salmonella in one 'blank' minced meat sample. This was probably caused by the

  18. PCR-RFLP Analysis of a fliC Gene Fragment in Avian Salmonella Isolates

    Directory of Open Access Journals (Sweden)

    Zohreh Ebrahimvandi

    2014-07-01

    Full Text Available Background: Salmonella are a genus of zoonotic bacteria of worldwide economic and health importance. Members of Salmonella enterica subspecies enterica are mainly associated with warm-blooded vertebrates and are usually transmitted by ingestion of food or watercontaminated by infected feces. Objectives: The aim of this study was to apply a PCR-RFLP method based on the fliC gene to identify the serotypes of Salmonella isolates from Karaj, Iran. Materials and Methods: A total of 30 Salmonella isolates were serotyped by specific antisera. For the PCR-RFLP method based on the fliC gene, extracted DNA was used as the template for amplifying the fliC gene (1500 bp using specific primers. PCR products were subjected to digestion using HhaI restriction endonuclease. Results: This study determined 30 serotypes as Salmonella durban (56.6%, Salmonella uno (23.3%, Salmonella enteritidis (3.3%, Salmonella tinda (3.3%, Salmonella mjimweme (3.3%, Salmonella Thompson (3.3%, Salmonella sIIO8 (3.3 % and Salmonella sIIO7 (3.3%. Observations indicated that HhaI is able to discriminate Salmonella tinda and Salmonella thompson, yet Salmonella enteritidis, Salmonella durban and Salmonella mjimweme had the same pattern with this enzyme. Also Salmonella sIIO8, Salmonella sIIO7 and Salmonella uno showed the same pattern. Thus, regarding the size and the number of resulting fragments from this enzyme, four patterns were obtained for HhaI. Conclusion: A large number of Salmonella serotypes need to be analyzed by the PCR-RFLP method and different enzymes must be used to give reliable results.

  19. p53-dependent non-coding RNA networks in chronic lymphocytic leukemia

    NARCIS (Netherlands)

    Blume, C. J.; Hotz-Wagenblatt, A.; Hüllein, J.; Sellner, L.; Jethwa, A.; Stolz, T.; Slabicki, M.; Lee, K.; Sharathchandra, A.; Benner, A.; Dietrich, S.; Oakes, C. C.; Dreger, P.; te Raa, D.; Kater, A. P.; Jauch, A.; Merkel, O.; Oren, M.; Hielscher, T.; Zenz, T.

    2015-01-01

    Mutations of the tumor suppressor p53 lead to chemotherapy resistance and a dismal prognosis in chronic lymphocytic leukemia (CLL). Whereas p53 targets are used to identify patient subgroups with impaired p53 function, a comprehensive assessment of non-coding RNA targets of p53 in CLL is missing. We

  20. Stably Integrated luxCDABE for Assessment of Salmonella Invasion Kinetics

    Directory of Open Access Journals (Sweden)

    Kelly N. Flentie

    2008-09-01

    Full Text Available Salmonella Typhimurium is a common cause of gastroenteritis in humans and also localizes to neoplastic tumors in animals. Invasion of specific eukaryotic cells is a key mechanism of Salmonella interactions with host tissues. Early stages of gastrointestinal cell invasion are mediated by a Salmonella type III secretion system, powered by the adenosine triphosphatase invC. The aim of this work was to characterize the invC dependence of invasion kinetics into disparate eukaryotic cells traditionally used as models of gut epithelium or neoplasms. Thus, a nondestructive real-time assay was developed to report eukaryotic cell invasion kinetics using lux+ Salmonella that contain chromosomally integrated luxCDABE genes. Bioluminescence-based invasion assays using lux+ Salmonella exhibited inoculum dose-response correlation, distinguished invasion-competent from invasion-incompetent Salmonella, and discriminated relative Salmonella invasiveness in accordance with environmental conditions that induce invasion gene expression. In standard gentamicin protection assays, bioluminescence from lux+ Salmonella correlated with recovery of colony-forming units of internalized bacteria and could be visualized by bioluminescence microscopy. Furthermore, this assay distinguished invasion-competent from invasion-incompetent bacteria independent of gentamicin treatment in real time. Bioluminescence reported Salmonella invasion of disparate eukaryotic cell lines, including neoplastic melanoma, colon adenocarcinoma, and glioma cell lines used in animal models of malignancy. In each case, Salmonella invasion of eukaryotic cells was invC dependent.

  1. Septic arthritis of the ankle due to Salmonella enteritidis.

    LENUS (Irish Health Repository)

    Dineen, Patrick F

    2011-06-01

    Salmonella septic arthritis in healthy, immunocompetent patients is extremely rare. We present the case of a 70-year-old man who presented with a one-day history of painful swelling of his ankle from which was aspirated pus which subsequently grew Salmonella enteritidis. There was no history of trauma or symptoms consistent with Salmonella enterocolitis. Our patient recovered fully after two weeks on intravenous ceftriaxone and six weeks on oral ciprofloxacin. Salmonella is a notifiable disease in the European Union and the United States of America, and is associated with outbreaks as a result of food contamination. The nature of Salmonella arthritis and its appropriate management are outlined.

  2. SALMONELLA SPECIES

    African Journals Online (AJOL)

    DR. AMINU

    ... of Salmonella species serotypes in relation to age and sex among children, ..... However, most antimicrobials show sufficient selective toxicity to be of value in ... salmonellosis should be given good attention (Barrow et al., 2007). To reduce ...

  3. Growth of Escherichia coli O157:H7, Non-O157 Shiga Toxin-Producing Escherichia coli , and Salmonella in Water and Hydroponic Fertilizer Solutions.

    Science.gov (United States)

    Shaw, Angela; Helterbran, Kara; Evans, Michael R; Currey, Christopher

    2016-12-01

    The desire for local, fresh produce year round is driving the growth of hydroponic growing systems in the United States. Many food crops, such as leafy greens and culinary herbs, grown within hydroponics systems have their root systems submerged in recirculating nutrient-dense fertilizer solutions from planting through harvest. If a foodborne pathogen were introduced into this water system, the risk of contamination to the entire crop would be high. Hence, this study was designed to determine whether Escherichia coli O157:H7, non-O157 Shiga toxin-producing E. coli , and Salmonella were able to survive and reproduce in two common hydroponic fertilizer solutions and in water or whether the bacteria would be killed or suppressed by the fertilizer solutions. All the pathogens grew by 1 to 6 log CFU/ml over a 24-h period, depending on the solution. E. coli O157:H7 reached higher levels in the fertilizer solution with plants (3.12 log CFU/ml), whereas non-O157 Shiga toxin-producing E. coli and Salmonella reached higher levels in the fertilizer solution without plants (1.36 to 3.77 log CFU/ml). The foodborne pathogens evaluated here survived for 24 h in the fertilizer solution, and populations grew more rapidly in these solutions than in plain water. Therefore, human pathogens entering the fertilizer solution tanks in hydroponic systems would be expected to rapidly propagate and spread throughout the system and potentially contaminate the entire crop.

  4. Prevalence and antimicrobial resistance of Salmonella serovars isolated from poultry in Ghana

    DEFF Research Database (Denmark)

    Andoh, Linda A.; Dalsgaard, Anders; Obiri-Danso, K.

    2016-01-01

    Poultry are possible sources of non-typhoidal Salmonella serovars which may cause foodborne human disease. We conducted a cross-sectional study to determine the prevalence of Salmonella serovars in egg-laying hens and broilers at the farm level and their susceptibility to antimicrobials commonly...... of antimicrobials). Of the resistant strains (n = 57), the most significant were to nalidixic acid (89·5%), tetracycline (80·7%), ciprofloxacin (64·9%), sulfamethazole (42·1%), trimethoprim (29·8%) and ampicillin (26·3%). All S. Kentucky strains were resistant to more than two antimicrobials and shared common...

  5. Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella

    Science.gov (United States)

    2009-01-01

    Background One of the major sources of human Salmonella infections is meat. Therefore, efficient and rapid monitoring of Salmonella in the meat production chain is necessary. Validation of alternative methods is needed to prove that the performance is equal to established methods. Very few of the published PCR methods for Salmonella have been validated in collaborative studies. This study describes a validation including comparative and collaborative trials, based on the recommendations from the Nordic organization for validation of alternative microbiological methods (NordVal) of a same-day, non-commercial real-time PCR method for detection of Salmonella in meat and carcass swabs. Results The comparative trial was performed against a reference method (NMKL-71:5, 1999) using artificially and naturally contaminated samples (60 minced veal and pork meat samples, 60 poultry neck-skins, and 120 pig carcass swabs). The relative accuracy was 99%, relative detection level 100%, relative sensitivity 103% and relative specificity 100%. The collaborative trial included six laboratories testing minced meat, poultry neck-skins, and carcass swabs as un-inoculated samples and samples artificially contaminated with 1–10 CFU/25 g, and 10–100 CFU/25 g. Valid results were obtained from five of the laboratories and used for the statistical analysis. Apart from one of the non-inoculated samples being false positive with PCR for one of the laboratories, no false positive or false negative results were reported. Partly based on results obtained in this study, the method has obtained NordVal approval for analysis of Salmonella in meat and carcass swabs. The PCR method was transferred to a production laboratory and the performance was compared with the BAX Salmonella test on 39 pork samples artificially contaminated with Salmonella. There was no significant difference in the results obtained by the two methods. Conclusion The real-time PCR method for detection of Salmonella in meat

  6. Anaerobiosis induced virulence of Salmonella typhi

    DEFF Research Database (Denmark)

    Kapoor, Sarika; Singh, R D; Sharma, P C

    2002-01-01

    , we examined the effect of anaerobiosis on the virulence of Salmonella Typhi, a Gram negative bacteria which invades through the gut mucosa and is responsible for typhoid fever. METHODS: Salmonella Typhi (ty2) was cultured in aerobic and anaerobic conditions to compare its virulence by rabbit ileal...

  7. Survival of Salmonella spp. and fecal indicator bacteria in Vietnamese biogas digesters receiving pig slurry

    DEFF Research Database (Denmark)

    Luu, Huong Quynh; Forslund, Anita; Madsen, Henry

    2014-01-01

    . and the fecal indicator bacteria, enterococci, E. coli, and spores of Clostridium perfringens in biogas digesters operated by small-scale Vietnamese pig farmers. The serovar and antimicrobial susceptibility of the Salmonella spp. isolated were also established. The study was conducted in 12 farms (6 farms...

  8. 76 FR 81513 - Guidance for Industry: Prevention of Salmonella

    Science.gov (United States)

    2011-12-28

    ...] Guidance for Industry: Prevention of Salmonella Enteritidis in Shell Eggs During Production, Storage, and... ``Prevention of Salmonella Enteritidis in Shell Eggs During Production, Storage, and Transportation.'' The... final rule ``Prevention of Salmonella Enteritidis in Shell Eggs During Production, Storage, and...

  9. Test results of Salmonella serotyping in the Member States of the European Union. (Collaborative study III amongst the National Reference Laboratories for Salmonella)

    NARCIS (Netherlands)

    Voogt N; Maas HME; Leeuwen WJ van; Henken AM; MGB

    1998-01-01

    Het Communautair Referentie Laboratorium (CRL) voor Salmonella heeft een derde ringonderzoek voor de serotypering van Salmonella georganiseerd. Alle Nationale Referentie Laboratoria (NRLs) voor Salmonella van de Europese Unie deden aan het onderzoek mee. Het belangrijkste doel was het

  10. Transmission of Salmonella between wildlife and meat-production animals in Denmark

    DEFF Research Database (Denmark)

    Skov, M. N.; Madsen, J. J.; Rahbek, C.

    2008-01-01

    Aims: To investigate the transmission of Salmonella spp. between production animals (pigs and cattle) and wildlife on production animal farms in Denmark. Methods and Results: In the winter and summer of 2001 and 2002, 3622 samples were collected from Salmonella-infected and noninfected herds...... of pigs and cattle and surrounding wildlife. Salmonella was detected in wildlife on farms carrying Salmonella-positive production animals and only during the periods when Salmonella was detected in the production animals. The presence of Salmonella Typhimurium in wild birds significantly correlated...... to their migration pattern and food preference. Conclusions: Salmonella was transmitted from infected herds of production animals (cattle and pigs) to wildlife that lived amongst or in close proximity to them. Significance and Impact of the Study: Salmonella in animal food products is associated with the occurrence...

  11. Prevalence and susceptibility of salmonella Typhi and salmonella ...

    African Journals Online (AJOL)

    Methods: Blood samples collected from presumptive typhoid fever patients from Ahmadu Bello University (ABU), Federal College of Education (FCE) and presumptive typhoid fever patients that attended two private clinics (Salama Clinics and Savanna Polyclinics) in Zaria were cultured for Salmonella species and identified ...

  12. Salmonella bacteraemia among healthcare workers and their dependents

    International Nuclear Information System (INIS)

    Raza, A.; Sultan, F.; Mahboob, A.; Nazeer, S. H.; Nizammudin, S.

    2014-01-01

    Objectives: To determine the incidence and resistance pattern of Salmonella infection in healthcare workers and their dependents. Methods: The retrospective analysis was conducted at Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, and comprised records of employees and their dependents with bacteraemia from January 2007 to December 2011. Person-years were calculated using data from the human resources department. SPSS 19 was used for statistical analyses. Results: Of the total 2532 records available, 82(3.23%) patients were identified with Salmonella bacteraemia. Of them, 34(41.5%) patients were in age group 1-10, 15(18.3%) in 11-20, 26(31.7%) in 21-30, and 7(8.5%) were above 30 years. Besides, 48(58.5%) were males. Salmonella typhi was found in 44(53.7%) patients, Salmonella paratyphi A in 35(42.7%) and Salmonella species in 3(3.7%) patients. The yearly incidence of Salmonella infection in the study population ranged from 206 to 596 per 100000 person-years. Ciprofloxacin resistance was noted to be 56 (68.2%) followed by Ampicillin 29 (35.3%) and Co-trimoxazole 24 (29.2%). No strains were resistant to Cefiximeor Ceftriaxone. Conclusion: The yearly incidence of Salmonella bacteraemia ranged from 200 to 600 per 100000 person years. There was significant quinolone resistance among the isolates. (author)

  13. Preexisting Salmonella-specific immunity interferes with the subsequent development of immune responses against the Salmonella strains delivering H9N2 hemagglutinin.

    Science.gov (United States)

    Hajam, Irshad Ahmed; Lee, John Hwa

    2017-06-01

    Recombinant Salmonella strains expressing foreign heterologous antigens have been extensively studied as promising live vaccine delivery vehicles. In this study, we constructed attenuated smooth (S-HA) and rough (R-HA) Salmonella strains expressing hemagglutinin (HA) of H9N2, a low pathogenic avian influenza A virus. We then investigated the HA-specific immune responses following oral immunization with either S-HA or R-HA strain in chicken model. We further examined the effects of the preexisting anti-Salmonella immunity on the subsequent elicitation of the HA and the Salmonella ompA specific immune responses. Our results showed that primary immunization with either the S-HA or the R-HA strain elicited comparable HA-specific immune responses and the responses were significantly (pSalmonella vector control. When chickens were pre-immunized with the smooth Salmonella carrier alone and then vaccinated with either S-HA or R-HA strain 3, 6 and 9 weeks later, respectively, significant reductions were seen for HA-specific immune responses at week 6, a point which corresponded to the peak of the primary Salmonella-specific antibody responses. No reductions were seen at week 3 and 9, albeit, the HA-specific immune responses were boosted at week 9, a point which corresponded to the lowest primary Salmonella-specific antibody responses. The ompA recall responses remain refractory at week 3 and 6 following deliberate immunization with the carrier strain, but were significantly (pSalmonella immunity inhibits antigen-specific immune responses and this effect could be avoided by carefully selecting the time point when carrier-specific immune responses are relatively low. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Saccharomyces boulardii prevention of the hepatic injury induced by Salmonella Enteritidis infection.

    Science.gov (United States)

    Wu, Daichao; Teng, Da; Wang, Xiumin; Dai, Changsong; Wang, Jianhua

    2014-10-01

    Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella Enteritidis) is the predominant cause of serovar-associated food-borne outbreaks in many countries and causes significant clinical symptoms of liver injury, enteritis, and diarrheal diseases. Saccharomyces boulardii is used in clinical application for prophylaxis and the treatment of a variety of diseases caused by bacterial infection. We used a mouse model of Salmonella Enteritidis infection, which included pretreatment with S. boulardii, to reveal the protection mechanisms of S. boulardii against Salmonella Enteritidis infection, including the translocation of Salmonella Enteritidis to the liver 10 days after Salmonella Enteritidis challenge, and the colonisation of Salmonella Enteritidis and the formation of hepatic tissue lesions in mice after Salmonella Enteritidis challenge on the 10th day. Compared with Salmonella Enteritidis infection in mice, S. boulardii decreased Salmonella Enteritidis translocation to the liver by 96%, and 99% of Salmonella Enteritidis colonised the cecum on the 10th day. Saccharomyces boulardii also abated hepatic tissue injury caused by the infiltration of neutrophilic granulocytes, lymphocytes, and plasmocytes by decreasing the translocation of Salmonella to the liver. These findings demonstrated that S. boulardii is an effective agent in the prevention of the hepatic injury induced by Salmonella Enteritidis infection in a mouse model.

  15. Prevalence of Salmonella spp. in oysters in the United States.

    Science.gov (United States)

    Brands, Danielle A; Inman, Allison E; Gerba, Charles P; Maré, C John; Billington, Stephen J; Saif, Linda A; Levine, Jay F; Joens, Lynn A

    2005-02-01

    Food-borne diseases such as salmonellosis can be attributed, in part, to the consumption of raw oysters. To determine the prevalence of Salmonella spp. in oysters, oysters harvested from 36 U.S. bays (12 each from the West, East, and Gulf coasts in the summer of 2002, and 12 bays, four per coast, in the winter of 2002-2003) were tested. Salmonella was isolated from oysters from each coast of the United States, and 7.4% of all oysters tested contained Salmonella. Isolation tended to be bay specific, with some bays having a high prevalence of Salmonella, while other bays had none. Differences in the percentage of oysters from which Salmonella was isolated were observed between the summer and winter months, with winter numbers much lower probably due to a variety of weather-related events. The vast majority (78/101) of Salmonella isolates from oysters were Salmonella enterica serovar Newport, a major human pathogen, confirming the human health hazard of raw oyster consumption. Contrary to previous findings, no relationship was found between the isolation of fecal coliforms and Salmonella from oysters, indicating a necessity for specific monitoring for Salmonella and other pathogens rather than the current reliance on fecal coliform testing.

  16. Molecular Epidemiology of Nontyphoidal Salmonella in Poultry and Poultry Products in India: Implications for Human Health.

    Science.gov (United States)

    Saravanan, Sellappan; Purushothaman, Venketaraman; Murthy, Thippichettypalayam Ramasamy Gopala Krishna; Sukumar, Kuppannan; Srinivasan, Palani; Gowthaman, Vasudevan; Balusamy, Mohan; Atterbury, Robert; Kuchipudi, Suresh V

    2015-09-01

    Human infections with non-typhoidal Salmonella (NTS) serovars are increasingly becoming a threat to human health globally. While all motile Salmonellae have zoonotic potential, Salmonella Enteritidis and Salmonella Typhimurium are most commonly associated with human disease, for which poultry are a major source. Despite the increasing number of human NTS infections, the epidemiology of NTS in poultry in India has not been fully understood. Hence, as a first step, we carried out epidemiological analysis to establish the incidence of NTS in poultry to evaluate the risk to human health. A total of 1215 samples (including poultry meat, tissues, egg and environmental samples) were collected from 154 commercial layer farms from southern India and screened for NTS. Following identification by cultural and biochemical methods, Salmonella isolates were further characterized by multiplex PCR, allele-specific PCR, enterobacterial repetitive intergenic consensus (ERIC) PCR and pulse field gel electrophoresis (PFGE). In the present study, 21/1215 (1.73 %) samples tested positive for NTS. We found 12/392 (3.06 %) of tissue samples, 7/460 (1.52 %) of poultry products, and 2/363 (0.55 %) of environmental samples tested positive for NTS. All the Salmonella isolates were resistant to oxytetracycline, which is routinely used as poultry feed additive. The multiplex PCR results allowed 16/21 isolates to be classified as S. Typhimurium, and five isolates as S. Enteritidis. Of the five S. Enteritidis isolates, four were identified as group D Salmonella by allele-specific PCR. All of the isolates produced different banding patterns in ERIC PCR. Of the thirteen macro restriction profiles (MRPs) obtained by PFGE, MRP 6 was predominant which included 6 (21 %) isolates. In conclusion, the findings of the study revealed higher incidence of contamination of NTS Salmonella in poultry tissue and animal protein sources used for poultry. The results of the study warrants further investigation

  17. Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues.

    Science.gov (United States)

    Castellano, Leandro; Stebbing, Justin

    2013-03-01

    MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression. They are characterized by specific maturation processes defined by canonical and non-canonical biogenic pathways. Analysis of ∼0.5 billion sequences from mouse data sets derived from different tissues, developmental stages and cell types, partly characterized by either ablation or mutation of the main proteins belonging to miRNA processor complexes, reveals 66 high-confidence new genomic loci coding for miRNAs that could be processed in a canonical or non-canonical manner. A proportion of the newly discovered miRNAs comprises mirtrons, for which we define a new sub-class. Notably, some of these newly discovered miRNAs are generated from untranslated and open reading frames of coding genes, and we experimentally validate these. We also show that many annotated miRNAs do not present miRNA-like features, as they are neither processed by known processing complexes nor loaded on AGO2; this indicates that the current miRNA miRBase database list should be refined and re-defined. Accordingly, a group of them map on ribosomal RNA molecules, whereas others cannot undergo genuine miRNA biogenesis. Notably, a group of annotated miRNAs are Dgcr8 independent and DICER dependent endogenous small interfering RNAs that derive from a unique hairpin formed from a short interspersed nuclear element.

  18. Thirteenth CRL-Salmonella interlaboratory comparison study on typing of Salmonella spp. : Dertiende CRL-Salmonella ringonderzoek voor de typering van Salmonella spp.

    NARCIS (Netherlands)

    Berk PA; Maas HME; de Pinna E; Mooijman KA; LZO; cib

    2010-01-01

    De Nationale Referentie Laboratoria (NRL's) van de 27 Europese lidstaten scoorden goed bij de kwaliteitscontrole op Salmonella-typering in 2008. Vier laboratoria hadden hiervoor een herkansing nodig. Daarnaast is een analyse van alle NRL's als groep uitgevoerd, waaruit bleek dat zij 97 % van de

  19. Sixteenth EURL-Salmonella interlaboratory comparison study on typing of Salmonella spp. : Zestiende EURL-Salmonella ringonderzoek voor de typering van Salmonella spp.

    NARCIS (Netherlands)

    Jacobs-Reitsma WF; Pol-Hofstad IE; Maas HME; de Pinna E; Mooijman KA; LZO; cib

    2012-01-01

    De 28 Nationale Referentie Laboratoria (NRL's) van de 27 Europese lidstaten scoorden in 2011 goed bij de kwaliteitscontrole om Salmonella te typeren. Twee laboratoria hadden hiervoor een herkansing nodig. Alle NRL's samen konden gemiddeld genomen aan 97 procent van de geteste stammen de juiste naam

  20. Salmonella burden in Lebanon.

    Science.gov (United States)

    Malaeb, M; Bizri, A R; Ghosn, N; Berry, A; Musharrafieh, U

    2016-06-01

    Salmonellosis is a disease that represents a major public health concern in both developing and developed countries. The aim of this article is to evaluate the public health burden of Salmonella illness in Lebanon. The current scope of the Salmonella infection problem was assessed in relation to disease incidence and distribution with respect to age, gender and district. Factors that provide a better understanding of the magnitude of the problem were explored and highlighted. Data reported to the Epidemiologic Surveillance Department at the Lebanese Ministry of Public Health between 2001 and 2013 was reviewed. Information obtained was compared to information reported regionally and globally. The estimated true incidence was derived using multipliers from the CDC and Jordan. A literature review of all published data from Lebanon about Salmonella susceptibility/resistance patterns and its serious clinical complications was conducted. The estimated incidence was 13·34 cases/100 000 individuals, most cases occurred in the 20-39 years age group with no significant gender variation. Poor and less developed districts of Lebanon had the highest number of cases and the peak incidence was in summer. Reflecting on the projected incidence derived from the use of multipliers indicates a major discrepancy between what is reported and what is estimated. We conclude that data about Salmonella infection in Lebanon and many Middle Eastern and developing countries lack crucial information and are not necessarily representative of the true incidence, prevalence and burden of illness.

  1. Antimicrobial resistance in zoonotic nontyphoidal Salmonella: an alarming trend?

    Science.gov (United States)

    Michael, G B; Schwarz, S

    2016-12-01

    Zoonotic bacteria of the genus Salmonella have acquired various antimicrobial resistance properties over the years. The corresponding resistance genes are commonly located on plasmids, transposons, gene cassettes, or variants of the Salmonella Genomic Islands SGI1 and SGI2. Human infections by nontyphoidal Salmonella isolates mainly result from ingestion of contaminated food. The two predominantly found Salmonella enterica subsp. enterica serovars in the USA and in Europe are S. Enteritidis and S. Typhimurium. Many other nontyphoidal Salmonella serovars have been implicated in foodborne Salmonella outbreaks. Summary reports of the antimicrobial susceptibility patterns of nontyphoidal Salmonella isolates over time suggest a moderate to low level of antimicrobial resistance and multidrug-resistance. However, serovar-specific analyses showed in part a steady state, a continuous decline, or a recent increase in resistance to certain antimicrobial agents. Resistance to critically important antimicrobial agents, e.g. third-generation cephalosporins and (fluoro)quinolones is part of many monitoring programmes and the corresponding results confirm that extended-spectrum β-lactamases are still rarely found in nontyphoidal Salmonella serovars, whereas resistance to (fluoro)quinolones is prevalent at variable frequencies among different serovars from humans and animals in different countries. Although it is likely that nontyphoidal Salmonella isolates from animals represent a reservoir for resistance determinants, it is mostly unknown where and when Salmonella isolates acquired resistance properties and which exchange processes have happened since then. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  2. Elimination of salmonella from animal glandular products.

    Science.gov (United States)

    De Fiebre, C W; Burck, K T; Feldman, D

    1969-03-01

    Methods for the elimination of salmonellae from selected powdered pharmaceuticals of animal glandular origin were studied. Terminal heat treatment under carefully controlled conditions was effective for pancreatin-a powder containing proteolytic, amylolytic, and lipolytic enzymes prepared from hog pancreas glands. Use of this method resulted in a significant reduction in the number of salmonella-positive batches and also reduced the testing procedures required to confirm the absence of viable salmonellae among the majority of samples tested. Powders such as stomach substance and thyroid, in which the biological activity is not enzyme in nature, were treated successfully with acidified organic solvents. Other methods were investigated but were not suitable because of a deleterious effect on the biological activity or physical properties of the product or an inability to effect salmonella elimination.

  3. Elimination of Salmonellae from Animal Glandular Products

    Science.gov (United States)

    De Fiebre, Conrad W.; Burck, Kenneth T.; Feldman, David

    1969-01-01

    Methods for the elimination of salmonellae from selected powdered pharmaceuticals of animal glandular origin were studied. Terminal heat treatment under carefully controlled conditions was effective for pancreatin—a powder containing proteolytic, amylolytic, and lipolytic enzymes prepared from hog pancreas glands. Use of this method resulted in a significant reduction in the number of salmonella-positive batches and also reduced the testing procedures required to confirm the absence of viable salmonellae among the majority of samples tested. Powders such as stomach substance and thyroid, in which the biological activity is not enzyme in nature, were treated successfully with acidified organic solvents. Other methods were investigated but were not suitable because of a deleterious effect on the biological activity or physical properties of the product or an inability to effect salmonella elimination. PMID:5780395

  4. Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

    Directory of Open Access Journals (Sweden)

    Walid Mottawea

    2018-05-01

    Full Text Available Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.

  5. Efeitos da Salmonella Enteritidis experimentalmente inoculada na saúde gastrintestinal de perus Effects of experimentally inoculated Salmonella Enteritidis on the gastrointestinal health of turkeys

    Directory of Open Access Journals (Sweden)

    Carla Yoko Tanikawa de Andrade

    2012-03-01

    Full Text Available Avaliaram-se os efeitos de Salmonella Enteritidis sobre a colonização e o desenvolvimento do trato intestinal, a conversão alimentar e o ganho de peso em perus. Um total de 135 perus de corte de 1 dia foi distribuído em três tratamentos: controle; perus oriundos de ovos inoculados com Salmonella Enteritidis via casca e perus desafiados com água de bebida com Salmonella Enteritidis. Aos 10, 20 e 28 dias, avaliaram-se as variáveis de desempenho e coletaram-se amostras para avaliação bacteriana, biometria e histomorfometria. Realizaram-se também, nos dias 1, 15 e 28 de idade, coletas de mecônio/excretas de todas as aves. A colonização intestinal aumentou durante a fase inicial quando Salmonella foi inoculada via casca. O intestino apresentou maior peso ao 1º, 10º e 28º dias quando Salmonella esteve presente, sem diferença no comprimento. Salmonella Enteritidis foi capaz de colonizar o trato intestinal, estabelecer infecção, reduzir o desempenho das aves e modificar as estruturas celulares do intestino. A contaminação da casca do ovo antes da incubação propiciou a ocorrência de infecções ao nascimento, e a frequência de isolamento de Salmonella Enteritidis persistiu até 28 dias de idade. A inoculação de Salmonella pela água de bebida gerou aves infectadas, porém com menor nível de infecção com o avançar da idade. O desempenho de aves inoculadas com Salmonella Enteritidis é menor e isso confirma potenciais prejuízos para a produção avícola.The effects of Salmonella Enteritidis on the colonization and development of the intestinal tract, feed conversion and weight gain were evaluated. A total of 135 day old turkeys were assigned to three treatments: control; turkeys from eggs inoculated with Salmonella Enteritidis via shell and turkeys challenged with drinking water with Salmonella Enteritidis. At 10, 20 and 28 days, the performance variables were evaluated and samples were collected to perform bacterial

  6. The eleventh CRL-Salmonella workshop, 9 May 2006, Saint Malo, France

    NARCIS (Netherlands)

    Mooijman KA; MGB

    2006-01-01

    De elfde workshop georganiseerd door het Communautair Referentie Laboratorium voor Salmonella (CRL-Salmonella) werd gehouden op 9 mei 2006 in Saint Malo, Frankrijk. Deelnemers waren vertegenwoordigers van de nationale Referentie Laboratoria voor Salmonella (NRLs-Salmonella) van de lidstaten van de

  7. SMM-system: A mining tool to identify specific markers in Salmonella enterica.

    Science.gov (United States)

    Yu, Shuijing; Liu, Weibing; Shi, Chunlei; Wang, Dapeng; Dan, Xianlong; Li, Xiao; Shi, Xianming

    2011-03-01

    This report presents SMM-system, a software package that implements various personalized pre- and post-BLASTN tasks for mining specific markers of microbial pathogens. The main functionalities of SMM-system are summarized as follows: (i) converting multi-FASTA file, (ii) cutting interesting genomic sequence, (iii) automatic high-throughput BLASTN searches, and (iv) screening target sequences. The utility of SMM-system was demonstrated by using it to identify 214 Salmonella enterica-specific protein-coding sequences (CDSs). Eighteen primer pairs were designed based on eighteen S. enterica-specific CDSs, respectively. Seven of these primer pairs were validated with PCR assay, which showed 100% inclusivity for the 101 S. enterica genomes and 100% exclusivity of 30 non-S. enterica genomes. Three specific primer pairs were chosen to develop a multiplex PCR assay, which generated specific amplicons with a size of 180bp (SC1286), 238bp (SC1598) and 405bp (SC4361), respectively. This study demonstrates that SMM-system is a high-throughput specific marker generation tool that can be used to identify genus-, species-, serogroup- and even serovar-specific DNA sequences of microbial pathogens, which has a potential to be applied in food industries, diagnostics and taxonomic studies. SMM-system is freely available and can be downloaded from http://foodsafety.sjtu.edu.cn/SMM-system.html. Copyright © 2011 Elsevier B.V. All rights reserved.

  8. SEROTYPES AND ANTIMICROBIAL RESISTANCE OF SALMONELLA ENTERICA SSP IN CENTRAL THAILAND, 2001-2006

    DEFF Research Database (Denmark)

    Pantip, Sirichote; Aroon, B.; Kanokwan, Tienmanee

    2010-01-01

    This study was carried out to elucidate the epidemiological trends and antimicrobial susceptibilities against Salmonella serovars among Thai patients and asymptomatic carriers during 2001-2006 in central Thailand. A total of 1,401 human and 260 non-human isolates from various sources were include...

  9. Targeting Non-Coding RNAs in Plants with the CRISPR-Cas Technology is a Challenge yet Worth Accepting.

    Science.gov (United States)

    Basak, Jolly; Nithin, Chandran

    2015-01-01

    Non-coding RNAs (ncRNAs) have emerged as versatile master regulator of biological functions in recent years. MicroRNAs (miRNAs) are small endogenous ncRNAs of 18-24 nucleotides in length that originates from long self-complementary precursors. Besides their direct involvement in developmental processes, plant miRNAs play key roles in gene regulatory networks and varied biological processes. Alternatively, long ncRNAs (lncRNAs) are a large and diverse class of transcribed ncRNAs whose length exceed that of 200 nucleotides. Plant lncRNAs are transcribed by different RNA polymerases, showing diverse structural features. Plant lncRNAs also are important regulators of gene expression in diverse biological processes. There has been a breakthrough in the technology of genome editing, the CRISPR-Cas9 (clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9) technology, in the last decade. CRISPR loci are transcribed into ncRNA and eventually form a functional complex with Cas9 and further guide the complex to cleave complementary invading DNA. The CRISPR-Cas technology has been successfully applied in model plants such as Arabidopsis and tobacco and important crops like wheat, maize, and rice. However, all these studies are focused on protein coding genes. Information about targeting non-coding genes is scarce. Hitherto, the CRISPR-Cas technology has been exclusively used in vertebrate systems to engineer miRNA/lncRNAs, but it is still relatively unexplored in plants. While briefing miRNAs, lncRNAs and applications of the CRISPR-Cas technology in human and animals, this review essentially elaborates several strategies to overcome the challenges of applying the CRISPR-Cas technology in editing ncRNAs in plants and the future perspective of this field.

  10. Targeting non-coding RNAs in Plants with the CRISPR-Cas technology is a challenge yet worth accepting

    Directory of Open Access Journals (Sweden)

    Jolly eBasak

    2015-11-01

    Full Text Available Non-coding RNAs (ncRNAs have emerged as versatile master regulator of biological functions in recent years. MicroRNAs (miRNAs are small endogenous ncRNAs of 18-24 nucleotides in length that originates from long self-complementary precursors. Besides their direct involvement in developmental processes, plant miRNAs play key roles in gene regulatory networks and varied biological processes. Alternatively, long ncRNAs (lncRNAs are a large and diverse class of transcribed ncRNAs whose length exceed that of 200 nucleotides. Plant lncRNAs are transcribed by different RNA polymerases, showing diverse structural features. Plant lncRNAs also are important regulators of gene expression in diverse biological processes. There has been a breakthrough in the technology of genome editing, the CRISPR-Cas9 (clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9 technology, in the last decade. CRISPR loci are transcribed into ncRNA and eventually form a functional complex with Cas9 and further guide the complex to cleave complementary invading DNA. The CRISPR-Cas technology has been successfully applied in model plants such as Arabidopsis and tobacco and important crops like wheat, maize and rice. However, all these studies are focused on protein coding genes. Information about targeting non-coding genes is scarce. Hitherto, the CRISPR-Cas technology has been exclusively used in vertebrate systems to engineer miRNA/lncRNAs, but it is still relatively unexplored in plants. While briefing miRNAs, lncRNAs and applications of the CRISPR-Cas technology in human and animals, this review essentially elaborates several strategies to overcome the challenges of applying the CRISPR-Cas technology in editing ncRNAs in plants and the future perspective of this field.

  11. Bilateral breast abscesses due to Salmonella Enterica serotype typhi

    Directory of Open Access Journals (Sweden)

    Gagandeep Singh

    2011-01-01

    Full Text Available Focal infection is an uncommon complication of Salmonella septicemia, particularly in immunocompetent patients. The localization of Salmonella infection to breast tissue is regarded as a rare event. We report a case of bilateral breast abscesses due to Salmonella enterica serotype Typhi in a nonlactating female and highlight the fact that Salmonella spp. should be included in differential diagnosis of abscesses in individuals coming from endemic areas with the history of recent typhoid fever and should be treated accordingly.

  12. Definitive Radiotherapy of Non-Small Cell Lung Cancer

    International Nuclear Information System (INIS)

    Lee, Jong Young; Park, Kyung Ran

    1995-01-01

    Purpose : The effect of dose escalation of up to 6500 cGy on local control and survival was investigated in locally advanced non-small cell lung cancer. Materials and Methods : Ninety eight patients with biopsy-proven unresectable non-small cell lung cancer without distant metastases or medically inoperable patients with lower-stage were treated with definitive radiotherapy alone. Group A were treated by thoracic irradiation, 6000 cGy or less in total tumor dose with daily fractions of 180 to 200 cGy: and group B was treated with 6500 cGy of same daily fractions. Results : The actuarial overall survival rate for the entire group was 54% at 1 year, 26.6% at 2 years and 16.4% at 3 years with a median survival time of 13 months. Statistically significant prognostic factors that affect survival rate were stage and N-stage. However, no improvement in local control and survival has been seen with higher dose radiotherapy(group B). Conclusion : Dose escalation of up to 6500 cGy was no effect on local control and survival rate. To increase the survival rate of non-small cell lung cancer hyperfractionated radiotherapy or concurrent chemoradiotherapy should be considered

  13. Expression of coding (mRNA) and non-coding (microRNA) RNA in lung tissue and blood isolated from pigs suffering from bacterial pleuropneumonia

    DEFF Research Database (Denmark)

    Skovgaard, Kerstin; Schou, Kirstine Klitgaard; Wendt, Karin Tarp

    2010-01-01

    MicroRNAs are small non-coding RNA molecules (18-23 nt), that regulate the activity of other genes at the post-transcriptional level. Recently it has become evident that microRNA plays an important role in modulating and fine tuning innate and adaptive immune responses. Still, little is known about...... the impact of microRNAs in the development and pathogenesis of lung infections. Expression of microRNA known to be induced by bacterial (i.e., LPS) ligands and thus supposed to play a role in the regulation of antimicrobial defence, were studied in lung tissue and in blood from pigs experimentally infected...... with Actinobacillus pleuropneumoniae (AP). Expression differences of mRNA and microRNA were quantified at different time points (6h, 12h, 24h, 48h PI) using reverse transcription quantitative real-time PCR (Rotor-Gene and Fluidigm). Expression profiles of miRNA in blood of seven animals were further studied using mi...

  14. Coconut and Salmonella Infection

    Science.gov (United States)

    Schaffner, Carl P.; Mosbach, Klaus; Bibit, Venuso C.; Watson, Colin H.

    1967-01-01

    Raw, unprocessed coconut supports the growth of salmonellae as well as that of other enteric bacteria, salmonellae being particularly resistant to subsequent desiccation. Original contamination is not due to carriers or to polluted water supplies, but to contact with bacteria-containing soils followed by dispersion via infected coconut milk and shells. Pasteurization of raw coconut meat in a water bath at 80 C for 8 to 10 min effectively killed such bacteria, did not injure the product, and provided a prophylactic method now widely used by the coconut industry. PMID:5340650

  15. Isolation and identification of Salmonella spp. in drinking water, streams, and swine wastewater by molecular techniques in Taiwan

    Science.gov (United States)

    Kuo, C.; Hsu, B.; Shen, T.; Tseng, S.; Tsai, J.; Huang, K.; Kao, P.; Chen, J.

    2013-12-01

    Salmonella spp. is a common water-borne pathogens and its genus comprises more than 2,500 serotypes. Major pathogenic genotypes which cause typhoid fever, enteritis and other intestinal-type diseases are S. Typhimurium, S. Enteritidis, S. Stanley, S. Agona, S.Albany, S. Schwarzengrund, S. Newport, S. Choleraesuis, and S. Derby. Hence, the identification of the serotypes of Salmonella spp. is important. In the present study, the analytical procedures include direct concentration method, non-selective pre-enrichment method and selective enrichment method of Salmonella spp.. Both selective enrichment method and cultured bacteria were detected with specific primers of Salmonella spp. by polymerase chain reaction (PCR). At last, the serotypes of Salmonella were confirmed by using MLST (multilocus sequence typing) with aroC, dnaN, hemD, hisD, purE, sucA, thrA housekeeping genes to identify the strains of positive samples. This study contains 121 samples from three different types of water sources including the drinking water (51), streams (45), and swine wastewater (25). Thirteen samples with positive invA gene are separated from culture method. The strains of these positive samples which identified from MLST method are S. Albany, S. Typhimurium, S. Newport, S. Bareilly, and S. Derby. Some of the serotypes, S. Albany, S. Typhimurium and S. Newport, are highly pathogenic which correlated to human diarrhea. In our results, MLST is a useful method to identify the strains of Salmonella spp.. Keywords: Salmonella, PCR, MLST.

  16. Diversity and Antimicrobial Resistance Genotypes in Non-Typhoidal Salmonella Isolates from Poultry Farms in Uganda

    Directory of Open Access Journals (Sweden)

    Terence Odoch

    2018-02-01

    Full Text Available Non-typhoidal Salmonella (NTS are foodborne pathogens of global public health significance. The aim of this study was to subtype a collection of 85 NTS originating from poultry farms in Uganda, and to evaluate a subgroup of phenotypically resistant isolates for common antimicrobial resistance genes and associated integrons. All isolates were subtyped by pulsed-field gel electrophoresis (PFGE. Phenotypically resistant isolates (n = 54 were screened by PCR for the most relevant AMR genes corresponding to their phenotypic resistance pattern, and all 54 isolates were screened by PCR for the presence of integron class 1 and 2 encoding genes. These genes are known to commonly encode resistance to ampicillin, tetracycline, ciprofloxacin, trimethoprim, sulfonamide and chloramphenicol. PFGE revealed 15 pulsotypes representing 11 serotypes from 75 isolates, as 10 were non-typable. Thirty one (57.4% of the 54 resistant isolates carried at least one of the seven genes (blaTEM-1, cmlA, tetA, qnrS, sul1, dhfrI, dhfrVII identified by PCR and six (11% carried class 1 integrons. This study has shown that a diversity of NTS-clones are present in Ugandan poultry farm settings, while at the same time similar NTS-clones occur in different farms and areas. The presence of resistance genes to important antimicrobials used in human and veterinary medicine has been demonstrated, hence the need to strengthen strategies to combat antimicrobial resistance at all levels.

  17. 78 FR 42451 - Animal Feeds Contaminated With Salmonella Microorganisms

    Science.gov (United States)

    2013-07-16

    .... FDA-2013-N-0253] Animal Feeds Contaminated With Salmonella Microorganisms AGENCY: Food and Drug... revoking an advisory opinion on animal feeds contaminated with Salmonella microorganisms. This action is... articulated in a final compliance policy guide (CPG) on Salmonella in food for animals. DATES: This rule is...

  18. Comparing validation of four ELISA-systems for detection of Salmonella derby- and Salmonella infantis-infected pigs.

    Science.gov (United States)

    Roesler, Uwe; Szabo, Istvan; Matthies, Claudia; Albrecht, Kerstin; Leffler, Martin; Scherer, Kathrin; Nöckler, Karsten; Lehmann, Jörg; Methner, Ulrich; Hensel, Andreas; Truyen, Uwe

    2011-01-01

    The objective of this study was the comparative evaluation of four indirect Salmonella ELISA tests at study time approved in Germany to detect Salmonella infection in pigs.Three tests are based on a LPS-antigen mix and directed against specific IgG antibodies. The fourth test is based on a purified S. Typhimurium whole-cell lysate antigen and discriminates between Salmonella-specific IgM-, IgA-, and IgG- antibodies. In a longitudinal study, two groups of six weeks old hybrid piglets were orally infected with a porcine S. Infantis or S. Derby strain. Clinical and bacteriological parameters were monitored weekly during an observation period of 130 days after infection and serum samples were investigated in parallel with the respective ELISAs. Apparently, the LPS-based ELISA systems used in this study failed to recognize S. Infantis-infected pigs although those animals shed the pathogen in high amounts throughout the study until day 81 post infection (p. i.). In contrast, the isotype-specific Salmonella Typhimurium whole-cell-lysate based ELISA was capable of detecting Salmonella-infected pigs from day ten p. i. at all tested serotypes and revealed the highest sensitivity in detection of S. Infantis-infected pigs. Furthermore, it became apparent that the often used surveillance cut-off value of 40 OD% is not appropriate for intra-vitam detection of S. Infantis- and S. Derby-infected pigs. In contrast, the cut-off values of the ELISAs given by the suppliers result in considerable higher detection rates.

  19. Increased colon cancer risk after severe Salmonella infection

    OpenAIRE

    Mughini-Gras, Lapo; Schaapveld, Michael; Kramers, Jolanda; Mooij, Sofie; Neefjes-Borst, E. Andra; van Pelt, Wilfrid; Neefjes, Jacques

    2018-01-01

    Background Colon cancer constitutes one of the most frequent malignancies. Previous studies showed that Salmonella manipulates host cell signaling pathways and that Salmonella Typhimurium infection facilitates colon cancer development in genetically predisposed mice. This epidemiological study examined whether severe Salmonella infection, usually acquired from contaminated food, is associated with increased colon cancer risk in humans. Methods and findings We performed a nationwide registry-b...

  20. Chasing Salmonella Typhimurium in free range egg production system.

    Science.gov (United States)

    Chousalkar, Kapil; Gole, Vaibhav; Caraguel, Charles; Rault, Jean-Loup

    2016-08-30

    Free range production systems are becoming a major source of egg production in Australia and worldwide. This study investigated shedding and ecology of Salmonella Typhimurium and Salmonella species in a free range layer flock, wild birds and foxes in the vicinity of the free range farm in different seasons. Shedding of Salmonella was significantly higher in summer. Within the shed, overall, Salmonella prevalence was highest in dust. Corticosterone level in faeces was highest in spring and lowest in winter. There was no direct association between the Salmonella shedding (MPN/gm) and corticosterone levels in faeces. Salmonella Typhimurium MLVA types isolated from fox and wild birds were similar to MLVA types isolated from layer flock and reported during human food borne illness. Wild birds and foxes appear to play an important role in S. Typhimurium ecology and food safety. Environmental factors could play a role in evolution of S. Typhimurium in free range environment. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

  1. Detection of Salmonella enterica in meat in less than 5 hours by a low-cost and non-complex sample preparation method

    DEFF Research Database (Denmark)

    Fachmann, Mette Sofie Rousing; Löfström, Charlotta; Hoorfar, Jeffrey

    2017-01-01

    peptone water, and a real-time PCR compatible sample preparation method, based on filtration, centrifugation, and enzymatic digestion, followed by fast cycling real-time PCR detection. The method was validated in an un-paired, comparative study against the Nordic Committee on Food Analysis (NMKL......, and help contribute to improved food safety. While the cost of analysis and hands-on time of the presented rapid method were comparable to reference culture methods, the fast product release by this method can provide the meat industry with a competitive advantage. Not only will the abattoirs save costs......Salmonella is recognised as one of the most important foodborne bacteria, and has a wide health and socioeconomical impact worldwide. Fresh pork meat is one of the main sources of Salmonella and efficient and fast methods for detection are therefore necessary. Current methods for Salmonella...

  2. Increased colon cancer risk after severe Salmonella infection.

    Directory of Open Access Journals (Sweden)

    Lapo Mughini-Gras

    Full Text Available Colon cancer constitutes one of the most frequent malignancies. Previous studies showed that Salmonella manipulates host cell signaling pathways and that Salmonella Typhimurium infection facilitates colon cancer development in genetically predisposed mice. This epidemiological study examined whether severe Salmonella infection, usually acquired from contaminated food, is associated with increased colon cancer risk in humans.We performed a nationwide registry-based study to assess colon cancer risk after diagnosed Salmonella infection. National infectious disease surveillance records (1999-2015 for Dutch residents aged ≥20 years when diagnosed with salmonellosis (n = 14,264 were linked to the Netherlands Cancer Registry. Salmonella-infected patients were laboratory-confirmed under medical consultation after 1-2 weeks of illness. These datasets also contained information on Salmonella serovar and type of infection. Colon cancer risk (overall and per colon subsite among patients with a diagnosed Salmonella infection was compared with expected colon cancer risk in the general population. Data from the nationwide registry of histo- and cytopathology (PALGA and Statistics Netherlands (CBS allowed assessing potential effects of age, gender, latency, socioeconomic status, genetic predisposition, inflammatory bowel disease (IBD, and tumor features. We found that compared to the general population, colon cancer risk was significantly increased (standardized incidence ratio [SIR] 1.54; 95%CI 1.09-2.10 among patients with Salmonella infection diagnosed <60 years of age. Such increased risk concerned specifically the ascending/transverse colon (SIR 2.12; 95%CI 1.38-3.09 after S. Enteritidis infection (SIR 2.97; 95%CI 1.73-4.76. Salmonellosis occurred more frequently among colon cancer patients with pre-infectious IBD, a known risk factor for colon cancer. Colon tumors of patients with a history of Salmonella infection were mostly of low grade

  3. Increased colon cancer risk after severe Salmonella infection

    Science.gov (United States)

    Mooij, Sofie; Neefjes-Borst, E. Andra; van Pelt, Wilfrid; Neefjes, Jacques

    2018-01-01

    Background Colon cancer constitutes one of the most frequent malignancies. Previous studies showed that Salmonella manipulates host cell signaling pathways and that Salmonella Typhimurium infection facilitates colon cancer development in genetically predisposed mice. This epidemiological study examined whether severe Salmonella infection, usually acquired from contaminated food, is associated with increased colon cancer risk in humans. Methods and findings We performed a nationwide registry-based study to assess colon cancer risk after diagnosed Salmonella infection. National infectious disease surveillance records (1999–2015) for Dutch residents aged ≥20 years when diagnosed with salmonellosis (n = 14,264) were linked to the Netherlands Cancer Registry. Salmonella-infected patients were laboratory-confirmed under medical consultation after 1–2 weeks of illness. These datasets also contained information on Salmonella serovar and type of infection. Colon cancer risk (overall and per colon subsite) among patients with a diagnosed Salmonella infection was compared with expected colon cancer risk in the general population. Data from the nationwide registry of histo- and cytopathology (PALGA) and Statistics Netherlands (CBS) allowed assessing potential effects of age, gender, latency, socioeconomic status, genetic predisposition, inflammatory bowel disease (IBD), and tumor features. We found that compared to the general population, colon cancer risk was significantly increased (standardized incidence ratio [SIR] 1.54; 95%CI 1.09–2.10) among patients with Salmonella infection diagnosed transverse colon (SIR 2.12; 95%CI 1.38–3.09) after S. Enteritidis infection (SIR 2.97; 95%CI 1.73–4.76). Salmonellosis occurred more frequently among colon cancer patients with pre-infectious IBD, a known risk factor for colon cancer. Colon tumors of patients with a history of Salmonella infection were mostly of low grade. Conclusions Patients diagnosed with severe

  4. Systemic bacteraemia in children presenting with clinical pneumonia and the impact of non-typhoid salmonella (NTS).

    Science.gov (United States)

    Schwarz, Norbert G; Sarpong, Nimako; Hünger, Frank; Marks, Florian; Acquah, Samuel Ek; Agyekum, Alex; Nkrumah, Bernard; Loag, Wibke; Hagen, Ralf M; Evans, Jennifer A; Dekker, Denise; Fobil, Julius N; Meyer, Christian G; May, Jürgen; Adu-Sarkodie, Yaw

    2010-11-04

    The diagnosis and antimicrobial treatment of pneumonia in African children in the absence of diagnostic means such as x-ray facilities or microbiological laboratories relies primarily on clinical symptoms presented by the patients. In order to assess the spectrum of bacterial pathogens, blood cultures were performed in children fulfilling the clinical criteria of pneumonia. In total, 1032 blood cultures were taken from children between 2 months and 5 years of age who were admitted to a rural hospital in Ghana between September 2007 and July 2009. Pneumonia was diagnosed clinically and according to WHO criteria classified as "non-severe pneumonia" and "severe pneumonia" ("severe pneumonia" includes the WHO categories "severe pneumonia" and "very severe pneumonia"). The proportion of bacteriaemia with non-typhoid salmonella (NTS) was similar in children with pneumonia (16/173, 9.2%) compared to children hospitalized for other reasons (112/859, 13%). NTS were the predominant organisms isolated from children with clinical pneumonia and significantly more frequent than Streptococcus pneumoniae (8/173, 4.6%). Nine percent (9/101) of children presenting with severe pneumonia and 10% (7/72) of children with non-severe pneumonia were infected with NTS. Nineteen out of 123 NTS isolates (15%) were susceptible to aminopenicillins (amoxycillin/ampicillin), 23/127 (18%) to chlorampenicol, and 23/98 (23%) to co-trimoxazole. All NTS isolates were sensitive to ceftriaxone and ciprofloxacin. In Sub-saharan Africa, sepsis with NTS should be considered in children with symptoms of pneumonia and aminopenicillins might often not be the adequate drugs for treatment.

  5. Effect of waste milk pasteurization on fecal shedding of Salmonella in pre-weaned calves

    Science.gov (United States)

    To determine if pasteurization of non-saleable waste milk influences fecal Salmonella concentrations, prevalence, or antimicrobial susceptibility and serotype of cultured isolates, 211 Holstein dairy calves were housed on a single commercial dairy in the southwestern United States and randomly allot...

  6. Risks Involved in the Use of Enrofloxacin for Salmonella Enteritidis or Salmonella Heidelberg in Commercial Poultry

    Science.gov (United States)

    Morales-Barrera, Eduardo; Calhoun, Nicole; Lobato-Tapia, Jose L.; Lucca, Vivian; Prado-Rebolledo, Omar; Hernandez-Velasco, Xochitl; Merino-Guzman, Ruben; Petrone-García, Victor M.; Latorre, Juan D.; Mahaffey, Brittany D.; Teague, Kyle D.; Graham, Lucas E.; Wolfenden, Amanda D.; Baxter, Mikayla F. A.; Hargis, Billy M.; Tellez, Guillermo

    2016-01-01

    The objectives of the present study were to evaluate the risks involved in the use of Enrofloxacin for Salmonella Enteritidis (SE) or Salmonella Heidelberg (SH) in commercial poultry and determine the effects of a probiotic as an antibiotic alternative. Two experiments were conducted to evaluate the risks involved in the use of Enrofloxacin for SE or SH in commercial poultry. Experiment 1 consisted of two trials. In each trial, chickens were assigned to one of three groups; control + SE challenged; Enrofloxacin 25 mg/kg + SE; and Enrofloxacin 50 mg/kg + SE. Chickens received Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, all groups received fresh water without any treatment. All chickens were orally gavaged with 107 cfu/chick of SE at 7 days of age and euthanized on 8 days of age. In Experiment 2, turkey poults were assigned to one of the three groups; control + SH; probiotic + SH; and Enrofloxacin 50 mg/kg + SH. Poults received probiotic or Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, poults received fresh water without any treatment. Poults were orally gavaged with 107 cfu/poult of SH at 7 days of age. Poults were weighed and humanely killed 24 h post-SH challenge to evaluate serum concentration of fluorescein isothiocyanate-dextran to evaluate intestinal permeability, metagenomics, and SH infection. In both trials of Experiment 1, chickens treated with Enrofloxacin were more susceptible to SE organ invasion and intestinal colonization when compared with control non-treated chickens (P < 0.05). In Experiment 2, poults treated with 50 mg/kg of Enrofloxacin showed an increase in body weight, however, this group also showed an increase in SH susceptibility, intestinal permeability, and lower proportion of Firmicutes and Bacteroidetes, but with control group had the highest proportion of Proteobacteria. By contrast, poults that received the probiotic had the highest

  7. TASS code topical report. V.1 TASS code technical manual

    International Nuclear Information System (INIS)

    Sim, Suk K.; Chang, W. P.; Kim, K. D.; Kim, H. C.; Yoon, H. Y.

    1997-02-01

    TASS 1.0 code has been developed at KAERI for the initial and reload non-LOCA safety analysis for the operating PWRs as well as the PWRs under construction in Korea. TASS code will replace various vendor's non-LOCA safety analysis codes currently used for the Westinghouse and ABB-CE type PWRs in Korea. This can be achieved through TASS code input modifications specific to each reactor type. The TASS code can be run interactively through the keyboard operation. A simimodular configuration used in developing the TASS code enables the user easily implement new models. TASS code has been programmed using FORTRAN77 which makes it easy to install and port for different computer environments. The TASS code can be utilized for the steady state simulation as well as the non-LOCA transient simulations such as power excursions, reactor coolant pump trips, load rejections, loss of feedwater, steam line breaks, steam generator tube ruptures, rod withdrawal and drop, and anticipated transients without scram (ATWS). The malfunctions of the control systems, components, operator actions and the transients caused by the malfunctions can be easily simulated using the TASS code. This technical report describes the TASS 1.0 code models including reactor thermal hydraulic, reactor core and control models. This TASS code models including reactor thermal hydraulic, reactor core and control models. This TASS code technical manual has been prepared as a part of the TASS code manual which includes TASS code user's manual and TASS code validation report, and will be submitted to the regulatory body as a TASS code topical report for a licensing non-LOCA safety analysis for the Westinghouse and ABB-CE type PWRs operating and under construction in Korea. (author). 42 refs., 29 tabs., 32 figs

  8. Generation of a gene cassette for genetically engineered Salmonella Enteritidis in the specific region of the sipC gene

    Directory of Open Access Journals (Sweden)

    M Ghasemi

    2017-05-01

    Full Text Available Introduction: Salmonellosis is an infection caused by eating contaminated food with Salmonella, and it can occur in humans and other animals. Salmonella has acquired the ability to create the infection due to the presence of several virulence genes. One of the virulence genes of salmonella is sipC gene that coding the SipC protein. The aim of this study was creating the gene cassette to genetically engineered Salmonella enteritidis in the specific region of the sipC gene. Methods: In this study, after DNA extraction from Salmonella, the upstream and downstream regions of the sipC gene was amplified based on PCR method. The PCR products were cloned with T/A cloning method and they were inserted into the pGEM vector. In order to generate the final gene cassette, each of the upstream and downstream regions of the sipC gene was subcloned into the pET32 vector, and cloning accuracy was assessed by PCR and enzyme digestion methods. Results: Amplification of the 320 bp upstream and 206 bp downstream of sipC gene was successful by PCR method. T/A cloning of these fragments were caused the formation of two pGEM-up and pGEM-down recombinant vectors. Results that were confirmed the sub-cloning accuracy indicate the formation of the final pET32-up-down gene cassette. Conclusion: The generated gene cassette in this study was considered as a multi-purpose cassette that is able to specific gene manipulation of Salmonella sipC gene by homologous recombination matched. This gene cassette has the necessary potential for sipC gene deletion or insertion of any useful gene instead of sipC gene.

  9. Salmonella infection and carriage in reptiles in a zoological collection.

    Science.gov (United States)

    Clancy, Meredith M; Davis, Meghan; Valitutto, Marc T; Nelson, Kenrad; Sykes, John M

    2016-05-01

    OBJECTIVE To identify important subspecies and serovars of Salmonella enterica in a captive reptile population and clinically relevant risk factors for and signs of illness in Salmonella-positive reptiles. DESIGN Retrospective cross-sectional study. ANIMALS 11 crocodilians (4 samples), 78 snakes (91 samples), 59 lizards (57 samples), and 34 chelonians (23 samples) at the Bronx Zoo from 2000 through 2012. PROCEDURES Data pertaining to various types of biological samples obtained from reptiles with positive Salmonella culture results and the reptiles themselves were analyzed to determine period prevalence of and risk factors for various Salmonella-related outcomes. RESULTS Serovar distribution differences were identified for sample type, reptile phylogenetic family, and reptile origin and health. Salmonella enterica subsp enterica was the most common subspecies in Salmonella cultures (78/175 [45%]), identified across all reptilian taxa. Salmonella enterica subsp diarizonae was also common (42/175 [24%]) and was recovered almost exclusively from snakes (n = 33), many of which had been clinically ill (17). Clinically ill reptiles provided 37% (64) of Salmonella cultures. Factors associated with an increased risk of illness in reptiles with a positive culture result were carnivorous diet and prior confiscation. Snakes had a higher risk of illness than other reptile groups, whereas lizards had a lower risk. Bony changes, dermatitis, and anorexia were the most common clinical signs. CONCLUSIONS AND CLINICAL RELEVANCE This study provided new information on Salmonella infection or carriage and associated clinical disease in reptiles. Associations identified between serovars or subspecies and reptile groups or clinical disease can guide management of Salmonella-positive captive reptiles.

  10. Salmonella Dublin i oksekød, 2014

    DEFF Research Database (Denmark)

    Aabo, Søren; Hansen, Tina Beck

    Case-by-case overvågningen af dansk og udenlandsk fersk kød af kvæg ophørte ved årsskiftet til 2013 som følge af meget få fund. I 2012 blev der imidlertid påvist Salmonella i 14,3 % af de undersøgte partier af fersk dansk oksekød, mens man i samme periode ikke så den samme stigning i fund af...... Salmonella på slagterierne. Det er derfor muligt, at der er andre kilder til salmonellas forekomst i det ferske oksekød. En del oksekød opskæres typisk på andre virksomheder end på slagteriet, og krydskontaminering med Salmonella her kan derfor være en af årsagerne til det høje fund, da disse virksomheder...... typisk forarbejder store mængder dansk og udenlandsk kød i de samme produktionslinjer. Siden planlægningen af dette projekt er forekomsten af Salmonella Dublin faldet i oksekød, men projektet er blevet gennemført som oprindeligt planlagt. Formålet med dette projekt har været at afklare forekomsten af...

  11. Effect of dietary Bacillus coagulans supplementation on growth performance and immune responses of broiler chickens challenged by Salmonella enteritidis.

    Science.gov (United States)

    Zhen, Wenrui; Shao, Yujing; Gong, Xiuyan; Wu, Yuanyuan; Geng, Yanqiang; Wang, Zhong; Guo, Yuming

    2018-04-11

    This study was conducted to evaluate the protective efficacy of dietary Bacillus coagulans (B. coagulans) supplementation in birds receiving Salmonella enteritidis (SE). Two hundred and forty 1-day-old Cobb broilers were randomly assigned to 2 × 2 factorial arrangements of treatments with 2 levels of dietary B. coagulans (0 or 400 mg/kg) and 2 levels of SE challenge (0 or 1 × 109 SE between d 9 to 11). Results showed that SE infection did not affect growth performance, but caused intestinal inflammation and barrier function impairment by reducing intestinal goblet cells and beneficial bacteria numbers, increasing cecal Salmonella colonization and liver Salmonella invasion, downregulating jejunal mucin-2 (at 7 and 17 d post-infection, DPI), TLR2 (at 7 and 17 DPI), TLR4 (at 17 DPI), TNFSF15 (at 7 and 17 DPI) gene mRNA levels, and upregulating jejunal IFN-γ mRNA levels (at 17 DPI) compared to uninfected birds. Moreover, SE infection also elevated the concentration of jejunal anti-Salmonella IgA and sera anti-Salmonella IgG compared to uninfected birds. However, chickens received B. coagulans diets showed significant increase in body weight gain and weight gain to feed intake ratio from d 15 to 21, alkaline phosphatase activity (at 7 DPI), cecal Lactobacilli and Bifidobacterium numbers (at 7 DPI; at 17 DPI), villous height: crypt ratio (at 17 DPI), and goblet cell numbers (at 7 and 17 DPI), whereas exhibiting reduced jejunal crypt depth (at 17 DPI), cecal Escherichia coli (at 7, 17, and 31 DPI), and Salmonella (at 7 and 17 DPI) levels compared with the non-supplemented birds, regardless of SE infection. In addition, B. coagulans supplement upregulated lysozyme mRNA levels (at 17 DPI), downregulated IFN-γ mRNA levels (at 7 and 17 DPI), showed an increased trend in Fowlicidin-2 mRNA levels (at 7 DPI) and a reduced trend in liver Salmonella load compared to the non-supplemented control. These data indicated that B. coagulans has a protective effect in SE infected

  12. Molecular characterization of Salmonella Paratyphi B dT+ and Salmonella Heidelberg from poultry and retail chicken meat in Colombia by pulsed-field gel electrophoresis

    Science.gov (United States)

    Salmonella Paratyphi B dT+ variant (also termed Salmonella Java) and Salmonella Heidelberg are human pathogens frequently isolated from poultry. As a step towards implementing the Colombian Integrated Program for Antimicrobial Resistant Surveillance (COIPARS), this study characterized molecular patt...

  13. Isolation, serotype diversity and antibiogram of Salmonella enterica isolated from different species of poultry in India

    Directory of Open Access Journals (Sweden)

    Irfan Ahmad Mir

    2015-07-01

    Conclusions: Occurrence of high proportion of serovars in our study which can cause serious gastroenteritis in humans is a matter of concern. Salmonella Altona has been detected for the first time in India from poultry. This serotype is known to cause serious outbreaks of gastroenteritis in humans. Multidrug resistant isolates were recovered at high percentage which can be attributed to non-judicious use of antibiotics both in prophylaxis and treatment regimen. This observation draws serious attention as poultry serves as an important source of transmission of these multidrug resistant Salmonella serovars to humans.

  14. Salmonella serotypes in reptiles and humans, French Guiana.

    Science.gov (United States)

    Gay, Noellie; Le Hello, Simon; Weill, François-Xavier; de Thoisy, Benoit; Berger, Franck

    2014-05-14

    In French Guiana, a French overseas territory located in the South American northern coast, nearly 50% of Salmonella serotypes isolated from human infections belong to serotypes rarely encountered in metropolitan France. A reptilian source of contamination has been investigated. Between April and June 2011, in the area around Cayenne, 151 reptiles were collected: 38 lizards, 37 snakes, 32 turtles, 23 green iguanas and 21 caimans. Cloacal swab samples were collected and cultured. Isolated Salmonella strains were identified biochemically and serotyped. The overall carriage frequency of carriage was 23.2% (95% confidence interval: 16.7-30.4) with 23 serotyped strains. The frequency of Salmonella carriage was significantly higher for wild reptiles. Near two-thirds of the Salmonella serotypes isolated from reptiles were also isolated from patients in French Guiana. Our results highlight the risk associated with the handling and consumption of reptiles and their role in the spread of Salmonella in the environment. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Joint beam design and user selection over non-binary coded MIMO interference channel

    Science.gov (United States)

    Li, Haitao; Yuan, Haiying

    2013-03-01

    In this paper, we discuss the problem of sum rate improvement for coded MIMO interference system, and propose joint beam design and user selection over interference channel. Firstly, we have formulated non-binary LDPC coded MIMO interference networks model. Then, the least square beam design for MIMO interference system is derived, and the low complexity user selection is presented. Simulation results confirm that the sum rate can be improved by the joint user selection and beam design comparing with single interference aligning beamformer.

  16. Long non-coding RNA expression profiles in hereditary haemorrhagic telangiectasia

    DEFF Research Database (Denmark)

    Tørring, Pernille M; Larsen, Martin Jakob; Kjeldsen, Anette D

    2014-01-01

    transcriptome, we wanted to assess whether lncRNAs play a role in the molecular pathogenesis of HHT manifestations. By microarray technology, we profiled lncRNA transcripts from HHT nasal telangiectasial and non-telangiectasial tissue using a paired design. The microarray probes were annotated using the GENCODE...... v.16 dataset, identifying 4,810 probes mapping to 2,811 lncRNAs. Comparing HHT telangiectasial tissue with HHT non-telangiectasial tissue, we identified 42 lncRNAs that are differentially expressed (qUsing GREAT, a tool that assumes cis-regulation, we showed that differently expressed lncRNAs...... to the TGF-β signalling pathway. The exact mechanism of how haploinsufficiency of ENG and ACVRL1 leads to HHT manifestations remains to be identified. As long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression and constitute a sizable fraction of the human...

  17. Mechanical characteristics of historic mortars from tests on small-sample non-standard on small-sample non-standard specimens

    Czech Academy of Sciences Publication Activity Database

    Drdácký, Miloš; Slížková, Zuzana

    2008-01-01

    Roč. 17, č. 1 (2008), s. 20-29 ISSN 1407-7353 R&D Projects: GA ČR(CZ) GA103/06/1609 Institutional research plan: CEZ:AV0Z20710524 Keywords : small-sample non-standard testing * lime * historic mortar Subject RIV: AL - Art, Architecture, Cultural Heritage

  18. Code Cactus; Code Cactus

    Energy Technology Data Exchange (ETDEWEB)

    Fajeau, M; Nguyen, L T; Saunier, J [Commissariat a l' Energie Atomique, Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France)

    1966-09-01

    This code handles the following problems: -1) Analysis of thermal experiments on a water loop at high or low pressure; steady state or transient behavior; -2) Analysis of thermal and hydrodynamic behavior of water-cooled and moderated reactors, at either high or low pressure, with boiling permitted; fuel elements are assumed to be flat plates: - Flowrate in parallel channels coupled or not by conduction across plates, with conditions of pressure drops or flowrate, variable or not with respect to time is given; the power can be coupled to reactor kinetics calculation or supplied by the code user. The code, containing a schematic representation of safety rod behavior, is a one dimensional, multi-channel code, and has as its complement (FLID), a one-channel, two-dimensional code. (authors) [French] Ce code permet de traiter les problemes ci-dessous: 1. Depouillement d'essais thermiques sur boucle a eau, haute ou basse pression, en regime permanent ou transitoire; 2. Etudes thermiques et hydrauliques de reacteurs a eau, a plaques, a haute ou basse pression, ebullition permise: - repartition entre canaux paralleles, couples on non par conduction a travers plaques, pour des conditions de debit ou de pertes de charge imposees, variables ou non dans le temps; - la puissance peut etre couplee a la neutronique et une representation schematique des actions de securite est prevue. Ce code (Cactus) a une dimension d'espace et plusieurs canaux, a pour complement Flid qui traite l'etude d'un seul canal a deux dimensions. (auteurs)

  19. The Aster code; Code Aster

    Energy Technology Data Exchange (ETDEWEB)

    Delbecq, J.M

    1999-07-01

    The Aster code is a 2D or 3D finite-element calculation code for structures developed by the R and D direction of Electricite de France (EdF). This dossier presents a complete overview of the characteristics and uses of the Aster code: introduction of version 4; the context of Aster (organisation of the code development, versions, systems and interfaces, development tools, quality assurance, independent validation); static mechanics (linear thermo-elasticity, Euler buckling, cables, Zarka-Casier method); non-linear mechanics (materials behaviour, big deformations, specific loads, unloading and loss of load proportionality indicators, global algorithm, contact and friction); rupture mechanics (G energy restitution level, restitution level in thermo-elasto-plasticity, 3D local energy restitution level, KI and KII stress intensity factors, calculation of limit loads for structures), specific treatments (fatigue, rupture, wear, error estimation); meshes and models (mesh generation, modeling, loads and boundary conditions, links between different modeling processes, resolution of linear systems, display of results etc..); vibration mechanics (modal and harmonic analysis, dynamics with shocks, direct transient dynamics, seismic analysis and aleatory dynamics, non-linear dynamics, dynamical sub-structuring); fluid-structure interactions (internal acoustics, mass, rigidity and damping); linear and non-linear thermal analysis; steels and metal industry (structure transformations); coupled problems (internal chaining, internal thermo-hydro-mechanical coupling, chaining with other codes); products and services. (J.S.)

  20. Parotid abscess due to salmonella enteritidis: A case report.

    Science.gov (United States)

    Reyes, Cesar V; Jensen, JoAnne D

    2006-01-01

    Salmonella infection of the parotid gland is rare. An instance in a 50-year-old man of Salmonella enteritidis parotiditis initially recognized by microbial culture of a fine needle aspiration cytology material is described. The identified predisposing factor was chronic alcoholic abuse. For the infection source, a carrier state of salmonella parotitis was postulated, which progressed to focal abscess and was subsequently complicated by bacteremia and hematogenous spread to the liver, spleen and lungs. Salmonella should be included in the differential consideration of head and neck abscesses in immunocompromised individuals and treated aggressively.