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Sample records for pedv field isolates

  1. Novel Approach for Isolation and Identification of Porcine Epidemic Diarrhea Virus (PEDV) Strain NJ Using Porcine Intestinal Epithelial Cells

    PubMed Central

    Shi, Wen; Jia, Shuo; Zhao, Haiyuan; Yin, Jiyuan; Wang, Xiaona; Yu, Meiling; Ma, Sunting; Wu, Yang; Chen, Ying; Fan, Wenlu; Xu, Yigang; Li, Yijing

    2017-01-01

    Porcine epidemic diarrhea virus (PEDV), which is the causative agent of porcine epidemic diarrhea in China and other countries, is responsible for serious economic losses in the pork industry. Inactivated PEDV vaccine plays a key role in controlling the prevalence of PEDV. However, consistently low viral titers are obtained during the propagation of PEDV in vitro; this represents a challenge to molecular analyses of the virus and vaccine development. In this study, we successfully isolated a PEDV isolate (strain NJ) from clinical samples collected during a recent outbreak of diarrhea in piglets in China, using porcine intestinal epithelial cells (IEC). We found that the isolate was better adapted to growth in IECs than in Vero cells, and the titer of the IEC cultures was 104.5 TCID50/0.1 mL at passage 45. Mutations in the S protein increased with the viral passage and the mutations tended towards attenuation. Viral challenge showed that the survival of IEC-adapted cultures was higher at the 45th passage than at the 5th passage. The use of IECs to isolate and propagate PEDV provides an effective approach for laboratory-based diagnosis of PEDV, as well as studies of the epidemiological characteristics and molecular biology of this virus. PMID:28117718

  2. Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation

    PubMed Central

    Diep, Nguyen Van; Norimine, Junzo; Sueyoshi, Masuo; Lan, Nguyen Thi; Yamaguchi, Ryoji

    2017-01-01

    Since late 2013, after an absence of seven years, outbreaks of porcine epidemic diarrhea virus (PEDV) infection have reemerged and swept rapidly across Japan, resulting in significant economic losses. In this study, we report the emergence, mixed infection, and genetic characterization of 15 novel field PEDV variants with large genomic deletions. The sizes of deletion varied between 582 nt (194 aa) and 648 nt (216 aa) at positions 28–714 (10–238) on the S gene (protein). Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. These variants were found in eight primary and nine recurrent outbreaks, and they might be associated with persistent PEDV infection in the farms. Full-length S and ORF3 genes of eight variants derived from 2 samples were characterized. This is the first report of mixed infections caused by various genotypes of PEDV and would be important for the studies of viral isolation, pathogenesis, and molecular epidemiology of the disease. PMID:28095455

  3. Oleanane triterpenes from the flowers of Camellia japonica inhibit porcine epidemic diarrhea virus (PEDV) replication.

    PubMed

    Yang, Jun-Li; Ha, Thi-Kim-Quy; Dhodary, Basanta; Pyo, Euisun; Nguyen, Ngoc Hieu; Cho, Hyomoon; Kim, Eunhee; Oh, Won Keun

    2015-02-12

    Porcine epidemic diarrhea virus (PEDV) infections have resulted in a severe economic loss in the swine industry in many countries due to no effective treatment approach. Fifteen oleanane triterpenes (1-15), including nine new ones (1-4 and 10-14), were isolated from the flowers of Camellia japonica, and their molecular structures were determined by extensive spectroscopic methods. These compounds were evaluated for their antiviral activity against PEDV replication, and the structure-activity relationships (SARs) were discussed. Compounds 6, 9, 11, and 13 showed most potent inhibitory effects on PEDV replication. They were found to inhibit PEDV genes encoding GP6 nucleocapsid, GP2 spike, and GP5 membrane protein synthesis based on RT-PCR data. Western blot analysis also demonstrated their inhibitory effects on PEDV GP6 nucleocapsid and GP2 spike protein synthesis during viral replication. The present study suggested the potential of compounds 6, 9, 11, and 13 as promising scaffolds for treating PEDV infection via inhibiting viral replication.

  4. Evaluation of two real-time polymerase chain reaction assays for porcine epidemic diarrhea virus (PEDV) to assess PEDV transmission in growing pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In April 2013 a porcine epidemic diarrhea virus (PEDV) epidemic began in the United States. As part of the response, real-time RT-PCR assays to detect PEDV were developed by several Veterinary Diagnostic Laboratories. This study evaluated RT-PCR PEDV assays that detect the N gene (gN) and S gene (gS...

  5. Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak in US swine

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Porcine epidemic diarrhea virus (PEDV) was detected for the first time in US swine in April 2013 and has caused significant economic loss. Obtaining a US PEDV isolate that can grow efficiently in cell culture is critical for PEDV pathogenesis study, diagnostic assays and vaccine development. It was ...

  6. Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea.

    PubMed

    Lee, Dong-Kyu; Park, Choi-Kyu; Kim, Seong-Hee; Lee, Changhee

    2010-05-01

    Porcine epidemic diarrhea virus (PEDV) has plagued the domestic swine industry in Korea causing significant economic impacts on pig production nationwide. In the present study, we determined the complete nucleotide sequences of the spike (S) glycoprotein genes of seven Korean PEDV isolates. The entire S genes of all isolates were found to be nine nucleotides longer in length than other PEDV reference strains. This size difference was due to the combined presence of notable 15 bp insertion and 6 bp deletion within the N-terminal region of the S1 domain of the Korean isolates. In addition, the largest number of amino acid variations was accumulated in the S1 N-terminal region, leading to the presence of hypervariability in the isolates. Sequence comparisons at the peptide level of the S proteins revealed that all seven Korean isolates shared diverse similarities ranging from a 93.6% to 99.6% identity with each other but exhibited a 92.2% to 93.7% identity with other reference strains. Collectively, the sequence analysis data indicate the diversity of the PEDV isolates currently prevalent in Korea that represents a heterogeneous group. Phylogenetic analyses showed two separate clusters, in which all Korean field isolates were grouped together in the second cluster (group 2). The results indicate that prevailing isolates in Korea are phylogenetically more closely related to each other rather than other reference strains. Interestingly, the tree topology based on the nucleotide sequences representing the S1 domain or the S1 N-terminal region most nearly resembled the full S gene-based phylogenetic tree. Therefore, our data implicates a potential usefulness of the partial S protein gene including the N-terminal region in unveiling genetic relatedness of PEDV isolates.

  7. Complete Genome Sequence of Variant Porcine Epidemic Diarrhea Virus Strain CH/HNZZ47/2016 Isolated from Suckling Piglets in China

    PubMed Central

    Liu, Xinsheng; Zhang, Qiaoling; Fang, Yuzhen; Zhou, Peng; Lu, Yanzhen; Xiao, Shuai; Dong, Zhaoliang

    2017-01-01

    ABSTRACT Porcine epidemic diarrhea virus (PEDV) could cause an acute and highly contagious enteric disease in swine. Here, we report the complete genome sequence of PEDV strain CH/HNZZ47/2016 isolated from suckling piglets with mild diarrhea in Henan Province, China. It will help understand the molecular and evolutionary characteristics of PEDV in China. PMID:28254990

  8. Molecular characterization of pig epidemic diarrhoea viruses isolated in Japan from 2013 to 2014.

    PubMed

    Suzuki, Tohru; Murakami, Satoshi; Takahashi, Osamu; Kodera, Aya; Masuda, Tsuneyuki; Itoh, Sakie; Miyazaki, Ayako; Ohashi, Seiichi; Tsutsui, Toshiyuki

    2015-12-01

    Since October 2013, approximately 1000 outbreaks of porcine epidemic diarrhoea (PED) have occurred, spanning almost all prefectures of Japan, after a period of seven years without a reported case. In order to consider occurrence factor of PED outbreaks, we determined the whole-genome sequences of 38 PED virus (PEDV) strains from diarrheal samples collected at swine farms in 18 prefectures between 2013 and 2014 using next-generation sequencing technology. Using these data, we investigated genetic variation among the recent Japanese PEDV strains and the genetic relationships between these strains and global PEDV strains isolated recently from multiple swine-industrial countries. Eleven out of 38 PEDV strains were isolated successfully on Vero cells with trypsin treatment and subjected to genome sequence analysis. In a comparative genome analysis, we detected two novel PEDV variants, TTR-2/JPN/2014 and MYG-1/JPN/2014, with large deletions in the spike and ORF3 genes, respectively. A phylogenetic analysis based on the spike gene showed that the 38 Japanese PEDV strains were classified into two PEDV types: the North American type with high virulence (n=34) and the INDEL type (n=4). In addition, the recent Japanese PEDV isolates had a close relationship to global PEDV strains isolated in recent years than to the classical PEDV strains detected in Japan the past decades ago. Moreover, the phylogenetic dendrogram of the complete genomes also indicated that the 38 Japanese PEDV strains, including the two novel PEDV variants discovered in this study, are closely related to the PEDV strains that were widespread in the United States and Korea in 2013-2014. These findings suggest that the re-emergence of PED outbreaks since the last reported case in 2006 was caused by the introduction of recent PEDV strains to Japan from overseas.

  9. Evaluation of two real-time polymerase chain reaction assays for Porcine epidemic diarrhea virus (PEDV) to assess PEDV transmission in growing pigs.

    PubMed

    Miller, Laura C; Crawford, Kimberly K; Lager, Kelly M; Kellner, Steven G; Brockmeier, Susan L

    2016-01-01

    In April 2013, a Porcine epidemic diarrhea virus (PEDV) epidemic began in the United States. As part of the response, real-time reverse transcription polymerase chain reaction (RT-PCR) assays to detect PEDV were developed by several veterinary diagnostic laboratories. Our study evaluated RT-PCR PEDV assays that detect the N gene (gN) and S gene (gS) for their ability to detect PEDV infection and the transmission potential of pigs experimentally exposed to PEDV. Detection limits and quantification cycle (Cq) values of real-time RT-PCR were assayed for PEDV samples and positive controls for both gN and gS. The limit of detection for the gN assay was 10(-6) (mean Cq: 39.82 ± 0.30) and 10(-5) (mean Cq: 39.39 ± 0.72) for the gS assay with PEDV strain USA/Colorado/2013. Following recommended guidelines, rectal swabs (n = 1,064) were tested; 354 samples were positive by gN assay and 349 samples were positive by gS assay (Cq ≤ 34.99), 710 samples were negative by gN assay and 715 were negative by gS assay (Cq > 34.99) of which 355 and 344 were "undetermined" (i.e., undetected within a threshold of 40 RT-PCR cycles, by gN and gS assays, respectively). The coefficient of variation (intra-assay variation) ranged from 0.00% to 2.65% and interassay variation had an average of 2.75%. PEDV could be detected in rectal swabs from all pigs for ~2 weeks postinfection at which time the prevalence began to decrease until all pigs were RT-PCR negative by 5 weeks postinfection. Our study demonstrated that RT-PCR assays functioned well to detect PEDV and that the gN assay was slightly better.

  10. Immune responses induced by DNA vaccines bearing Spike gene of PEDV combined with porcine IL-18

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Porcine epidemic diarrhea virus (PEDV) is the causative agent of porcine epidemic diarrhea, a highly contagious enteric disease of swine. The Spike (S) protein is one of the main structural proteins of PEDV capable of inducing neutralizing antibodies in vivo. Herein, we generated three distinct DNA ...

  11. Development of the full-length cDNA clones of two porcine epidemic diarrhea disease virus isolates with different virulence

    PubMed Central

    Li, Jie; Jin, Zhonghui; Gao, Yueyi; Zhou, Lei; Ge, Xinna; Guo, Xin; Yang, Hanchun

    2017-01-01

    The recently emerged highly virulent variants of porcine epidemic and diarrhea virus (PEDV) remain a huge threat to the worldwide swine industry. Here, we describe the development of a bacterial artificial chromosome (BAC) reverse genetics system for PEDV based on two recent Chinese field isolates, namely CHM2013 and BJ2011C. Phylogenetically, CHM2013 is closely related to the vaccine strain SM98 whereas the isolate BJ2011C belongs to the GIIb group, a cluster that contains many recent pandemic strains. The full-length cDNA clones of the two isolates were constructed into BAC under the control of CMV promoter. The rescued viruses rBJ2011C and rCHM2013 were found to replicate at the kinetics similar to their respective parental viruses in cell culture. When tested in the 2-day-old pig model, rBJ2011C caused severe diarrhea of piglets with extensive damages to the intestinal epithelium, leading to 100% fatality within 48 hours. In contrast, the rCHM2013-inoculated piglets all survived with only very minor tissue damage observed. Thus, we have successfully established a convenient platform for PEDV genome manipulation. This study also represents the first description of a DNA-launched reverse genetics system for the highly virulent PEDV. PMID:28301551

  12. Production impact & time to stability in sow herds infected with porcine epidemic diarrhea virus (PEDV).

    PubMed

    Goede, Dane; Morrison, Robert B

    2016-01-01

    PEDV was first detected in United States in May, 2013. The virus spread through the swine industry and was reported in 30 US states by June, 2014 (Morrison and Goede, 2014). There are limited data describing the impact on production in sow farms. Veterinarians attempt to control the virus in sow herds with a program that stimulates herd immunity. There are no data on how long it takes with this control program to achieve a stable state of consistently produce weaned pigs that are not infected with the virus. This study involved participants and data from an existing program called the Swine Health Monitoring Project. Veterinarians were invited to share production data from 429 herds infected with PEDV. These data, in conjunction with diagnostic reports, were used to estimate the time required for the herd to produce PEDV PCR negative pigs and the production loss. Of the 429 infected herds that achieved the stable state of weaning PEDV PCR negative pigs, the median time was 28 weeks, ranging from 7 to 64 weeks. A median of 2.7 piglets/inventoried sow were not weaned and the average time required to recover to baseline production was 10 weeks in 183 herds. Herd infected in quarters 3 or 4 of the year had approximately twice the negative impact. These data are valuable for veterinarians in advising clients on the anticipated impact and time to re-achieve a stable state with regards to PEDV.

  13. Complete Genome Sequences of Porcine Epidemic Diarrhea Virus Strains JSLS-1/2015 and JS-2/2015 Isolated from China.

    PubMed

    Tao, Jie; Li, Benqiang; Zhang, Chunling; Liu, Huili

    2016-11-10

    Two porcine epidemic diarrhea virus (PEDV) strains, JSLS-1/2015 and JS-2/2015, were isolated from piglets with watery diarrhea in South China. Two genomic sequences were highly homologous to the attenuated DR13 strain. Furthermore, JSLS-1/2015 contains a 24-amino-acid deletion in open reading frame 1b, which was first reported in PEDV isolates.

  14. Reactivity of anti-PEDV structural protein antibodies to porcine enteric coronaviruses: diagnostic implications.

    PubMed

    Gimenez-Lirola, Luis Gabriel; Zhang, Jianqiang; Carrillo-Avila, Jose Antonio; Chen, Qi; Magtoto, Ronaldo; Poonsuk, Korakrit; Baum, David H; Piñeyro, Pablo; Zimmerman, Jeffrey

    2017-02-15

    The development of porcine epidemic diarrhea virus (PEDV) antibody-based assays is important for detecting infected animals, confirming previous virus exposure, and monitoring sow herd immunity. However, the potential cross-reactivity among porcine coronaviruses is a major concern for the development of pathogen-specific assays. In this study, we used serum samples (n = 792) from pigs of precisely known infection status and a multiplex fluorescent microbead-based immunoassay and/or enzyme-linked immunoassay platform to characterize the antibody response against PEDV whole-virus (WV) particles and recombinant polypeptides derived from the four PEDV structural proteins, i.e., spike (S), nucleocapsid (N), membrane (M), and envelope (E). Antibody assay cut-off values were selected to provide 100% diagnostic specificity for each target. The earliest IgG antibody response was observed at days 7--10 post-infection, mainly directed against S1 polypeptides. With the exception of non-reactive protein E, we observed a similar antibody ontogeny and pattern of seroconversion for S1, N, M, and WV antigens. Recombinant S1 provided the best diagnostic sensitivity, regardless of PEDV strain, with no cross-reactivity detected against transmissible gastroenteritis virus (TGEV), porcine respiratory coronavirus (PRCV), or porcine deltacoronavirus (PDCoV) pig antisera. The WV particles showed some cross-reactivity against TGEV Miller and TGEV Purdue antisera, while N protein presented some cross-reactivity against TGEV Miller. The M protein was highly cross-reactive against TGEV and PRCV antisera. Differences in the antibody response against specific PEDV structural proteins have important implications in the development and performance of antibody assays for the diagnosis of PEDV enteric disease.

  15. Lactogenic immunity and vaccines for porcine epidemic diarrhea virus (PEDV): historical and current concepts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Morbidity, mortality, and loss of productivity from enteric diseases in neonatal piglets cost swine producers millions of dollars annually. In 2013-2014, the porcine epidemic diarrhea virus (PEDV) outbreak led to $900 million to $1.8 billion in annual losses to US swine producers. Passive lactogeni...

  16. PEDV exposure protects pigs against homologous re-exposure 44 days later

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction PEDV emerged in the US during 2013 and rapidly spread from farm to farm causing high morbidity and mortality resulting in high economic losses to the US swine industry. As the virus made its way through swine dense populations there were many questions on degree and length of protection...

  17. Monitoring Survivability and Infectivity of Porcine Epidemic Diarrhea Virus (PEDv) in the Infected On-Farm Earthen Manure Storages (EMS)

    PubMed Central

    Tun, Hein M.; Cai, Zhangbin; Khafipour, Ehsan

    2016-01-01

    In recent years, porcine epidemic diarrhea virus (PEDv) has caused major epidemics, which has been a burden to North America’s swine industry. Low infectious dose and high viability in the environment are major challenges in eradication of this virus. To further understand the viability of PEDv in the infected manure, we longitudinally monitored survivability and infectivity of PEDv in two open earthen manure storages (EMS; previously referred to as lagoon) from two different infected swine farms identified in the province of Manitoba, Canada. Our study revealed that PEDv could survive up to 9 months in the infected EMS after the initial outbreak in the farm. The viral load varied among different layers of the EMS with an average of 1.1 × 105 copies/ml of EMS, independent of EMS temperature and pH. In both studied EMS, the evidence of viral replication was observed through increased viral load in the later weeks of the samplings while there was no new influx of infected manure into the EMS, which was suggestive of presence of potential alternative hosts for PEDv within the EMS. Decreasing infectivity of virus over time irrespective of increased viral load suggested the possibility of PEDv evolution within the EMS and perhaps in the new host that negatively impacted virus infectivity. Viral load in the top layer of the EMS was low and mostly non-infective suggesting that environmental factors, such as UV and sunlight, could diminish the replicability and infectivity of the virus. Thus, frequent agitation of the EMS that could expose virus to UV and sunlight might be a potential strategy for reduction of PEDv load and infectivity in the infected EMS. PMID:27014197

  18. Monitoring Survivability and Infectivity of Porcine Epidemic Diarrhea Virus (PEDv) in the Infected On-Farm Earthen Manure Storages (EMS).

    PubMed

    Tun, Hein M; Cai, Zhangbin; Khafipour, Ehsan

    2016-01-01

    In recent years, porcine epidemic diarrhea virus (PEDv) has caused major epidemics, which has been a burden to North America's swine industry. Low infectious dose and high viability in the environment are major challenges in eradication of this virus. To further understand the viability of PEDv in the infected manure, we longitudinally monitored survivability and infectivity of PEDv in two open earthen manure storages (EMS; previously referred to as lagoon) from two different infected swine farms identified in the province of Manitoba, Canada. Our study revealed that PEDv could survive up to 9 months in the infected EMS after the initial outbreak in the farm. The viral load varied among different layers of the EMS with an average of 1.1 × 10(5) copies/ml of EMS, independent of EMS temperature and pH. In both studied EMS, the evidence of viral replication was observed through increased viral load in the later weeks of the samplings while there was no new influx of infected manure into the EMS, which was suggestive of presence of potential alternative hosts for PEDv within the EMS. Decreasing infectivity of virus over time irrespective of increased viral load suggested the possibility of PEDv evolution within the EMS and perhaps in the new host that negatively impacted virus infectivity. Viral load in the top layer of the EMS was low and mostly non-infective suggesting that environmental factors, such as UV and sunlight, could diminish the replicability and infectivity of the virus. Thus, frequent agitation of the EMS that could expose virus to UV and sunlight might be a potential strategy for reduction of PEDv load and infectivity in the infected EMS.

  19. Tissue localization, shedding, virus carriage, antibody response, and aerosol transmission of porcine epidemic diarrhea virus (PEDV) following inoculation of 4 week-old feeder pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Porcine epidemic diarrhea virus (PEDV) emerged in the U.S. in April 2013 and caused significant losses to the swine industry. The purpose of this investigation was to determine tissue localization, shedding patterns, virus carriage, antibody response, and aerosol transmission of PEDV following inocu...

  20. Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique.

    PubMed

    Sun, Dongbo; Shi, Hongyan; Guo, Donghua; Chen, Jianfei; Shi, Da; Zhu, Qinghe; Zhang, Xin; Feng, Li

    2015-06-15

    Recent outbreaks of porcine epidemic diarrhea virus (PEDV) have caused widespread concern. The identification of proteins associated with PEDV infection might provide insight into PEDV pathogenesis and facilitate the development of novel antiviral strategies. We analyzed the differential protein profile of PEDV-infected Vero E6 cells using mass spectrometry and an isobaric tag for relative and absolute quantification. A total of 126 proteins were identified that were differentially expressed between the PEDV-infected and mock-infected groups (P<0.05, quantitative ratio ≥1.2), among which the expression of 58 proteins was up-regulated and that of 68 proteins was down-regulated in the PEDV-infected Vero E6 cells, involving in integrin β2/β3, cystatin-C. The Gene Ontology analysis indicated that the molecular function of the differentially expressed proteins (DEPs) was primarily related to binding and catalytic activity, and that the biological functions in which the DEPs are involved included metabolism, organismal systems, cellular processes, genetic information processing, environmental information processing, and diseases. Among the disease-related functions, certain anti-viral pathways and proteins, such as the RIG-I-like receptor, Rap1, autophagy, mitogen-activated protein kinase, PI3K-Akt and Jak-STAT signaling pathways, and integrin β2/β3 and cystatin-C proteins, represented potential factors in PEDV infection. Our findings provide valuable insight into PEDV-Vero E6 cell interactions.

  1. Performance assessment of a real-time polymerase chain reaction assay for porcine epidemic diarrhea virus to assess PEDV transmission in growing pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    PEDV was first diagnosed in the U.S. in April 2013 as sporadic cases of diarrhea in young piglets with high mortality. Real-time RT-PCR is a high throughput test system that has potential to detect PEDV during the acute phase of the infection or pre-seroconversion. A study in nursery pigs was conduc...

  2. Gradient isolator for flow field of fuel cell assembly

    DOEpatents

    Ernst, William D.

    1999-01-01

    Isolator(s) include isolating material and optionally gasketing material strategically positioned within a fuel cell assembly. The isolating material is disposed between a solid electrolyte and a metal flow field plate. Reactant fluid carried by flow field plate channel(s) forms a generally transverse electrochemical gradient. The isolator(s) serve to isolate electrochemically a portion of the flow field plate, for example, transversely outward from the channel(s), from the electrochemical gradient. Further, the isolator(s) serve to protect a portion of the solid electrolyte from metallic ions.

  3. Gradient isolator for flow field of fuel cell assembly

    DOEpatents

    Ernst, W.D.

    1999-06-15

    Isolator(s) include isolating material and optionally gasketing material strategically positioned within a fuel cell assembly. The isolating material is disposed between a solid electrolyte and a metal flow field plate. Reactant fluid carried by flow field plate channel(s) forms a generally transverse electrochemical gradient. The isolator(s) serve to isolate electrochemically a portion of the flow field plate, for example, transversely outward from the channel(s), from the electrochemical gradient. Further, the isolator(s) serve to protect a portion of the solid electrolyte from metallic ions. 4 figs.

  4. Temperature field in rubber vibration isolators

    NASA Astrophysics Data System (ADS)

    Abdulhadi, M. Issa

    1985-02-01

    The temperature field inside a vibrating rubber solid cylinder is investigated. The rubber cylinder, a specimen of a vibration isolator rubber (Neoprene GR), is subjected to a repeatedly cyclic compressive force by means of an electrodynamic shaker. In the experimental investigation the temperatures at 16 different locations inside the cylinder have been measured by means of copper-constantan thermocouples. After the estimation of the heat generated per unit volume per unit time with the help of the estimated damping and stiffness coefficients of rubber, one can attempt the solution of the heat conduction equation describing the temperature field inside the rubber specimen. The values of the temperature found from the analytical investigation compare fairly well with the experimental measurements.

  5. Nucleocapsid Interacts with NPM1 and Protects it from Proteolytic Cleavage, Enhancing Cell Survival, and is Involved in PEDV Growth

    PubMed Central

    Shi, Da; Shi, Hongyan; Sun, Dongbo; Chen, Jianfei; Zhang, Xin; Wang, Xiaobo; Zhang, Jialin; Ji, Zhaoyang; Liu, Jianbo; Cao, Liyan; Zhu, Xiangdong; Yuan, Jing; Dong, Hui; Wang, Xin; Chang, Tiecheng; Liu, Ye; Feng, Li

    2017-01-01

    Porcine epidemic diarrhea virus (PEDV) replicates in the cytoplasm of infected cells, but its nucleocapsid (N) protein localizes specifically to the nucleolus. The mechanism of nuclear translocation, and whether N protein associates with particular nucleolar components, is unknown. In this study, we confirm that a nucleolar phosphoprotein nucleophosmin (NPM1) interacts and co-localizes with the N protein in the nucleolus. In vitro binding studies indicated that aa 148–294 of N and aa 118–188 of NPM1 were required for binding. Interestingly, N protein importation into the nucleolus is independent of the ability of NPM1 to shuttle between the nucleus and the cytoplasm. Furthermore, overexpression of NPM1 promoted PEDV growth, while knockdown of NPM1 suppressed PEDV growth. In addition, binding of N protein to NPM1 protects it from proteolytic degradation by caspase-3, leading to increased cell survival. Taken together, our studies demonstrate a specific interaction of the N protein with the host cell protein NPM1 in the nucleolus. The results suggest potential linkages among viral strategies for the regulation of cell survival activities, possibly through an interaction of N protein with NPM1 which prevents its proteolytic cleavage and enhances cell survival, thus ultimately promoting the replication of PEDV. PMID:28045037

  6. Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV)

    PubMed Central

    Trudeau, Michaela P.; Verma, Harsha; Sampedro, Fernando; Urriola, Pedro E.; Shurson, Gerald C.; McKelvey, Jessica; Pillai, Suresh D.; Goyal, Sagar M.

    2016-01-01

    Infection with porcine epidemic diarrhea virus (PEDV) causes diarrhea, vomiting, and high mortality in suckling pigs. Contaminated feed has been suggested as a vehicle of transmission for PEDV. The objective of this study was to compare thermal and electron beam processing, and the inclusion of feed additives on the inactivation of PEDV in feed. Feed samples were spiked with PEDV and then heated to 120–145°C for up to 30 min or irradiated at 0–50 kGy. Another set of feed samples spiked with PEDV and mixed with Ultracid P (Nutriad), Activate DA (Novus International), KEM-GEST (Kemin Agrifood), Acid Booster (Agri-Nutrition), sugar or salt was incubated at room temperature (~25°C) for up to 21 days. At the end of incubation, the virus titers were determined by inoculation of Vero-81 cells and the virus inactivation kinetics were modeled using the Weibull distribution model. The Weibull kinetic parameter delta represented the time or eBeam dose required to reduce virus concentration by 1 log. For thermal processing, delta values ranged from 16.52 min at 120°C to 1.30 min at 145°C. For eBeam processing, a target dose of 50 kGy reduced PEDV concentration by 3 log. All additives tested were effective in reducing the survival of PEDV when compared with the control sample (delta = 17.23 days). Activate DA (0.81) and KEM-GEST (3.28) produced the fastest inactivation. In conclusion, heating swine feed at temperatures over 130°C or eBeam processing of feed with a dose over 50 kGy are effective processing steps to reduce PEDV survival. Additionally, the inclusion of selected additives can decrease PEDV survivability. PMID:27341670

  7. Magnetic field decay in isolated neutron stars

    NASA Technical Reports Server (NTRS)

    Goldreich, Peter; Reisenegger, Andreas

    1992-01-01

    Three mechanisms that promote the loss of magnetic flux from an isolated neutron star - Ohmic decay, ambipolar diffusion, and Hall drift - are investigated. Equations of motions are solved for charged particles in the presence of a magnetic field and a fixed background of neutrons, while allowing for the creation and destruction of particles by weak interactions. Although these equations apply to normal neutrons and protons, the present interpretations of their solutions are extended to cover cases of neutron superfluidity and proton superconductivity. The equations are manipulated to prove that, in the presence of a magnetic force, the charged particles cannot be simultaneously in magnetostatic equilibrium and chemical equilibrium with the neutrons. The application of the results to real neutron stars is discussed.

  8. Survivability of porcine epidemic diarrhea virus (PEDV) in bovine plasma submitted to spray drying processing and held at different time by temperature storage conditions.

    PubMed

    Pujols, Joan; Segalés, Joaquim

    2014-12-05

    Bovine plasma was inoculated with porcine epidemic diarrhea virus (PEDV) at an average final titer of 4.2 log10 TCID50/mL to determine the effect of spray drying on viral inactivation. Using a laboratory scale drier, inoculated plasma was spray dried at 200 °C inlet temperature and either 70 or 80 °C throughout substance. Both liquid and dried samples were subjected to three passages on VERO cell monolayers to determine PEDV infectivity. Results indicated liquid samples contained infective virus, but none of the spray dried samples were infectious. Also, survivability of PEDV inoculated on spray dried bovine plasma (SDBP) and stored at 4, 12 or 22 °C was determined for 7, 14 and 21 days. Commercial SDBP powder was inoculated with PEDV to an average final titer of 2.8 log10 TCID50/g. Five samples per time and temperature conditions were subjected to three passages on VERO cell monolayers to determine PEDV infectivity. The virus was non-infectious for all samples stored at 22 °C at 7, 14 and 21 days. PEDV was infective in 1 out of 5 samples stored at 12 °C at 7 days, but none of the samples stored for 14 and 21 days were infectious in cell culture. For samples stored at 4 °C, 4 out of 5 samples were infectious at 7 days, 1 out of 5 samples were infectious at 14 days, but none were infectious at 21 days. In summary, PEDV was not infectious on cell culture within 7 days when stored at room temperature and within 21 days when stored at refrigerated temperature.

  9. Soft hairs on isolated horizon implanted by electromagnetic fields

    NASA Astrophysics Data System (ADS)

    Mao, Pujian; Wu, Xiaoning; Zhang, Hongbao

    2017-03-01

    Inspired by the recent proposal of soft hair on black holes in Hawking et al (2016 Phys. Rev. Lett. 116 231301), we have shown that an isolated horizon carries soft hairs implanted by electromagnetic fields. The solution space and the asymptotic symmetries of Einstein–Maxwell theory have been worked out explicitly near the isolated horizon. The conserved current has been computed and an infinite number of near horizon charges have been introduced from the electromagnetic fields associated with the asymptotic U(1) symmetry near the horizon, which indicates the fact that the isolated horizon carries a large amount of soft electric hairs. The soft electric hairs, i.e. asymptotic U(1) charges, are shown to be equivalent to the electric multipole moments of isolated horizons. It is further argued that the isolated horizon supertranslation is from the ambiguity of its foliation and an analogue of memory effect on horizon can be expected.

  10. Sensitivity of porcine epidemic diarrhea virus (PEDV) to pH and heat treatment in the presence or absence of porcine plasma.

    PubMed

    Quist-Rybachuk, G V; Nauwynck, H J; Kalmar, I D

    2015-12-31

    Emergence of porcine epidemic diarrhea virus (PEDV) resulted in massive neonatal mortality in the North-American and Asian pork industry. Measures to prevent its geographical spread are of utmost importance to safeguard susceptible porcine populations. The major infection route is direct or indirect faecal-oral contact. Adequate biosafety measures should be in place at all levels of the swine production chain, including feed and feed ingredients. Present study aimed to investigate the sensitivity of PEDV to thermal inactivation at neutral and alkaline pH in presence or absence of porcine plasma. Cell culture medium and porcine plasma at different pH (7.2, 9.2, 10.2) and temperature conditions (4 °C, 40 °C, 44 °C, 48 °C) were inoculated to a final titer of 5.5 log10 TCID50 PEDV/ml, incubated for up to 120 min and the residual infectivity was determined by endpoint dilution assay. Irrespective of presence of plasma, PEDV was not sensitive to pH 7.2-10.2 at 4 °C. At moderate temperatures (≥40 °C), both alkaline pH and presence of plasma potentiated thermal inactivation. Inactivation of 8 log10 TCID50/ml plasma within 30 min (8D value<30 min) by moderate pH and temperature would denote potential industrial processing conditions that ensure safety towards PEDV while limiting denaturation of bioactive components. Virus-spiked plasma required heat treatment of 40 °C and alkalinization to pH 9.2 to achieve 8 log10 reduction within such time. At pH 10.2 and 48 °C, the 8D value was 4.6 min in plasma and 15.2 min in MEM. Here we propose heat-alkalinity-time (HAT) pasteurization as a highly efficient method to inactivate PEDV during industrial processing of porcine plasma.

  11. Change in antimicrobial susceptibility of Mycoplasma gallisepticum field isolates.

    PubMed

    Gharaibeh, Saad; Al-Rashdan, Mohammad

    2011-06-02

    This study compares the antimicrobial susceptibility over time between two groups of Mycoplasma gallisepticum (MG) isolates from the same geographical area. Minimum inhibitory concentration of 13 antimicrobials was determined against two groups of MG isolates from chickens. Group 1 strains (n=22) were isolated in 2004-2005 while group 2 strains (n=7) were isolated in 2007-2008. Minimum inhibitory concentration 50 for group 1 versus group 2 was 4/4, 0.5/0.5, ≤ 0.031/≥ 64, ≤ 0.031/2, ≤ 0.031/0.125, 1/0.5, 1/1, ≤ 0.031/≤ 0.031, ≤ 0.031/2, ≤ 0.031/2, 1/4, ≤ 0.031/0.062, and 0.062/2 μg/ml against gentamicin, spectinomycin, erythromycin, tilmicosin, tylosin, florfenicol, thiamphenicol, tiamulin, ciprofloxacin, enrofloxacin, chlortetracycline, doxycycline, and oxytetracycline, respectively. There was a statistically significant increase in resistance of group 2 to erythromycin, tilmicosin, tylosin, ciprofloxacin, enrofloxacin, chlortetracycline, doxycycline, and oxytetracycline. This dramatic increase in resistance against 8 antimicrobials belonging to three different families of antimicrobials in a relatively short period of time appears to be rare and of concern. The cause of this increased resistance observed in group 2 of MG isolates was not determined and should be further investigated. Monitoring of MG field strain susceptibility is highly recommended to implement successful treatment and prophylaxis programs in endemic areas.

  12. Antimicrobial susceptibility testing of Spanish field isolates of Brachyspira hyodysenteriae.

    PubMed

    Hidalgo, A; Carvajal, A; García-Feliz, C; Osorio, J; Rubio, P

    2009-08-01

    This study is the first conducted in Spain to evaluate antimicrobial susceptibility of field isolates of Brachyspira hyodysenteriae. One hundred and eight isolates of the bacterium, recovered from different Spanish swine farms between 2000 and 2007, were investigated. The minimum inhibitory concentrations (MIC) of erythromycin, tylosin, tiamulin, valnemulin, clindamycin and lincomycin were determined using a broth microdilution technique. Most of the isolates showed poor susceptibility to erythromycin (MIC(90)>256 microg/ml), tylosin (MIC(90)>256 microg/ml), clindamycin (MIC(90)>4 microg/ml) and lincomycin (MIC(90)=128 microg/ml). Reduced susceptibility to tiamulin and valnemulin was observed with a MIC>2 microg/ml in 17.6% and 7.41% of the B. hyodysenteriae isolates, respectively. Moreover, a survival analysis permitted the detection of an increasing trend in the MIC values for almost all the antimicrobials used in the treatment of swine dysentery when comparing recent isolates (from 2006 to 2007) with those recovered in earlier years (between 2000 and 2004).

  13. Pathogenesis of porcine epidemic diarrhea virus isolate (US/Iowa/18984/2013) in 3-week-old weaned pigs.

    PubMed

    Madson, D M; Magstadt, D R; Arruda, P H E; Hoang, H; Sun, D; Bower, L P; Bhandari, M; Burrough, E R; Gauger, P C; Pillatzki, A E; Stevenson, G W; Wilberts, B L; Brodie, J; Harmon, K M; Wang, C; Main, R G; Zhang, J; Yoon, K J

    2014-11-07

    Porcine epidemic diarrhea virus (PEDV) is associated with clinical diarrhea in naïve swine of all ages. This report describes timing of antibody generation and disease progression following infection with a US PEDV isolate by assessing fecal viral shedding, morphometric analysis of intestinal lesions, and magnitude of immunohistochemical staining. Sixty-three, 3-week-old pigs were randomly allocated into control (n=27) and challenged (n=36) groups. Challenged pigs were administered 1 mL of 1 × 10(3) PFU/mL of US/Iowa/18984/2013 PEDV isolate by oro-gastric gavage. Three control and four challenged pigs were necropsied on days post-inoculation (dpi) 1, 2, 3, 4, 7, and weekly thereafter, until study termination on dpi 35. Clinical disease, fecal shedding, body weight, and temperature were monitored during the study period. Diarrhea was observed in challenged pigs beginning for some on dpi 2, affecting a majority of pigs by dpi 6 and subsiding by dpi 10. Average daily gain was significantly lower (P<0.001) for one week post-infection in challenged pigs. PEDV was detected in feces by PCR on dpi 1 and continued in a subset of pigs until dpi 24. PEDV-specific antigen was detected in villous enterocytes of challenged pigs by immunohistochemistry (IHC) on dpi 1, 2, 3, 4, 7, and 14. Microscopic lesions included severe diffuse atrophic enteritis with significantly reduced (P<0.001) villous length observed on dpi 3, 4, and 7. Under the conditions of this study, fecal shedding of PEDV and IHC staining can precede and continue beyond the observation of clinical signs, thus increasing the risk of viral transmission.

  14. Simulations of magnetic fields in isolated disc galaxies

    NASA Astrophysics Data System (ADS)

    Pakmor, Rüdiger; Springel, Volker

    2013-06-01

    Magnetic fields are known to be dynamically important in the interstellar medium of our own Galaxy, and they are ubiquitously observed in diffuse gas in the haloes of galaxies and galaxy clusters. Yet, magnetic fields have typically been neglected in studies of the formation of galaxies, leaving their global influence on galaxy formation largely unclear. Here we extend our magnetohydrodynamics (MHD) implementation in the moving-mesh code AREPO to cosmological problems which include radiative cooling and the formation of stars. In particular, we replace our previously employed divergence cleaning approach with a Powell eight-wave scheme, which turns out to be significantly more stable, even in very dynamic environments. We verify the improved accuracy through simulations of the magneto-rotational instability in accretion discs, which reproduce the correct linear growth rate of the instability. Using this new MHD code, we simulate the formation of isolated disc galaxies similar to the Milky Way using idealized initial conditions with and without magnetic fields. We find that the magnetic field strength is quickly amplified in the initial central starburst and the differential rotation of the forming disc, eventually reaching a saturation value. At this point, the magnetic field pressure in the interstellar medium becomes comparable to the thermal pressure, and a further efficient growth of the magnetic field strength is prevented. The additional pressure component leads to a lower star formation rate at late times compared to simulations without magnetic fields, and induces changes in the spiral arm structures of the gas disc. In addition, we observe highly magnetized fountain-like outflows from the disc. These results are robust with numerical resolution and are largely independent of the initial magnetic seed field strength assumed in the initial conditions, as the amplification process is rapid and self-regulated. Our findings suggest an important influence of

  15. Extensive population synthesis of isolated neutron stars with field decay

    NASA Astrophysics Data System (ADS)

    Popov, S. B.; Boldin, P. A.; Miralles, J. A.; Pons, J. A.; Posselt, B.

    2011-09-01

    We perform population synthesis studies of different types of neutron stars (thermally emitting isolated neutron stars, normal radio pulsars, magnetars) taking into account the magnetic field decay and using results from the most recent advances in neutron star cooling theory. For the first time, we confront our results with observations using simultaneously the Log N--Log S distribution for nearby isolated neutron stars, the Log N--Log L distribution for magnetars, and the distribution of radio pulsars in the P--Ṗ diagram. For this purpose, we fix a baseline neutron star model (all microphysics input), and other relevant parameters to standard values (velocity distribution, mass spectrum, etc.), only allowing to vary the initial magnetic field strength. We find that our theoretical model is consistent with all sets of data if the initial magnetic field distribution function follows a log-normal law with < log(B0/[G])>~13.25 and σlog B0~0.6. The typical scenario includes about 10% of neutron stars born as magnetars, significant magnetic field decay during the first million years of a NS life (only about a factor of 2 for low field neutron stars but more than an order of magnitude for magnetars), and a mass distribution function dominated by low mass objects. This model explains satisfactorily all known populations. Evolutionary links between different subclasses may exist, although robust conclusions are not yet possible. We apply the obtained field distribution and the model of decay to study long-term evolution of neuton stars till the stage of accretion from the interstellar medium. It is shown that though the subsonic propeller stage can be relatively long, initially highly magnetized neutron stars (B0>~1013 G) reach the accretion regime within the Galactic lifetime if their kick velocities are not too large. The fact that in previous studies made >10 years ago, such objects were not considered results in a slight increase of the Accretor fraction in

  16. Laboratory bioassays and field-cage trials of Metarhizium spp. isolates with field-collected Mormon crickets (Anabrus simplex)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Mormon cricket, Anabrus simplex, is an important pest in the western United States. This study evaluates the virulence of 32 isolates of Metarhizium towards field-collected Mormon crickets. Additionally, several isolates were tested in outdoor field-cage studies. All 32 Metarhizium isolates were...

  17. Archaeoglobus fulgidus Isolated from Hot North Sea Oil Field Waters

    PubMed Central

    Beeder, Janiche; Nilsen, Roald Kåre; Rosnes, Jan Thomas; Torsvik, Terje; Lien, Torleiv

    1994-01-01

    A hyperthermophilic sulfate reducer, strain 7324, was isolated from hot (75°C) oil field waters from an oil production platform in the Norwegian sector of the North Sea. It was enriched on a complex medium and isolated on lactate with sulfate. The cells were nonmotile, irregular coccoid to disc shaped, and 0.3 to 1.0 μm wide. The temperature for growth was between 60 and 85°C with an optimum of 76°C. Lactate, pyruvate, and valerate plus H2 were utilized as carbon and energy sources with sulfate as electron acceptor. Lactate was completely oxidized to CO2. The cells contained an active carbon monoxide dehydrogenase but no 2-oxoglutarate dehydrogenase activity, indicating that lactate was oxidized to CO2 via the acetyl coenzyme A/carbon monoxide dehydrogenase pathway. The cells produced small amounts of methane simultaneously with sulfate reduction. F420 was detected in the cells which showed a blue-green fluorescence at 420 nm. On the basis of morphological, physiological, and serological features, the isolate was classified as an Archaeoglobus sp. Strain 7324 showed 100% DNA-DNA homology with A. fulgidus Z, indicating that it belongs to the species A. fulgidus. Archaeoglobus sp. has been selectively enriched and immunomagnetically captured from oil field waters from three different platforms in the North Sea. Our results show that strain 7324 may grow in oil reservoirs at 70 to 85°C and contribute to hydrogen sulfide formation in this environment. Images PMID:16349231

  18. Investigating the Density of Isolated Field Elliptical Galaxies

    NASA Astrophysics Data System (ADS)

    Ulgen, E. Kaan

    2016-02-01

    In this thesis, 215.590 elliptical galaxies with M(r) ≤ -21 in the CFHTLS-W1 field which is covering 72 sq. deg on the sky are examined . Criterion given by Smith et al. (2004) has been used to determine isolated elliptical galaxies. 118 isolated elliptical galaxies have been determined in total. By using g, r and i photometric bands, the true-colour images of candidates are produced and visually inspected. In order to have a clean list of IfEs some candidates are excluded from the final sample after visual inspection. The final sample consists of 60 IfEs which corresponds to the 0.027 per cent of the whole sample. In other words, IfE density in the W1 is 0.8 IfE / sq.deg. Since the formation of the ellipticals in the isolated regions is not known clearly, it is crucial to determine IfEs and compare their photometric and morphological properties to the normal or cluster ellipticals. When the (g-i) distributions of three different elliptical galaxy class are compared, it is found that they have almost the same colours. When the redshift distributions of the galaxies are considered, it can be seen that IfEs formed later than the cluster and normal ellipticals. The average redshift of IfEs is determined as zphot=0.284, while for normal and cluster ellipticals, it is, respectively, 0.410 and 0.732. In addition, when the effective radii of the three elliptical systems are considered, it is found that the IfEs are bigger than the other two elliptical classes.

  19. Characterization of field isolates of Magnaporthe oryzae with mating type, DNA fingerprinting, and pathogenicity assays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Due to the harmful nature of the rice blast fungus, Magnaporthe oryzae, it is beneficial to characterize field isolates to help aid in the deployment of resistance (R) genes in rice. In the present study, 190 field isolates of M. oryzae, collected from rice fields of Yunnan province in China, were a...

  20. Magnetic field inhibits isolated lymphocytes' proliferative response to mitogen stimulation.

    PubMed

    Roman, Adam; Zyss, Tomasz; Nalepa, Irena

    2005-04-01

    We aimed to find out how the exposure of isolated lymphocytes to a pulsed magnetic field (MF) affected their in vitro proliferative response to mitogenic stimulation. Cells were exposed to MF of various intensities (0.3, 0.6, and 1.2 T) at a constant frequency of 30 Hz, for a period of 60, 180, and 330 s. Then, the proliferative response of splenocytes was induced by optimal concentrations of concanavalin A (Con A; mitogenic toward T cells), bacterial lipopolysaccharide (LPS; mitogenic toward B cells), or pokeweed mitogen (PWM; mitogenic toward both populations). We found that the exposure of lymphocytes to the MF profoundly inhibited their proliferative response to mitogens. The suppressive action of the MF on B and T cell proliferation was intensified when a cooperative response of those two lymphocyte populations was simultaneously induced by PWM. The inhibitory effect of MF depended on the exposure time and MF intensity. Prolonged exposure and/or a stronger intensity of the MF weakened its inhibitory influence on the response of lymphocyte to mitogenic stimulation. The data show that an exposure to MF may influence the activity of lymphocytes in their response to mitogenic stimuli.

  1. Flavobacterium anhuiense sp. nov., isolated from field soil.

    PubMed

    Liu, Huan; Liu, Rui; Yang, Shou-Yun; Gao, Wei-Kai; Zhang, Chong-Xing; Zhang, Ke-Yun; Lai, Ren

    2008-04-01

    A novel strain, D3T, isolated from a field-soil sample obtained from Anhui Province, PR China, was characterized taxonomically by using a polyphasic approach. The cells were Gram-negative, yellow-pigmented rods devoid of flagella, but showing gliding motility. The organism was able to grow at 5-37 degrees C and at pH 4.0-10.0. A comparative 16S rRNA gene sequence analysis indicated that strain D3T is a member of the genus Flavobacterium, sharing highest sequence similarity with the type strain of Flavobacterium defluvii (96.7 %). The major isoprenoid quinone was MK-6 and the predominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 omega 7c and/or iso-C15 : 0 2-OH) and C16 : 0. The DNA G+C content was 31.4 mol%. On the basis of phylogenetic and phenotypic data, strain D3T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium anhuiense sp. nov. is proposed. The type strain is D3T (=KCTC 22128T = CGMCC 1.6859T).

  2. Mechanics of isolated extended bodies in classical field theories

    NASA Astrophysics Data System (ADS)

    Harte, Abraham Isaiah

    2007-08-01

    This thesis discusses a number of issues related to the description and motion of extended matter distributions in certain classical field theories. Particular emphasis is placed on general relativity and Maxwell theory, although many results also apply in related formalisms. They are obtained by extending and applying a series of ideas originally developed by W. G. Dixon to understand the mechanics of isolated bodies. Since this formalism is not well- known, we provide an extensive review in a unified form. This elucidates the structure of an object's stress-energy tensor and electromagnetic current vector. Multipole decompositions of these objects are also studied in considerable detail, and are designed to automatically "factor out" the relevant conservation laws. In the case of charge-current vectors, we show how to extend these results to also take into account the assumed smoothness and compactness of the physical matter. This allows essentially all reasonable current configurations with a given total charge to be parameterized without any reference to the spacetime structure. Such constructions provide natural methods for comparing the properties of current distributions in different systems. They also simplify the study of "rigid" currents. It is found that such objects cannot generally exist without allowing for the presence of singularities. An even stronger result applies to the nonexistence of rigid number density vectors in systems where the total number of particles is fixed. These formal developments are applied in various way to study the motions of various compact extended bodies. The first case considered here is that of an uncharged test mass embedded in a spatially-flat Friedmann-Robertson-Walker universe. It is shown that even with zero (global) momentum, such an object may adjust its mass and trajectory merely by changing shape. Mass shifts are in fact unavoidable in almost all cases, and could be significant for galactic superclusters. This

  3. Permanent-magnet Faraday isolator with the field intensity of 25 kOe

    SciTech Connect

    Mironov, E A; Snetkov, I L; Voitovich, A V; Palashov, O V

    2013-08-31

    A Faraday isolator with a single magneto-optical element is constructed and experimentally tested. It provides the isolation ratio of 30 dB at an average laser radiation power of 650 W. These parameters are obtained by increasing the field intensity in the magnetic system of the isolator and employing a low-absorption magneto-optical element. (elements of laser devices)

  4. Novosphingobium colocasiae sp. nov., isolated from a taro field.

    PubMed

    Chen, Wen-Ming; Chen, Jhen-Ci; Huang, Cheng-Wen; Young, Chiu-Chung; Sheu, Shih-Yi

    2016-02-01

    A novel bacterial strain, designated Teta-03T, was isolated from a taro field in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain Teta-03T were aerobic, Gram-stain-negative, rod-shaped and non-motile and formed bright yellow colonies. Growth occurred at 10-37 °C (optimum, 20 °C), with 0-1.0 % (w/v) NaCl (optimum, 0 %) and at pH 3.0-9.0 (optimum, pH 7.0-8.0). The major fatty acids (>10 %) of strain Teta-03T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine, an uncharacterized glycolipid and an uncharacterized aminolipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.0 mol%. On the basis of 16S rRNA gene sequence analysis, strain Teta-03T was shown to belong to the genus Novosphingobium and showed highest similarity to Novosphingobium barchaimii LL02T (96.8 %). Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Teta-03T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium colocasiae sp. nov. is proposed. The type strain is Teta-03T ( = LMG 27385T = KCTC 32255T).

  5. Flavobacterium ginsengiterrae sp. nov., isolated from a ginseng field.

    PubMed

    Kim, Sang-Rae; Kim, Yeon-Ju; Nguyen, Ngoc-Lan; Min, Jin-Woo; Jeon, Ji-Na; Yang, Dong-Uk; Yang, Deok-Chun

    2011-01-01

    A novel strain of Flavobacterium, DCY55(T), a Gram-negative, yellow-pigmented, rod-shaped, non-spore-forming and gliding-motile bacterium, was isolated from the soil of a ginseng field in South Korea. Phylogenetic analysis, based on the 16S rRNA sequence, demonstrated that strain DCY55(T) belongs to the genus Flavobacterium within the family Flavobacteriaceae. Strain DCY55(T) showed the highest similarity with F. johnsoniae UW101(T) (97.1%), F. ginsenosidimutans THG 01(T) (96.8%), F. defluvii EMB 117(T) (96.6%), F. banpakuense 15F3(T) (96.3%) and F. anhuiense D3(T) (95.8%). Chemotaxonomic results showed that strain DCY55(T) predominantly contains menaquinone MK-6, that its DNA G+C content is 36.1mol%, and that its major cellular fatty acids are iso-C(15:0), summed feature 3 (comprising iso-C(15:0) 2-OH and/or C(16:1) ω 7c) and C(16:0). The chemotaxonomic and genotypic characteristics support the taxonomic classification of strain DCY55(T) to the genus Flavobacterium. The results of physiological and biochemical tests confirmed that strain DCY55(T) is distinct from previously validated species. We conclude that strain DCY55(T) should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium ginsengiterrae sp. nov. is proposed, with the type strain DCY55(T) (=KCTC 23319(T) = JCM 17337(T)).

  6. CPm gene diversity in field isolates of Citrus tristeza virus from Colombia.

    PubMed

    Oliveros-Garay, Oscar Arturo; Martinez-Salazar, Natalhie; Torres-Ruiz, Yanneth; Acosta, Orlando

    2009-01-01

    The nucleotide sequence diversity of the CPm gene from 28 field isolates of Citrus tristeza virus (CTV) was assessed by SSCP and sequence analyses. These isolates showed two major shared haplotypes, which differed in distribution: A1 was the major haplotype in 23 isolates from different geographic regions, whereas R1 was found in isolates from a discrete region. Phylogenetic reconstruction clustered A1 within an independent group, while R1 was grouped with mild isolates T30 from Florida and T385 from Spain. Some isolates contained several minor haplotypes, which were very similar to, and associated with, the major haplotype.

  7. Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae

    PubMed Central

    Díez-Delgado, Iratxe; Contreras, Marinela; Vicente, Joaquín; Cabezas-Cruz, Alejandro; Manrique, Marina; Tobes, Raquel; López, Vladimir; Romero, Beatriz; Domínguez, Lucas; Garrido, Joseba M.; Gortazar, Christian

    2015-01-01

    Here we report the complete genome sequences of field isolates of Mycobacterium bovis and the related mycobacterial species, Mycobacterium caprae. The genomes of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different virulence, prevalence, and host distribution phenotypes were sequenced. PMID:26112781

  8. Rhizobium ipomoeae sp. nov., isolated from a water convolvulus field.

    PubMed

    Sheu, Shih-Yi; Chen, Zih-Han; Young, Chiu-Chung; Chen, Wen-Ming

    2016-04-01

    A bacterial strain, designated shin9-1T, was isolated from a water sample taken from a water convolvulus field in Taiwan and characterized using a polyphasic taxonomical approach. Cells of strain shin9-1T were aerobic, Gram-stain-negative, rod-shaped and surrounded by a thick capsule and formed cream-coloured colonies. Growth occurred at 10-45 °C (optimum, 30 °C), with 0-3.0% NaCl (optimum, 0.5%) and at pH 7.0-9.0 (optimum, pH 7.0). Strain shin9-1T did not form nodules on a legume plant, Macroptilium atropurpureum, and the nodulation genes nodA, nodC and the nitrogenase reductase gene nifH were not detected by PCR. Phylogenetic analyses based on 16S rRNA and three housekeeping gene sequences (recA, atpD and rpoB) showed that strain shin9-1T belonged to the genus Rhizobium. Strain shin9-1T had the highest level of 16S rRNA gene sequence similarity with respect to Rhizobium daejeonense L61T (97.6 %). The major fatty acid of strain shin9-1T was C18:1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and several uncharacterized lipids. The DNA G+C content was 58.3 mol%. The DNA-DNA relatedness of strain shin9-1T with respect to recognized species of the genus Rhizobium was less than 70%. Phenotypic characteristics of the novel strain also differed from those of the most closely related species of the genus Rhizobium. On the basis of the phylogenetic inference and phenotypic data, strain shin9-1T should be classified as a representative of a novel species, for which the name Rhizobium ipomoeae sp. nov. is proposed. The type strain is shin9-1T (=LMG 27163T=KCTC 32148T).

  9. Vector-component isolation of an arbitrary modulating electric field in zincblende electro-optic probes

    NASA Astrophysics Data System (ADS)

    Reano, Ronald M.; Whitaker, John F.; Katehi, Linda P. B.

    2005-08-01

    Analysis of the field-induced linear birefringence in zincblende crystals shows that one can obtain complete isolation of a single vector component of an arbitrary modulating electric field. For an optical probe beam path aligned parallel to the [110] direction and an optical probe beam polarization aligned parallel to the [110] direction, the field-induced birefringence occurs only for the component of the modulating electric field aligned parallel to the [110] direction. Measurements using a modulating electric field with known polarization and electro-optic probes machined from (110) gallium arsenide wafers demonstrate an alignment-limited isolation between orthogonal modulating electric field components of 17 dB.

  10. Improvement of device isolation using field implantation for GaN MOSFETs

    NASA Astrophysics Data System (ADS)

    Jiang, Ying; Wang, Qingpeng; Zhang, Fuzhe; Li, Liuan; Shinkai, Satoko; Wang, Dejun; Ao, Jin-Ping

    2016-03-01

    Gallium nitride (GaN) metal-oxide-semiconductor field-effect transistors (MOSFETs) with boron field implantation isolation and mesa isolation were fabricated and characterized. The process of boron field implantation was altered and subsequently conducted after performing high-temperature ohmic annealing and gate oxide thermal treatment. Implanted regions with high resistivity were achieved. The circular MOSFET fabricated in the implanted region showed an extremely low current of 6.5 × 10-12 A under a gate voltage value up to 10 V, thus demonstrating that the parasitic MOSFET in the isolation region was eliminated by boron field implantation. The off-state drain current of the rectangular MOSFET with boron field implantation was 5.5 × 10-11 A, which was only one order of magnitude higher than the 6.6 × 10-12 A of the circular device. By contrast, the rectangular MOSFET with mesa isolation presented an off-state drain current of 3.2 × 10-9 A. The field isolation for GaN MOSFETs was achieved by using boron field implantation. The implantation did not reduce the field-effect mobility. The isolation structure of both mesa and implantation did not influence the subthreshold swing, whereas the isolation structure of only the implantation increased the subthreshold swing. The breakdown voltage of the implanted region with 5 μm spacing was up to 901.5 V.

  11. Interferometric optical isolator employing a nonreciprocal phase shift operated in a unidirectional magnetic field.

    PubMed

    Yokoi, Hideki; Shoji, Yuya; Shin, Etsu; Mizumoto, Tetsuya

    2004-08-20

    An interferometric optical isolator that employs a nonreciprocal phase shift was studied. The optical isolator consisted of an interferometer with distinct layer structures. A traveling light wave underwent distinct nonreciprocal phase shifts such that the optical isolator could be operated in a unidirectional magnetic field. The optical isolator, in which the waveguide had a HfO2 cladding layer in one of the arms, was designed at a wavelength of 1.55 microm. The propagation distance of the nonreciprocal phase shifter required for the isolator's operation was less than 1.5 mm. The device's total length was less than 2 mm. An optical isolator with distinct layer structures was fabricated and evaluated. An isolation ratio of approximately 9.9 dB was obtained in the unidirectional magnetic field.

  12. Characterization of Isolates of Meloidogyne from Rice-Wheat Production Fields in Nepal

    PubMed Central

    Pokharel, Ramesh R.; Abawi, George S.; Zhang, Ning; Duxbury, John M.; Smart, Christine D.

    2007-01-01

    Thirty-three isolates of root-knot nematode were recovered from soil samples from rice-wheat fields in Nepal and maintained on rice cv. BR 11. The isolates were characterized using morphology, host range and DNA sequence analyses in order to ascertain their identity. Results indicated phenotypic similarity (juvenile measurements, perennial pattern, host range and gall shape) of the Nepalese isolates with Meloidogyne graminicola, with minor variations. The rice varieties LA 110 and Labelle were susceptible to all of the Nepalese isolates, but differences in the aggressiveness of the isolates were observed. Phylogenetic analyses based on the sequences of partial internal transcribed spacer (ITS) of the rRNA genes indicated that all Nepalese isolates formed a distinct clade with known isolates of M. graminicola with high bootstrap support. Furthermore, two groups were identified within the M. graminicola clade. No correlation between ITS haplotype and aggressiveness or host range was found among the tested isolates. PMID:19259491

  13. Molecular-genetic analysis of field isolates of Avian Leucosis Viruses in the Russian Federation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Commercial poultry farms in 14 regions of Russian Federation were monitored for avian leukosis virus (ALV) infection using virus isolation tests and serology. Results indicated the presence of two subgroups of ALV in farms located in 11 of 14 regions. Analysis of the genomes of 12 field isolates of...

  14. The association of serotype and pulsed-field gel electrophoresis genotype in isolates of Streptococcus pneumoniae isolated in Israel.

    PubMed

    Bar-Meir, M; Naaman, G; Assous, M; Korenman, Z; Valinsky, L; Picard, E

    2015-05-01

    The relationship between Streptococcus pneumoniae isolates causing invasive infections in children admitted to a single center in central Israel was examined by pulsed-field gel electrophoresis (PFGE) and serotyping. Although there was a close correlation between serotype and PFGE clone, the genetic diversity varied by serotype, with some genotypes comprising multiple serotypes. Additionally, clones C and D were associated with higher penicillin minimum inhibitory concentrations. Serotyping alone may be insufficient for epidemiological mapping of pneumococcal isolates in the era of pneumococcal conjugate polysaccharide vaccines.

  15. Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pulsed-field gel electrophoresis (PFGE) is the most applied and effective genetic typing method for epidemiological studies and investigation of foodborne outbreaks caused by different pathogens, including Staphylococcus aureus. The technique relies on analysis of large DNA fragments generated by th...

  16. In vivo evaluation of the pathogenicity of field isolates of infectious bronchitis virus.

    PubMed

    Avellaneda, G E; Villegas, P; Jackwood, M W; King, D J

    1994-01-01

    The pathogenicity of 13 field isolates of infectious bronchitis virus (IBV) isolated from Georgia broiler farms from 1989 to 1992 was evaluated using the IBV and Escherichia coli mixed-infection model. Based on the clinical signs, mortality, and lesions, the isolates were classified as high, intermediate, and low in pathogenicity. The in vivo classification was compared with the serotype classification results obtained by reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism analysis. The high-pathogenicity group was composed of five isolates representing three serotypes: Arkansas, Georgia variant (GAV), and Massachusetts. Isolates in the intermediate- and low-pathogenicity groups were all representatives of the Connecticut serotype, except for one isolate, which belonged to the Massachusetts serotype.

  17. Genetic variability of Aspergillus flavus isolates from a Mississippi corn field.

    PubMed

    Solorzano, Cesar D; Abbas, Hamed K; Zablotowicz, Robert M; Chang, Perng-Kuang; Jones, Walker A

    2014-01-01

    A nontoxigenic Aspergillus flavus strain, K49, is currently being tested as a biological control agent in corn fields in the Mississippi Delta. However, little is known about the overall genetic diversity of A. flavus from year to year in corn fields and specifically in Mississippi. Our objective was to assess the genetic variability of A. flavus isolates from different seasons, inoculum sources, and years, from a no-till corn field. Of the 175 A. flavus isolates examined, 74 and 97 had the typical norB-cypA type I (1.5 kb) and type II (1.0 kb) deletion patterns, respectively. Variability in the sequence of the omtA gene of the majority of the field isolates (n = 118) was compared to strain K49. High levels of haplotypic diversity (24 omtA haplotypes; Hd = 0.61 ± 0.04) were found. Among the 24 haplotypes, two were predominant, H1 (n = 71), which consists of mostly toxigenic isolates, and H49 (n = 18), which consists of mostly atoxigenic isolates including K49. Toxigenic isolates were prevalent (60%) in this natural population. Nonetheless, about 15% of the population likely shared the same ancestral origin with K49. This study provides valuable information on the diversity of A. flavus. This knowledge can be further used to develop additional biological control strains.

  18. Isolated magnetic field structures in Mercury's magnetosheath as possible analogues for terrestrial magnetosheath plasmoids and jets

    NASA Astrophysics Data System (ADS)

    Karlsson, Tomas; Liljeblad, Elisabet; Kullen, Anita; Raines, Jim M.; Slavin, James A.; Sundberg, Torbjörn

    2016-09-01

    We have investigated MESSENGER magnetic field data from the Mercury magnetosheath and near solar wind, to identify isolated magnetic field structures (defined as clear, isolated changes in the field magnitude). Their properties are studied in order to determine if they may be considered as analogues to plasmoids and jets known to exist in Earth's magnetosheath. Both isolated decreases of the magnetic field absolute value ('negative magnetic field structures') and increases ('positive structures') are found in the magnetosheath, whereas only negative structures are found in the solar wind. The similar properties of the solar wind and magnetosheath negative magnetic field structures suggests that they are analogous to diamagnetic plasmoids found in Earth's magnetosheath and near solar wind. The latter have earlier been identified with solar wind magnetic holes. Positive magnetic field structures are only found in the magnetosheath, concentrated to a region relatively close to the magnetopause. Their proximity to the magnetopause, their scale sizes, and the association of a majority of the structures with bipolar magnetic field signatures identify them as flux transfer events (which generally are associated with a decrease of plasma density in the magnetosheath). The positive magnetic field structures are therefore not likely to be analogous to terrestrial paramagnetic plasmoids but possibly to a sub-population of magnetosheath jets. At Earth, a majority of magnetosheath jets are associated with the quasi-parallel bow shock. We discuss some consequences of the findings of the present investigation pertaining to the different nature of the quasi-parallel bow shock at Mercury and Earth.

  19. Enzyme Mini-Test for Field Identification of Leishmania isolates from U.S. Military Personnel.

    DTIC Science & Technology

    1983-08-15

    TEST FOR FIELD IDENTIFICATION OF LEISHMANIA ISOLATES FROM U. S. MILITARY PERSONNEL Annual Report RICHARD D. KREUTZER 15 AUGUST 1983 Supported by U. S... LEISHMANIA ISOLATES FROM U. S. MILITARY PERSONNEL 1. PERFORMING ORG. REPORT NUMBER 7. AUTHOR(s) 8. CONTRACT OR GRANT NUMBER(&) Richard D. Kreutzer DAMD1...SUPPLEMENTARY NOTES N/A 19. KEY WORDS (Continue on reverse side If noceawaetnd Identify by block number) Leishmania ; electrophoresis; identification

  20. Identification of Strain-Specific Sequences That Distinguish a Mycoplasma gallisepticum Vaccine Strain from Field Isolates

    PubMed Central

    Ricketts, Camir; Pickler, Larissa; Maurer, John; Ayyampalayam, Saravanaraj; García, Maricarmen

    2016-01-01

    ABSTRACT Despite attempts to control avian mycoplasmosis through management, vaccination, and surveillance, Mycoplasma gallisepticum continues to cause significant morbidity, mortality, and economic losses in poultry production. Live attenuated vaccines are commonly used in the poultry industry to control avian mycoplasmosis; unfortunately, some vaccines may revert to virulence and vaccine strains are generally difficult to distinguish from natural field isolates. In order to identify genome differences among vaccine revertants, vaccine strains, and field isolates, whole-genome sequencing of the M. gallisepticum vaccine strain ts-11 and several “ts-11-like” strains isolated from commercial flocks was performed using Illumina and 454 pyrosequencing and the sequenced genomes compared to the M. gallisepticum Rlow reference genome. The collective contigs for each strain were annotated using the fully annotated Mycoplasma reference genome. The analysis revealed genetic differences among vlhA alleles, as well as among genes annotated as coding for a cell wall surface anchor protein (mg0377) and a hypothetical protein gene, mg0359, unique to M. gallisepticum ts-11 vaccine strain. PCR protocols were designed to target 5 sequences unique to the M. gallisepticum ts-11 strain: vlhA3.04a, vlhA3.04b, vlhA3.05, mg0377, and mg0359. All ts-11 isolates were positive for the five gene alleles tested by PCR; however, 5 to 36% of field isolates were also positive for at least one of the alleles tested. A combination of PCR tests for vlhA3.04a, vlhA3.05, and mg0359 was able to distinguish the M. gallisepticum ts-11 vaccine strain from field isolates. This method will further supplement current approaches to quickly distinguish M. gallisepticum vaccine strains from field isolates. PMID:27847370

  1. Isolated short attosecond pulse generation in an orthogonally polarized multicycle chirped laser field

    SciTech Connect

    Xu Junjie

    2011-03-15

    We theoretically demonstrate the generation of a high-order harmonic and isolated attosecond pulse in an orthogonally polarized laser field, which is synthesized by an 800-nm chirped laser pulse and an 800-nm chirp-free laser pulse. Owing to the instantaneous frequency increasingly reducing close to the center of the driving pulse, the extreme ultraviolet supercontinuum for the chirped synthesized field is even broader than that for an orthogonal chirp-free two-color laser field. It is found that the broadband supercontinuum spectrum can be achieved for the driving pulse with ten and above optical cycles. After phase compensation an isolated attosecond pulse with a duration of {approx}16 as is produced. Furthermore, the optimization of the chirping rate parameters is investigated to achieve cutoff extension and an isolated short attosecond pulse.

  2. Generation of isolated attosecond extreme ultraviolet pulses employing nanoplasmonic field enhancement: optimization of coupled ellipsoids

    NASA Astrophysics Data System (ADS)

    Stebbings, S. L.; Süßmann, F.; Yang, Y.-Y.; Scrinzi, A.; Durach, M.; Rusina, A.; Stockman, M. I.; Kling, M. F.

    2011-07-01

    The production of extreme ultraviolet (XUV) radiation via nanoplasmonic field-enhanced high-harmonic generation (HHG) in gold nanostructures at MHz repetition rates is investigated theoretically in this paper. Analytical and numerical calculations are employed and compared in order to determine the plasmonic fields in gold ellipsoidal nanoparticles. The comparison indicates that numerical calculations can accurately predict the field enhancement and plasmonic decay, but may encounter difficulties when attempting to predict the oscillatory behavior of the plasmonic field. Numerical calculations for coupled symmetric and asymmetric ellipsoids for different carrier-envelope phases (CEPs) of the driving laser field are combined with time-dependent Schrödinger equation simulations to predict the resulting HHG spectra. The studies reveal that the plasmonic field oscillations, which are controlled by the CEP of the driving laser field, play a more important role than the nanostructure configuration in finding the optimal conditions for the generation of isolated attosecond XUV pulses via nanoplasmonic field enhancement.

  3. Two-color field for the generation of an isolated attosecond pulse in water-window region.

    PubMed

    Chen, Wenxiang; Chen, Guanglong; Kim, Dong Eon

    2011-10-10

    For the investigation of various ultrafast electron dynamics, an isolated attosecond pulse in a broad spectral range is necessary. The generation of isolated attosecond pulses demands the manipulation of the electric field of a laser. We propose a two-color field scheme for generating an isolated attosecond pulse in the water-window region. Two-color fields are generated by mixing two equally-strong pulsed color fields. The investigation shows that an isolated attosecond pulse with a photon energy of near 500 eV and a pulse duration of 125 - 188 attoseconds can be generated using 10 - 15 fs FWHM laser fields.

  4. Quantitative Field Testing Heterodera glycines from Metagenomic DNA Samples Isolated Directly from Soil under Agronomic Production

    PubMed Central

    Li, Yan; Lawrence, Gary W.; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P.

    2014-01-01

    A quantitative PCR procedure targeting the Heterodera glycines ortholog of the Caenorhabditis elegans uncoordinated-78 gene was developed. The procedure estimated the quantity of H. glycines from metagenomic DNA samples isolated directly from field soil under agronomic production. The estimation of H. glycines quantity was determined in soil samples having other soil dwelling plant parasitic nematodes including Hoplolaimus, predatory nematodes including Mononchus, free-living nematodes and biomass. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from field soil. PMID:24587100

  5. Enhancing isolation of antenna arrays by simultaneously blocking and guiding magnetic field lines using magnetic metamaterials

    NASA Astrophysics Data System (ADS)

    Liu, Zhaotang; Wang, Jiafu; Qu, Shaobo; Zhang, Jieqiu; Ma, Hua; Xu, Zhuo; Zhang, Anxue

    2016-10-01

    In this article, we propose to enhance the isolation of antenna arrays by manipulating the near-field magnetic coupling between adjacent antennas using magnetic metamaterials (MMs). Due to the artificially designed negative or large permeability, MMs can concentrate or block the magnetic field lines where they are located, which allows us to tune the near-field magnetic coupling strengths between antennas. MMs can play a two-fold role in enhancing antenna isolation. On one hand, the magnetic fields can be blocked in gaps between adjacent antennas using MMs with negative permeability; on the other hand, the magnetic fields can be pulled towards the borders of the antenna array using MMs with large permeability. As an example, we demonstrated a four-element patch antenna array with split-ring resonators (SRR) integrated in the substrate. The measured results show that the isolation can be enhanced by more than 10 dB with the integration of SRRs, even if the gap between antennas is only about 0.082λ. This work provides an effective alternative to the design of high-isolation antenna arrays.

  6. Molecular Typing by Pulsed-Field Gel Electrophoresis of Spanish Animal and Human Listeria monocytogenes Isolates

    PubMed Central

    Vela, A. I.; Fernandez-Garayzabal, J. F.; Vazquez, J. A.; Latre, M. V.; Blanco, M. M.; Moreno, M. A.; de la Fuente, L.; Marco, J.; Franco, C.; Cepeda, A.; Rodriguez Moure, A. A.; Suarez, G.; Dominguez, L.

    2001-01-01

    A total of 153 strains of Listeria monocytogenes isolated from different sources (72 from sheep, 12 from cattle, 18 from feedstuffs, and 51 from humans) in Spain from 1989 to 2000 were characterized by pulsed-field gel electrophoresis. The strains of L. monocytogenes displayed 55 pulsotypes. The 84 animal, 51 human, and 18 feedstuff strains displayed 31, 29, and 7 different pulsotypes, respectively, indicating a great genetic diversity among the Spanish L. monocytogenes isolates studied. L. monocytogenes isolates from clinical samples and feedstuffs consumed by the diseased animals were analyzed in 21 flocks. In most cases, clinical strains from different animals of the same flock had identical pulsotypes, confirming the existence of a listeriosis outbreak. L. monocytogenes strains with pulsotypes identical to those of clinical strains were isolated from silage, potatoes, and maize stalks. This is the first study wherein potatoes and maize stalks are epidemiologically linked with clinical listeriosis. PMID:11722943

  7. Optimum design of bridges with superelastic-friction base isolators against near-field earthquakes

    NASA Astrophysics Data System (ADS)

    Ozbulut, Osman E.; Hurlebaus, Stefan

    2010-04-01

    The seismic response of a multi-span continuous bridge isolated with novel superelastic-friction base isolator (S-FBI) is investigated under near-field earthquakes. The isolation system consists of a flat steel-Teflon sliding bearing and a superelastic NiTi shape memory alloy (SMA) device. Sliding bearings limit the maximum seismic forces transmitted to the superstructure to a certain value that is a function of friction coefficient of sliding interface. Superelastic SMA device provides restoring capability to the isolation system together with additional damping characteristics. The key design parameters of an S-FBI system are the natural period of the isolated, yielding displacement of SMA device, and the friction coefficient of the sliding bearings. The goal of this study is to obtain optimal values for each design parameter by performing sensitivity analyses of the isolated bridge. First, a three-span continuous bridge is modeled as a two-degrees-of-freedom with S-FBI system. A neuro-fuzzy model is used to capture rate-dependent nonlinear behavior of SMA device. A time-dependent method which employs wavelets to adjust accelerograms to match a target response spectrum with minimum changes on the other characteristics of ground motions is used to generate ground motions used in the simulations. Then, a set of nonlinear time history analyses of the isolated bridge is performed. The variation of the peak response quantities of the isolated bridge is shown as a function of design parameters. Also, the influence of temperature variations on the effectiveness of S-FBI system is evaluated. The results show that the optimum design of the isolated bridge with S-FBI system can be achieved by a judicious specification of design parameters.

  8. Strain field reconstruction in shallow trench isolation structures by CBED and LACBED

    NASA Astrophysics Data System (ADS)

    Spessot, A.; Frabboni, S.; Balboni, R.; Armigliato, A.

    2006-12-01

    Using a combination of the CBED and the LACBED techniques in the transmission electron microscopy (TEM), we have investigated the strain field in the silicon active region of a shallow trench isolation structure, underlying a TiSi 2 layer. Starting from the analysis of the deformation in a sample, thinned for TEM analysis, we have reconstructed the displacement field, simulating the split HOLZ lines visible in the experimental CBED patterns. From the comparison between the experimental LACBED patterns, taken in a suitable sample orientation to evidence the stressors distribution in the polycrystalline silicide layer, and the corresponding dynamically simulated ones, we have reproduced the strain field in the unthinned, bulk sample.

  9. Spore-Forming Thermophilic Sulfate-Reducing Bacteria Isolated from North Sea Oil Field Waters

    PubMed Central

    Rosnes, Jan Thomas; Torsvik, Terje; Lien, Torleiv

    1991-01-01

    Thermophilic sulfate-reducing bacteria were isolated from oil field waters from oil production platforms in the Norwegian sector of the North Sea. Spore-forming rods dominated in the enrichments when lactate, propionate, butyrate, or a mixture of aliphatic fatty acids (C4 through C6) was added as a carbon source and electron donor. Representative strains were isolated and characterized. The isolates grew autotrophically on H2-CO2 and heterotrophically on fatty acids such as formate, propionate, butyrate, caproate, valerate, pyruvate, and lactate and on alcohols such as methanol, ethanol, and propanol. Sulfate, sulfite, and thiosulfate but not nitrate could be used as an electron acceptor. The temperature range for growth was 43 to 78°C; the spores were extremely heat resistant and survived 131°C for 20 min. The optimum pH was 7.0. The isolates grew well in salt concentrations ranging from 0 to 800 mmol of NaCl per liter. Sulfite reductase P582 was present, but cytochrome c and desulfoviridin were not found. Electron micrographs revealed a gram-positive cell organization. The isolates were classified as a Desulfotomaculum sp. on the basis of spore formation, general physiological characteristics, and submicroscopic organization. To detect thermophilic spore-forming sulfate-reducing bacteria in oil field water, polyvalent antisera raised against antigens from two isolates were used. These bacteria were shown to be widespread in oil field water from different platforms. The origin of thermophilic sulfate-reducing bacteria in the pore water of oil reservoirs is discussed. Images PMID:16348538

  10. Genetic diversity and relationships among Venezuelan equine encephalitis virus field isolates from Colombia and Venezuela.

    PubMed

    Moncayo, A C; Medina, G M; Kalvatchev, Z; Brault, A C; Barrera, R; Boshell, J; Ferro, C; Freier, J E; Navarro, J C; Salas, R; De Siger, J; Vasquez, C; Walder, R; Weaver, S C

    2001-12-01

    During field studies of enzootic Venezuelan equine encephalitis (VEE) viruses associated with epizootic emergence, a large number of virus isolates were made in sylvatic foci of Venezuela and Colombia. To rapidly characterize these isolates, antigenic subtypes were determined by means of immunofluorescence and by single-strand conformational polymorphism (SSCP) analysis by use of an 856-bp fragment from the P62 gene, which we used to distinguish genetic variants. Representative isolates were sequenced to assess the sensitivity of SSCP to detect genetic differences. The SSCP analysis distinguished isolates differing by as little as 1 nucleotide; overall, differences of > or = 1 nucleotide were recognized 89% of the time, and the sensitivity to distinguish strains that differed by only 1 or 4 nucleotides was 17 and 57%, respectively. Phylogenetic analyses of representative sequences showed that all recent isolates from the Catatumbo region of western Venezuela and the middle Magdalena Valley of Colombia were closely related to epizootic subtype IAB and IC strains; strains from Yaracuy and Miranda States were more distantly related. Cocirculation of the same virus genotype in both Colombian and Venezuelan foci indicated that these viruses are readily transported between enzootic regions separated by > 300 km. The SSCP analysis appears to be a simple, fast, and relatively efficient method of screening VEE virus isolates to identify meaningful genetic variants.

  11. A new spiroplasma isolate from the field cricket (Gryllus bimaculatus) in Taiwan.

    PubMed

    Nai, Yu-Shin; Su, Ping-Yi; Hsu, Yu-Hsiang; Chiang, Ching-Hao; Kim, Jae Su; Chen, Yue-Wen; Wang, Chung-Hsiung

    2014-07-01

    We briefly described the morphology and transmission pathway of a Spiroplasma sp. isolated from the field cricket, Gryllus bimaculatus in Taiwan, followed by the phylogenetic analysis based on the 16S rRNA gene sequence. The cricket spiroplasma infected the hemolymph, gut, muscle tissues and tracheal cells; therefore we suggest that the pathogen invaded tissues and organs from the hemolymph through the tracheal system and the endoplasmic reticular system. Based on 16S rRNA gene sequences and the phylogeny, this spiroplasma was most closely related to Spiroplasma platyhelix (Identity=95%) isolated from the dragonfly Pachydiplax longipennis and belongs to the Ixodetis clade.

  12. Salmonella Gallinarum field isolates from laying hens are related to the vaccine strain SG9R.

    PubMed

    Van Immerseel, F; Studholme, D J; Eeckhaut, V; Heyndrickx, M; Dewulf, J; Dewaele, I; Van Hoorebeke, S; Haesebrouck, F; Van Meirhaeghe, H; Ducatelle, R; Paszkiewicz, K; Titball, R W

    2013-10-09

    Salmonella enterica subspecies enterica serotype Gallinarum can cause severe systemic disease in chickens and a live Salmonella Gallinarum 9R vaccine (SG9R) has been used widely to control disease. Using whole-genome sequencing we found point mutations in the pyruvate dehydrogenase (aceE) and/or lipopolysaccharide 1,2-glucosyltransferase (rfaJ) genes that likely explain the attenuation of the SG9R vaccine strain. Molecular typing using Pulsed Field Gel Electrophoresis and Multiple-Locus Variable number of tandem repeat Analysis showed that strains isolated from different layer flocks in multiple countries and the SG9R vaccine strain were similar. The genome of one Salmonella Gallinarum field strain, isolated from a flock with a mortality peak and selected on the basis of identical PFGE and MLVA patterns with SG9R, was sequenced. We found 9 non-silent single-nucleotide differences distinguishing the field strain from the SG9R vaccine strain. Our data show that a Salmonella Gallinarum field strain isolated from laying hens is almost identical to the SG9R vaccine. Mutations in the aceE and rfaJ genes could explain the reversion to a more virulent phenotype. Our results highlight the importance of using well defined gene deletion mutants as vaccines.

  13. Improved isolation of archeomagnetic signals by combined low temperature and alternating field demagnetization

    NASA Astrophysics Data System (ADS)

    Borradaile, Graham J.; Lagroix, France; Trimble, Dale

    2001-09-01

    Conventional alternating field (AF) demagnetization of the magnetite-bearing claystone foundations of a Saxon or late medieval lime kiln in Lincolnshire, England fail to isolate stable characteristic remanences, or remanences compatible with possible contemporary geomagnetic field orientations. Consolidation of the material prevented thermal demagnetization. When low temperature demagnetization (LTD) precedes AF demagnetization, however, the vector plots show a stable characteristic (primary) component. Magnetic anisotropy measurements show that the LTD did not significantly disturb the mineral fabric of the claystone, that the mineral fabric did not deflect the palaeofield, and that AF demagnetization did not induce a field-impressed anisotropy during the experiments. Anisotropy of low-field magnetic susceptibility (AMS) is affected by all minerals, and therefore the anisotropy of the magnetite was isolated by measuring anisotropy of anhysteretic remanence (AARM); this is of more relevance in evaluating the potential for palaeofield deflection. Thus, we conclude that LTD preceding AF demagnetization is responsible for improving the isolation of a characteristic remanence, which then favours a late medieval age for the kiln foundation.

  14. Identification and Comparison of Receptor Binding Characteristics of the Spike Protein of Two Porcine Epidemic Diarrhea Virus Strains

    PubMed Central

    Deng, Feng; Ye, Gang; Liu, Qianqian; Navid, Muhammad Tariq; Zhong, Xiaoli; Li, Youwen; Wan, Chunyun; Xiao, Shaobo; He, Qigai; Fu, Zhen F.; Peng, Guiqing

    2016-01-01

    Porcine epidemic diarrhea virus (PEDV), a member of Alphacoronavirus, has caused huge economic losses for the global pork industry recently. The spike (S) protein mediates PEDV entry into host cells. Herein, we investigated the interactions between the S protein and its receptor porcine aminopeptidase N (pAPN) or co-receptor sugars. The C-terminal domain (CTD) of the S1 domain is bound to pAPN. The prototype strain demonstrated similar receptor-binding activity compared with the variant field isolate. Three loops at the tips of the β-barrel domains did not play crucial roles in the PEDV S-pAPN association, indicating that PEDV conforms to a different receptor recognition model compared with transmissible gastroenteritis virus (TGEV), porcine respiratory CoV (PRCV), and human coronavirus NL63 (HCoV-NL63). The N-terminal domain (NTD) of the PEDV S1 domain could bind sugar, a possible co-receptor for PEDV. The prototype strain exhibited weaker sugar-binding activity compared with the variant field isolate. Strategies targeting the receptor binding domain (RBD) may be helpful for developing vaccines or antiviral drugs for PEDV. Understanding the differences in receptor binding between the prototype and the variant strains may provide insight into PEDV pathogenesis. PMID:26907329

  15. Hy-wire and fast electric field change measurements near an isolated thunderstorm, appendix C

    NASA Technical Reports Server (NTRS)

    Holzworth, R. H.; Levine, D. M.

    1983-01-01

    Electric field measurements near an isolated thunderstorm at 6.4 km distance are presented from both a tethered balloon experiment called Hy-wire and also from ground based fast and slow electric field change systems. Simultaneous measurements were made of the electric fields during several lightning flashes at the beginning of the storm which the data clearly indicate were cloud-to-ground flashes. In addition to providing a comparison between the Hy-wire technique for measuring electric fields and more traditional methods, these data are interesting because the lightning flashes occurred prior to changes in the dc electric field, although Hy-wire measured changes in the dc field of up to 750 V/m in the direction opposite to the fair weather field a short time later. Also, the dc electric field was observed to decay back to its preflash value after each flash. The data suggest that Hy-wire was at the field reversal distance from this storm and suggest the charge realignment was taking place in the cloud with a time constant on the order of 20 seconds.

  16. Investigation of the Sterol Composition and Azole Resistance in Field Isolates of Septoria tritici

    PubMed Central

    Joseph-Horne, T.; Hollomon, D.; Manning, N.; Kelly, S. L.

    1996-01-01

    We report here a biochemical study of resistance to azole antifungal agents in a field isolate (S-27) of a fungal phytopathogen. Isolates of Septoria tritici were compared in vitro, and their responses reflected that observed in the field, with S-27 exhibiting resistance relative to RL2. In untreated cultures, both RL2 and S-27 contained isomers of ergosterol and ergosta-5,7-dienol, although in differing concentrations. Under azole treatment, this phytopathogen exhibited a response similar to that of other pathogenic fungi, with a reduction in desmethyl sterols and an accumulation of 14(alpha)-methyl sterols, indicative of inhibition of the P450-mediating sterol 14(alpha)-demethylase. Growth arrest was attributed to the reduction of ergosterol combined with an accumulation of nonutilizable sterols. Strain S-27 exhibited an azole-resistant phenotype which was correlated with decreased cellular content of azole. PMID:16535210

  17. Comparative analysis of field-isolate and monkey-adapted Plasmodium vivax genomes.

    PubMed

    Chan, Ernest R; Barnwell, John W; Zimmerman, Peter A; Serre, David

    2015-03-01

    Significant insights into the biology of Plasmodium vivax have been gained from the ability to successfully adapt human infections to non-human primates. P. vivax strains grown in monkeys serve as a renewable source of parasites for in vitro and ex vivo experimental studies and functional assays, or for studying in vivo the relapse characteristics, mosquito species compatibilities, drug susceptibility profiles or immune responses towards potential vaccine candidates. Despite the importance of these studies, little is known as to how adaptation to a different host species may influence the genome of P. vivax. In addition, it is unclear whether these monkey-adapted strains consist of a single clonal population of parasites or if they retain the multiclonal complexity commonly observed in field isolates. Here we compare the genome sequences of seven P. vivax strains adapted to New World monkeys with those of six human clinical isolates collected directly in the field. We show that the adaptation of P. vivax parasites to monkey hosts, and their subsequent propagation, did not result in significant modifications of their genome sequence and that these monkey-adapted strains recapitulate the genomic diversity of field isolates. Our analyses also reveal that these strains are not always genetically homogeneous and should be analyzed cautiously. Overall, our study provides a framework to better leverage this important research material and fully utilize this resource for improving our understanding of P. vivax biology.

  18. Forecasting the Feasibility of Implementing Isolation Perimeters Between GM and non-GM Maize Fields Under Agricultural Conditions

    NASA Astrophysics Data System (ADS)

    Devos, Yann; Cougnon, Mathias; Thas, Olivier; De Clercq, Eva M.; Cordemans, Karl; Reheul, Dirk

    2008-10-01

    Although spatially isolating genetically modified (GM) maize fields from non-GM maize fields is a robust on-farm strategy to keep the adventitious presence of GM material in the harvests of neighboring non-GM maize fields due to cross-fertilizations below established labeling thresholds (and thus to ensure the spatial co-existence between maize cropping systems), the practical implementation of isolation perimeters attracted little research efforts. In this study, the feasibility of implementing isolation perimeters around GM maize fields is investigated. Using Geographic Information System datasets and Monte Carlo simulations, various scenarios differing in shares and spatial distributions of GM maize were tested for various isolation perimeters in six agricultural areas in Flanders. Factors that affect the feasibility of implementing isolation perimeters are discussed.

  19. Pulsed-field gel electrophoresis and ribotype profiles of clinical and environmental Vibrio vulnificus isolates.

    PubMed Central

    Tamplin, M L; Jackson, J K; Buchrieser, C; Murphree, R L; Portier, K M; Gangar, V; Miller, L G; Kaspar, C W

    1996-01-01

    Vibrio vulnificus belongs to the autochthonous bacterial flora of warm estuarine waters. It can cause life-threatening extraintestinal disease in persons who have underlying illness and who consume raw shellfish or contact wounds with estuarine water. Currently, very little is known about genetic diversity within this species. In this report, we describe high-level variation in restriction fragment length polymorphism profiles among 53 clinical and 78 environmental isolates, as determined by pulsed-field gel electrophoresis. In contrast, ribotype profiles showed greater similarity. When combined ribotype profiles of clinical and environmental isolates were analyzed, four predominant clusters were observed. Interestingly, a low number (16%) of clinical isolates were found in cluster C, compared with clusters A, B, and D (range, 50 to 83%). In addition, 83% of all Hawaiian isolates were located in a single cluster, indicating a possible relationship between geography and genotype. We also report that spontaneous translucent colonial morphotypes were distinct by both restriction fragment length polymorphism and biochemical profiles, compared with opaque parent strains. PMID:8837412

  20. The limitations of pulsed-field gel electrophoresis for analysis of Yersinia enterocolitica isolates.

    PubMed

    Gilpin, B J; Robson, B; Lin, S; Hudson, J A; Weaver, L; Dufour, M; Strydom, H

    2014-09-01

    This study describes the analysis of 432 isolates of Yersinia enterocolitica by pulsed-field gel electrophoresis (PFGE). PFGE had a high level of discrimination with biotype 1A isolates (Simpson's Diversity Index 0.997), but with the clinically important biotypes 2, 3 and 4, the discriminatory ability of PFGE was so low as to severely limit its usefulness (DI <0.6). For biotypes 2, 3 and 4, 79% or more of isolates of each biotype were of just three different PFGE profiles. Because of this, four known outbreaks of yersiniosis would not have been identified by PFGE analysis. However, a previously unrecognized potential outbreak of yersiniosis caused by biotype 4 isolates was identified on the basis of a rare PFGE genotype with spatial and temporal clustering. We conclude that PFGE has a very limited application to the genotyping of Y. enterocolitica biotypes 2, 3 and 4, and inferences based on finding indistinguishable PFGE profiles among cases or between cases and sources need to be substantiated using alternative typing tools, or strong epidemiological evidence.

  1. Incipient Fault Detection and Isolation of Field Devices in Nuclear Power Systems Using Principal Component Analysis

    SciTech Connect

    Kaistha, Nitin; Upadhyaya, Belle R.

    2001-11-15

    An integrated method for the detection and isolation of incipient faults in common field devices, such as sensors and actuators, using plant operational data is presented. The approach is based on the premise that data for normal operation lie on a surface and abnormal situations lead to deviations from the surface in a particular way. Statistically significant deviations from the surface result in the detection of faults, and the characteristic directions of deviations are used for isolation of one or more faults from the set of typical faults. Principal component analysis (PCA), a multivariate data-driven technique, is used to capture the relationships in the data and fit a hyperplane to the data. The fault direction for each of the scenarios is obtained using the singular value decomposition on the state and control function prediction errors, and fault isolation is then accomplished from projections on the fault directions. This approach is demonstrated for a simulated pressurized water reactor steam generator system and for a laboratory process control system under single device fault conditions. Enhanced fault isolation capability is also illustrated by incorporating realistic nonlinear terms in the PCA data matrix.

  2. AquaPathogen X--A template database for tracking field isolates of aquatic pathogens

    USGS Publications Warehouse

    Emmenegger, Evi; Kurath, Gael

    2012-01-01

    AquaPathogen X is a template database for recording information on individual isolates of aquatic pathogens and is available for download from the U.S. Geological Survey (USGS) Western Fisheries Research Center (WFRC) website (http://wfrc.usgs.gov). This template database can accommodate the nucleotide sequence data generated in molecular epidemiological studies along with the myriad of abiotic and biotic traits associated with isolates of various pathogens (for example, viruses, parasites, or bacteria) from multiple aquatic animal host species (for example, fish, shellfish, or shrimp). The simultaneous cataloging of isolates from different aquatic pathogens is a unique feature to the AquaPathogen X database, which can be used in surveillance of emerging aquatic animal diseases and clarification of main risk factors associated with pathogen incursions into new water systems. As a template database, the data fields are empty upon download and can be modified to user specifications. For example, an application of the template database that stores the epidemiological profiles of fish virus isolates, called Fish ViroTrak (fig. 1), was also developed (Emmenegger and others, 2011).

  3. Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Isolates Determined by Pulsed-Field Gel Electrophoresis: Comparison of Isolates from Avian Wildlife, Domestic Animals, and the Environment in Norway

    PubMed Central

    Refsum, Thorbjørn; Heir, Even; Kapperud, Georg; Vardund, Traute; Holstad, Gudmund

    2002-01-01

    The molecular epidemiology of 142 isolates of Salmonella enterica serovar Typhimurium from avian wildlife, domestic animals, and the environment in Norway was investigated using pulsed-field gel electrophoresis (PFGE) and computerized numerical analysis of the data. The bacterial isolates comprised 79 isolates from wild-living birds, including 46 small passerines and 26 gulls, and 63 isolates of nonavian origin, including 50 domestic animals and 13 environmental samples. Thirteen main clusters were discernible at the 90% similarity level. Most of the isolates (83%) were grouped into three main clusters. These were further divided into 20 subclusters at the 95% similarity level. Isolates from passerines, gulls, and pigeons dominated within five subclusters, whereas isolates from domestic animals and the environment belonged to many different subclusters with no predominance. The results support earlier results that passerines constitute an important source of infection to humans in Norway, whereas it is suggested that gulls and pigeons, based on PFGE analysis, represent only a minor source of human serovar Typhimurium infections. Passerines, gulls, and pigeons may also constitute a source of infection of domestic animals and feed plants or vice versa. Three isolates from cattle and a grain source, of which two were multiresistant, were confirmed as serovar Typhimurium phage type DT 104. These represent the first reported phage type DT 104 isolates from other sources than humans in Norway. PMID:12406755

  4. Field studies on two rock phosphate solubilizing actinomycete isolates as biofertilizer sources

    NASA Astrophysics Data System (ADS)

    Mba, Caroline C.

    1994-03-01

    Recently biotechnology is focusing attention on utilization of biological resources to solve a number of environmental problems such as soil fertility management. Results of microbial studies on earthworm compost in the University of Nigeria farm identified a number of rock phosphate solubilizing actinomycetes. Two of these, isclates 02 and 13, were found to be efficient rock phosphate (RP) solubilizers and fast-growing cellulolytic microbes producing extracellular hydrolase enzymes. In this preliminary field study the two microbial isolates were investigated with respect to their effects on the growth of soybean and egusi as well as their effect on the incidence of toxicity of poultry droppings. Application of these isolates in poultry manure-treated field plots, as microbial fertilizers, brought about yield increases of 43% and 17% with soybeans and 19% and 33% with egusi, respectively. Soil properties were also improved. With isolates 02 and 13, the soil available phosphorus increased at the five-leaf stage, while N-fixation in the soil increased by 45% or 11% relative to control. It was further observed that air-dried poultry manure after four days of incubation was still toxic to soybean. The toxic effect of the applied poultry manure was reduced or eliminated with microbial fertilizers 02 or 13, respectively. The beneficial effects of the microbial organic fertilizer are discussed. Justification for more intensive research on rock phosphate organic fertilizer is highlighted.

  5. Identification of Brucella ovis exclusive genes in field isolates from Argentina.

    PubMed

    Alvarez, Lucía Paula; García-Effrón, Guillermo; Robles, Carlos Alejandro

    2016-03-01

    Brucellosis caused by Brucella ovis is one of the most important infectious diseases of sheep. The aim of this study was to determine the presence of genes both inside and outside the specific B. ovis pathogenicity island 1 (BOPI-1) in a large collection of field isolates of B. ovis and other Brucella spp. from Argentina. The BOV_A0500 gene from B. ovis BOPI-1 was identified in all 104 B. ovis isolates studied. The BOPI-1 complete sequence was found to be conserved in 10 B. ovis strains from the collection, for which whole genome sequencing was performed. The BOV_0198 gene, which is outside BOPI-1 and considered exclusive to B. ovis, showed 90-100% identity with genomic regions of B. ovis, B. melitensis, B. abortus, B. canis, B. suis, B. microti, B. ceti and B. pinnipedialis. The results demonstrate that BOPI-1 is the only exclusive genetic region of B. ovis and marine Brucella spp. and that it is highly conserved in B. ovis field isolates from Argentina.

  6. [In vitro cultivation of fields isolates of Plasmodium falciparum in Mali].

    PubMed

    Djimde, A A; Kirkman, L; Kassambara, L; Diallo, M; Plowe, C V; Wellems, T E; Doumbo, O K

    2007-02-01

    Malaria immunology, molecular biology and pathogenicity studies often require the adaptation of Plasmodium falciparum field isolates to continuous in vitro cultivation. For this purpose we have established propagation protocols of asexual erythrocytic stages of P. falciparum samples from malaria patients or asymptomatic carriers in Mali. The parasites were grown in standard culture medium supplemented by human serum and in a culture medium without human serum but supplemented by AlbuMax 1. The candle jar environment and tissue culture flasks gassed with 5% CO2, 5% O2 and 90% N2 obtained from a portable gas mixer were used. Protocols for parasite cultivation in a resource-poor setting were developed. These protocols were successfully applied to fresh isolates in Mali as well as to blood samples frozen in liquid nitrogen and shipped to a laboratory in U.S.A.

  7. Characterization of Listeria monocytogenes isolates from cattle and ground beef by pulsed-field gel electrophoresis.

    PubMed

    Foerster, Claudia; Vidal, Lorena; Troncoso, Miriam; Figueroa, Guillermo

    2012-01-01

    The aims of this study were to determine the occurrence of Listeria monocytogenes in cattle feces and ground beef, to characterize these strains by pulsed-field gel electrophoresis and to compare them to three listeria strains found in humans. Cattle from different origins (n = 250) and ground beef obtained from supermarkets (n = 40) were sampled. The results show low occurrence in cattle feces (0.4 %) but a higher presence in ground beef (37 %). An important part of the ground beef strains (80 %) had > 95 % similarity with a strain isolated from a human sporadic case and the ATCC 19115 used as control. The strain isolated from cattle feces had 93 % similarity to clone 009, previously associated with a listeriosis outbreak related to cheese. Cattle and ground beef can harbor virulent L. monocytogenes strains. Further studies in animals and animal products are needed to improve listeriosis control.

  8. First clinical isolates of Cronobacter spp. (Enterobacter sakazakii) in Argentina: characterization and subtyping by pulsed-field gel electrophoresis.

    PubMed

    Asato, Valeria C; Vilches, Viviana E; Pineda, María G; Casanueva, Enrique; Cane, Alejandro; Moroni, Mirian P; Brengi, Silvina P; Pichel, Mariana G

    2013-01-01

    Cronobacter species are opportunistic pathogens associated with severe infections in neonates and immunocompromised infants. From January 2009 through September 2010, two cases of neonatal infections associated with Cronobacter malonaticus and one case associated with Cronobacter sakazakii, two of them fatal, were reported in the same hospital. These are the first clinical isolates of Cronobacter spp. in Argentina. The objective of this work was to characterize and subtype clinical isolates of Cronobacter spp. in neonate patients, as well as to establish the genetic relationship between these isolates and the foodborne isolates previously identified in the country. Pulsed-field gel electrophoresis analysis showed a genetic relationship between the C. malonaticus isolates from two patients. Different results were found when the pulsed-field gel electrophoresis patterns of clinical isolates were compared with those deposited in the National Database of Cronobacter spp.

  9. Geobacter luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud.

    PubMed

    Viulu, Samson; Nakamura, Kohei; Okada, Yurina; Saitou, Sakiko; Takamizawa, Kazuhiro

    2013-02-01

    A novel species of Fe(III)-reducing bacterium, designated strain OSK6(T), belonging to the genus Geobacter, was isolated from lotus field mud in Japan. Strain OSK6(T) was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, gram-negative, motile, straight rod-shaped bacterium, 0.6-1.9 µm long and 0.2-0.4 µm wide. The growth of the isolate occurred at 20-40 °C with optima of 30-37 °C and pH 6.5-7.5 in the presence of up to 0.5 g NaCl l(-1). The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6(T) was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6(T) is closely related to Geobacter daltonii and Geobacter toluenoxydans with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6(T) is described as a representative of a novel species, Geobacter luticola sp. nov.; the type strain is OSK6(T) ( = DSM 24905(T) = JCM 17780(T)).

  10. Sulfur oxidation in rice field soil: activity, enumeration, isolation and characterization of thiosulfate-oxidizing bacteria.

    PubMed

    Stubner, S; Wind, T; Conrad, R

    1998-12-01

    In rice paddy fields the bulk soil is anoxic, but oxygenated zones occur in the surrounding of the rice roots to where oxygen is transported via the aerenchyma system of the rice plants. In the anaerobic soil compartments sulfate is consumed by sulfate-reducing bacteria. In the rhizosphere the reduced sulfur compounds can be reoxidized by sulfur-oxidizing bacteria. Measurements of the potential activity of thiosulfate-oxidizing bacteria in soil slurries derived from planted rice soil microcosms showed turnover rates of 2-6 mumol d-1 g-dw-1. Thiosulfate was oxidized to sulfate with tetrathionate as intermediate. Most probable number (MPN) enumeration with three aerobic media and one anaerobic nitrate-amended medium showed that thiosulfate-oxidizing bacteria were abundant in paddy soil and in rhizosphere soil at numbers of 10(5) to 10(6) per gram dry weight soil. Nine isolates of S-oxidizing bacteria were obtained from enrichment cultures or from the highest dilutions of the MPN series and were affiliated to four different phylogenetic groups. These isolates were characterized by physiological properties and by comparative 16S rDNA sequence analysis. Three isolates (TA1-AE1, TA1-A1 and TA12-21) were shown to be facultatively chemolithoautotrophic strains of Ancylobacter aquaticus. Three further isolates (Tv6-2b, Z2A-6A and Z4A-2A) were also facultatively chemolithoautotrophic and were affiliated with the Xanthobacter sp. group, probably representing new strains of X. flavus or X. tagetidis. Strain SZ-2111 was phylogenetically related to Bosea thiooxidans. However, the genus Bosea is described as obligately heterotrophic, whereas strain 5Z-2111 was able to grow autotrophically. The isolates 5Z-C1 and TBW3 were obligate chemolithoautotrophs and were closely affiliated with Thiobacillus thioparus. Our results showed that S-oxidizing bacteria were abundant and active in rice paddy soil and consisted of physiologically and phylogenetically diverse populations.

  11. Genetic Variability and Geographical Distribution of Mycotoxigenic Fusarium verticillioides Strains Isolated from Maize Fields in Texas

    PubMed Central

    Ortiz, Carlos S.; Richards, Casey; Terry, Ashlee; Parra, Joselyn; Shim, Won-Bo

    2015-01-01

    Maize is the dominant cereal crop produced in the US. One of the main fungal pathogens of maize is Fusarium verticillioides, the causative agent of ear and stalk rots. Significantly, the fungus produces a group of mycotoxins - fumonisins - on infested kernels, which have been linked to various illnesses in humans and animals. Nonetheless, durable resistance against F. verticillioides in maize is not currently available. In Texas, over 2.1 million acres of maize are vulnerable to fumonisin contamination, but understanding of the distribution of toxigenic F. verticillioides in maize-producing areas is currently lacking. Our goal was to investigate the genetic variability of F. verticillioides in Texas with an emphasis on fumonisin trait and geographical distribution. A total of 164 F. verticillioides cultures were isolated from 65 maize-producing counties. DNA from each isolate was extracted and analyzed by PCR for the presence of FUM1- a key fumonisin biosynthesis gene - and mating type genes. Results showed that all isolates are in fact F. verticillioides capable of producing fumonisins with a 1:1 mating-type gene ratio in the population. To further study the genetic diversity of the population, isolates were analyzed using RAPD fingerprinting. Polymorphic markers were identified and the analysis showed no clear correlation between the RAPD profile of the isolates and their corresponding geographical origin. Our data suggest the toxigenic F. verticillioides population in Texas is widely distributed wherever maize is grown. We also hypothesize that the population is fluid, with active movement and genetic recombination occurring in the field. PMID:26361468

  12. Molecular Typing of Vibrio cholerae O1 Isolates from Thailand by Pulsed-field Gel Electrophoresis

    PubMed Central

    Tapchaisri, Pramuan; Na-Ubol, Mathukorn; Tiyasuttipan, Watcharee; Chaiyaroj, Sansanee C.; Yamasaki, Shinji; Wongsaroj, Thitima; Hayashi, Hideo; Nair, G. Balakrish; Chongsa-Nguan, Manas; Kurazono, Hisao; Chaicumpa, Wanpen

    2008-01-01

    The aim of the present study was to genotypically characterize Vibrio cholerae strains isolated from cholera patients in various provinces of Thailand. Two hundred and forty V. cholerae O1 strains, isolated from patients with cholera during two outbreaks, i.e. March 1999–April 2000 and December 2001–February 2002, in Thailand, were genotypically characterized by NotI digestion and pulsed-field gel electrophoresis (PFGE). In total, 17 PFGE banding patterns were found and grouped into four Dice-coefficient clusters (PF-I to PF-IV). The patterns of V. cholerae O1, El Tor reference strains from Australia, Peru, Romania, and the United States were different from the patterns of reference isolates from Asian countries, such as Bangladesh, India, and Thailand, indicating a close genetic relationship or clonal origin of the isolates in the same geographical region. The Asian reference strains, regardless of their biotypes and serogroups (classical O1, El Tor O1, O139, or O151), showed a genetic resemblance, but had different patterns from the strains collected during the two outbreaks in Thailand. Of 200 Ogawa strains collected during the first outbreak in Thailand, two patterns (clones)—PF-I and PF-II—predominated, while other isolates caused sporadic cases and were grouped together as pattern PF-III. PF-II also predominated during the second outbreak, but none of the 40 isolates (39 Inaba and 1 Ogawa) of the second outbreak had the pattern PF-I; a minority showed a new pattern—PF-IV, and others caused single cases, but were not groupable. In summary, this study documented the sustained appearance of the pathogenic V. cholerae O1 clone PF-II, the disappearance of clones PF-I and PF-III, and the emergence of new pathogenic clones during the two outbreaks of cholera. Data of the study on molecular characteristics of indigenous V. cholerae clinical isolates have public-health implications, not only for epidemic tracing of existing strains but also for the

  13. Isolation, identification and field tests of the sex pheromone of the carambola fruit borer, Eucosma notanthes.

    PubMed

    Hung, C C; Hwang, J S; Hung, M D; Yen, Y P; Hou, R F

    2001-09-01

    Two components, (Z)-8-dodecenyl acetate (Z8-12:Ac) and (Z)-8-dodecenol (Z8-12:OH), were isolated from sex pheromone glands of the carambola fruit borer, Eucosma notanthes, and were identified by GC, and GC-MS, chemical derivatization, and comparison of retention times. The ratio of the alcohol to acetate in the sex pheromone extracts was 2.7. However, synthetic mixtures (1 mg) in ratios ranging from 0.5 to 1.5 were more effective than other blends in trapping male moths in field tests.

  14. Breakdown characteristics of an isolated conducting object in a uniform electric field

    NASA Technical Reports Server (NTRS)

    Grothaus, M. G.; Trost, T. F.

    1986-01-01

    A laboratory experiment was conducted to determine the physical processes involved in the electrical breakdown of a particular spark gap arrangement. The gap consists of an isolated conducting ellipsoid located midway between two large flat electrodes. Gradual increase of the applied electric field, E, in the gap produces corona on the ellipsoid tips followed by flashover in a leader-arc sequence. The leader phase consists of the abrupt formation of ionized channels which partially bridge the gap and then decay prior to the arc. Measurements of dE/dt and of current were made, and photographs were taken with an image converter. Experimental parameters are listed.

  15. Induction of avirulence by AVR-Pita1 in virulent U.S. field isolates of Magnaporthe oryzae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The AVR-Pita1 gene, from the Chinese isolate O-137 of Magnaporthe oryzae, is an effector that determines the efficacy of the Pi-ta rice blast resistance gene. In the present study, the avirulence function of AVR-Pita1 was induced by transformation of field isolates (TM2, ZN19, B2 and B8) that origin...

  16. Induction of avirulence in U.S. virulent field isolates of Magnaporthe oryzae by AVR-Pita 1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The AVR-Pita1 gene, from the Chinese isolate O-137 of Magnaporthe oryzae, is an effector that determines the efficacy of the Pi-ta rice blast resistance gene. In the present study, the avirulence function of AVR-Pita1 was induced in field isolates (TM2, ZN19, B2 and B8) that originally were virule...

  17. Genetic diversity demonstrated by pulsed field gel electrophoresis of Salmonella enterica isolates obtained from diverse sources in Mexico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was conducted to determine the genetic diversity of Salmonella isolates recovered from a variety of sources using pulsed-field gel electrophoresis (PFGE) to assess their possible relatedness. Salmonella was isolated from ca. 52% of samples from a pepper var. Bell production system. A to...

  18. Isolation and purification of {sup 14}C-atrazine metabolites from field grown sugarcane and sorghum

    SciTech Connect

    Ash, S.G.; Larson, J.D.; Talaat, R.E.

    1996-10-01

    Sugarcane and sorghum plants were grown in separate field plots and treated with [2,4,6-{sup 14}C]-Atrazine (according to standard agricultural practices and at levels approximating the maximum usage rate) in partial fulfillment of EPA registration requirements. Sugarcane leaves were collected just before the final (fourth) test material application and at final harvest; canes were collected only at final harvest. Atrazine and a total of 20 metabolites of atrazine, accounting for 45.1% of the total radioactive residues, were isolated and characterized from prefourth application sugarcane leaves. Sorghum forage samples were collected 30 days after treatment (30 DAT), and at silage stage; mature fodder and grain were collected at final harvest. Two additional metabolites of atrazine were isolated and characterized from 30 DAT sorghum. Flowcharts describing the extraction and fractionation procedures used for isolation and purification of selected metabolites will be presented. The mass spectra as well as proposed metabolic pathways for these metabolites will be presented in an accompanying abstract.

  19. Comparison of Haemophilus parasuis reference strains and field isolates by using random amplified polymorphic DNA and protein profiles

    PubMed Central

    2012-01-01

    Background Haemophilus parasuis is the causative agent of Glässer’s disease and is a pathogen of swine in high-health status herds. Reports on serotyping of field strains from outbreaks describe that approximately 30% of them are nontypeable and therefore cannot be traced. Molecular typing methods have been used as alternatives to serotyping. This study was done to compare random amplified polymorphic DNA (RAPD) profiles and whole cell protein (WCP) lysate profiles as methods for distinguishing H. parasuis reference strains and field isolates. Results The DNA and WCP lysate profiles of 15 reference strains and 31 field isolates of H. parasuis were analyzed using the Dice and neighbor joining algorithms. The results revealed unique and reproducible DNA and protein profiles among the reference strains and field isolates studied. Simpson’s index of diversity showed significant discrimination between isolates when three 10mer primers were combined for the RAPD method and also when both the RAPD and WCP lysate typing methods were combined. Conclusions The RAPD profiles seen among the reference strains and field isolates did not appear to change over time which may reflect a lack of DNA mutations in the genes of the samples. The recent field isolates had different WCP lysate profiles than the reference strains, possibly because the number of passages of the type strains may affect their protein expression. PMID:22703293

  20. The magnetic field of an isolated neutron star from X-ray cyclotron absorption lines.

    PubMed

    Bignami, G F; Caraveo, P A; De Luca, A; Mereghetti, S

    2003-06-12

    Isolated neutron stars are highly magnetized, fast-rotating objects that form as an end point of stellar evolution. They are directly observable in X-ray emission, because of their high surface temperatures. Features in their X-ray spectra could in principle reveal the presence of atmospheres, or be used to estimate the strength of their magnetic fields through the cyclotron process, as is done for X-ray binaries. Almost all isolated neutron star spectra observed so far appear as featureless thermal continua. The only exception is 1E1207.4-5209 (refs 7-9), where two deep absorption features have been detected, but with insufficient definition to permit unambiguous interpretation. Here we report a long X-ray observation of the same object in which the star's spectrum shows three distinct features, regularly spaced at 0.7, 1.4 and 2.1 keV, plus a fourth feature of lower significance, at 2.8 keV. These features vary in phase with the star's rotation. The logical interpretation is that they are features from resonant cyclotron absorption, which allows us to calculate a magnetic field strength of 8 x 10(10) G, assuming the absorption arises from electrons.

  1. Epitope analysis of capsid and matrix proteins of North American ovine lentivirus field isolates.

    PubMed Central

    Marcom, K A; Pearson, L D; Chung, C S; Poulson, J M; DeMartini, J C

    1991-01-01

    Monoclonal antibodies (MAbs) directed against two phenotypically distinct ovine lentivirus (OvLV) strains were generated by fusion of BALB/c SP2/0-Ag 14 myeloma cells with spleen cells from mice immunized with purified OvLV. Hybridomas were selected by indirect enzyme-linked immunosorbent assay (ELISA) and analysis of reactivity on immunoblots. The majority (17 of 21) of the MAbs recognized the gag-encoded capsid protein, CA p27, of both strains. Four other MAbs recognized a smaller structural protein, presumably a matrix protein, MA p17. Three distinct epitopes on CA p27 and one on MA p17 were distinguished by the MAbs with competition ELISA. MAbs from each epitope group were able to recognize 17 North American field isolates of OvLV and the closely related caprine arthritis-encephalitis virus (CAEV). Analysis of the data indicated that these epitopes were highly conserved among naturally occurring isolates. A representative MAb from each epitope group of anti-CA p27 MAbs reacted with four field strains of OvLV and CAEV on immunoblots. An anti-MA p17 MAb recognized the same OvLV strains on immunoblots but failed to recognize CAEV. MAbs which recognize conserved epitopes of gag-encoded lentivirus proteins (CA p27 and MA p17) are valuable tools. These MAbs can be used to develop sensitive diagnostic assays and to study the pathogenesis of lentivirus infections in sheep and goats. Images PMID:1715884

  2. Genotypic diversity in Babesia bovis field isolates and vaccine strains from South Africa.

    PubMed

    Combrink, M P; Troskie, P C; Pienaar, R; Latif, A A; Mans, B J

    2014-01-31

    Genotypic diversity in Babesia bovis (cause of Asiatic redwater in cattle) vaccine strains and field isolates from South Africa were investigated using the Bv80 gene as well as microsatellites. The S11 vaccine strain possessed both A and B alleles of the Bv80 gene, as well as genotypic diversity within each allele type as defined by repeat variation resulting in different amplicon sizes. Rapid serial passage of vaccine strain from passage S10 to S24 resulted in loss of genotypic diversity that yielded a single allele A genotype with an amplicon size of 558 bp. This suggested that clonal selection occurred during rapid passaging. Extensive genotypic diversity exists in 44 field isolates characterized with both Bv80 A and B alleles, but can be readily distinguished from the S24 vaccine strain using either the Bv80 allele specific PCR assays or using multi-locus micro-satellite typing. This indicated that no recent documented clinical cases of Asiatic redwater were caused by the reversion to virulence of the current vaccine strain.

  3. Subthalamic local field potentials in Parkinson's disease and isolated dystonia: An evaluation of potential biomarkers.

    PubMed

    Wang, Doris D; de Hemptinne, Coralie; Miocinovic, Svjetlana; Qasim, Salman E; Miller, Andrew M; Ostrem, Jill L; Galifianakis, Nicholas B; San Luciano, Marta; Starr, Philip A

    2016-05-01

    Local field potentials (LFP) recorded from the subthalamic nucleus in patients with Parkinson's disease (PD) demonstrate prominent oscillations in the beta (13-30 Hz) frequency range, and reduction of beta band spectral power by levodopa and deep brain stimulation (DBS) is correlated with motor symptom improvement. Several features of beta activity have been theorized to be specific biomarkers of the parkinsonian state, though these have rarely been studied in non-parkinsonian conditions. To compare resting state LFP features in PD and isolated dystonia and evaluate disease-specific biomarkers, we recorded subthalamic LFPs from 28 akinetic-rigid PD and 12 isolated dystonia patients during awake DBS implantation. Spectral power and phase-amplitude coupling characteristics were analyzed. In 26/28 PD and 11/12 isolated dystonia patients, the LFP power spectrum had a peak in the beta frequency range, with similar amplitudes between groups. Resting state power did not differ between groups in the theta (5-8 Hz), alpha (8-12 Hz), beta (13-30 Hz), broadband gamma (50-200 Hz), or high frequency oscillation (HFO, 250-350 Hz) bands. Analysis of phase-amplitude coupling between low frequency phase and HFO amplitude revealed significant interactions in 19/28 PD and 6/12 dystonia recordings without significant differences in maximal coupling or preferred phase. Two features of subthalamic LFPs that have been proposed as specific parkinsonian biomarkers, beta power and coupling of beta phase to HFO amplitude, were also present in isolated dystonia, including focal dystonias. This casts doubt on the utility of these metrics as disease-specific diagnostic biomarkers.

  4. A Natural Electromagnetic Fields Effect on Healthy Volunteers During Long-Term Experiment with Isolation

    NASA Astrophysics Data System (ADS)

    Gurfinkel, Yury I.; Mikhailov, Valery M.; Ushakov, Boris B.

    2008-06-01

    There were investigated four healthy volunteers at the age of 37, 40, 41 and 48 during the baseline 240-d isolation period starting from July 3, 1999 in the frame of SFINCSS-99 - "SIMULATION OF FLIGHT OF INTERNATIONAL CREW ON SPACE STATION". Before a starting of experiment with long-term isolation were carried out measurements of magnetic properties of module and sleeping places. With the regularity of 3 times a week each subject made records of no less then 3 video episodes with the total length of one minute minimum at the same time between 1 and 2 p.m. Applying vital non-invasive computer capillaroscopy of nailbed has allowed quantitatively estimating a capillary blood velocity (CBV). The microcirculation parameters obtained during experiment were compared to local indexes of geomagnetic activity. About 1500 episodes were recorded on laser disks and analyzed. Parameters of microcirculation were compared with other physiological parameters monitored in the experiment. CBV investigation during the most intensive magnetic storm for the period of isolation (A-index- 44) show, that CBV at all volunteers was considerably slowed down. The greatest delay of blood flow velocity revealed at the subject which the factor of shielding of a constant magnetic field at the level of the sleeping berth has made 2,0. CBV at the subject has made 498 ± 46 μm/s with (- 65,8 % from base line). Least delay of a CBV is revealed at the subject which the factor of shielding of a constant magnetic field at the level of the sleeping berth has made 3, 15 (-12 % from base line).

  5. Necrotic enteritis potential in a model system using Clostridium perfringens isolated from field outbreaks.

    PubMed

    Chalmers, G; Bruce, H L; Toole, D L; Barnum, D A; Boerlin, P

    2007-12-01

    Necrotic enteritis is an enteric disease of avian species caused by the anaerobic bacterium Clostridium perfringens. The disease is regularly controlled in the broiler chicken industry with antimicrobials in feed but is reemerging in areas such as Europe where there is a ban on antimicrobials as growth promoters. To study prospective therapies, researchers must be able to reproduce this disease in a controlled environment, but this is not always possible because of differences in the pathogenicity of C. perfringens strains. Our objective was to test the potential of five isolates (SNECP43, 44, 47, 49, and 50), taken from field cases of necrotic enteritis, at recreating the disease in a controlled challenge experiment. SNECP43 and 50 were derived from a common clone, with SNECP50 passed in vivo and SNECP43 subcultured in vitro. Four hundred birds were divided into 16 pens, with three pens each receiving one of five treatments, with one control pen. Day-old birds were raised on a high wheat-based diet to promote necrotic enteritis development and were challenged with between 3.4 x 10(9) and 3.2 x 10(11) colony-forming units (cfu) of C. perfringens in feed for a period of 24 hr starting on day 13 of the challenge experiment. Lesion scores were assessed on two birds per pen sacrificed on day 17 and on any dead birds during the 25-day study. Growth performance was assessed up to 25 days, and mortality recorded throughout. Only SNECP50 produced necrotic enteritis mortalities significantly different (P < or = 0.05) from the control. The five isolates were also typed using pulsed-field gel electrophoresis to assess their genetic relatedness. All epidemiologically unrelated isolates were deemed genetically unrelated, whereas SNECP43 and 50 differed by only a single minor band. Toxin type was assessed using polymerase chain reaction (PCR), which was also used for the detection of the gene encoding the beta2-toxin.

  6. Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control.

  7. Plasmodium falciparum field isolates use complement receptor 1 (CR1) as a receptor for invasion of erythrocytes.

    PubMed

    Awandare, Gordon A; Spadafora, Carmenza; Moch, J Kathleen; Dutta, Sheetij; Haynes, J David; Stoute, José A

    2011-05-01

    A majority of Plasmodium falciparum strains invade erythrocytes through interactions with sialic acid (SA) on glycophorins. However, we recently reported that complement receptor 1 (CR1) is a SA-independent invasion receptor of many laboratory strains of P. falciparum. To determine the role of CR1 in erythrocyte invasion among P. falciparum field isolates, we tested eight isolates obtained from children in Kenya. All the parasites examined were capable of invading in a SA-independent manner, and invasion of neuraminidase-treated erythrocytes was nearly completely blocked by anti-CR1 and soluble CR1 (sCR1). In addition, anti-CR1 and sCR1 partially inhibited invasion of intact erythrocytes in a majority of isolates tested. Sequencing of the hypervariable region of P. falciparum AMA-1 showed considerable diversity among all the isolates. These data demonstrate that CR1 mediates SA-independent erythrocyte invasion in P. falciparum field isolates.

  8. Quantum interference control of an isolated resonance lifetime in the weak-field limit.

    PubMed

    García-Vela, A

    2015-11-21

    Resonance states play an important role in a large variety of physical and chemical processes. Thus, controlling the resonance behavior, and particularly a key property like the resonance lifetime, opens up the possibility of controlling those resonance mediated processes. While such a resonance control is possible by applying strong-field approaches, the development of flexible weak-field control schemes that do not alter significantly the system dynamics still remains a challenge. In this work, one such control scheme within the weak-field regime is proposed for the first time in order to modify the lifetime of an isolated resonance state. The basis of the scheme suggested is quantum interference between two pathways induced by laser fields, that pump wave packet amplitude to the target resonance under control. The simulations reported here show that the scheme allows for both enhancement and quenching of the resonance survival lifetime, being particularly flexible to achieve large lifetime enhancements. Control effects on the resonance lifetime take place only while the pulse is operating. In addition, the conditions required to generate the two interfering quantum pathways are found to be rather easy to meet for general systems, which makes the experimental implementation straightforward and implies the wide applicability of the control scheme.

  9. Molecular typing of Japanese field isolates and live commercial vaccine strain of Mycoplasma synoviae using improved pulsed-field gel electrophoresis and vlhA gene sequencing.

    PubMed

    Harada, Kazuki; Kijima-Tanaka, Mayumi; Uchiyama, Mariko; Yamamoto, Tomoko; Oishi, Koji; Arao, Megumi; Takahashi, Toshio

    2009-12-01

    In the present study, pulsed-field gel electrophoresis (PFGE) and vlhA gene sequence analysis were applied and verified for typing the Mycoplasma synoviae live vaccine MS-H strain and field isolates from diseased chickens in Japan. The previously published PFGE protocol using SmaI digestion could not allow the discrimination of two of the 11 M. synoviae field isolates from the vaccine strain and had relatively low discrimination power (D = 0.885). On the other hand, our new PFGE protocols using BlnI and BamHI digestions as well as the vlhA sequence analysis allowed the discrimination of all 11 M. synoviae field isolates from the vaccine strain. In addition, these PFGE protocols using BlnI and BamHI digestions generated unique fragment patterns in epidemiologically unrelated isolates, including those with identical SmaI-digested patterns or vlhA gene sequences (D = 0.987 and 1.000, respectively), and generated indistinguishable or closely related patterns in epidemiologically related isolates. Therefore, we believe that they would be useful tools to determine whether M. synoviae clinical isolates from diseased chickens are derived from the vaccine strain or wild-type strain and to further elucidate the epidemiology of M. synoviae infection.

  10. Phytophthora infestans field isolates from Gansu province, China are genetically highly diverse and show a high frequency of self fertility.

    PubMed

    Han, Miao; Liu, Gang; Li, Ji-Ping; Govers, Francine; Zhu, Xiao-Qiong; Shen, Chong-Yao; Guo, Li-Yun

    2013-01-01

    The genetic diversity of 85 isolates of Phytophthora infestans collected in 2007 from Gansu province in China was determined and compared with 21 isolates collected before 2004. Among them, 70 belonged to the A1 mating type and 15 were self-fertile (SF). The mitochondrial DNA haplotypes revealed both Ia (25%) and IIa (75%) haplotypes. Metalaxyl resistance occurred with high frequency (54%) in Gansu. Simple sequence repeat (SSR) genotyping revealed 26 genotypes (13 from the Tianshui region) among the 85 isolates, and 18 genotypes among the 21 isolates collected before 2004, without overlap in genotypes detected in the two groups. Cluster analysis showed clear subdivisions within the different mating type isolates. Among Gansu's isolates, Nei's and Shannon's diversity indices were highest in isolates collected in Tianshui where both A1 and SF isolates were found. Analysis of molecular variance of isolates from Gansu indicated that 51% and 49% of the variance was explained by within-area and among-area variance, respectively. The results suggest that the occurrence of SF isolates increases the risk of sexual reproduction, the formation of oospore as initial inocula in the field, and affects the genotypic diversity in the population.

  11. Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil.

    PubMed

    Sakai, Sanae; Conrad, Ralf; Liesack, Werner; Imachi, Hiroyuki

    2010-12-01

    A novel hydrogenotrophic methanogen, designated strain MRE50(T), was isolated from a methanogenic consortium, which was originally established from an Italian rice field soil. Cells were non-motile rods, 1.3-2.8 μm long and 0.4-0.7 μm wide. Coccoid cells were also observed in cultures at the late-exponential phase of growth. Strain MRE50(T) grew at 37-55 °C (optimally at 45 °C), at pH 6-7.8 (optimally at pH 7.0) and in the presence of 0-20 g NaCl l(-1). The isolate utilized H(2)/CO(2) and formate for growth and methane production. Phylogenetic analyses of the 16S rRNA gene and the methanogen-specific marker gene mcrA showed that strain MRE50(T) is affiliated with the order Methanocellales, previously known as uncultured archaeal group Rice Cluster I. Based on both 16S rRNA gene and mcrA gene sequences, strain MRE50(T) was related most closely to Methanocella paludicola SANAE(T). Levels of sequence similarity were 92.5 and 86.1 %, respectively, indicating that strains MRE50(T) and Methanocella paludicola SANAE(T) represent different species within the genus Methanocella. In addition, although these strains shared phenotypic properties including cell morphology and substrate utilization, they differed with respect to susceptibility to antibiotics, and temperature and NaCl ranges for growth. Given the phenotypic differences and the distinct phylogenetic placement of the new isolate relative to the type species of the genus Methanocella, strain MRE50(T) is considered to represent a novel species of the genus Methanocella, for which the name Methanocella arvoryzae sp. nov. is proposed. The type strain is MRE50(T) (=NBRC 105507(T) =DSM 22066(T)).

  12. Isolated high-harmonic XUV photon absorption and NIR strong-field tunnel ionization

    NASA Astrophysics Data System (ADS)

    Bryan, W. A.; Frassetto, F.; Froud, C. A.; Turcu, I. C. E.; King, R. B.; Calvert, C. R.; Nemeth, G. R. A. J.; Villoresi, P.; Poletto, L.; Springate, E.

    2012-01-01

    Extreme ultraviolet (XUV) pulses with a duration of tens of femtoseconds initiate 4s-1 or 4p-1 photoionization of krypton, which populates highly excited satellite states through the electron correlation. The excited ions are then tunnel ionized to Kr2+4s-14p-1 or 4p-2 by a strong-field near-infrared (NIR) pulse of a similar duration. The XUV pulses are produced by high harmonic generation in a gas jet and we employ a state-of-the-art time-preserving monochromator to isolate individual XUV harmonic orders. An enhancement of the Kr2+ yield as a function of harmonic photon energy and XUV-pump NIR-probe delay is observed and compared with a two-step model, which allows the population of the satellite states to be inferred. Furthermore, relative 4s and 4p satellite excitation cross-sections are predicted at the photon energies studied. This proof-of-principle experiment demonstrates that isolated harmonics can be employed to pump specific electronic states, which will be highly complementary to synchrotron, attosecond and x-ray free-electron laser studies of complex systems.

  13. Attosecond Lighthouses: How To Use Spatiotemporally Coupled Light Fields To Generate Isolated Attosecond Pulses

    NASA Astrophysics Data System (ADS)

    Vincenti, H.; Quéré, F.

    2012-03-01

    Under the effect of even simple optical components, the spatial properties of femtosecond laser beams can vary over the duration of the light pulse. We show how using such spatiotemporally coupled light fields in high harmonic generation experiments (e.g., in gases or dense plasmas) enables the production of attosecond lighthouses, i.e., sources emitting a collection of angularly well-separated light beams, each consisting of an isolated attosecond pulse. This general effect opens the way to a new generation of light sources, particularly suitable for attosecond pump-probe experiments, and provides a new tool for ultrafast metrology, for instance, giving direct access to fluctuations of the carrier-envelope relative phase of even the most intense ultrashort lasers.

  14. Isolation and Characterization of a Novel Facultative Anaerobic Filamentous Fungus from Japanese Rice Field Soil

    PubMed Central

    Tonouchi, Akio

    2009-01-01

    A novel filamentous fungus strain designated RB-1 was isolated into pure culture from Japanese rice field soil through an anaerobic role tube technique. The strain is a mitosporic fungus that grows in both aerobic and strict anaerobic conditions using various mono-, di-, tri-, and polysaccharides with acetate and ethanol productions. The amount of acetate produced was higher than that of ethanol in both aerobic and anaerobic cultures. The characteristic verrucose or punctuate conidia of RB-1 closely resembled those of some strains of the genus Thermomyces, a thermophilic or mesophilic anamorphic ascomycete. However, based on phylogenetic analysis with the small subunit (SSU) and large subunit (LSU) rDNA sequences, RB-1 was characterized as a member of the class Lecanoromycetes of the phylum Ascomycota. Currently, RB-1 is designated as an anamorphic ascomycete and is phylogenetically considered an incertae sedis within the class Lecanoromycetes. PMID:20148171

  15. Isolated horizons, p-form matter fields, topology, and the black-hole/string correspondence principle

    SciTech Connect

    Liko, Tomas

    2009-04-15

    We study the mechanics of D-dimensional isolated horizons (IHs) for Einstein gravity in the presence of arbitrary p-form matter fields. This generalizes the analysis of Copsey and Horowitz to nonstationary spacetimes and therefore the local first law in D>4 dimensions to include nonmonopolar (dipole) charges. The only requirement for the local first law to hold is that the action has to be differentiable. The resulting conserved charges are all intrinsic to the horizon and are independent of the topology of the horizon cross sections. We explicitly calculate the local charges for five-dimensional black holes and black rings that are relevant within the context of superstring theory. We conclude with some comments on the black-hole/string correspondence principle and argue that IHs (or some other quasilocal variant) should play a fundamental role in superstring theory.

  16. Isolation and identification of pathogenic microorganisms at wastewater-irrigated fields: ratios in air and wastewater

    SciTech Connect

    Teltsch, B.; Kedmi, S.; Bonnet, L.; Borenzstajn-Rotem, Y.; Katzenelson, E.

    1980-06-01

    Samples of air and corresponding wastewater samples were taken at wastewater spray-irrigated fields. The concentrations of salmonellae and enteroviruses present in these samples were determined and compared with those of coliforms, and the ratios between them were calculated. The most common Salmonella serotype in the air was Salmonella ohio, whereas in the wastewater, Salmonella anatum was the most common. Enteroviruses isolated and identified were poliovirus, echovirus, and coxsackievirus type B. From the ratios of salmonellas to coliforms and enteroviruses to coliforms in the air, as compared to these ratios in the wastewater, it was concluded that the suitability of coliforms as an indication of airborne contamination caused by spray irrigation is questionable.

  17. Pulsed-field gel electrophoresis patterns of Escherichia coli O157 isolates from Kansas feedlots.

    PubMed

    Sargeant, J M; Shi, X; Sanderson, M W; Renter, D G; Nagaraja, T G

    2006-01-01

    This study investigated the prevalence and distribution of Escherichia coli O157 genetic types within and among feedlots using pulsed-field gel electrophoresis to separate XbaI-digested DNA. The study population consisted of 300 pens of cattle in 30 feedlots in Kansas that were sampled (feces, water, and water sediment) within a month of being shipped for slaughter. The prevalence of E. coli O157 was 8.5% in feces, 3.1% in water, and 4.5% in water sediment samples. A total of 424 E. coli O157 isolates were characterized by pulsed-field gel electrophoresis, and 139 subtypes (100% Dice similarity with no band differences) were identified. The majority of subtypes (70/139) was identified only once, but nine were identified 10 or more times. Identical subtypes were recovered from both feces and water tanks in 10 feedlots. The majority of subtypes were identified in only one feedlot, and the number of subtypes ranged from one to 23 within a feedlot and from one to seven within a pen. There were 10 feedlots with at least 15 positive samples. In these 10 feedlots, the most common subtype accounted for 16.9-78.6% of the isolates. Common subtypes differed among feedlots. In eight of the 10 feedlots, the most common subtype was identified in multiple pens. The results support a complex ecology for E. coli O157 in feedlot operations, with factors associated with exposure and transmission likely acting at a common level for multiple feedlots, within feedlots, and within pens of cattle.

  18. Integrative conjugative elements are widespread in field isolates of Mycoplasma species pathogenic for ruminants.

    PubMed

    Tardy, Florence; Mick, Virginie; Dordet-Frisoni, Emilie; Marenda, Marc Serge; Sirand-Pugnet, Pascal; Blanchard, Alain; Citti, Christine

    2015-03-01

    Comparative genomics have revealed massive horizontal gene transfer (HGT) between Mycoplasma species sharing common ruminant hosts. Further results pointed toward an integrative conjugative element (ICE) as an important contributor of HGT in the small-ruminant-pathogen Mycoplasma agalactiae. To estimate the prevalence of ICEs in ruminant mycoplasmas, we surveyed their occurrence in a collection of 166 field strains representing 4 (sub)species that are recognized as major pathogens. Based on available sequenced genomes, we first defined the conserved, minimal ICE backbone as composed of 4 coding sequences (CDSs) that are evenly distributed and predicted to be essential for ICE chromosomal integration-excision and horizontal transfer. Screening of the strain collection revealed that these 4 CDSs are well represented in ruminant Mycoplasma species, suggesting widespread occurrence of ICEs. Yet their prevalence varies within and among species, with no correlation found with the individual strain history. Extrachromosomal ICE forms were also often detected, suggesting that ICEs are able to circularize in all species, a first and essential step in ICE horizontal transfer. Examination of the junction of the circular forms and comparative sequence analysis of conserved CDSs clearly pointed toward two types of ICE, the hominis and spiroplasma types, most likely differing in their mechanism of excision-integration. Overall, our data indicate the occurrence and maintenance of functional ICEs in a large number of field isolates of ruminant mycoplasmas. These may contribute to genome plasticity and gene exchanges and, presumably, to the emergence of diverse genotypes within pathogenic mycoplasmas of veterinary importance.

  19. Characterization of Chinese Porcine Epidemic Diarrhea Virus with Novel Insertions and Deletions in Genome

    PubMed Central

    Fan, Baochao; Jiao, Dian; Zhao, Xiaona; Pang, Fengjiao; Xiao, Qi; Yu, Zhengyu; Mao, Aihua; Guo, Rongli; Yuan, Wanzhe; Zhao, Pandeng; He, Kongwang; Li, Bin

    2017-01-01

    Outbreaks of porcine epidemic diarrhoea virus (PEDV) have caused great economic losses to the global pig industry. PEDV strains with variants in the spike (S) gene have been reported in several countries. To better understand the molecular epidemiology and genetic diversity of PEDV field isolates, in this study, we characterised the complete genome sequence of a novel PEDV variant JSCZ1601 from a outbreak in China in 2016. The PEDV isolate was 28,033 nucleotides (nt) in length without the polyadenylated sequences. Phylogenetic analysis based on the full-length genome sequence of JSCZ1601 grouped it with the pandemic variants determined post-2010 into group 2 (G2). However, the S gene of JSCZ1601 formed a new subgroup separated from the subgroups containing the other G2 strains. Comparative analysis of the amino acids encoded by the S genes revealed the N-terminal of the deduced JSCZ1601 S protein had a novel two-amino-acid deletion (N58 and S59) compared with all identified genogroups. Further, compared with the reference strains, a ‘G’ insertion was detected in the 5′ terminal of the 5′UTR of the JSCZ1601. The animal experiment revealed that this strain was high pathogenic to neonatal pigs. Taken together, a PEDV strain with the new molecular characterizations and phylogenies was found in mainland China. It is necessary to strengthen the monitoring of PEDV variations. PMID:28276526

  20. Bacillus depressus sp. nov., isolated from soil of a sunflower field.

    PubMed

    Wei, Xuexin; Xin, Di; Xin, Yuhua; Zhang, Hao; Wang, Tianying; Zhang, Jianli

    2016-01-01

    A Gram-stain positive, rod-shaped, endospore-forming and aerobic bacterium, designated BZ1(T), was isolated from a soil sample collected from a sunflower field in Wuyuan county, Inner Mongolia, China. On the basis of 16S rRNA gene sequence analysis, the isolate was found to be a member of the genus Bacillus and the close phylogenetic relatives to be Bacillus gottheilii WCC 4585(T), Bacillus oceanisediminis H2(T), Bacillus mesonae FJAT-13985(T) and Bacillus horneckiae DSM 23495(T) with 98.3, 98.1, 98.0 and 97.6 % sequence similarity, respectively. Strain BZ1(T) was found to grow at 6-40 °C (optimum 30-33 °C), pH 6.0-9.0 (optimum pH 7.0) and 0-5.5 % (w/v) NaCl (optimum 0.5 %). The cell wall diamino acid of the peptidoglycan of strain BZ1(T) was identified as meso-diaminopimelic acid and the predominant respiratory quinone as MK-7. The major cellular fatty acids were found to be iso-C15:0, anteiso-C15:0 and iso-C14:0, and the polar lipids to consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The novel strain was found to have a DNA G + C content 44.5 mol%. DNA-DNA hybridization with closely related strains was low. Based on phenotypic, phylogenetic and chemotaxonomic results, it is concluded that strain BZ1(T) represents a novel species within the genus Bacillus, for which we propose the name Bacillus depressus sp. nov. The type strain is BZ1(T) (= CGMCC 1.15124(T) = KCTC 33643(T)).

  1. Sub-inhibitory concentrations of penicillin G induce biofilm formation by field isolates of Actinobacillus pleuropneumoniae.

    PubMed

    Hathroubi, S; Fontaine-Gosselin, S-È; Tremblay, Y D N; Labrie, J; Jacques, M

    2015-09-30

    Actinobacillus pleuropneumoniae is a Gram-negative bacterium and causative agent of porcine pleuropneumonia. This is a highly contagious disease that causes important economic losses to the swine industry worldwide. Penicillins are extensively used in swine production and these antibiotics are associated with high systemic clearance and low oral bioavailability. This may expose A. pleuropneumoniae to sub-inhibitory concentrations of penicillin G when the antibiotic is administered orally. Our goal was to evaluate the effect of sub-minimum inhibitory concentration (MIC) of penicillin G on the biofilm formation of A. pleuropneumoniae. Biofilm production of 13 field isolates from serotypes 1, 5a, 7 and 15 was tested in the presence of sub-MIC of penicillin G using a polystyrene microtiter plate assay. Using microscopy techniques and enzymatic digestion, biofilm architecture and composition were also characterized after exposure to sub-MIC of penicillin G. Sub-MIC of penicillin G significantly induced biofilm formation of nine isolates. The penicillin G-induced biofilms contained more poly-N-acetyl-D-glucosamine (PGA), extracellular DNA and proteins when compared to control biofilms grown without penicillin G. Additionally, penicillin G-induced biofilms were sensitive to DNase which was not observed with the untreated controls. Furthermore, sub-MIC of penicillin G up-regulated the expression of pgaA, which encodes a protein involved in PGA synthesis, and the genes encoding the envelope-stress sensing two-component regulatory system CpxRA. In conclusion, sub-MICs of penicillin G significantly induce biofilm formation and this is likely the result of a cell envelope stress sensed by the CpxRA system resulting in an increased production of PGA and other matrix components.

  2. Pontibacter amylolyticus sp. nov., isolated from a deep-sea sediment hydrothermal vent field.

    PubMed

    Wu, Yue-Hong; Zhou, Peng; Jian, Shu-Ling; Liu, Zhen-Sheng; Wang, Chun-Sheng; Oren, Aharon; Xu, Xue-Wei

    2016-04-01

    A Gram-stain-negative, short rod-shaped bacterium, designated 9-2T, was isolated from a sediment sample collected from a hydrothermal vent field on the south-west Indian Ridge. It formed red colonies, produced carotenoid-like pigments and did not produce bacteriochlorophyll a. Strain 9-2T was positive for hydrolysis of DNA, gelatin and starch, but negative for hydrolysis of aesculin and Tween 60. The sole respiratory quinone was menaquinone-7 (MK-7). The main polar lipids consisted of phosphatidylethanolamine, one unidentified phospholipid and two unidentified polar lipids. The principal fatty acids (>5%) were summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B), iso-C15:0 and iso-C17:0 3-OH. The genomic DNA G+C content was 49.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 9-2T should be assigned to the genus Pontibacter. Levels of 16S rRNA gene sequence similarity between the new isolate and the type strains of Pontibacter species with validly published names were in the range 94.0-96.5%. On the basis of phenotypic and genotypic data, strain 9-2T represents a novel species of the genus Pontibacter, for which the name Pontibacter amylolyticus sp. nov. is proposed. The type strain is 9-2T (=CGMCC 1.12749T=JCM 19653T=MCCC 1K00278T).

  3. Erysipelothrix rhusiopathiae: genetic characterization of midwest US isolates and live commercial vaccines using pulsed-field gel electrophoresis.

    PubMed

    Opriessnig, T; Hoffman, L J; Harris, D L; Gaul, S B; Halbur, P G

    2004-03-01

    This is the first report of molecular characterization of US erysipelas field isolates and vaccine strains of Erysipelothrix rhusiopathiae by pulsed-field gel electrophoresis (PFGE). Erysipelas in pigs is mainly caused by E. rhusiopathiae serotypes 1a, 1b, and 2. In 2001, erysipelas reemerged as a clinical problem in pigs in the midwestern United States. In this work 90 erysipelas isolates (58 recent and 28 archived field isolates as well as 4 live-vaccine strains) were genetically characterized. Because of the limited availability of antiserum, 74/90 isolates (44/58 recent isolates) were serotyped. The serotype of the majority (79.6%) of the 44 recent isolates tested was determined to be 1a, 13.6% were serotype 1b, and 6.8% of recent isolates were serologically untypeable. Among all 90 isolates, 23 different PFGE patterns were identified. There were 43 isolates identified as serotype 1a with 4 genetic patterns: 38/43, 1A(I); 3/43, 1A(III); 1/43, 1B(V); and 1/43, 3B. Sixteen serotype 1b isolates had 11 unique genetic patterns: 4/16 were genotype 1B(III), 2/16 were genotype 3A(I), and 1/16 was in genotype groups 1A(V), 1A(VI), 1A(VII), 1B(I), 1B(IV), 1B(VII), 2, 4, and 5. Six genetic patterns were distinguished among the 10 serotype 2 isolates: 1A(IV) (1/10), 1A(V) (1/10), 1B(VI) (1/10), 2 (4/10), 7 (1/10), and 8 (2/8). Erysipelas vaccine strains (modified live) were similar to each other but different from current field strains, sharing 78.6% identity with the most prevalent genotype 1A(I) based on the PFGE-SmaI pattern. Compared with serotyping, PFGE genotyping is a more distinguishing technique, easy to perform and not dependent on the limited availability of antiserum.

  4. Influence of day-length and isolates of Phytophthora infestans on field resistance to late blight of potato.

    PubMed

    Mihovilovich, E; Munive, S; Bonierbale, M

    2010-04-01

    Main and interaction effects of day-length and pathogen isolate on the reaction and expression of field resistance to Phytophthora infestans were analyzed in a sample of standard clones for partial resistance to potato late blight, and in the BCT mapping population derived from a backcross of Solanum berthaultii to Solanum tuberosum. Detached leaves from plants grown in field plots exposed to short- and long day-length conditions were independently inoculated with two P. infestans isolates and incubated in chambers under short- and long photoperiods, respectively. Lesion growth rate (LGR) was used for resistance assessment. Analysis of variance revealed a significant contribution of genotype x isolate x day-length interaction to variation in LGR indicating that field resistance of genotypes to foliar late blight under a given day-length depended on the infecting isolate. An allele segregating from S. berthaultii with opposite effects on foliar resistance to late blight under long- and short day-lengths, respectively, was identified at a quantitative trait locus (QTL) that mapped on chromosome 1. This allele was associated with positive (decreased resistance) and negative (increased resistance) additive effects on LGR, under short- and long day-length conditions, respectively. Disease progress on whole plants inoculated with the same isolate under field conditions validated the direction of its effect in short day-length regimes. The present study suggests the occurrence of an isolate-specific QTL that displays interaction with isolate behavior under contrasting environments, such as those with different day-lengths. This study highlights the importance of exposing genotypes to a highly variable population of the pathogen under contrasting environments when stability to late blight resistance is to be assessed or marker-assisted selection is attempted for the manipulation of quantitative resistance to late blight.

  5. Plasmodium falciparum Field Isolates Commonly Use Erythrocyte Invasion Pathways That Are Independent of Sialic Acid Residues of Glycophorin A

    PubMed Central

    Okoyeh, Jude Nnaemeka; Pillai, C. R.; Chitnis, Chetan E.

    1999-01-01

    Erythrocyte invasion by malaria parasites is mediated by specific molecular interactions. Sialic acid residues of glycophorin A are used as invasion receptors by Plasmodium falciparum. In vitro invasion studies have demonstrated that some cloned P. falciparum lines can use alternate receptors independent of sialic acid residues of glycophorin A. It is not known if invasion by alternate pathways occurs commonly in the field. In this study, we used in vitro growth assays and erythrocyte invasion assays to determine the invasion phenotypes of 15 P. falciparum field isolates. Of the 15 field isolates tested, 5 multiply in both neuraminidase and trypsin-treated erythrocytes, 3 multiply in neuraminidase-treated but not trypsin-treated erythrocytes, and 4 multiply in trypsin-treated but not neuraminidase-treated erythrocytes; 12 of the 15 field isolates tested use alternate invasion pathways that are not dependent on sialic acid residues of glycophorin A. Alternate invasion pathways are thus commonly used by P. falciparum field isolates. Typing based on two polymorphic markers, MSP-1 and MSP-2, and two microsatellite markers suggests that only 1 of the 15 field isolates tested contains multiple parasite genotypes. Individual P. falciparum lines can thus use multiple invasion pathways in the field. These observations have important implications for malaria vaccine development efforts based on EBA-175, the P. falciparum protein that binds sialic acid residues of glycophorin A during invasion. It may be necessary to target parasite ligands responsible for the alternate invasion pathways in addition to EBA-175 to effectively block erythrocyte invasion by P. falciparum. PMID:10531229

  6. Laboratory and field evaluations for efficacy of a fast-killing baculovirus isolate from Spodoptera frugiperda

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three biopesticide parameters were evaluated for a fast-killing isolate (3AP2) Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) and a wild-type isolate (Sf3) of the same baculovirus. Both isolates were evaluated for virus production using in vivo methods, for speed of kill based on bioas...

  7. Phylogenetic analysis of field isolates of feline calcivirus (FCV) in Japan by sequencing part of its capsid gene.

    PubMed

    Sato, Y; Ohe, K; Murakami, M; Fukuyama, M; Furuhata, K; Kishikawa, S; Suzuki, Y; Kiuchi, A; Hara, M; Ishikawa, Y; Taneno, A

    2002-04-01

    The molecular epidemiology of the infectious disease caused by feline calcivirus (FCV) in Japan was investigated by analysing the phylogenetic relationship among 21 Japanese field isolates, including the F4 strain, and 30 global isolates. Parts of the capsid gene (B-F) of the isolates were amplified by RT-PCR, and the amino acid sequences were compared with those from the global isolates. Thirty-seven and 14 out of a total of 51 isolates were clustered into two distinct genogroups, I and II respectively, by UPGMA and NJ analysis. Seven of the 21 Japanese isolates (33%) fell into group I together with 30 global isolates, while the other 14 Japanese isolates (67%) belonged to group II. The bootstrap repetition analysis of groups I and II formed by the NJ method gave a value of 99.00%. The 14 latter Japanese isolates were clearly separated from the isolates in group I, and they were different from any previously known FCV, forming a new genogroup, which implies that this lineage has been confined to Japan. Comparing the amino acid sequences shared by groups I and II, the amino acid at position 377 in B region was asparagine (Asn or Asp (NH2)) in group I, while it was lysine (Lys) in all the strains in group II. Similarly, the amino acid at position 539 in the F region was alanine (Ala) or proline (Pro) in group I, while it was valine (Val) in group II; glycine (Gly) at position 557 in group I was serine (Ser) in Group II; and phenylalanine (Phe) or leucine (Leu) at position 566 in genogroup I was tyrosine (Tyr) in group II.

  8. DNA Hybridization Probe for Use in Determining Restricted Nodulation among Bradyrhizobium japonicum Serocluster 123 Field Isolates

    PubMed Central

    Sadowsky, Michael J.; Cregan, Perry B.; Keyser, Harold H.

    1990-01-01

    Several soybean plant introduction (PI) genotypes have recently been described which restrict nodulation of Bradyrhizobium japonicum serocluster 123 in an apparently serogroup-specific manner. While PI 371607 restricts nodulation of strains in serogroup 123 and some in serogroup 127, those in serogroup 129 are not restricted. When DNA regions within and around the B. japonicum I-110 common nodulation genes were used as probes to genomic DNA from the serogroup strains USDA 123, USDA 127, and USDA 129, several of the probes differentially hybridized to the nodulation-restricted and -unrestricted strains. One of the gene regions, cloned in plasmid pMJS12, was subsequently shown to hybridize to 4.6-kilobase EcoRI fragments from DNAs from nodulation-restricted strains and to larger fragments in nodulation-unrestricted strains. To determine if the different hybridization patterns could be used to predict nodulation restriction, we hybridized pMJS12 to EcoRI-digested genomic DNAs from uncharacterized serocluster 123 field isolates. Of the 36 strains examined, 15 were found to have single, major, 4.6-kilobase hybridizing EcoRI fragments. When tested for nodulation, 80% (12 of 15) of the strains were correctly predicted to be restricted for nodulation of the PI genotypes. In addition, hybridization patterns obtained with pMJS12 and nodulation phenotypes on PI 371607 indicated that there are at least three types of serogroup 127 strains. Our results suggest that the pMJS12 gene probe may be useful in selecting compatible host-strain combinations and in determining the suitability of field sites for the placement of soybean genotypes containing restrictive nodulation alleles. Images PMID:16348217

  9. Spontaneous rhythmic field potentials of isolated mouse hippocampal-subicular-entorhinal cortices in vitro.

    PubMed

    Wu, C P; Huang, H L; Asl, M Nassiri; He, J W; Gillis, J; Skinner, F K; Zhang, L

    2006-10-15

    The rodent hippocampal circuit is capable of exhibiting in vitro spontaneous rhythmic field potentials (SRFPs) of 1-4 Hz that originate from the CA3 area and spread to the CA1 area. These SRFPs are largely correlated with GABA-A IPSPs in pyramidal neurons and repetitive discharges in inhibitory interneurons. As such, their generation is thought to result from cooperative network activities involving both pyramidal neurons and GABAergic interneurons. Considering that the hippocampus, subiculum and entorhinal cortex function as an integrated system crucial for memory and cognition, it is of interest to know whether similar SRFPs occur in hippocampal output structures (that is, the subiculum and entorhinal cortex), and if so, to understand the cellular basis of these subicular and entorhinal SRFPs as well as their temporal relation to hippocampal SRFPs. We explored these issues in the present study using thick hippocampal-subicular-entorhinal cortical slices prepared from adult mice. SRFPs were found to spread from the CA1 area to the subicular and entorhinal cortical areas. Subicular and entorhinal cortical SRFPs were correlated with mixed IPSPs/EPSPs in local pyramidal neurons, and their generation was dependent upon the activities of GABA-A and AMPA glutamate receptors. In addition, the isolated subicular circuit could elicit SRFPs independent of CA3 inputs. We hypothesize that the SRFPs represent a basal oscillatory activity of the hippocampal-subicular-entorhinal cortices and that the subiculum functions as both a relay and an amplifier, spreading the SRFPs from the hippocampus to the entorhinal cortex.

  10. Laboratory and field evaluation of selective media for isolation of group B streptococci.

    PubMed Central

    Gray, B M; Pass, M A; Dillon, H C

    1979-01-01

    Problems encountered with currently recommended selective media for group B streptococci (GBS) (selective broth medium and CNA agar) prompted a searach for alternative culture methods in ongoing epidemiological studies. Previously recommended inhibitory agents were tested in vitro. Gentamicin, alone or in combination with nalidixic acid, proved inhibitory for many GBS strains. Among other agents tested, polymyxin was most complementary to the gram-negative spectrum of nalidixic acid, without compromising GBS growth. Crystal violet provided the simplest, most economical staphylococcal inhibitor. Broth and agar media, constituted with these three agents and designated NPC, were evaluated in vitro and in field studies. This investigation represents the first direct comparison of broth media containing inhibitory agents for the preferential isolation of GBS. In maternal colonization studies, NPC broth proved superior to Todd-Hewitt broth containing nalidixic acid and gentamicin at concentrations employed in the previously described selective broth medium (95% versus 59% recovery). Our comparisons were done without added sheep blood since GBS grow well in Todd-Hewitt broth. NPC broth proved more sensitive than NPC agar for detecting GBS colonization in newborns. The NPC agar medium was useful for further purification of broth cultures and quantitative culture techniques. PMID:379037

  11. Biodegradation of buprofezin by Rhodococcus sp. strain YL-1 isolated from rice field soil.

    PubMed

    Li, Chao; Zhang, Ji; Wu, Zhi-Guo; Cao, Li; Yan, Xin; Li, Shun-Peng

    2012-03-14

    A buprofezin-degrading bacterium, YL-1, was isolated from rice field soil. YL-1 was identified as Rhodococcus sp. on the basis of the comparative analysis of 16S rDNA sequences. The strain could use buprofezin as the sole source of carbon and nitrogen for growth and was able to degrade 92.4% of 50 mg L(-1) buprofezin within 48 h in liquid culture. During the degradation of buprofezin, four possible metabolites, 2-tert-butylimino-3-isopropyl-1,3,5-thiadiazinan-4-one, N-tert-butyl-thioformimidic acid formylaminomethyl ester, 2-isothiocyanato-2-methyl-propane, and 2-isothiocyanato-propane, were identified using gas chromatography-mass spectrometry (GC-MS) analysis. The catechol 2,3-dioxygenase activity was strongly induced during the degradation of buprofezin. A novel microbial biodegradation pathway for buprofezin was proposed on the basis of these metabolites. The inoculation of soils treated with buprofezin with strain YL-1 resulted in a higher degradation rate than that observed in noninoculated soils, indicating that strain YL-1 has the potential to be used in the bioremediation of buprofezin-contaminated environments.

  12. Brevibacillus ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field.

    PubMed

    Baek, Sang-Hoon; Im, Wan-Taek; Oh, Hyun Woo; Lee, Jung-Sook; Oh, Hee-Mock; Lee, Sung-Taik

    2006-11-01

    A Gram-positive, rod-shaped, spore-forming bacterium, Gsoil 3088T, was isolated from soil from a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 3088T was shown to belong to the family Paenibacillaceae, being related to Brevibacillus centrosporus (96.6%), Brevibacillus borstelensis (96.3%), Brevibacillus parabrevis (96.1%), Brevibacillus formosus (96.1%), Brevibacillus brevis (96.1%) and Brevibacillus laterosporus (96.0%). The phylogenetic distances from other validly described species within the genus Brevibacillus were greater than 4.0% (i.e. there was less than 96.0% similarity). The G+C content of the genomic DNA was 52.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; fatty acid profile, iso-C15:0, iso-C14:0 and anteiso-C15:0) supported the affiliation of strain Gsoil 3088T to the genus Brevibacillus. The results of physiological and biochemical tests allowed strain Gsoil 3088T to be distinguished genotypically and phenotypically from Brevibacillus species with validly published names. Strain Gsoil 3088T, therefore, represents a novel species of the genus Brevibacillus, for which the name Brevibacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3088T (=KCTC 13938T=LMG 23403T).

  13. Flavobacterium panacisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Jung, Sun Young; Kim, Yeon-Ju; Hoang, Van-An; Jin, Yan; Nguyen, Ngoc-Lan; Oh, Keun Huyn; Yang, Deok-Chun

    2016-09-01

    A novel bacterial strain, designated DCY70(T), was isolated from soil of a ginseng field in Republic of Korea and was characterized in order to determine its taxonomic position. The strain was Gram-reaction negative, yellow-pigmented, rod-shaped and catalase- and oxidase-positive. Based on the 16S rRNA gene sequence similarity, strain DCY70(T) was shown to belong to the genus Flavobacterium, most closely related to Flavobacterium oncorhynchi 631-08(T) (98.4 %), Flavobacterium plurextorum 1126-1H-08(T) (97.9 %), Flavobacterium chilense LM-09-Fp(T) (97.9 %) and Flavobacterium chungangense CJ(T) (97.7 %). The chemotaxonomic characteristics showed only menaquinone-6 (MK-6), iso-C15:0, iso-C15:0 3OH, iso-C17:0 3OH and summed feature 3 as major cellular fatty acids. Polar lipids were phosphatidylethanolamine (PE), two unidentified aminolipids, four unidentified polar lipids and one unidentified phospholipid. The DNA G+C content was 34.9 mol%. Based on the phylogenetic, phenotypic and genotypic data, a novel species, Flavobacterium panacisoli sp. nov., is proposed (=KCTC 32393(T) = JCM 19162(T)).

  14. Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field.

    PubMed

    Im, Wan-Taek; Liu, Qing-Mei; Lee, Kang-Jin; Kim, Se-Young; Lee, Sung-Taik; Yi, Tae-Hoo

    2010-07-01

    A Gram-negative, aerobic or facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium (strain Gsoil 3165(T)) was isolated from soil of a ginseng field in Pocheon, South Korea. Its taxonomic position was determined by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 3165(T) was shown to belong to the family Comamonadaceae, class Betaproteobacteria, and was related most closely to the type strains of Variovorax boronicumulans (98.9 % similarity), Variovorax paradoxus (98.3 %), Variovorax soli (98.2 %) and Variovorax dokdonensis (96.6 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 3165(T) and the type strains of other species in the family Comamonadaceae were less than 97.0 %. The G+C content of the genomic DNA of strain Gsoil 3165(T) was 66 mol%. Phenotypic and chemotaxonomic data (Q-8 as the major ubiquinone; C(16 : 0) and C(17 : 0) cyclo as major fatty acids) supported the affiliation of strain Gsoil 3165(T) to the genus Variovorax. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 3165(T) from recognized Variovorax species. Gsoil 3165(T) is therefore considered to represent a novel species of the genus Variovorax, for which the name Variovorax ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3165(T) (=KCTC 12583(T) =LMG 23392(T)).

  15. Pulsed-Field Gel Electrophoresis Genotyping of Taylorella equigenitalis Isolates Collected in the United States from 1978 to 2010▿

    PubMed Central

    Aalsburg, Alan M.; Erdman, Matthew M.

    2011-01-01

    Taylorella equigenitalis is the etiologic agent of contagious equine metritis (CEM), a venereal disease of horses. A total of 82 strains of T. equigenitalis isolated in the United States were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of genomic DNA with restriction enzyme ApaI. Twenty-eight of those strains isolated from horses in the 2009 U.S. outbreak (CEM09) were further analyzed with NotI and NaeI enzymes. When ApaI alone was used for analysis, the 82 isolates clustered into 15 different genotypes that clearly defined groups of horses with known epidemiological connections. The PFGE profiles of the CEM09 isolates were indistinguishable after digestion with ApaI, NotI, and NaeI and did not match those of isolates from previous U.S. outbreaks in 1978 and 2006 or of any other isolate from the National Veterinary Services Laboratories (NVSL) culture library. Coupled with the fact that the CEM09 isolates are epidemiologically related, these results suggest a common source for the outbreak not linked to previous occurrences of CEM in the United States. PMID:21191049

  16. Fabrication and investigation on field-dependent properties of natural rubber based magneto-rheological elastomer isolator

    NASA Astrophysics Data System (ADS)

    Ain Abd Wahab, Nurul; Amri Mazlan, Saiful; Ubaidillah; Kamaruddin, Shamsul; Intan Nik Ismail, Nik; Choi, Seung-Bok; Haziq Rostam Sharif, Amirul

    2016-10-01

    This study presents a laminated magnetorheological elastomer (MRE) isolator which applies to vibration control in practice. The proposed isolator is fabricated with multilayer MRE sheets associated with the natural rubber (NR) as a matrix, and steel plates. The fabricated MRE isolator is then magnetically analysed to achieve high magnetic field intensity which can produce high damping force required for effective vibration control. Subsequently, the NR-based MRE specimen is tested to identify the field-dependent rheological properties such as storage modulus with 60 weight percentage of carbonyl iron particles. It is shown from this test that the MR effect of MRE specimen is quantified to reach up to 120% at 0.8 T. Following the design stage, the electromagnetic simulation using the finite element method magnetic (FEMM) software is carried out for analysing the magnetic flux distribution in the laminated MRE isolator. The laminated MRE isolator is then examined to a series of compression for static and dynamic test under various applied currents using the dynamic fatigue machine and biaxial dynamic testing machine. It is shown that the static compression force is increased by 14.5% under strong magnetic field compared to its off-state. Meanwhile, the dynamic compression test results show that the force increase of the laminated MRE isolator is up to 16% and 7% for low and high frequency respectively. From the results presented in this work, it is demonstrated that the full-scale concept of the MRE isolator can be one of the potential candidates for vibration control applications by tunability of the dynamic stiffness.

  17. Confirming and identifying new loci for rice blast disease resistance using magnaporthe oryzae field isolates in the US

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative trait loci (QTL) in rice play important roles in controlling rice blast disease. In the present study, 10 field isolates of the races IA1, IB1, IB17, and IC1 of U.S. rice blast fungus Magnaporthe oryzae collected in 1996 and 2009 were used to identify blast resistance QTL with a recombi...

  18. Complete genome sequence of Cupriavidus basilensis 4G11, isolated from the Oak Ridge Field Research Center site

    DOE PAGES

    Ray, Jayashree; Waters, R. Jordan; Skerker, Jeffrey M.; ...

    2015-05-14

    Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field Research Center (FRC) site. Here, we report the complete genome sequence and annotation of Cupriavidus basilensis 4G11. The genome contains 8,421,483 bp, 7,661 predicted protein-coding genes, and a total GC content of 64.4%.

  19. Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site.

    PubMed

    Ray, Jayashree; Waters, R Jordan; Skerker, Jeffrey M; Kuehl, Jennifer V; Price, Morgan N; Huang, Jiawen; Chakraborty, Romy; Arkin, Adam P; Deutschbauer, Adam

    2015-05-14

    Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field Research Center (FRC) site. Here, we report the complete genome sequence and annotation of Cupriavidus basilensis 4G11. The genome contains 8,421,483 bp, 7,661 predicted protein-coding genes, and a total GC content of 64.4%.

  20. Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site

    PubMed Central

    Ray, Jayashree; Waters, R. Jordan; Skerker, Jeffrey M.; Kuehl, Jennifer V.; Price, Morgan N.; Huang, Jiawen; Chakraborty, Romy; Arkin, Adam P.

    2015-01-01

    Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field Research Center (FRC) site. Here, we report the complete genome sequence and annotation of Cupriavidus basilensis 4G11. The genome contains 8,421,483 bp, 7,661 predicted protein-coding genes, and a total GC content of 64.4%. PMID:25977418

  1. Complete Genome Sequence of a Potential Novel Bacillus sp. Strain, FJAT-18017, Isolated from a Potato Field

    PubMed Central

    Liu, Guo-Hong; Wang, Jie-Ping; Che, Jian-Mei; Chen, Qian-Qian

    2017-01-01

    ABSTRACT Bacillus sp. strain FJAT-18017 was isolated from a potato field in Xinjiang, China. This paper is the first report, to our knowledge, to demonstrate the fully sequenced and completely annotated genome of Bacillus sp. FJAT-18017. The genome size is 5,265,521 bp. The average G+C content was 42.42%. PMID:28104649

  2. Porcine Epidemic Diarrhea Virus 3C-Like Protease-Mediated Nucleocapsid Processing: Possible Link to Viral Cell Culture Adaptability.

    PubMed

    Jaru-Ampornpan, Peera; Jengarn, Juggragarn; Wanitchang, Asawin; Jongkaewwattana, Anan

    2017-01-15

    Porcine epidemic diarrhea virus (PEDV) causes severe diarrhea and high mortality rates in newborn piglets, leading to massive losses to the swine industry worldwide during recent epidemics. Intense research efforts are now focusing on defining viral characteristics that confer a growth advantage, pathogenicity, or cell adaptability in order to better understand the PEDV life cycle and identify suitable targets for antiviral or vaccine development. Here, we report a unique phenomenon of PEDV nucleocapsid (N) cleavage by the PEDV-encoded 3C-like protease (3Cpro) during infection. The identification of the 3Cpro cleavage site at the C terminus of N supported previous observations that PEDV 3Cpro showed a substrate requirement slightly different from that of severe acute respiratory syndrome coronavirus (SARS-CoV) 3Cpro and revealed a greater flexibility in its substrate recognition site. This cleavage motif is present in the majority of cell culture-adapted PEDV strains but is missing in emerging field isolates. Remarkably, reverse-genetics-derived cell culture-adapted PEDVAVCT12 harboring uncleavable N displayed growth retardation in Vero E6-APN cells compared to the wild-type virus. These observations altogether shed new light on the investigation and characterization of the PEDV nucleocapsid protein and its possible link to cell culture adaptation.

  3. Identification and onion pathogenicity of Burkholderia cepacia complex isolates from the onion rhizosphere and onion field soil.

    PubMed

    Jacobs, Janette L; Fasi, Anthony C; Ramette, Alban; Smith, James J; Hammerschmidt, Raymond; Sundin, George W

    2008-05-01

    Burkholderia cepacia complex strains are genetically related but phenotypically diverse organisms that are important opportunistic pathogens in patients with cystic fibrosis (CF,) as well as pathogens of onion and banana, colonizers of the rhizospheres of many plant species, and common inhabitants of bulk soil. Genotypic identification and pathogenicity characterization were performed on B. cepacia complex isolates from the rhizosphere of onion and organic soils in Michigan. A total of 3,798 putative B. cepacia complex isolates were recovered on Pseudomonas cepacia azelaic acid tryptamine and trypan blue tetracycline semiselective media during the 2004 growing season from six commercial onion fields located in two counties in Michigan. Putative B. cepacia complex isolates were identified by hybridization to a 16S rRNA gene probe, followed by duplex PCR using primers targeted to the 16S rRNA gene and recA sequences and restriction fragment length polymorphism analysis of the recA sequence. A total of 1,290 isolates, 980 rhizosphere and 310 soil isolates, were assigned to the species B. cepacia (160), B. cenocepacia (480), B. ambifaria (623), and B. pyrrocinia (27). The majority of isolates identified as B. cepacia (85%), B. cenocepacia (90%), and B. ambifaria (76%) were pathogenic in a detached onion bulb scale assay and caused symptoms of water soaking, maceration, and/or necrosis. A phylogenetic analysis of recA sequences from representative B. cepacia complex type and panel strains, along with isolates collected in this study, revealed that the B. cenocepacia isolates associated with onion grouped within the III-B lineage and that some strains were closely related to strain AU1054, which was isolated from a CF patient. This study revealed that multiple B. cepacia complex species colonize the onion rhizosphere and have the potential to cause sour skin rot disease of onion. In addition, the onion rhizosphere is a natural habitat and a potential environmental source

  4. Comparison of genetic diversity and population structure between two Schistosoma japonicum isolates--the field and the laboratory.

    PubMed

    Bian, Chao-Rong; Gao, Yu-Meng; Lamberton, Poppy H L; Lu, Da-Bing

    2015-06-01

    Schistosomiasis japonicum is one of the most important human parasitic diseases, and a number of studies have recently elucidated the difference in biological characteristics of S. japonicum among different parasite isolates, for example, between the field and the laboratory isolates. Therefore, the understanding of underlying genetic mechanism is of both theoretical and practical importance. In this study, we used six microsatellite markers to assess genetic diversity, population structure, and the bottleneck effect (a sharp reduction in population size) of two parasite populations, one field and one laboratory. A total of 136 S. japonicum cercariae from the field and 86 from the laboratory, which were genetically unique within single snails, were analyzed. The results showed bigger numbers of alleles and higher allelic richness in the field parasite population than in the laboratory indicating lower genetic diversity in the laboratory parasites. A bottleneck effect was detected in the laboratory population. When the field and laboratory isolates were combined, there was a clear distinction between two parasite populations using the software Structure. These genetic differences may partially explain the previously observed contrasted biological traits.

  5. Co-transmission of the non-transmissible South African Babesia bovis S24 vaccine strain during mixed infection with a field isolate.

    PubMed

    Combrink, M P; Troskie, P C; de Klerk, D G; Pienaar, R; Latif, A A; Mans, B J

    2015-03-01

    The South African Babesia bovis live blood vaccine, originating from a field isolate attenuated by 23 serial syringe passages in splenectomized calves, has lost the ability to infect the natural vector Rhipicephalus (Boophilus) microplus. In this study, infection with mixed parasites from the vaccine strain and a field isolate, resulted in transmission of both genotype populations. Comparing the field isolate and transmitted combination indicated no significant difference in their virulence, while challenge of vaccinated cattle with these isolates showed the ability of the vaccine to protect against both. Limiting dilution of the transmitted combination, followed by infection of splenectomized cattle (n=34) yielded no single infections for the vaccine strain genotype, seven clonal lines of the field isolate and one mixture of vaccine strain and field isolate. Only one of two field isolate clonal lines selected for vector transmission study was transmitted. Showing that B. bovis isolates can contain both tick transmissible and non-transmissible subpopulations. The findings of this study also indicate the probability of vaccine co-infection transmission occurring in the field, which may result in new genotype populations of B. bovis. However, the impact of this recombination with field isolates is considered negligible since a genotypically diverse population of B. bovis is already present in South Africa.

  6. In vitro screening of compounds against laboratory and field isolates of human hookworm reveals quantitative differences in anthelmintic susceptibility.

    PubMed

    Treger, Rebecca S; Otchere, Joseph; Keil, Martin F; Quagraine, Josephine E; Rai, Ganesha; Mott, Bryan T; Humphries, Debbie L; Wilson, Michael; Cappello, Michael; Vermeire, Jon J

    2014-01-01

    A panel of 80 compounds was screened for anthelmintic activity against a laboratory strain of Ancylostoma ceylanicum and field isolates of hookworm obtained from school children in the Kintampo North District of the Brong Ahafo Region of Ghana. Although the laboratory strain of A. ceylanicum was more susceptible to the compounds tested than the field isolates of hookworm, a twofold increase in compound concentration resulted in comparable egg hatch percent inhibition for select compounds. These data provide evidence that the efficacy of anthelmintic compounds may be species-dependent and that field and laboratory strains of hookworm differ in their sensitivities to the anthelmintics tested. These data also suggest that both compound concentration and hookworm species must be considered when screening to identify novel anthelmintic compounds.

  7. Susceptibility of GT1-7 cells to mouse-passaged field scrapie isolates with a long incubation.

    PubMed

    Miyazawa, Kohtaro; Okada, Hiroyuki; Iwamaru, Yoshifumi; Masujin, Kentaro; Yokoyama, Takashi

    2014-01-01

    A typical feature of scrapie in sheep and goats is the accumulation of disease-associated prion protein. Scrapie consists of many strains with different biological properties. Nine natural sheep scrapie cases were transmitted to wild-type mice and mouse-passaged isolates were classified into 2 types based on incubation time: short and long. These 2 types displayed a distinct difference in their pathology. We attempted to transmit these mouse-passaged isolates to 2 murine cell lines (GT1-7 and L929) to compare their properties. All of the isolates were transmitted to L929 cells. However, only mouse-passaged field isolates with a long incubation time were transmitted to GT1-7 cells. This specific susceptibility of GT1-7 cells was also confirmed with a primary-passaged isolate that was not completely adapted to the new host species. Characterization of the mechanisms of the specific susceptibility of GT1-7 cells to isolates with a long incubation time may lead to a greater understanding of the differences among prion strains.

  8. Antitrypanosomal activity of aloin and its derivatives against Trypanosoma congolense field isolate

    PubMed Central

    2014-01-01

    Background There is an urgent need for the development of new, cheap, safe and highly effective drugs against African trypanosomiasis that affects both man and livestock in sub-Saharan Africa including Ethiopia. In the present study the exudate of Aloe gilbertii, an endemic Aloe species of Ethiopia, aloin, aloe-emodin and rhein were tested for their in vitro and in vivo antitrypanosomal activities against Trypanosoma congolense field isolate. Aloin was prepared from the leaf exudate of A. gilbertii by acid catalyzed hydrolysis. Aloe-emodin was obtained by oxidative hydrolysis of aloin, while rhein was subsequently derived from aloe-emodin by oxidation. In vitro trypanocidal activity tests were conducted on parasites obtained from infected mice, while mice infected with T. congolense were used to evaluate in vivo antitrypanosomal activity of the test substances. Results Results of the study showed that all the test substances arrested parasites motility at effective concentration of 4.0 mg/ml within an incubation period ranging from 15 to 40 min. Moreover, the same concentration of the test substances caused loss of infectivity of the parasites to mice during 30 days observation period. Among the tested substances, rhein showed superior activity with minimum inhibitory concentration (MIC) of 0.4 mg/ml. No adverse reactions were observed when the test substances were administered at a dose of 2000 mg/kg. Rhein at doses of 200 and 400 mg/kg, and the exudate, aloin and aloe-emodin at a dose of 400 mg/kg reduced the level of parasitaemia significantly (P < 0.05) and improved anaemia. Conclusion The results obtained in this investigation indicate that aloin and its derivatives particularly rhein have the potential to be used as a scaffold for the development of safe and cost effective antitrypanosomal drugs that can be useful in the continuing fight against African trypanosomiasis. PMID:24612613

  9. The Genotypic and Phenotypic Stability of Plasmodium falciparum Field Isolates in Continuous In Vitro Culture

    PubMed Central

    Yeda, Redemptah; Ingasia, Luicer A.; Cheruiyot, Agnes C.; Okudo, Charles; Chebon, Lorna J.; Cheruiyot, Jelagat; Akala, Hoseah M.; Kamau, Edwin

    2016-01-01

    The Plasmodium falciparum in vitro culture system is critical for genotypic and phenotypic analyses of the parasites. For genotypic analysis, the genomic DNA can be obtained directly from the patient blood sample or from culture adapted parasites whereas for phenotypic analysis, immediate ex vivo or in vitro culture adapted parasites are used. However, parasite biology studies have not investigated whether culture adaptation process affects genotypic and/or phenotypic characteristics of the parasites in short- or long-term cultures. Here, we set out to study the dynamics and stability of parasite genetic and phenotypic profiles as field isolate parasites were adapted in continuous cultures. Parasites collected from three different patients presenting with uncomplicated malaria were adapted and maintained in drug-free continuous cultures. Aliquots from the continuous cultures were collected every 24–48 hours for analyses. Each aliquot was treated as a separate parasite sample. For genetic analysis, microsatellite (MS) typing and single nucleotide polymorphism (SNP) analyses of 23 drug resistance markers were done. The 50% inhibitory concentrations (IC50) for some of the samples were also established for four antimalarial drugs. Samples from each patient (parasite-line) were compared as they were passed through the continuous culture. Data revealed genotypic and phenotypic profiles for the three parasite-lines fluctuated from one generation to the next with no specific pattern or periodicity. With few exceptions, multilocus analysis revealed samples from each parasite-line had high genetic diversity with unique haplotypes. Interestingly, changes in MS and SNP profiles occurred simultaneously. The difference in the IC50s of samples in each parasite-line reached statistical significance. However, phenotypic changes did not correspond or correlate to genotypic changes. Our study revealed parasite genetic and phenotypic characteristics fluctuates in short- and long

  10. Molecular characterization of field infectious bursal disease virus isolates from Nigeria

    PubMed Central

    Nwagbo, Ijeoma O.; Shittu, Ismaila; Nwosuh, Chika I.; Ezeifeka, George O.; Odibo, Frederick J. C.; Michel, Linda O.; Jackwood, Daral J.

    2016-01-01

    Aim: To characterize field isolates of infectious bursal disease virus (IBDV) from outbreaks in nine states in Nigeria through reverse transcription polymerase chain reaction (RT-PCR) and sequence analysis of portions of the VP2 and VP1 genes and to determine the presence or absence of reassortant viruses. Materials and Methods: A total of 377 bursa samples were collected from 201 suspected IBD outbreaks during 2009 to 2014 from nine states in Nigeria. Samples were subjected to RT-PCR using VP2 and VP1 gene specific primers, and the resulting PCR products were sequenced. Results: A total of 143 samples were positive for IBDV by RT-PCR. These assays amplified a 743 bp fragment from nt 701 to 1444 in the IBDV VP2 hypervariable region (hvVP2) of segment A and a 722 bp fragment from nt 168 to 889 in the VP1 gene of segment B. RT-PCR products were sequenced, aligned and compared with reference IBDV sequences obtained from GenBank. All but one hvVP2 sequence showed similarity to very virulent IBDV (vvIBDV) reference strains, yet only 3 of the VP1 67 VP1 sequences showed similarity to the VP1 gene of vvIBDV. Phylogenetic analysis revealed a new lineage of Nigerian reassortant IBDV strains. Conclusion: Phylogenetic analysis of partial sequences of genome segment A and B of IBDV in Nigeria confirmed the existence of vvIBDV in Nigeria. In addition, we noted the existence of reassortant IBDV strains with novel triplet amino acid motifs at positions 145, 146 and 147 in the reassorted Nigerian IBDV. PMID:28096615

  11. Brevibacillus halotolerans sp. nov., isolated from saline soil sample collected from paddy field.

    PubMed

    Song, Jinlong; Wang, Yanwei; Song, Yi; Zhao, Bingqiang; Wang, Huimin; Zhou, Shan; Kong, Delong; Guo, Xiang; Li, Yanting; He, Mingxiong; Ma, Kedong; Ruan, Zhiyong; Yan, Yanchun

    2016-10-17

    Two novel aerobic bacteria, designated strains LAM0312T and LAM0313, were isolated from saline soil sample collected from paddy field in Dezhou city, Shandong Province in China. The Cells of these strains were Gram-stain positive, sporogenous, rod-shaped and motile with peritrichous flagella. The optimal growth temperature and pH were 30 ºC and pH 7.0-8.0, repesctively. Strain LAM0312T was found to be able to grow in the presence of 12 % (w/v) NaCl. The major fatty acids of strains were identified as anteiso-C15:0 and iso-C15:0. The dominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, glycolipids, five unidentitied lipids and phosphatidylmonomethylethanolamine. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. The predominant menaquinone was identified as menaquinone-7. The G+C content of genomic DNA of strains LAM0312T and LAM0313 were 45.0 mol% and 46.0 mol%, respectively as determined by the Tm method. The 16S rRNA gene sequence similarity analysis indicated that the strains were closely related to Brevibacillus laterosporus DSM 25T and Brevibacillus fluminis JCM 15716T with 98.5 % and 96.4 % sequence similarity, respectively. The DNA-DNA hybridization values between strain LAM0312T and LAM0313 was 92 ± 0.6 % (reciprocal 90 ± 0.2 %)and the value between LAM0312T andBrevibacillus laterosporus DSM 25T was 48 ± 0.5 % (reciprocal 40 ± 0.4 %). On the basis of the phenotypic, phylogenetic and chemotaxonomic characteristics, the strains are proposed to represent a novel species of the genus Brevibacillus, for which the name Brevibacillus halotolerans sp. nov. is proposed. The type strain is LAM0312T (=ACCC 06527T =JCM 30849T).

  12. Flavobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Kim, Yeon-Ju; Kim, Sang-Rae; Nguyen, Ngoc-Lan; Yang, Deok-Chun

    2013-11-01

    A novel bacterial strain, designated DCY54(T), was isolated from a field cultivated with ginseng in Yongin, Republic of Korea. Cells were Gram-reaction-negative, yellow-pigmented, rod-shaped, non-spore-forming, and strictly aerobic. They were motile by gliding and produced flexirubin-type pigments. Growth occurred optimally at 25-30 °C, at pH 5.0-7.0 and in the presence of 0-1 % NaCl. The 16S rRNA sequence analysis demonstrated that strain DCY54(T) was most closely related to Flavobacterium defluvii EMB117(T) (96.9 %). The only isoprenoid quinone of strain DCY 54(T) was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major cellular fatty acids (>15 %) were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The DNA G+C content was 33.3 mol%. Phylogenetic inference and phenotypic data supported affiliation of strain DCY54(T) to the genus Flavobacterium. Several physiological and biochemical tests differentiated strain DCY54(T) from the species of the genus Flavobacterium with validly published names. On the basis of data from a polyphasic study, strain DCY54(T) represents a novel species of the genus Flavobacterium for which the name Flavobacterium ginsengisoli sp. nov. is proposed. The type strain is DCY54(T) ( = KCTC 23318(T) = JCM 17336(T)).

  13. Sensitivity of Penicillium expansum field isolates to tebuconazole, iprodione, fludioxonil and cyprodinil and characterization of fitness parameters and patulin production.

    PubMed

    Karaoglanidis, George S; Markoglou, Anastasios N; Bardas, George A; Doukas, Eleftherios G; Konstantinou, Sotiris; Kalampokis, John F

    2011-01-31

    A total of 236 Penicillium expansum field isolates from decayed apple fruit collected from packinghouses and processing industries located in the region of Imathia, Northern Greece were tested for their sensitivity to tebuconazole, fludioxonil, iprodione and cyprodinil. Preliminary fungitoxicity tests on the response of the isolates showed several phenotypes, distinguished according to their sensitivity to fungicides tested. The EC(50) values ranged from 0.64 to 5 (average = 0.98) μg/ml for iprodione, 0.9 to 7.3 (average = 2.66) μg/ml for tebuconazole, 0.008 to 1.28 (average = 0.55) μg/ml for cyprodinil and from 0.013 to 0.47 (average = 0.08) μg/ml for fludioxonil. A bimodal distribution of the EC(50) values of isolates with distinct sensitive and resistant populations to fludioxonil and tebuconazole were observed. In the case of cyprodinil, a much broader, hundred-fold, range of sensitivity was found, probably indicating that some isolates are relatively insensitive to cyprodinil compared to the most sensitive ones. Isolates exhibiting simultaneously reduced sensitivity to tebuconazole and fludioxonil or tebuconazole and iprodione or to tebuconazole and cyprodinil were also observed at low frequencies. A small portion of the population (7.5%) showed multiple resistance to tebuconazole, fludioxonil and iprodione. Study of fitness determining parameters showed that the resistance to tebuconazole, fludioxonil and iprodione had a significant adverse effect on mycelial growth rate and pathogenicity. Contrary to that, these fitness parameters were not affected in the isolates showing reduced sensitivity to cyprodinil. Analysis of patulin production on YES-agar growth medium and on artificially inoculated apple fruit showed that all isolates were mycotoxigenic. Most of the cyprodinil-insensitive isolates produced patulin at concentrations similar to or relatively higher (up to 1.5-fold on growth medium) than the sensitive ones. In contrast, a significant reduction

  14. One-day pulsed-field gel electrophoresis protocol for rapid determination of emetic Bacillus cereus isolates.

    PubMed

    Kaminska, Paulina S; Fiedoruk, Krzysztof; Jankowska, Dominika; Mahillon, Jacques; Nowosad, Karol; Drewicka, Ewa; Zambrzycka, Monika; Swiecicka, Izabela

    2015-04-01

    Bacillus cereus, the Gram-positive and spore-forming ubiquitous bacterium, may cause emesis as the result of food intoxication with cereulide, a heat-stable emetic toxin. Rapid determination of cereulide-positive B. cereus isolates is of highest importance due to consequences of this intoxication for human health and life. Here we present a 1-day pulsed-field gel electrophoresis for emetic B. cereus isolates, which allows rapid and efficient determination of their genomic relatedness and helps determining the source of intoxication in case of outbreaks caused by these bacilli.

  15. Aflatoxin Production of Species and Strains of the Aspergillus flavus Group Isolated from Field Crops

    PubMed Central

    Schroeder, H. W.; Boller, R. A.

    1973-01-01

    Peanuts, cottonseed, rice, and sorghum from Texas were sampled over a 3-year period. To insure adequate isolation of alfatoxin-producing species of fungi, low-quality lots were sampled at a rate greater than their respective proportional representation. Aflatoxins were found each year in peanut and cottonseed and were found in 2 of 3 years in rice and sorghum. Aflatoxins were detected in all four crops. The Aspergillus flavus group was much more prevalent in peanut and rice than in cottonseed and sorghum. Of the isolates of the A. flavus group, 96% from peanuts, 79% from cottonseed, 49% from sorghum, and 35% from rice produced aflatoxins. The average toxin production of isolates from rice was much less than that from peanuts, cottonseed, or sorghum. More than 90% of all isolates of the A. flavus group were identified as the species A. flavus. A. parasiticus was isolated from all four crops. Only A. parasiticus produced aflatoxin G. PMID:4197766

  16. Analysis of Genetic Diversity of Streptococcus suis Clinical Isolates from Pigs in Spain by Pulsed-Field Gel Electrophoresis

    PubMed Central

    Vela, Ana I.; Goyache, Joaquin; Tarradas, Carmen; Luque, Inmaculada; Mateos, Ana; Moreno, Miguel A.; Borge, Carmen; Perea, J. Anselmo; Domínguez, Lucas; Fernández-Garayzábal, José F.

    2003-01-01

    Pulsed-field gel electrophoresis (PFGE) was used to investigate the diversity of Streptococcus suis isolates of various serotypes recovered from swine clinical samples in Spain. Capsular types 9 (64.9%) and 2 (14.8%) were the most frequently isolated serotypes followed by serotype 7 (5.9%) and serotype 8 (4.3%). The PFGE results of this study with 60 different pulsotypes indicate a great genetic diversity among the S. suis isolates, which is consistent with the broad distribution of S. suis in the swine population. Forty-five percent of the pulsotypes corresponded to single isolates, no pulsotype was common to all farms, and at least 3 different pulsotypes were isolated in 56% of herds in which more than 3 clinical isolates were analyzed. These results reveal a great diversity both between and within herds throughout the strains of S. suis studied, demonstrating that different strains of S. suis are associated with infection in pigs. Some pulsotypes were more frequently isolated and exhibited a wider distribution over herds than others, and were the unique or predominant strains in several herds, suggesting the existence of a prevalent or a few prevalent clones responsible for a large proportion of clinical cases. Overall, the great genetic heterogeneity of the clinical strains of S. suis, the isolation of different strains within the same herd, and the predominance of particular strains in some herds are evidence that infection by S. suis is a dynamic process and reinforce the idea that the epidemiology of S. suis infection is very complex. PMID:12791872

  17. Analysis of genetic diversity of Streptococcus suis clinical isolates from pigs in Spain by pulsed-field gel electrophoresis.

    PubMed

    Vela, Ana I; Goyache, Joaquin; Tarradas, Carmen; Luque, Inmaculada; Mateos, Ana; Moreno, Miguel A; Borge, Carmen; Perea, J Anselmo; Domínguez, Lucas; Fernández-Garayzábal, José F

    2003-06-01

    Pulsed-field gel electrophoresis (PFGE) was used to investigate the diversity of Streptococcus suis isolates of various serotypes recovered from swine clinical samples in Spain. Capsular types 9 (64.9%) and 2 (14.8%) were the most frequently isolated serotypes followed by serotype 7 (5.9%) and serotype 8 (4.3%). The PFGE results of this study with 60 different pulsotypes indicate a great genetic diversity among the S. suis isolates, which is consistent with the broad distribution of S. suis in the swine population. Forty-five percent of the pulsotypes corresponded to single isolates, no pulsotype was common to all farms, and at least 3 different pulsotypes were isolated in 56% of herds in which more than 3 clinical isolates were analyzed. These results reveal a great diversity both between and within herds throughout the strains of S. suis studied, demonstrating that different strains of S. suis are associated with infection in pigs. Some pulsotypes were more frequently isolated and exhibited a wider distribution over herds than others, and were the unique or predominant strains in several herds, suggesting the existence of a prevalent or a few prevalent clones responsible for a large proportion of clinical cases. Overall, the great genetic heterogeneity of the clinical strains of S. suis, the isolation of different strains within the same herd, and the predominance of particular strains in some herds are evidence that infection by S. suis is a dynamic process and reinforce the idea that the epidemiology of S. suis infection is very complex.

  18. Isolation and Characterization of Mobile Genetic Elements from Microbial Assemblages Obtained from the Field Research Center Site

    SciTech Connect

    Patricia Sobecky; Cassie Hodges; Kerri Lafferty; Mike Humphreys; Melanie Raimondo; Kristin Tuttle; Tamar Barkay

    2004-03-17

    Considerable knowledge has been gained from the intensive study of a relatively limited group of bacterial plasmids. Recent efforts have begun to focus on the characterization of, at the molecular level, plasmid populations and associated mobile genetic elements (e.g., transposons, integrons) occurring in a wider range of aquatic and terrestrial habitats. Surprisingly, however, little information is available regarding the incidence and distribution of mobile genetic elements extant in contaminated subsurface environments. Such studies will provide greater knowledge on the ecology of plasmids and their contributions to the genetic plasticity (and adaptation) of naturally occurring subsurface microbial communities. We requested soil cores from the DOE NABIR Field Research Center (FRC) located on the Oak Ridge Reservation. The cores, received in February 2003, were sampled from four areas on the Oak Ridge Site: Area 1, Area 2, Area 3 (representing contaminated subsurface locales) and the background reference sites. The average core length (24 in) was subdivided into three profiles and soil pH and moisture content were determined. Uranium concentration was also determined in bulk samples. Replicate aliquots were fixed for total cell counts and for bacterial isolation. Four different isolation media were used to culture aerobic and facultative microbes from these four study areas. Colony forming units ranged from a minimum of 100 per gram soil to a maximum of 10,000 irrespective of media composition used. The vast majority of cultured subsurface isolates were gram-positive isolates and plasmid characterization was conducted per methods routinely used in the Sobecky laboratory. The percentage of plasmid incidence ranged from 10% to 60% of all isolates tested. This frequency appears to be somewhat higher than the incidence of plasmids we have observed in other habitats and we are increasing the number of isolates screened to confirm this observation. We are also

  19. Genetic Diversity and Symbiotic Efficiency of Nodulating Rhizobia Isolated from Root Nodules of Faba Bean in One Field

    PubMed Central

    Lan, Qin; Wang, Ke; Liu, Ming; Peng, Dan; Zhang, Xiaoping; Chen, Qiang; Zhao, Ke; Zeng, Xiangzhong; Xu, Kai Wei

    2016-01-01

    Thirty-one nodulating rhizobium strains were collected from root nodules of spring and winter type faba bean cultivars grown in micro ecoarea, i.e. the same field in Chengdu plain, China. The symbiotic efficiency and phylogeny of these strains were studied. Effectively nitrogen fixing strains were isolated from both winter type and spring type cultivars. Based on phylogenetic analysis of 16S rRNA gene and concatenated sequence of atpD, glnII and recA genes, the isolates were assigned as Rhizobium anhuiense and a potential new Rhizobium species. The isolates were diverse on symbiosis related gene level, carrying five, four and three variants of nifH, nodC and nodD, respectively. Strains carrying similar gene combinations were trapped by both winter and spring cultivars, disagreeing with the specificity of symbiotic genotypes to reported earlier faba bean ecotypes. PMID:27936180

  20. Analysis of Genomic Diversity among Helicobacter pylori Strains Isolated from Iranian Children by Pulsed Field Gel Electrophoresis

    PubMed Central

    Falsafi, Tahereh; Sotoudeh, Nazli; Feizabadi, Mohammad-Mehdi; Mahjoub, Fatemeh

    2014-01-01

    Objective: Presence of genomic diversity among Helicobacter pylori (H. pylori) strains have been suggested by numerous investigators. Little is known about diversity of H. pylori strains isolated from Iranian children and their association with virulence of the strains. Our purpose was to assess the degree of genomic diversity among H. pylori strains isolated from Iranian-children, on the basis of vacA genotype, cagA status of the strains, sex, age as well as the pathological status of the patients. Methods: Genomic DNA from 44 unrelated H. pylori strains isolated during 1997–2009, was examined by pulse-field gel electrophoresis (PFGE). Pathological status of the patients was performed according to the modified Sydney-system and genotype/status of vacA/cagA genes was determined by PCR. PFGE was performed using XbaI restriction-endonuclease and the field inversion-gel electrophoresis system. Findings: No significant relationship was observed between the patterns of PFGE and the cagA/vacA status/genotype. Also no relationship was observed between age, sex, and pathological status of the children and the PFGE patterns of their isolates. Similar conclusion was obtained by Total Lab software. However, more relationship was observed between the strains isolated in the close period (1997–2009, 2001–2003, 2005–2007, and 2007–2009) and more difference was observed among those obtained in the distant periods (1997 and 2009). Conclusion: H. pylori strains isolated from children in Iran are extremely diverse and this diversity is not related to their virulence characteristics. Occurrence of this extreme diversity may be related to adaptation of H. pylori strains to variable living conditions during transmission between various host individuals. PMID:26019775

  1. Draft Genome Sequence of the Field Isolate Brucella melitensis Strain Bm IND1 from India.

    PubMed

    Rao, Sashi Bhushan; Gupta, Vivek K; Kumar, Mukesh; Hegde, Nagendra R; Splitter, Gary A; Reddanna, Pallu; Radhakrishnan, Girish K

    2014-05-29

    Brucella spp. are facultative intracellular bacterial pathogens causing the zoonotic disease brucellosis. Here, we report the draft genome sequence of the Brucella melitensis strain from India designated Bm IND1, isolated from stomach contents of an aborted goat fetus.

  2. Downregulation of mitogen-activated protein kinase 1 of Leishmania donovani field isolates is associated with antimony resistance.

    PubMed

    Ashutosh; Garg, Mansi; Sundar, Shyam; Duncan, Robert; Nakhasi, Hira L; Goyal, Neena

    2012-01-01

    Emergence of resistance to pentavalent antimonials has become a severe obstacle in the treatment of visceral leishmaniasis (VL) on the Indian subcontinent. The mechanisms operating in laboratory-generated strains are somewhat known, but the determinants of clinical antimony resistance are not well understood. By utilizing a DNA microarray expression profiling approach, we identified a gene encoding mitogen-activated protein kinase 1 (MAPK1) for the kinetoplast protozoan Leishmania donovani (LdMAPK1) that was consistently downregulated in antimony-resistant field isolates. The expression level of the gene was validated by real-time PCR. Furthermore, decreased expression of LdMAPK1 was also confirmed at the protein level in resistant isolates. Primary structure analysis of LdMAPK1 revealed the presence of all of the characteristic features of MAPK1. When expressed in Escherichia coli, the recombinant enzyme showed kinase activity with myelin basic protein as the substrate and was inhibited by staurosporine. Interestingly, overexpression of this gene in a drug-sensitive laboratory strain and a resistant field isolate resulted in increased the sensitivity of the transfectants to potassium antimony tartrate, suggesting that it has a role in antimony resistance. Our results demonstrate that downregulation of LdMAPK1 may be in part correlated with antimony drug resistance in Indian VL isolates.

  3. Existence of variant strains Fowlpox virus integrated with Reticuloendotheliosis virus in its genome in field isolates in Tanzania.

    PubMed

    Mzula, Alexanda; Masola, Selemani N; Kasanga, Christopher J; Wambura, Philemon N

    2014-06-01

    Fowlpox virus (FPV) is one example of poultry viruses which undergoes recombination with Reticuloendotheliosis virus (REV). Trepidation had been raised, and it was well established on augmented pathogenicity of the FPV upon integration of the full intact REV. In this study, we therefore intended at assessing the integration of REV into FPV genome of the field isolates obtained in samples collected from different regions of Tanzania. DNA extraction of 85 samples (scabs) was performed, and FPV-specific PCR was done by the amplification of the highly conserved P4b gene. Evaluation of FPV-REV recombination was done to FPV-specific PCR positively identified samples by amplifying the env gene and REV long terminal repeats (5' LTR). A 578-bp PCR product was amplified from 43 samples. We are reporting for the first time in Tanzania the existence of variant stains of FPV integrated with REV in its genome as 65 % of FPV identified isolates were having full intact REV integration, 21 % had partial FPV-REV env gene integration and 5 % had partial 5' LTR integration. Despite of the fact that FPV-REV integrated stains prevailed, FPV-REV-free isolates (9 %) also existed. In view of the fact that full intact REV integration is connected with increased pathogenicity of FPV, its existence in the FPV genome of most field isolates could have played a role in increased endemic, sporadic and recurring outbreaks in selected areas in Tanzania.

  4. Isolation of RNA from field-grown jute (Corchorus capsularis) plant in different developmental stages for effective downstream molecular analysis.

    PubMed

    Samanta, Pradipta; Sadhukhan, Sanjoy; Das, Subrata; Joshi, Alpana; Sen, Soumitra K; Basu, Asitava

    2011-10-01

    Jute (Corchorus capsularis), as a natural fibre producing plant species, ranks next to cotton only. Today, biotechnological approach has been considered as most accepted means for any genetic improvement of plant species. However, genetic control of the fibre development in jute has not yet been explored sufficiently for desired genetic improvement. One of the major impediments in exploring the genetic architecture in this crop at molecular level is the availability of good quality RNA from field-grown plant tissues mostly due to the presence of high amount of mucilage and phenolics. Development of a suitable RNA isolation method is becoming essential for deciphering developmental stage-specific gene expression pattern related to fibre formation in this crop species. A combination of modified hot borate buffer followed by isopycnic centrifugation (termed as HBIC) was adopted and found to be the best isolation method yielding sufficient quantity (~350-500 μg/gm fresh tissue) and good quality (A(260/280) ratio 1.88 to 1.91) RNA depending on the developmental stage of stem tissue from field-grown jute plant. The poly A(+) RNA purified from total RNA isolated by the present method was found amenable to efficient RT-PCR and cDNA library construction. The present development of RNA isolation was found to be appropriate for gene expression analysis related to fibre formation in this economically important jute plant in near future.

  5. Generating Isolated Elliptically Polarized Attosecond Pulses Using Bichromatic Counterrotating Circularly Polarized Laser Fields

    NASA Astrophysics Data System (ADS)

    Medišauskas, Lukas; Wragg, Jack; van der Hart, Hugo; Ivanov, Misha Yu.

    2015-10-01

    We theoretically demonstrate the possibility to generate both trains and isolated attosecond pulses with high ellipticity in a practical experimental setup. The scheme uses circularly polarized, counterrotating two-color driving pulses carried at the fundamental and its second harmonic. Using a model Ne atom, we numerically show that highly elliptic attosecond pulses are generated already at the single-atom level. Isolated pulses are produced by using few-cycle drivers with controlled time delay between them.

  6. Isolation of Buggy Creek virus (Togaviridae: Alphavirus) from field-collected eggs of Oeciacus vicarius (Hemiptera: Cimicidae).

    PubMed

    Brown, Charles R; Moore, Amy T; Young, Ginger R; Padhi, Abinash; Komar, Nicholas

    2009-03-01

    Alphaviruses (Togaviridae) rarely have been found to be vertically transmitted from female arthropods to their progeny. We report two isolations of Buggy Creek virus (BCRV), an ecologically unusual alphavirus related to western equine encephalomyelitis virus, from field-collected eggs of cimicid swallow bugs (Oeciacus vicarius Horvath), the principal vector for BCRV. Ten percent of egg pools were positive for BCRV, and we estimated minimum infection rates to be 1.03 infected eggs per 1,000 tested. The results show potential vertical transmission of BCRV, represent one of the few isolations of any alphavirus from eggs or larvae of insects in the field, and are the first report of any virus in the eggs of cimicid bedbugs. The specialized ecological niche of BCRV in swallow bugs and at cliff swallow (Petrochelidon pyrrhonota Vieillot) nesting sites may promote vertical transmission of this virus.

  7. Flavobacterium aquaticum sp. nov., isolated from a water sample of a rice field.

    PubMed

    Subhash, Y; Sasikala, Ch; Ramana, Ch V

    2013-09-01

    Strain JC164(T) was isolated from a water sample from a rice field at Jamdih, Mau, Uttar Pradesh, India. Colonies of strain JC164(T) were brown-yellow and cells were Gram-stain-negative. Catalase, oxidase and amylase were present. iso-C(15:0), iso-C(16:0), iso-C15 1 G, iso-C(15:0) 3-OH and iso-C(14:0) were the predominant fatty acids with minor amounts of iso-C(16:0) 3-OH, anteiso-C(15:0), C(16:0), iso-C(16:1) H, iso-C(14:0) 3-OH and iso-C(13:0). Strain JC164(T) contained phosphatidylethanolamine and a few unidentified lipids (L1, L3 and L6) as major polar lipids. Bacteriohopane derivative 1 (BHD1) and diplopterol (DPL) were the major hopanoids. β-Carotene was one among the several spirilloxanthin series carotenoids present in strain JC164(T). Genomic DNA G+C content was 39.6 mol%. 16S rRNA gene sequence comparisons indicated that strain JC164(T) represents a member of the genus Flavobacterium (family Flavobacteriaceae, class Flavobacteriia). The most closely related taxa to strain JC164(T) were Flavobacterium sasangense YC6274(T) (98.5%), Flavobacterium cucumis R2A45-3(T) (98.1%), Flavobacterium cheniae NJ-26(T) (97.2%) and the novel strain possessed <95.1% sequence similarity with other members of the genus Flavobacterium. However, strain JC164(T) showed 12.5 ± 2, 13.6 ± 1 and 17.4 ± 2% genomic DNA association (based on DNA-DNA hybridization) with Flavobacterium sasangense KCTC 22246(T), Flavobacterium cucumis DSM 18830(T) and Flavobacterium cheniae CGMCC 1.6844(T), respectively. The distinct genomic difference and morphological, physiological and chemotaxonomic differences from the previously described taxa support the classification of strain JC164(T) as a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium aquaticum sp. nov. is proposed. The type strain is JC164(T) ( = KCTC 32196(T) = CGMCC 1.12398=LMG 27251(T)).

  8. Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field.

    PubMed

    Son, Heung-Min; Kook, Moochang; Park, Sang-Yong; Mavlonov, Gafurjon T; Yi, Tae-Hoo

    2013-12-01

    A Gram-staining negative, strictly aerobic, motile by gliding, non-spore-forming, pale yellow pigmented and rod-shaped bacterium designated strain THG-107(T) was isolated from soil of a ginseng field on Ganghwa Island in the Republic of Korea and its taxonomic position was investigated by using a polyphasic study. Growth of strain THG-107(T) was found to occur at 4-37 °C (optimum, 20-30 °C), at pH 5.5-10 (optimum, pH 7.0) and in the presence of 0-1 % (w/v) NaCl (optimum, absence) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain THG-107(T) was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium denitrificans ED5(T) (99.1 % similarity). The G+C content of the genomic DNA was determined to be 34.2 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. The only isoprenoid quinone detected in strain THG-107(T) was menaquinone-6 (MK-6) and the major polyamine was identified as homospermidine (82.9 %). The major polar lipid detected was phosphatidylethanolamine and the major cellular fatty acids were identified as iso-C15:0 (26.3 %), iso-C17:0 3OH (12.6 %) and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c; 11.6 %). Flexirubin-type pigments were found to be present. Strain THG-107(T) has β-glucosidase activity to convert ginsenosides Rb1 and Rd into Gyp17 and F2. DNA-DNA hybridization with F. denitrificans ED5(T) was 52 %. Strain THG-107(T) could be distinguished from F. denitrificans ED5(T) and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. Therefore, strain THG-107(T) is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium kyungheensis sp. nov. is proposed (type strain THG-107(T) = KACC 16219(T) = LMG 26575(T)).

  9. Pulsed-Field Gel Electrophoresis characterization of Listeria monocytogenes isolates from cheese manufacturing plants in São Paulo, Brazil.

    PubMed

    Barancelli, Giovana V; Camargo, Tarsila M; Gagliardi, Natália G; Porto, Ernani; Souza, Roberto A; Campioni, Fabio; Falcão, Juliana P; Hofer, Ernesto; Cruz, Adriano G; Oliveira, Carlos A F

    2014-03-03

    This study aimed to evaluate the occurrence of Listeria monocytogenes in cheese and in the environment of three small-scale dairy plants (A, B, C) located in the Northern region state of São Paulo, Brazil, and to characterize the isolates using conventional serotyping and PFGE. A total of 393 samples were collected and analyzed from October 2008 to September 2009. From these, 136 came from dairy plant A, where only L. seeligeri was isolated. In dairy plant B, 136 samples were analyzed, and L. innocua, L. seeligeri and L. welshimeri were isolated together with L. monocytogenes. In dairy plant C, 121 samples were analyzed, and L. monocytogenes and L. innocua were isolated. Cheese from dairy plants B and C were contaminated with Listeria spp, with L. innocua being found in Minas frescal cheese from both dairy plants, and L. innocua and L. monocytogenes in Prato cheese from dairy plant C. A total of 85 L. monocytogenes isolates were classified in 3 serotypes: 1/2b, 1/2c, and 4b, with predominance of serotype 4b in both dairy plants. The 85 isolates found in the dairy plants were characterized by genomic macrorestriction using ApaI and AscI with Pulsed Field Gel Electrophoresis (PFGE). Macrorestriction yielded 30 different pulsotypes. The presence of indistinguishable profiles repeatedly isolated during a 12-month period indicated the persistence of L. monocytogenes in dairy plants B and C, which were more than 100 km away from each other. Brine used in dairy plant C contained more than one L. monocytogenes lineage. The routes of contamination were identified in plants B and C, and highlighted the importance of using molecular techniques and serotyping to track L. monocytogenes sources of contamination, distribution, and routes of contamination in dairy plants, and to develop improved control strategies for L. monocytogenes in dairy plants and dairy products.

  10. Diversity of Campylobacter isolates from retail poultry carcasses and from humans as demonstrated by pulsed-field gel electrophoresis.

    PubMed

    Dickins, M Avery; Franklin, Sharon; Stefanova, Rossina; Schutze, Gordon E; Eisenach, Kathleen D; Wesley, Irene; Cave, M Donald

    2002-06-01

    Campylobacter spp. are a major contaminant of poultry. Eating undercooked chicken and handling raw poultry have been identified as risk factors for campylobacteriosis in humans. Previous studies have found Campylobacter spp. on 90% of poultry carcasses. In the present study, pulsed-field gel electrophoresis (PFGE) was used to assess the genetic diversity of strains on retail poultry carcasses. PFGE patterns of isolates from campylobacteriosis cases were compared to those from the poultry isolates. Over a 1-year study period (March 2000 through February 2001), whole fresh young chickens (n = 72) were obtained from three retail outlets in an urban community in the south-central United States. Campylobacter spp. were isolated from 82% of these carcasses. Strains (n = 70) were defined on the basis of their PFGE pattern. Sixty-seven percent of the carcasses from which Campylobacter spp. were isolated were contaminated with more than one PFGE-distinguishable strain. During the 1-year study period, most of the PFGE patterns (59%) were limited to isolates obtained from a single carcass. Forty-one percent of the PFGE-distinguishable strains were recovered from more than one carcass. Ninety-seven percent of the carcasses contaminated with the same strain were purchased at the same time from the same store. To examine the degree of genetic stability, four strains were followed in vitro over an estimated 1,000 doublings. The PFGE pattern of one of these isolates underwent minor changes during in vitro growth. The data indicate extensive variability in the PFGE patterns of Campylobacter spp. isolated from humans and from poultry carcasses. In spite of difficulties caused by such diversity and the fact that some carcasses are contaminated with more than one strain, the pattern variation provides a useful method for linking a particular strain to its source.

  11. Analysis of Molecular Epidemiology of Chilean Salmonella enterica Serotype Enteritidis Isolates by Pulsed-Field Gel Electrophoresis and Bacteriophage Typing

    PubMed Central

    Fernandez, Jorge; Fica, Alberto; Ebensperger, German; Calfullan, Hector; Prat, Soledad; Fernandez, Alda; Alexandre, Marcela; Heitmann, Ingrid

    2003-01-01

    Human Salmonella enterica serotype Enteritidis infections emerged in Chile in 1994. S. enterica serotype Enteritidis phage type 1 isolates predominated in the north, and phage type 4 isolates predominated in the central and southern regions. A study was planned to characterize this epidemic using the best discriminatory typing technique. Research involved 441 S. enterica serotype Enteritidis isolates, including clinical preepidemic samples (n = 74; 1975 to 1993) and epidemic (n = 199), food (n = 72), poultry (n = 57), and some Latin American (n = 39) isolates. The best method was selected based on a sample of preepidemic isolates, analyzing the discriminatory power (DP) obtained by phage typing and randomly amplified polymorphic DNA and pulsed-field gel electophoresis (PFGE) analysis. The highest DP was associated with BlnI PFGE-bacteriophage typing analysis (0.993). A total of 38 BlnI patterns (B patterns) were identified before the epidemic period, 19 since 1994, and only 4 in both periods. Two major clusters were identified by phylogenetic analysis, and the predominant B patterns clustered in the same branch. Combined analysis revealed that specific B pattern-phage type combinations (subtypes) disappeared before 1994, that different genotypes associated with S. enterica serotype Enteritidis phage type 4 had been observed since 1988, and that strain diversity increased before the expansion of S. enterica serotype Enteritidis in 1994. Predominant subtype B3-phage type 4 was associated with the central and southern regions, and subtype B38-phage type 1 was associated with the north (P < 0.0001). Food and poultry isolates matched the predominant S. enterica serotype Enteritidis subtypes, but isolates identified in neighboring countries (Peru and Bolivia) did not match S. enterica serotype Enteritidis subtypes identified in the north of Chile. The results of this work demonstrate that genetic diversity, replacement, and expansion of specific S. enterica serotype

  12. Pulsed-field gel electrophoresis typing, antibiotic resistance, and plasmid profiles of Escherichia coli strains isolated from foods.

    PubMed

    Uysal, Ahmet; Durak, Yusuf

    2012-11-01

    Bacterial contamination in foods and antimicrobial resistance levels of common pathogenic strains causing food-borne disease are important in human health. Thus, typing technologies are important tools to determine primary sources of bacterial contamination. In this study, 40 Escherichia coli strains isolated from 85 food samples were evaluated in terms of genetic diversity, susceptibility to certain antibiotics, and plasmid profiles. Pulsed-field gel electrophoresis was used to identify the genetic relations of E. coli isolates. It was determined that the 40 E. coli strains revealed 32 different pulsotypes represented by 6 subtypes. Antibiotic susceptibility tests conducted by using a disc diffusion method against 15 antibiotics showed that although the isolates revealed 14 different types of resistance profiles, the strains showed the greatest resistance to ampicillin (77.5%), followed by ticarcillin-clavulanic acid (30%), tetracycline (22.5%), and cephalothin (14.5%). Plasmid isolations studies of the strains conducted by the method of alkaline lysis revealed that 18 (45%) of 40 E. coli strains contain 31 different plasmid bands ranging between 64.4 and 1 kb. The results showed that PFGE was a powerful method in tracking sources of food contamination and that the antibiotic resistance levels of food isolates were high and should be monitored.

  13. Effector Polymorphisms of the Sunflower Downy Mildew Pathogen Plasmopara halstedii and Their Use to Identify Pathotypes from Field Isolates.

    PubMed

    Gascuel, Quentin; Bordat, Amandine; Sallet, Erika; Pouilly, Nicolas; Carrere, Sébastien; Roux, Fabrice; Vincourt, Patrick; Godiard, Laurence

    2016-01-01

    The obligate biotroph oomycete Plasmopara halstedii causes downy mildew on sunflower crop, Helianthus annuus. The breakdown of several Pl resistance genes used in sunflower hybrids over the last 25 years came along with the appearance of new Pl. halstedii isolates showing modified virulence profiles. In oomycetes, two classes of effector proteins, key players of pathogen virulence, are translocated into the host: RXLR and CRN effectors. We identified 54 putative CRN or RXLR effector genes from transcriptomic data and analyzed their genetic diversity in seven Pl. halstedii pathotypes representative of the species variability. Pl. halstedii effector genes were on average more polymorphic at both the nucleic and protein levels than random non-effector genes, suggesting a potential adaptive dynamics of pathogen virulence over the last 25 years. Twenty-two KASP (Competitive Allele Specific PCR) markers designed on polymorphic effector genes were genotyped on 35 isolates belonging to 14 Pl. halstedii pathotypes. Polymorphism analysis based on eight KASP markers aims at proposing a determination key suitable to classify the eight multi-isolate pathotypes into six groups. This is the first report of a molecular marker set able to discriminate Pl. halstedii pathotypes based on the polymorphism of pathogenicity effectors. Compared to phenotypic tests handling living spores used until now to discriminate Pl. halstedii pathotypes, this set of molecular markers constitutes a first step in faster pathotype diagnosis of Pl. halstedii isolates. Hence, emerging sunflower downy mildew isolates could be more rapidly characterized and thus, assessment of plant resistance breakdown under field conditions should be improved.

  14. Diversity of pulsed-field gel electrophoresis patterns of cereulide-producing isolates of Bacillus cereus and Bacillus weihenstephanensis.

    PubMed

    Castiaux, Virginie; N'guessan, Elise; Swiecicka, Izabela; Delbrassinne, Laurence; Dierick, Katelijne; Mahillon, Jacques

    2014-04-01

    Bacillus cereus is an important foodborne pathogen causing diarrhoea, emesis and in, rare cases, lethal poisonings. The emetic syndrome is caused by cereulide, a heat-stable toxin. Originally considered as a rather homogenous group, the emetic strains have since been shown to display some diversity, including the existence of two clusters of mesophilic B. cereus and psychrotolerant B. weihenstephanensis. Using pulsed-field gel electrophoresis (PFGE) analysis, this research aimed to better understand the diversity and spatio-temporal occurrence of emetic strains originating from environmental or food niches vs. those isolated from foodborne cases. The diversity was evaluated using a set of 52 B. cereus and B. weihenstephanensis strains isolated between 2000 and 2011 in ten countries. PFGE analysis could discriminate 17 distinct profiles (pulsotypes). The most striking observations were as follows: (1) more than one emetic pulsotype can be observed in a single outbreak; (2) the number of distinct isolates involved in emetic intoxications is limited, and these potentially clonal strains frequently occurred in successive and independent food poisoning cases; (3) isolates from different countries displayed identical profiles; and (4) the cereulide-producing psychrotolerant B. weihenstephanensis were, so far, only isolated from environmental niches.

  15. Virus excretion and antibody dynamics in goats inoculated with a field isolate of peste des petits ruminants virus.

    PubMed

    Liu, W; Wu, X; Wang, Z; Bao, J; Li, L; Zhao, Y; Li, J

    2013-11-01

    A field isolate of peste des petits ruminants virus (PPRV) from an outbreak in Tibet, China, was inoculated into goats to investigate the dynamics of virus excretion and antibody production. Further, animals received PPRV vaccine strain Nigeria 75/1. Ocular, nasal and oral samples were tested for the presence of virus antigen by one-step real-time qualitative RT-PCR (qRT-PCR); competitive ELISA (c-ELISA) was used for the measurement of specific antibodies against PPRV. Virus particles could be detected as early as day 3 post-inoculation (pi) and virus excretion lasted for up to day 26 pi. All four goats inoculated with the PPRV field isolate were seropositive as early as day 10 pi. In animals inoculated with the vaccine strain, antibody was detected at day 14 pi, and levels of neutralizing antibodies remained above the protection threshold level (1 : 8) for 8 months. Both virus particles and neutralizing antibodies were detected earlier in goats challenged with the field isolate than in those receiving the vaccine strain.

  16. Field collection and genetic classification of tick-borne Rickettsiae and Rickettsiae-like pathogens from South Texas: Coxiella burnetii isolated from field-collected Amblyomma cajennense.

    PubMed

    Sanders, David M; Parker, Jill E; Walker, Wes W; Buchholz, Matt W; Blount, Keith; Kiel, Johnathan L

    2008-12-01

    We are reporting the first known isolation of the Q-fever agent Coxiella burnetii from field-collected cayenne ticks Amblyomma cajennense in North America. Q-fever affects a number of domestic ungulates where it can lead to abortion in sheep and goats. There is far less known about the disease's effects on wild species, primarily because of the tendency of the disease to self resolve and to provide long-term immunity to subsequent infections. The first recovery of C. burnetii in North America was from the tick species Dermacentor andersoni. Since the original isolation C. burnetii has been recovered from five other North American tick species. The currently accepted mode for the majority of human infections is inhalation. The Centers for Disease Control and Prevention, Division of Viral and Rickettsial Diseases, Rickettsial Zoonoses Branch asserts the Q-fever agent as requiring as few as one organism to cause disease via inhalation in susceptible humans. However, with more and more isolations from ticks, evidence linking C. burnetii and ticks is mounting. The true role of tick species as competent vectors is still unconfirmed. Preemptive field collections of possible vector arthropods, hosts, and reservoirs can provide invaluable baseline environmental data that will prove supportive in follow-up studies and abatement efforts.

  17. Aquaporin 2 mutations in Trypanosoma brucei gambiense field isolates correlate with decreased susceptibility to pentamidine and melarsoprol.

    PubMed

    Graf, Fabrice E; Ludin, Philipp; Wenzler, Tanja; Kaiser, Marcel; Brun, Reto; Pyana, Patient Pati; Büscher, Philippe; de Koning, Harry P; Horn, David; Mäser, Pascal

    2013-01-01

    The predominant mechanism of drug resistance in African trypanosomes is decreased drug uptake due to loss-of-function mutations in the genes for the transporters that mediate drug import. The role of transporters as determinants of drug susceptibility is well documented from laboratory-selected Trypanosoma brucei mutants. But clinical isolates, especially of T. b. gambiense, are less amenable to experimental investigation since they do not readily grow in culture without prior adaptation. Here we analyze a selected panel of 16 T. brucei ssp. field isolates that (i) have been adapted to axenic in vitro cultivation and (ii) mostly stem from treatment-refractory cases. For each isolate, we quantify the sensitivity to melarsoprol, pentamidine, and diminazene, and sequence the genomic loci of the transporter genes TbAT1 and TbAQP2. The former encodes the well-characterized aminopurine permease P2 which transports several trypanocides including melarsoprol, pentamidine, and diminazene. We find that diminazene-resistant field isolates of T. b. brucei and T. b. rhodesiense carry the same set of point mutations in TbAT1 that was previously described from lab mutants. Aquaglyceroporin 2 has only recently been identified as a second transporter involved in melarsoprol/pentamidine cross-resistance. Here we describe two different kinds of TbAQP2 mutations found in T. b. gambiense field isolates: simple loss of TbAQP2, or loss of wild-type TbAQP2 allele combined with the formation of a novel type of TbAQP2/3 chimera. The identified mutant T. b. gambiense are 40- to 50-fold less sensitive to pentamidine and 3- to 5-times less sensitive to melarsoprol than the reference isolates. We thus demonstrate for the first time that rearrangements of the TbAQP2/TbAQP3 locus accompanied by TbAQP2 gene loss also occur in the field, and that the T. b. gambiense carrying such mutations correlate with a significantly reduced susceptibility to pentamidine and melarsoprol.

  18. Isolation and Characterization of Strains CVO and FWKO B, Two Novel Nitrate-Reducing, Sulfide-Oxidizing Bacteria Isolated from Oil Field Brine

    PubMed Central

    Gevertz, Diane; Telang, Anita J.; Voordouw, Gerrit; Jenneman, Gary E.

    2000-01-01

    Bacterial strains CVO and FWKO B were isolated from produced brine at the Coleville oil field in Saskatchewan, Canada. Both strains are obligate chemolithotrophs, with hydrogen, formate, and sulfide serving as the only known energy sources for FWKO B, whereas sulfide and elemental sulfur are the only known electron donors for CVO. Neither strain uses thiosulfate as an energy source. Both strains are microaerophiles (1% O2). In addition, CVO grows by denitrification of nitrate or nitrite whereas FWKO B reduces nitrate only to nitrite. Elemental sulfur is the sole product of sulfide oxidation by FWKO B, while CVO produces either elemental sulfur or sulfate, depending on the initial concentration of sulfide. Both strains are capable of growth under strictly autotrophic conditions, but CVO uses acetate as well as CO2 as its sole carbon source. Neither strain reduces sulfate; however, FWKO B reduces sulfur and displays chemolithoautotrophic growth in the presence of elemental sulfur, hydrogen, and CO2. Both strains grow at temperatures between 5 and 40°C. CVO is capable of growth at NaCl concentrations as high as 7%. The present 16s rRNA analysis suggests that both strains are members of the epsilon subdivision of the division Proteobacteria, with CVO most closely related to Thiomicrospira denitrifcans and FWKO B most closely related to members of the genus Arcobacter. The isolation of these two novel chemolithotrophic sulfur bacteria from oil field brine suggests the presence of a subterranean sulfur cycle driven entirely by hydrogen, carbon dioxide, and nitrate. PMID:10831429

  19. Optimization of an antibiotic sensitivity assay for Mycoplasma hyosynoviae and susceptibility profiles of field isolates from 1997 to 2011.

    PubMed

    Schultz, K K; Strait, E L; Erickson, B Z; Levy, N

    2012-07-06

    Mycoplasma hyosynoviae is a common agent responsible for polyarthritis leading to decreased production in swine herds worldwide. Antimicrobial agents are used to combat infections; however breakpoints for M. hyosynoviae have not yet been established. A number of methods have previously been utilized to analyze minimum inhibitory concentrations (MICs) for antibiotics against M. hyosynoviae; however these techniques as currently described are not easily standardized between laboratories. A dry microbroth dilution method was conducted to compare the minimum inhibitory concentrations (MICs) for 18 antibiotics, representative of different classes, against 24 recent isolates (23 field isolates and the type strain) of M. hyosynoviae. The MICs were determined using standard, commercially available 96-well Sensititre(®) plates containing various freeze-dried antibiotics at a range of concentrations appropriate to their potency. Clindamycin (CLI), a lincosamide antibiotic, showed the highest activity and most consistent inhibition for all isolates with an MIC(50) of ≤ 0.12 μg/ml. Tiamulin (TIA), a pleuromutilin derivative, exhibited an MIC(50) of ≤ 0.25 μg/ml. The isolates had similar levels of susceptibility to the quinolones, enrofloxacin (ENRO) and danofloxacin (DANO), exhibiting an MIC(50) of 0.25 μg/ml and 0.5 μg/ml, respectively. For the macrolides, the MIC(50) for tylosin (TYLT) and tilmicosin (TIL) was ≤ 0.25 μg/ml and ≤ 2 μg/ml respectively, but was ≤ 16 μg/ml for tulathromycin (TUL). For the aminoglycosides, the MIC(50) for gentamicin (GEN) was ≤ 0.5 μg/ml, while spectinomycin (SPE) and neomycin (NEO) had an MIC(50) of ≤ 4 μg/ml. The tetracyclines, oxytetracycline (OXY) and chlortetracycline (CTET) both had an MIC(50) of ≤ 2 μg/ml. Florfenicol (FFN) exhibited a MIC(50) of ≤ 1 μg/ml. All isolates were resistant to penicillin (PEN), ampicillin (AMP), ceftiofur (TIO), trimethoprim/sulfamethoxazole (SXT), and sulphadimethoxine (SDM) at all

  20. Frequencies of virulence genes and pulse field gel electrophoresis fingerprints in Escherichia coli isolates from canine pyometra.

    PubMed

    Maluta, Renato P; Borges, Clarissa A; Beraldo, Lívia G; Cardozo, Marita V; Voorwald, Fabiana A; Santana, André M; Rigobelo, Everlon C; Toniollo, Gilson H; Avila, Fernando A

    2014-11-01

    Escherichia coli is the most common bacterial agent isolated from canine pyometra. The frequencies of 24 virulence genes and pulsed field gel electrophoresis (PFGE) profiles were determined for 23 E. coli isolates from cases of canine pyometra in Brazil. The frequencies of virulence genes were 91.3% fimH, 91.3% irp-2, 82.6% fyuA, 56.5% iroN, 47.8% traT, 39.1% usp, 34.8% sfaD/E, 34.8% tsh, 30.4% papC, 30.4% hlyA, 26.1% papGIII, 26.1% cnf-1, 21.7% papE/F, 21.7% iss, 17.4% iutA, 17.4% ompT, 17.4% cvaC, 17.4% hlyF, 17.4% iucD, 13.0% iucC, 13.0% astA, 4.3% papGII, 0% afaB/C and 0% papGI. The high frequency of yersiniabactin (fyuA and irp2) and salmochelin (iroN) genes suggests that iron uptake systems might be important in the pathogenesis of canine pyometra. PFGE profiles of 19 isolates were heterogeneous, confirming that E. coli isolates from canine pyometra are unlikely to be epidemic clones.

  1. Genetic Diversity of Streptococcus suis Strains Isolated from Pigs and Humans as Revealed by Pulsed-Field Gel Electrophoresis

    PubMed Central

    Berthelot-Hérault, Florence; Marois, Corinne; Gottschalk, Marcelo; Kobisch, Marylène

    2002-01-01

    The genetic diversity of 123 Streptococcus suis strains of capsular types 2, 1/2, 3, 7, and 9, isolated from pigs in France and from humans in different countries, was evaluated by pulsed-field gel electrophoresis (PFGE) of DNA restricted with SmaI. The method was highly discriminative (D = 0.98), results were reproducible, and the PFGE analysis was easy to interpret. Among all S. suis strains, 74 PFGE patterns were shown. At 60% homology, three groups (A, B, and C) were identified, and at 69% homology, eight subgroups (a to h) were observed. Strains isolated from diseased pigs or from humans were statistically clustered in group B, especially in subgroup d. By contrast, S. suis strains isolated from clinically healthy pigs were preferentially included in subgroup b of group A. Relationships could be established between capsular types 1/2, 3, and 9 and groups A, e, and B, respectively. S. suis strains isolated from humans were homogeneous, and a very high level of association between these strains and four DNA patterns was observed. The PFGE used in this study is a very useful tool for evaluating the genetic diversity of S. suis strains, and it would be used for epidemiological investigations. PMID:11825980

  2. Genetic diversity of Streptococcus suis strains isolated from pigs and humans as revealed by pulsed-field gel electrophoresis.

    PubMed

    Berthelot-Hérault, Florence; Marois, Corinne; Gottschalk, Marcelo; Kobisch, Marylène

    2002-02-01

    The genetic diversity of 123 Streptococcus suis strains of capsular types 2, 1/2, 3, 7, and 9, isolated from pigs in France and from humans in different countries, was evaluated by pulsed-field gel electrophoresis (PFGE) of DNA restricted with SmaI. The method was highly discriminative (D = 0.98), results were reproducible, and the PFGE analysis was easy to interpret. Among all S. suis strains, 74 PFGE patterns were shown. At 60% homology, three groups (A, B, and C) were identified, and at 69% homology, eight subgroups (a to h) were observed. Strains isolated from diseased pigs or from humans were statistically clustered in group B, especially in subgroup d. By contrast, S. suis strains isolated from clinically healthy pigs were preferentially included in subgroup b of group A. Relationships could be established between capsular types 1/2, 3, and 9 and groups A, e, and B, respectively. S. suis strains isolated from humans were homogeneous, and a very high level of association between these strains and four DNA patterns was observed. The PFGE used in this study is a very useful tool for evaluating the genetic diversity of S. suis strains, and it would be used for epidemiological investigations.

  3. Overexpression of ubiquitin and amino acid permease genes in association with antimony resistance in Leishmania tropica field isolates.

    PubMed

    Kazemi-Rad, Elham; Mohebali, Mehdi; Khadem-Erfan, Mohammad Bagher; Hajjaran, Homa; Hadighi, Ramtin; Khamesipour, Ali; Rezaie, Sassan; Saffari, Mojtaba; Raoofian, Reza; Heidari, Mansour

    2013-08-01

    The mainstay therapy against leishmaniasis is still pentavalent antimonial drugs; however, the rate of antimony resistance is increasing in endemic regions such as Iran. Understanding the molecular basis of resistance to antimonials could be helpful to improve treatment strategies. This study aimed to recognize genes involved in antimony resistance of Leishmania tropica field isolates. Sensitive and resistant L. tropica parasites were isolated from anthroponotic cutaneous leishmaniasis patients and drug susceptibility of parasites to meglumine antimoniate (Glucantime®) was confirmed using in vitro assay. Then, complementary DNA-amplified fragment length polymorphism (cDNA-AFLP) and real-time reverse transcriptase-PCR (RT-PCR) approaches were utilized on mRNAs from resistant and sensitive L. tropica isolates. We identified 2 known genes, ubiquitin implicated in protein degradation and amino acid permease (AAP3) involved in arginine uptake. Also, we identified 1 gene encoding hypothetical protein. Real-time RT-PCR revealed a significant upregulation of ubiquitin (2.54-fold), and AAP3 (2.86-fold) (P<0.05) in a resistant isolate compared to a sensitive one. Our results suggest that overexpression of ubiquitin and AAP3 could potentially implicated in natural antimony resistance.

  4. Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation fields.

    PubMed

    Tago, Kanako; Ishii, Satoshi; Nishizawa, Tomoyasu; Otsuka, Shigeto; Senoo, Keishi

    2011-01-01

    Denitrifiers can produce and consume nitrous oxide (N(2)O). While little N(2)O is emitted from rice paddy soil, the same soil produces N(2)O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N(2) in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N(2)-producing denitrifiers.

  5. Identification of antimony resistance markers in Leishmania tropica field isolates through a cDNA-AFLP approach.

    PubMed

    Kazemi-Rad, Elham; Mohebali, Mehdi; Khadem-Erfan, Mohammad Bagher; Saffari, Mojtaba; Raoofian, Reza; Hajjaran, Homa; Hadighi, Ramtin; Khamesipour, Ali; Rezaie, Sassan; Abedkhojasteh, Hoda; Heidari, Mansour

    2013-10-01

    Pentavalent antimonial compounds have been the first line therapy for leishmaniasis; unfortunately the rate of treatment failure of anthroponotic cutaneous leishmaniasis (ACL) is increasing due to emerging of drug resistance. Elucidation of the molecular mechanisms operating in antimony resistance is critical for development of new strategies for treatment. Here, we used a cDNA-AFLP approach to identify gene(s) which are differentially expressed in resistant and sensitive Leishmania tropica field isolates. We identified five genes, aquaglyceroporin (AQP1) acts in drug uptake, ATP-binding cassette (ABC) transporter (MRPA) involved in sequestration of drug, phosphoglycerate kinase (PGK) implicated in glycolysis metabolism, mitogen activated protein kinase (MAPK) and protein tyrosine phosphatase (PTP) responsible for phosphorylation pathway. The results were confirmed using real time RT-PCR which revealed an upregulation of MRPA, PTP and PGK genes and downregulation of AQP1 and MAPK genes in resistant isolate. To our knowledge, this is the first report of identification of PTP and PGK genes potentially implicated in resistance to antimonials. Our findings support the idea that distinct biomolecules might be involved in antimony resistance in L. tropica field isolates.

  6. New isolated gate bipolar transistor two-quadrant chopper power supply for a fast field cycling nuclear magnetic resonance spectrometer

    NASA Astrophysics Data System (ADS)

    Sousa, D. M.; Marques, G. D.; Sebastião, P. J.; Ribeiro, A. C.

    2003-10-01

    This work, presents, for the first time, an Isolated Gate Bipolar Transistor (IGBT) two-quadrant chopper power supply for a fast field cycling (FFC) nuclear magnetic resonance spectrometer. This power supply was designed to achieve a maximum current of 200 A with good efficiency, low semiconductor losses, low cost, and easy maintenance. Both energy storage circuits and dumping circuits are used to obtain switching times less than 2 ms between field levels in agreement with the FFC technique specifications. The current ripple at high currents is better than 1×10-4 and presents a specific shape which can be used for additional compensation using auxiliary circuits. The implemented power supply was tested and been continuously operating with a home-built FFC solenoidal magnet, associated cooling system, and rf units for fields between 0 and 0.2 T.

  7. POPULATION SYNTHESIS OF YOUNG ISOLATED NEUTRON STARS: THE EFFECT OF FALLBACK DISK ACCRETION AND MAGNETIC FIELD EVOLUTION

    SciTech Connect

    Fu, Lei; Li, Xiang-Dong

    2013-10-01

    The spin evolution of isolated neutron stars (NSs) is dominated by their magnetic fields. The measured braking indices of young NSs show that the spin-down mechanism due to magnetic dipole radiation with constant magnetic fields is inadequate. Assuming that the NS magnetic field is buried by supernova fallback matter and re-emerges after accretion stops, we carry out a Monte Carlo simulation of the evolution of young NSs, and show that most of the pulsars have braking indices ranging from –1 to 3. The results are compatible with the observational data of NSs associated with supernova remnants. They also suggest that the initial spin periods of NSs might occupy a relatively wide range.

  8. Efficacy of commercial canarypox vaccine for protecting Hawai'i 'Amakihi from field isolates of Avipoxvirus

    USGS Publications Warehouse

    Atkinson, Carter T.; Wiegand, Kimberly C.; Triglia, Dennis; Jarvi, Susan I.

    2010-01-01

    At least three variants of avian pox virus are present in Hawai‘i - Fowlpox from domestic poultry and a group of genetically distinct viruses that cluster within two clades (Pox Variant 1 and Pox Variant 2) that are most similar to Canarypox based on DNA sequence of the virus 4b core protein gene. We tested whether Hawai‘i ‘Amakihi can be protected from wild virus isolates with an attenuated live Canarypox vaccine that is closely related to isolates that cluster within clade 1 (Pox Variant 1) based on sequence of the attenuated Canarypox virus 4b core protein. Thirty-one (31) Hawai`i ‘Amakihi (Hemignathus virens) with no prior physical evidence of pox infection were collected on Mauna Kea from xeric, high elevation habitats with low pox prevalence and randomly divided into two groups. One group of 16 was vaccinated with Poximmune C® while the other group received a sham vaccination with virus diluent. Four of 15 (27%) vaccinated birds developed potentially life-threatening disseminated lesions or lesions of unusually long duration, while one bird never developed a vaccine-associated lesion or "take". After vaccine-associated lesions healed, vaccinated birds were randomly divided into three groups of five and challenged with either a wild isolate of Fowlpox, a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 1 (Pox Variant 1) or a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 2 (Pox Variant 2). Similarly, three random groups of five unvaccinated ‘Amakihi were challenged with the same virus isolates. Vaccinated and unvaccinated ‘Amakihi challenged with Fowlpox had transient infections with no clinical signs of infection. Mortality in vaccinated ‘Amakihi that were challenged with Pox Variant 1 and Pox Variant 2 ranged from 0% (0/5) for Pox Variant 1 to 60% (3/5) for Pox Variant 2. Mortality in unvaccinated ‘Amakihi ranged from 40% (2/5) for Pox Variant 1 to 100% (5/5) for Pox Variant 2. While the vaccine provided some

  9. Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype.

    PubMed

    Brown, Tyler S; Jacob, Christopher G; Silva, Joana C; Takala-Harrison, Shannon; Djimdé, Abdoulaye; Dondorp, Arjen M; Fukuda, Mark; Noedl, Harald; Nyunt, Myaing Myaing; Kyaw, Myat Phone; Mayxay, Mayfong; Hien, Tran Tinh; Plowe, Christopher V; Cummings, Michael P

    2015-03-01

    Multiple transcontinental waves of drug resistance in Plasmodium falciparum have originated in Southeast Asia before spreading westward, first into the rest of Asia and then to sub-Saharan Africa. In vitro studies have suggested that hypermutator P. falciparum parasites may exist in Southeast Asia and that an increased rate of acquisition of new mutations in these parasites may explain the repeated emergence of drug resistance in Southeast Asia. This study is the first to test the hypermutator hypothesis using field isolates. Using genome-wide SNP data from human P. falciparum infections in Southeast Asia and West Africa and a test for relative rate differences we found no evidence of increased relative substitution rates in P. falciparum isolates from Southeast Asia. Instead, we found significantly increased substitution rates in Mali and Bangladesh populations relative to those in populations from Southeast Asia. Additionally we found no association between increased relative substitution rates and parasite clearance following treatment with artemisinin derivatives.

  10. Experimental infection of young adult European breed sheep with Rift Valley fever virus field isolates.

    PubMed

    Busquets, Nuria; Xavier, F; Martín-Folgar, Raquel; Lorenzo, Gema; Galindo-Cardiel, Iván; del Val, Bernat Pérez; Rivas, Raquel; Iglesias, Javier; Rodríguez, Fernando; Solanes, David; Domingo, Mariano; Brun, Alejandro

    2010-10-01

    The increasing interest in Rift Valley fever virus (RVFV) and its potential impact on naive animal populations deserve revisiting experimental reproduction of RVFV infection, particularly in those animal breeds for which no data about their susceptibility to RVFV infection have ever been recorded. In this study we show the susceptibility of 9-10 weeks old European sheep (Ripollesa breed) to RVFV infection, showing a mild, subacute form of disease. Four different viral isolates efficiently replicated in vivo after subcutaneous experimental inoculation, and consistent viral loads in blood and virus shedding (variable in length depending on the RVFV isolate used) were detected, showing horizontal transmission to a noninfected, sentinel lamb. RVFV infection caused transient pyrexia in adult lambs and no other clinical symptoms were observed, with the exception of corneal opacity ("blue eye") found in 3 out of 16 subcutaneously inoculated sheep. In conclusion, adult sheep from this European breed are readily infected with RVFV without apparent clinical manifestations.

  11. [Production of a vaccine against enterotoxemia from Clostridium perfringens strains isolated in the field].

    PubMed

    Cherfaoui, S; Kadra, B

    1992-01-01

    We have isolated eight strains of C. perfringens from cases of enterotoxaemia. Five of these strains have revealed themselves toxic with respective types (type "A":2, type "C":2, type "D":1). In order to produce anti-enterotoxaemia vaccine, we have proceeded at the cultivation in fermenter of isolated strains and reference strains CWA 35, CWC and CWD AF. At the end of fermentation, we have evaluated the two following parameters: obtained biomass, and toxin titers. With the two classes of strains we reached an important biomass but toxins titers relatively weak comparatively to that which is usually required. It will be necessary then, to demonstrate the immunogen value of the produced vaccines by testing their efficacity.

  12. Site-specific distribution and competitive ability of indigenous bean-nodulating rhizobia isolated from organic fields in Minnesota.

    PubMed

    Wongphatcharachai, Manoosak; Wang, Ping; Staley, Christopher; Chun, Chan Lan; Ferguson, John A; Moncada, Kristine M; Sheaffer, Craig C; Sadowsky, Michael J

    2015-11-20

    Organic dry bean production systems have received increasing interest in many regions of the US, including Minnesota. Thus, improving biological N2 fixation would be highly beneficial for organic crop production. To date, only limited work has been done to select efficient N2-fixing rhizobia for organic dry bean production. In this study, soil samples from 25 organic fields in Minnesota, with a previous cropping history of dry beans, soybeans or both, were collected during May to July 2012. Genetic diversity of indigenous dry bean-rhizobia (511 isolates) was determined by using horizontal, fluorophore-enhanced, repetitive, extragenic, and palindromic-PCR (HFERP) DNA fingerprinting and isolates were classified as belonging to 58 different genotypes. The more abundant rhizobia isolated from bean nodules comprised 35.6% of the population. None of the isolates were identical to commonly-used commercial strains used in the U.S., including Rhizobium tropici CIAT899. Seventeen predominant genotypes were shown to represent two main species, Rhizobium leguminosarum bv. phaseoli (67.1%) and Rhizobium etli (30.2%). One of the indigenous strains, orgK9, displayed efficient N2-fixation and competitive ability relative to the commercial strains tested. The lack of large numbers of indigenous dry bean-rhizobia at most study sites will be useful to avoid competition problems between inoculant strains and indigenous rhizobia. This will allow inoculation with highly effective N2-fixing rhizobia, thus resulting in improved crop productivity. Our results highlight the existence of site-specific rhizobial genotypes in different organic fields and identify strains that may prove useful as novel inoculants for organic dry bean production systems.

  13. Isolation of Legionella species from Noyu (unattended natural hot springs in mountains and fields) samples in Japan.

    PubMed

    Furuhata, Katsunori; Edagawa, Akiko; Ishizaki, Naoto; Fukuyama, Masafumi

    2013-01-01

    In order to understand the habitation conditions of the bacteria of the genus Legionella in Noyu (unattended natural hot springs in mountains and fields) in Japan, isolation of Legionella spp. was attempted in the Noyu samples from 11 prefectures nationwide between May and September 2012, and the following results were obtained. Overall, Legionella spp. was isolated from 16 of 43 samples (37.2%). The species was isolated from the Hokkaido region to the Chugoku region but not from the Shikoku region to the Kyushu region. The number of bacteria detected was usually small, less than 5.0 × 10(1) CFU/100 ml, as found in 11 samples (68.8%), while counts of 10(2) or more to 10(3) or less CFU/100 ml were found in two samples (12.5%). Legionella pneumophila was the most commonly found strain, with 19 strains (90.5%) found, and was the dominant species. Regarding the serogrouping, four strains (21.1%) fell under group 1, the most common grouping, followed by three strains (15.8%) in group 3, two strains (10.5%) in group 5, etc. Moreover, the detected bacterial strains other than L. pneumophila included two strains (9.5%) of L. londiniensis. The temperature of the Noyu from which Legionella spp. was isolated was between 33.1°C and 41.5°C with a pH ranging from 5.2 to 8.1. The present report is the first report to clarify the habitation conditions of strains of Legionella spp. isolated from Noyu in Japan.

  14. Effector Polymorphisms of the Sunflower Downy Mildew Pathogen Plasmopara halstedii and Their Use to Identify Pathotypes from Field Isolates

    PubMed Central

    Gascuel, Quentin; Bordat, Amandine; Sallet, Erika; Pouilly, Nicolas; Carrere, Sébastien; Roux, Fabrice

    2016-01-01

    The obligate biotroph oomycete Plasmopara halstedii causes downy mildew on sunflower crop, Helianthus annuus. The breakdown of several Pl resistance genes used in sunflower hybrids over the last 25 years came along with the appearance of new Pl. halstedii isolates showing modified virulence profiles. In oomycetes, two classes of effector proteins, key players of pathogen virulence, are translocated into the host: RXLR and CRN effectors. We identified 54 putative CRN or RXLR effector genes from transcriptomic data and analyzed their genetic diversity in seven Pl. halstedii pathotypes representative of the species variability. Pl. halstedii effector genes were on average more polymorphic at both the nucleic and protein levels than random non-effector genes, suggesting a potential adaptive dynamics of pathogen virulence over the last 25 years. Twenty-two KASP (Competitive Allele Specific PCR) markers designed on polymorphic effector genes were genotyped on 35 isolates belonging to 14 Pl. halstedii pathotypes. Polymorphism analysis based on eight KASP markers aims at proposing a determination key suitable to classify the eight multi-isolate pathotypes into six groups. This is the first report of a molecular marker set able to discriminate Pl. halstedii pathotypes based on the polymorphism of pathogenicity effectors. Compared to phenotypic tests handling living spores used until now to discriminate Pl. halstedii pathotypes, this set of molecular markers constitutes a first step in faster pathotype diagnosis of Pl. halstedii isolates. Hence, emerging sunflower downy mildew isolates could be more rapidly characterized and thus, assessment of plant resistance breakdown under field conditions should be improved. PMID:26845339

  15. Comparison of Campylobacter isolates from poultry and humans: association between in vitro virulence properties, biotypes, and pulsed-field gel electrophoresis clusters.

    PubMed

    Nadeau, Eric; Messier, Serge; Quessy, Sylvain

    2003-10-01

    The in vitro virulence properties of 197 temporally and geographically related Campylobacter isolates from chicken broilers and humans were compared. Comparisons of the virulence properties associated with genotypes and biotypes were made. All isolates adhered to, and 63% invaded, INT-407 cells, whereas 13% were cytotoxic for CHO cells. CHO cell-cytotoxic extracts were also cytotoxic for INT-407 cells, but the sensitivity for Vero cells was variable. The proportion of isolates demonstrating a high invasiveness potential (>1,000 CFU ml(-1)) or Vero cell cytotoxicity was significantly higher for human than for poultry isolates. Invasiveness was associated with Campylobacter jejuni isolates of biotypes 1 and 2, whereas CHO and INT-407 cell cytotoxicity was associated with C. jejuni isolates of biotypes 3 and 4. Cytotoxic isolates were also clustered according to pulsed-field gel electrophoresis profiles.

  16. Landau-like theory for universality of critical exponents in quasistationary states of isolated mean-field systems.

    PubMed

    Ogawa, Shun; Yamaguchi, Yoshiyuki Y

    2015-06-01

    An external force dynamically drives an isolated mean-field Hamiltonian system to a long-lasting quasistationary state, whose lifetime increases with population of the system. For second order phase transitions in quasistationary states, two nonclassical critical exponents have been reported individually by using a linear and a nonlinear response theories in a toy model. We provide a simple way to compute the critical exponents all at once, which is an analog of the Landau theory. The present theory extends the universality class of the nonclassical exponents to spatially periodic one-dimensional systems and shows that the exponents satisfy a classical scaling relation inevitably by using a key scaling of momentum.

  17. Parainfluenza virus isolation enhancement utilizing a portable cell culture system in the field.

    PubMed Central

    Parkinson, A J; Muchmore, H G; Scott, L V; Miles, J A

    1980-01-01

    Using a portable minaturized cell culture system, enhanced recoveries of parainfluenza virus types 1 and 3 were made in the field from symptomatic human adult subjects working at remote Antarctic stations. PMID:6247369

  18. Differentiation of Erysipelothrix rhusiopathiae strains by nucleotide sequence analysis of a hypervariable region in the spaA gene: discrimination of a live vaccine strain from field isolates.

    PubMed

    Nagai, Shinya; To, Ho; Kanda, Akira

    2008-05-01

    Erysipelothrix rhusiopathiae causes erysipelas in swine and is considered a reemerging disease contributing substantially to economic losses in the swine industry. Since an attenuated live vaccine was commercialized in 1974 in Japan, outbreaks of acute septicemia or subacute urticaria of erysipelas have decreased dramatically. In contrast, a chronic form of erysipelas found during meat inspections in slaughterhouses has been increasing. In this study, a new strain-typing method was developed based on nucleotide sequencing of a hypervariable region in the surface protective antigen (spaA) gene for discrimination of the live vaccine strain from field isolates. Sixteen strains isolated from arthritic lesions found in slaughtered pigs were segregated into 4 major patterns: 1) identical nucleotide sequence with the vaccine strain: 3 isolates; 2) 1 nucleotide substitution (C to A) at position 555: 5 isolates; 3) 1 nucleotide substitution at various positions: 5 isolates; and 4) 2 nucleotide substitutions: 3 isolates. Isolates with the same nucleotide sequence as the vaccine strain were further characterized by other properties, including the mouse pathogenicity test. One strain isolated from pigs on a farm where the live vaccine had been used was found to be closely related to the vaccine strain. The phylogenetic tree constructed based on the spaA sequence suggests that the evolutionary distance of the isolates is related to the pathogenicity in mice. The new strain-typing system based on nucleotide sequencing of the spaA region is useful to discriminate the vaccine strain from field isolates.

  19. Characterization of Nivalenol-Producing Fusarium culmorum Isolates Obtained from the Air at a Rice Paddy Field in Korea

    PubMed Central

    Kim, Da-Woon; Kim, Gi-Yong; Kim, Hee-Kyoung; Kim, Jueun; Jeon, Sun Jeong; Lee, Chul Won; Lee, Hyang Burm; Yun, Sung-Hwan

    2016-01-01

    Together with the Fusarium graminearum species complex, F. culmorum is a major member of the causal agents of Fusarium head blight on cereals such as wheat, barley and corn. It causes significant yield and quality losses and results in the contamination of grain with mycotoxins that are harmful to humans and animals. In Korea, F. culmorum is listed as a quarantine fungal species since it has yet to be found in the country. In this paper, we report that two isolates (J1 and J2) of F. culmorum were collected from the air at a rice paddy field in Korea. Species identification was confirmed by phylogenetic analysis using multi-locus sequence data derived from five genes encoding translation elongation factor, histone H3, phosphate permease, a reductase, and an ammonia ligase and by morphological comparison with reference strains. Both diagnostic PCR and chemical analysis confirmed that these F. culmorum isolates had the capacity to produce nivalenol, the trichothecene mycotoxin, in rice substrate. In addition, both isolates were pathogenic on wheat heads and corn stalks. This is the first report on the occurrence of F. culmorum in Korea. PMID:27298593

  20. Kitasatospora sampliensis sp. nov., a novel actinobacterium isolated from soil of a sugar-cane field in India.

    PubMed

    Mayilraj, S; Krishnamurthi, S; Saha, P; Saini, H S

    2006-03-01

    Polyphasic characterization of an actinomycete strain VT-36(T) isolated from a sugar-cane field soil sample collected in Punjab State, India, revealed that the strain belongs to the genus Kitasatospora. The strain's chemotaxonomic characters and G+C content of DNA (76.5 mol%) were typical of members of the genus. Analysis of the 16S rRNA gene sequence supported the generic affiliation of the strain and showed that its closest phylogenetic relative was Kitasatospora putterlickiae F18-98T (= DSM 44665T) (98.3 % 16S rRNA gene sequence similarity). The similarities with type strains of all other Kitasatospora species were in the range 95.1-97.0 %. The results of DNA-DNA hybridization showed 54 % relatedness of the isolate and K. putterlickiae F18-98T. Based on the above data and the phenotypic differences from K. putterlickiae and other Kitasatospora species, it is proposed that the isolate should be classified as the type strain of a novel species, Kitasatospora sampliensis sp. nov., with strain VT-36T (= MTCC 6546T = DSM 44898T = JCM 13010T) as the type strain.

  1. Isolation of a new heterolobosean amoeba from a rice field soil: Vrihiamoeba italica gen. nov., sp. nov.

    PubMed

    Murase, Jun; Kawasaki, Michio; De Jonckheere, Johan F

    2010-08-01

    A heterolobosean amoeba strain 6_5F was isolated from an Italian rice field soil. Although 18S rRNA gene sequence analysis demonstrated that the new isolate was closely related to Stachyamoeba sp. ATCC 50324, further molecular analysis and morphological observation showed distinct differences amongst the two. The 5.8S rRNA gene was successfully amplified and sequenced for strain 6_5F but not for strain ATCC 50324. Trophozoites of strain ATCC 50324 transform into flagellate forms in the late stage of incubation before encystment, while strain 6_5F do not show flagellate forms under different conditions of the flagellation test. Light and electron microscopic observation showed the structural difference of cysts of strain 6_5F from strain ATCC 50324 and also from the type strain Stachyamoeba lipophora. The results show that the strain 6_5F is distinct from Stachyamoeba spp. and we propose a new genus and species for this isolate, Vrihiamoeba italica gen. nov., sp. nov.

  2. Anaerobranca zavarzinii sp. nov., an anaerobic, alkalithermophilic bacterium isolated from Kamchatka thermal fields.

    PubMed

    Kevbrin, Vadim; Boltyanskaya, Yulia; Garnova, Elena; Wiegel, Juergen

    2008-06-01

    A novel obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from a small and very shallow geothermally heated pool at Pushino (Kamchatka, Far East Russia). The bacterium, designated strain JW/VK-KS5Y(T), was a Gram staining negative, Gram type positive rod. The cells were sometimes branched, with a tendency to grow in long chains, and were non-sporulating and non-motile. The shortest observed doubling time was 28 min when the novel strain was grown at 54-60 degrees C in 120 mM sodium carbonate-containing medium at pH(25 degrees C) 8.5-9.0. The novel bacterium grew on yeast extract and soytone as sole carbon and energy sources but could also use fumarate, thiosulfate and sulfur as electron acceptors. The DNA G+C content was 32.5 mol%. Based on phylogenetic, DNA-DNA hybridization and phenotypic data, it was concluded that isolate JW/VK-KS5Y(T) (=VKM B-2436(T)=DSM 18970(T)) represents the type strain of a novel species, Anaerobranca zavarzinii sp. nov.

  3. A single-step method for RNA isolation from tropical crops in the field

    PubMed Central

    Breitler, J.-C.; Campa, C.; Georget, F.; Bertrand, B.; Etienne, H.

    2016-01-01

    The RNAzol RT reagent was used to provide pure RNA from human cells. We develop a protocol using RNAzol RT reagent to extract pure RNA from plants tissues and demonstrate that this RNA extraction method works not only at room temperature but also at elevated temperatures and provides the simplest and most effective single-step method to extract pure and undegraded RNA directly from tropical plants in the field. RNA extraction directly in a complex field environment opens up the way for studying gene-environment interactions at transcriptome level to decipher the complex regulatory network involved in multiple-stress responses. PMID:27922073

  4. Temporal abundance, parity, survival rates, and arbovirus isolation of field-collected container-inhabiting mosquitoes in eastern Tennessee.

    PubMed

    Gottfried, Kristy L; Gerhardt, Reid R; Nasci, Roger S; Crabtree, Mary B; Karabatsos, Nick; Burkhalter, Kristen L; Davis, Brent S; Panella, Nicholas A; Paulson, Dave J

    2002-09-01

    Surveillance of container-inhabiting mosquitoes was conducted from June 17 through November 9, 1998, at 2 1997 La Crosse virus (LAC) human case sites (Knox and Cocke counties, Tennessee). Mosquitoes were collected weekly with 2 dry ice-baited Centers for Disease Control miniature light traps, 2 omnidirectional Fay traps, and 40 oviposition traps at each site. A total of 8,408 mosquitoes, composed of Ochlerotatus triseriatus (n = 2,095) and Aedes albopictus (n = 6,313), were reared or collected and assayed for virus. The majority of host-seeking Ae. albopictus (n = 567) collected from July through October from both sites were dissected to determine parity status. Monthly parity rates ranged from 0.78 to 0.85 and 0.79 to 0.92 in Knox and Cocke counties, respectively. The high parity rates indicate that this population of Ae. albopictus has a high daily survival rate and may have a high vector potential. The temporal patterns in Ae. albopictus and Oc. triseriatus egg collections from both of the human case sites were significantly correlated, suggesting that the populations fluctuate in a similar manner across the eastern Tennessee region. Although LAC was not isolated from either species, one isolation of a California serogroup virus, most likely a subtype of Jamestown Canyon virus (JC), was recovered from a pool of 50 male Ae. albopictus reared from eggs collected at the Knox County site (minimum field infection rate of 1.89 per 1,000). This is the 1st report of a very closely related JC-like virus in Ae. albopictus and from Tennessee, as well as the 1st time this potential human pathogen has been isolated from transovarially infected field populations of Ae. albopictus.

  5. A Field-Suitable, Semisolid Aerobic Enrichment Medium for Isolation of Campylobacter jejuni in Small Numbers

    PubMed Central

    Jeffrey, J. S.; Hunter, A.; Atwill, E. R.

    2000-01-01

    The objective of this study was to produce an economical, easy to prepare, field-suitable enrichment medium for detection of Campylobacter jejuni in small numbers. A semisolid aerobic enrichment medium was developed. Rates of recovery from inoculated medium, sterile swabs, and mixed cultures of C. jejuni and coliform bacteria were tested. PMID:10747165

  6. From Isolation to Collaboration: Rethinking the Preservice Field Experience from a Community Perspective

    ERIC Educational Resources Information Center

    Bower, Laura A.; Klecka, Cari L.; Silva, Susan

    2010-01-01

    In this article, we report the action research that shaped the development of the Growing Career Educators project, a teacher-designed field experience for preservice teachers within a high school in the fifth-largest school district in the country. The research consisted of two cycles of action research, both of which focused on whether a…

  7. Analysing one isolated single walled carbon nanotube in the near-field domain with selective nanovolume Raman spectroscopy.

    PubMed

    Atalay, Han; Lefrant, Serge

    2004-09-01

    In this paper, we describe a new method to the selective nanovolume analysing of one isolated single walled carbon nanotube (SWNT). This concept is based on actually available imaging micro-spectrometry systems for working in near-field domain combined with a stigmatic solid immersion lens. This combination of different analytical methods, and modified and configured equipment entitles us to expand the functionality toward a three-dimensional (3D) nanovolume Raman mapping and photoluminescence intensity with a possible discrimination in polarization, as well as photoluminescence decaytime constant mapping with their unique combination. Subsequently, selective spectra can be acquired from the same location on the samples. By spectrally selecting a SWNT, we registered the spatial distribution of the emitted photons in x, y, z vectors to determine the position of a SWNT in the near-field domain. For the SWNTs that are localized with an accuracy better than 18 nm in the x, y and <1 nm in the z directions, we demonstrate an analytical sensitivity close to a single nanotube with unity throughput. This near-field capability is applied to resolve local variations unambiguously in the Raman spectrum along one single SWNT. Finally, in this paper, we report what we believe to be the first evidence of Raman mapping and 3D real optical imaging of carbon nanotubes with near-field resolution.

  8. An efficient thermotolerant and halophilic biosurfactant-producing bacterium isolated from Dagang oil field for MEOR application

    NASA Astrophysics Data System (ADS)

    Wu, Langping; Richnow, Hans; Yao, Jun; Jain, Anil

    2014-05-01

    Dagang Oil field (Petro China Company Limited) is one of the most productive oil fields in China. In this study, 34 biosurfactant-producing strains were isolated and cultured from petroleum reservoir of Dagang oil field, using haemolytic assay and the qualitative oil-displacement test. On the basis of 16S rDNA analysis, the isolates were closely related to the species in genus Pseudomonas, Staphylococcus and Bacillus. One of the isolates identified as Bacillus subtilis BS2 were selected for further study. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties at 37ºC as well as at higher temperature of 55ºC. The biosurfactant produced by the strain BS2 could reduce the surface tension of the culture broth from 70.87 mN/m to 28.97 mN/m after 8 days of incubation at 37ºC and to 36.15 mN/m after 20 days of incubation at 55ºC, respectively. The biosurfactant showed stability at high temperature (up to 120ºC), a wide range of pH (2 to 12) and salt concentrations (up to 12%) offering potential for biotechnology. Fourier transform infrared (FT-IR) spectrum of extracted biosurfactant tentatively characterized the produced biosurfactant as glycolipid derivative. Elemental analysis of the biosurfactant by energy dispersive X-ray spectroscopy (EDS) reveals that the biosurfactant was anionic in nature. 15 days of biodegradation of crude oil suggested a preferential usage of n-alkane upon microbial metabolism of BS2 as a carbon substrate and consequently also for the synthesis of biosurfactants. Core flood studies for oil release indicated 9.6% of additional oil recovery over water flooding at 37ºC and 7.2% of additional oil recovery at 55 ºC. Strain BS2 was characterized as an efficient biosurfactant-producing, thermotolerant and halophillic bacterium and has the potential for application for microbial enhanced oil recovery (MEOR) through water flooding in China's oil fields even in situ as adapted to reservoir chemistry and

  9. Genetic characterization of atypical enteropathogenic Escherichia coli isolates from ewes' milk, sheep farm environments, and humans by multilocus sequence typing and pulsed-field gel electrophoresis.

    PubMed

    Otero, Verónica; Rodríguez-Calleja, José-María; Otero, Andrés; García-López, María-Luisa; Santos, Jesús A

    2013-10-01

    A collection of 81 isolates of enteropathogenic Escherichia coli (EPEC) was obtained from samples of bulk tank sheep milk (62 isolates), ovine feces (4 isolates), sheep farm environment (water, 4 isolates; air, 1 isolate), and human stool samples (9 isolates). The strains were considered atypical EPEC organisms, carrying the eae gene without harboring the pEAF plasmid. Multilocus sequence typing (MLST) was carried out with seven housekeeping genes and 19 sequence types (ST) were detected, with none of them having been previously reported for atypical EPEC. The most frequent ST included 41 strains isolated from milk and human stool samples. Genetic typing by pulsed-field gel electrophoresis (PFGE) resulted in 57 patterns which grouped in 24 clusters. Comparison of strains isolated from the different samples showed phylogenetic relationships between milk and human isolates and also between milk and water isolates. The results obtained show a possible risk for humans due to the presence of atypical EPEC in ewes' milk and suggest a transmission route for this emerging pathogen through contaminated water.

  10. High-resolution melt PCR analysis for rapid identification of Chlamydia abortus live vaccine strain 1B among C. abortus strains and field isolates.

    PubMed

    Vorimore, Fabien; Cavanna, Noémie; Vicari, Nadia; Magnino, Simone; Willems, Hermann; Rodolakis, Annie; Siarkou, Victoria I; Laroucau, Karine

    2012-09-01

    We describe a novel high-resolution melt assay that clearly differentiates Chlamydia abortus live vaccine strain 1B from field C. abortus strains and field wild-type isolates based on previously described single nucleotide polymorphisms. This modern genotyping technique is inexpensive, easy to use, and less time-consuming than PCR-RFLP.

  11. Field and laboratory testing of seal materials proposed for the Waste Isolation Pilot Plant

    SciTech Connect

    Knowles, M.K.; Howard, C.L.

    1996-02-05

    The Small Scale Seal Performance Tests (SSSPT) were a series of in situ tests designed to evaluate the feasibility of various materials for sealing purposes. Testing was initiated in 1985 and concluded in 1995. Materials selected for the SSSPT included salt-saturated concrete, a 50%/50% mixture of crushed salt and bentonite, bentonite, and crushed salt. This paper presents a summary of the SSSPT field program, results of the in situ testing, and a discussion of post-testing laboratory studies of salt-saturated concrete. Results of the SSSPT support the use of salt-saturated concrete, compacted bentonite clay, and compacted crushed salt as sealing materials for the WIPP.

  12. Icelandic basaltic geothermal field: A natural analog for nuclear waste isolation in basalt

    SciTech Connect

    Ulmer, G.C.; Grandstaff, D.E. . Dept. of Geology)

    1984-11-21

    Analog studies of Icelandic geothermal fields have shown that the design of nuclear waste repositories in basalt can benefit by comparison to the data base already available from the development of these geothermal fields. A high degree of similarity exists between these two systems: their petrology, groundwater geochemistry, mineral solubilities, hydrologic parameters, temperature ranges, water-rock redox equilibria, hydrothermal pH values, and secondary mineralogies all show considerable overlap in the range of values. The experimentally-simulated hydrothermal studies of the basaltic nuclear waste repository rocks have, at this time, produced a data base that receives a strong confirmation from the Icelandic analog. Furthermore, the Icelandic analog should eventually be employed to extrapolate into higher and lower temperatures, into longer time-base chemical comparisons, and into more realistic mineral deposition studies, than have been possible in the laboratory evaluations of the nuclear waste repository designs. This eventual use of the Icelandic analog will require cooperative work with the Icelandic Geological Survey. 46 refs., 4 figs., 2 tabs.

  13. Methanolobus profundi sp. nov., a methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field.

    PubMed

    Mochimaru, Hanako; Tamaki, Hideyuki; Hanada, Satoshi; Imachi, Hiroyuki; Nakamura, Kohei; Sakata, Susumu; Kamagata, Yoichi

    2009-04-01

    A mesophilic, methylotrophic methanogen, strain MobM(T), was isolated from a natural gas field in Japan. Strain MobM(T) grew on methanol and methylamines, but not on H(2)/CO(2), formate, acetate or dimethyl sulfide. The cells were motile, irregular cocci (diameter, 0.9-1.2 microm) and occurred singly, in pairs, as tetracocci or (occasionally) as aggregates. Strain MobM(T) grew at 9-37 degrees C (optimally at 30 degrees C) and at pH 6.1-7.8 (optimally at pH 6.5). Sodium and magnesium were required for growth, at 0.1-1.0 M Na(+) (optimally at 0.35 M) and 10-400 mM Mg(2+) (optimally at 15-25 mM). The G+C content of the genomic DNA was 42.4 mol%. 16S rRNA gene sequencing revealed that the isolate is a member of the genus Methanolobus, but distinct from its closest neighbours, Methanolobus tindarius DSM 2278(T) (sequence similarity, 98.0 %) and Methanolobus vulcani DSM 3029(T) (98.1 %). On the basis of phenotypic and phylogenetic features of MobM(T), it is clear that this strain represents a novel species of the genus Methanolobus, for which the name Methanolobus profundi sp. nov. is proposed. The type strain is MobM(T) (=DSM 21213(T)=NBRC 104158(T)).

  14. Oxygen Implant Isolation of n-GaN Field-Effect Transistor Structures

    SciTech Connect

    Dang, G.; Cao, X.A.; Ren, F.; Pearton, S.J.; Han, J.; Baca, A.G.; Shul, R.J.

    1999-07-20

    Multiple-energy (30-325 keV) O{sup +} implantation into GaN field-effect transistor structures (n {approximately} 10{sup 18} cm{sup {minus}3}, 3000 {angstrom} thick) can produce as-implanted sheet resistances of 4 x 10{sup 12} {Omega}/{open_square}, provided care is taken to ensure compensation of the region up to the projected range of the lowest energy implant. The sheet resistance remains above 10{sup 7} {Omega}/{open_square} to annealing temperatures of {approximately} 650 C and displays an activation energy of 0.29 eV. No diffusion of the implanted oxygen was observed for anneals up to 800 C.

  15. Molecular detection of field isolates of Turkey Eimeria by polymerase chain reaction amplification of the cytochrome c oxidase I gene.

    PubMed

    Rathinam, T; Gadde, U; Chapman, H D

    2015-07-01

    Oocysts of Eimeria spp. were isolated from litter samples obtained from 30 commercial turkey farms. Genomic DNA was extracted from clean oocysts, and polymerase chain amplification of the species-specific cytochrome c oxidase subunit I (COI) gene was performed for five species of turkey Eimeria. The species tested were Eimeria adenoeides, Eimeria meleagrimitis, Eimeria meleagridis, Eimeria dispersa, and Eimeria gallopavonis. All DNA samples were positive for E. meleagrimitis, nine were positive for E. adenoeides, two were positive for E. dispersa, and none for E. meleagridis and E. gallopavonis. E. meleagrimitis occurred as a single species in 21 (70 %) of the farms while 9 (30 %) farms had a mixed species with E. meleagrimitis and E. adenoeides and 2 (7 %) were triple positive with E. meleagrimitis, E. adenoeides, and E. dispersa. This is the first account of the field prevalence of turkey Eimeria species using molecular methods.

  16. Biosynthesis of compatible solutes in rhizobial strains isolated from Phaseolus vulgaris nodules in Tunisian fields

    PubMed Central

    2010-01-01

    Background Associated with appropriate crop and soil management, inoculation of legumes with microbial biofertilizers can improve food legume yield and soil fertility and reduce pollution by inorganic fertilizers. Rhizospheric bacteria are subjected to osmotic stress imposed by drought and/or NaCl, two abiotic constraints frequently found in semi-arid lands. Osmostress response in bacteria involves the accumulation of small organic compounds called compatible solutes. Whereas most studies on rhizobial osmoadaptation have focussed on the model species Sinorhizobium meliloti, little is known on the osmoadaptive mechanisms used by native rhizobia, which are good sources of inoculants. In this work, we investigated the synthesis and accumulations of compatible solutes by four rhizobial strains isolated from root nodules of Phaseolus vulgaris in Tunisia, as well as by the reference strain Rhizobium tropici CIAT 899T. Results The most NaCl-tolerant strain was A. tumefaciens 10c2, followed (in decreasing order) by R. tropici CIAT 899, R. leguminosarum bv. phaseoli 31c3, R. etli 12a3 and R. gallicum bv. phaseoli 8a3. 13C- and 1H-NMR analyses showed that all Rhizobium strains synthesized trehalose whereas A. tumefaciens 10c2 synthesized mannosucrose. Glutamate synthesis was also observed in R. tropici CIAT 899, R. leguminosarum bv. phaseoli 31c3 and A. tumefaciens 10c2. When added as a carbon source, mannitol was also accumulated by all strains. Accumulation of trehalose in R. tropici CIAT 899 and of mannosucrose in A. tumefaciens 10c2 was osmoregulated, suggesting their involvement in osmotolerance. The phylogenetic analysis of the otsA gene, encoding the trehalose-6-phosphate synthase, suggested the existence of lateral transfer events. In vivo 13C labeling experiments together with genomic analysis led us to propose the uptake and conversion pathways of different carbon sources into trehalose. Collaterally, the β-1,2-cyclic glucan from R. tropici CIAT 899 was co

  17. Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae

    PubMed Central

    Gouré, Julien; Findlay, Wendy A; Deslandes, Vincent; Bouevitch, Anne; Foote, Simon J; MacInnes, Janet I; Coulton, James W; Nash, John HE; Jacques, Mario

    2009-01-01

    Background Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is a highly contagious respiratory pathogen that causes severe losses to the swine industry worldwide. Current commercially-available vaccines are of limited value because they do not induce cross-serovar immunity and do not prevent development of the carrier state. Microarray-based comparative genomic hybridizations (M-CGH) were used to estimate whole genomic diversity of representative Actinobacillus pleuropneumoniae strains. Our goal was to identify conserved genes, especially those predicted to encode outer membrane proteins and lipoproteins because of their potential for the development of more effective vaccines. Results Using hierarchical clustering, our M-CGH results showed that the majority of the genes in the genome of the serovar 5 A. pleuropneumoniae L20 strain were conserved in the reference strains of all 15 serovars and in representative field isolates. Fifty-eight conserved genes predicted to encode for outer membrane proteins or lipoproteins were identified. As well, there were several clusters of diverged or absent genes including those associated with capsule biosynthesis, toxin production as well as genes typically associated with mobile elements. Conclusion Although A. pleuropneumoniae strains are essentially clonal, M-CGH analysis of the reference strains of the fifteen serovars and representative field isolates revealed several classes of genes that were divergent or absent. Not surprisingly, these included genes associated with capsule biosynthesis as the capsule is associated with sero-specificity. Several of the conserved genes were identified as candidates for vaccine development, and we conclude that M-CGH is a valuable tool for reverse vaccinology. PMID:19239696

  18. Optimizing the HRP-2 In Vitro Malaria Drug Susceptibility Assay Using a Reference Clone to Improve Comparisons of Plasmodium falciparum Field Isolates

    DTIC Science & Technology

    2012-09-13

    analysed using the LC/MS system consisting of a reversed phase column (XTerra MS C18, 3.5 μm, 2.1 x 50 mm, Waters Corporation, MA, USA) and pre-column of...of such systems to evaluate field isolates for artemisinin resistance, particularly when used in isolation, without clinical correlation. The most...effort is the use of standardized Plasmodium falciparum reference clones to provide context for variability among the several assay systems

  19. Pulsed-field gel electrophoresis analysis of more than one clinical isolate of Campylobacter spp. from each of 49 patients in New Zealand.

    PubMed

    Gilpin, Brent; Robson, Beth; Lin, Susan; Scholes, Paula; On, Stephen

    2012-02-01

    Pulsed-field gel electrophoresis (PFGE) analysis demonstrated that while 76% of patients had only one genotype of campylobacter, 10% carried two different but related genotypes (Dice coefficients > 0.78), and 14% carried at least two unrelated genotypes (Dice coefficients < 0.65). This supports the clustering of Campylobacter isolates with similar PFGE patterns, highlights the need to analyze multiple isolates from both sources and patients, and confirms that caution should be exercised before epidemiological links between patients or sources are dismissed.

  20. Biological effects of gamma-irradiation on laboratory and field isolates of Eimeria tenella (Protozoa; Coccidia).

    PubMed

    Gilbert, J M; Fuller, A L; Scott, T C; McDougald, L R

    1998-06-01

    Sporulated oocysts of a field strain (FS-111) and a laboratory strain (WIS) of Eimeria tenella were exposed to 0, 50, 100, 150, or 200 Gy of gamma-radiation from a 60Co source. Irradiated oocysts of WIS and FS-111 were not significantly more fragile after irradiation as shown by the release of sporocysts after 5-105 s of vortex agitation with glass beads. Excystation was normal in both strains after treatment of the sporocysts with trypsin and sodium taurodeoxycholate, even in groups exposed to 200 Gy of radiation. Sporozoite release from irradiated sporocysts was more rapid than that from unirradiated sporocysts, primarily because of a shorter lag phase during the first 30 min. Irradiated sporozoites were slower to parasitize cultured chick kidney cells than were control sporozoites (4 h postinoculation), but after 24 h there was no significant difference (P < 0.05) between irradiated and control groups except for the WIS treated with 200 Gy. After 48 h, developing schizonts were reduced by 77-94% on exposure to 50-200 Gy. Strain FS-111 did not develop as well as WIS in vitro, but the effect of irradiation was similar. When irradiated oocysts of WIS or FS-111 were inoculated into chickens the prepatent period was unaffected, but fewer oocysts were produced, lesion scores were lower, and the weight gain was less strongly affected in proportion to the doses of radiation. These results suggest that the effects of radiation damage were largely confined to the mechanism of nuclear and cellular reproduction rather than other physiological processes.

  1. Biodegradation of 2,4-dichlorophenoxyacetic acid by bacteria with highly antibiotic-resistant pattern isolated from wheat field soils in Kurdistan, Iran.

    PubMed

    Karami, Solmaz; Maleki, Afshin; Karimi, Ebrahim; Poormazaheri, Helen; Zandi, Shiva; Davari, Behrooz; Salimi, Yahya Zand; Gharibi, Fardin; Kalantar, Enayatollah

    2016-12-01

    Recently, there has been increasing interest to clean up the soils contaminated with herbicide. Our aim was to determine the bioremediation of 2,4-dichlorophenoxyacetic acid (2,4-D) from wheat fields which have a long history of herbicide in Sanandaj. Based on our literature survey, this study is the first report to isolate and identify antimicrobial resistant bacteria from polluted wheat field soils in Sanandaj which has the capacity to degrade 2,4-D. From 150 2,4-D-exposed soil samples, five different bacteria were isolated and identified based on biochemical tests and 16S ribosomal RNA (rRNA). Pseudomonas has been the most frequently isolated genus. By sequencing the 16S rRNA gene of the isolated bacteria, the strains were detected and identified as a member of the genus Pseudomonas sp, Entrobacter sp, Bacillus sp, Seratia sp, and Staphylococcus sp. The sequence of Sanandaj 1 isolate displayed 87% similarity with the 16S rRNA gene of a Pseudomonas sp (HE995788). Similarly, all the isolates were compared to standard strains based on 16S rRNA. Small amounts of 2,4-D could be transmitted to a depth of 10-20 cm; however, in the depth of 20-40 cm, we could not detect the 2,4-D. The isolates were resistant to various antibiotics particularly, penicillin, ampicillin, and amoxicillin.

  2. Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field.

    PubMed

    Yang, Jung-Eun; Kim, Se-Young; Im, Wan-Taek; Yi, Tae-Hoo

    2011-06-01

    A Gram-negative, aerobic, non-motile, non-spore-forming, yellow-pigmented, rod-shaped bacterium, designated strain THG 01(T), was isolated from the soil of a ginseng field in Pocheon province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain THG 01(T) grew well at 25-37 °C and pH 6.0-7.5 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity data, strain THG 01(T) was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium anhuiense D3(T) (97.5 % similarity), Flavobacterium johnsoniae UW101(T) (96.8 %) and Flavobacterium denitrificans ED5(T) (96.7 %). 16S rRNA gene sequence similarities between the novel strain and members of other recognized species within the family Flavobacteriaceae were less than 96.7 %. The G+C content of the genomic DNA of strain THG 01(T) was 32.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone was MK-6 and major fatty acids were iso-C(15 : 0), iso-C(15 : 0) 3-OH and C(16 : 1)ω7c and/or C(16 : 1)ω6c ) supported the affiliation of strain THG 01(T) to the genus Flavobacterium. DNA-DNA hybridization experiments showed that DNA-DNA relatedness values between strain THG 01(T) and its closest phylogenetic neighbours were below 11 %. The results of physiological and biochemical tests enabled strain THG 01(T) to be differentiated genotypically and phenotypically from recognized species of the genus Flavobacterium. The isolate therefore represents a novel species, for which the name Flavobacterium ginsenosidimutans sp. nov. is proposed, with THG 01(T) ( = KACC 14525(T) = JCM 16720(T)) as the type strain.

  3. Phylogenetic analysis of classical swine fever virus (CSFV) field isolates from outbreaks in South and Central America.

    PubMed

    Pereda, A J; Greiser-Wilke, I; Schmitt, B; Rincon, M A; Mogollon, J D; Sabogal, Z Y; Lora, A M; Sanguinetti, H; Piccone, M E

    2005-06-01

    To date, there is little information concerning the epidemiological situation of classical swine fever (CSF) in the Americas. Besides summarizing the available data, genotyping of isolates from outbreaks in domestic pigs in several countries of South and Central America was performed. For this, a 190 base fragment of the E2 envelope glycoprotein gene was used. European strains and isolates, and historical isolates from the United States (US) were included for comparison. In contrast to the situation in most parts of Europe, where group 2 isolates predominate, it was found that all the isolates from the American continent analyzed belonged to group 1 and were further resolved into three subgroups. The Cuban isolates clustered in subgroup 1.2, whereas the isolates from Honduras and Guatemala clustered in subgroup 1.3. The remaining isolates from Argentina, Brazil, Colombia and Mexico generated four poorly resolved clusters in subgroup 1.1, together with the vaccine strains, with historical European and US isolates, and with a recent Russian isolate. While the vaccine strains and the historical European isolates formed a relatively distinct cluster, one of the US isolates clustered together with the Mexican, and another one with Colombian isolates. Historically, CSF (hog cholera) was observed almost simultaneously in the US and in Europe in the first half of the 19th century, and its origin remains a matter of discussion. Our results showed that the US isolates are closely related to isolates from South America, while appearance of isolates in Cuba on one hand and in Honduras and Guatemala on the other hand, seems to have been due to unrelated events. This allows to speculate that at least in the American continent, CSF virus may have appeared independently in several regions, and spreading may have been a secondary effect.

  4. Evaluation and improvement of a single nucleotide polymorphism-based PCR assay for rapid differentiation of live attenuated vaccine strains from field isolates of Erysipelothrix rhusiopathiae.

    PubMed

    Zhu, Weifeng; Li, Jingtao; Wang, Ya; Kang, Chao; Jin, Meilin; Chen, Huanchun

    2016-11-01

    A single nucleotide polymorphism-based PCR assay has been developed to differentiate the attenuated vaccine strain used in Japan from field isolates of Erysipelothrix rhusiopathiae found in pigs. However, this assay has been evaluated with only Japanese strains and isolates; therefore, it is unknown whether it could be used in other countries with E. rhusiopathiae strains and isolates of different genetic backgrounds. In our study, the PCR assay was evaluated using Chinese E. rhusiopathiae vaccine strains and field isolates. The PCR assay was able to differentiate the attenuated vaccine strains from the field isolates of E. rhusiopathiae in China but with a pattern different from that observed in Japan (only a single nucleotide polymorphism was detected in the Chinese vaccine strains compared with 5 in the Japanese vaccine strains). Importantly, either a DNA polymerase without 3' to 5' exonuclease activity or an exo(+) polymerase with an antibody inhibiting the proofreading activity was required. In conclusion, after evaluation and improvement, this fast differentiation assay can be extended from Japan to China.

  5. A Field Experiment to Assess the Rate of Infestation in Honey Bee Populations of Two Metarhizium anisopliae Isolates on Varroa destructor (Acari: Mesostigmata)

    PubMed Central

    Pirali-kheirabadi, Khodadad; Teixeira-da-Silva, Jaime A; Razzaghi-Abyaneh, Mehdi; Nazemnia, Mehdi

    2013-01-01

    Background: The protective effect of two isolates of an entomopathogenic fungus, Metarhizium anisopliae (DEMI 002 and Iran 437C) on the adult stage of Varroa destructor was evaluated in comparison with fluvalinate strips in the field. Methods: A total of 12 honey bee colonies were provided from an apiculture farm. The selected hives were divided into 4 groups (3 hives per group). The first group was the control, treated with distilled water. The other two groups were exposed to different fungi (M. anisopliae isolates DEMI 002 and Iran 437C) and the last group was treated with one strip of fluvalinate per colony. The number of fallen mites was counted using sticky traps during a 6-day period, six days before and after treatments. A fungal suspension at a concentration of 5× 106 conidia/mL was sprayed onto the frames and the number of fallen mites was counted. Results: Metarhizium anisopliae DEMI 002 and Iran 437C isolates were as effective (i.e., caused as much mite fall) as the fluvalinate strip in controlling bee colonies than no treatment. Conclusion: Both M. anisopliae isolates are promising candidates as agents in the control of Varroa mites under field conditions. Isolate DEMI 002 can be considered as a possible non-chemical biocontrol agent for controlling bee infestation with V. destructor in the field. In order to substantiate this hypothesis, tests are currently being performed using larger colonies and larger doses than tested in the present study in our beekeeping. PMID:23785691

  6. Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing

    PubMed Central

    Wang, Yun; Butler, Robert R.; Reddy, N. Rukma; Skinner, Guy E.; Larkin, John W.

    2015-01-01

    Clostridium sporogenes PA 3679 is a nonpathogenic, nontoxic model organism for proteolytic Clostridium botulinum used in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates of C. sporogenes PA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. All C. sporogenes PA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolytic C. botulinum strains, with clade I forming a distinct cluster with other C. sporogenes non-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession number AGAH00000000.1) than clade II isolates were. The genomic reference C. sporogenes PA 3679 (NCTC8594) genome and clade I C. sporogenes isolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use of C. sporogenes PA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization of C. sporogenes PA 3679 are of critical importance. PMID:26519392

  7. Identification of nif genes in N2-fixing bacterial strains isolated from rice fields along the Yangtze River Plain.

    PubMed

    Xie, Guang Hui; Cui, Zongjun; Yu, Jun; Yan, Jing; Hai, Weili; Steinberger, Yosef

    2006-01-01

    The aim of this research was to identify nifH and nifHDKYE ' genes in twenty strains of N2-fixing heterotrophic bacteria isolated from rice fields in the Yangtze River Plain. Southern hybridization of the total DNA from each strain was performed with the Klebsiella pneumoniae nifHDKYE ' gene probe (6.2 kb Eco RI fragment from pSA30) and the Azospirillum brasilense nifH gene probe (0.6 kb Eco RI-Hin dIII fragment from pHU8). We found that Eco RI fragments of total DNA from Aeromonas hydrophila HY2, Bacillus azotoformans FD, Bacillus licheniformis NCH1, NCH5, WH4, Bacillus brevis NC2, Bacillus pumilus NC12, Bacillus cereus NCH2, Citrobacter freundii HY5, HY9, Derxia gummosa HZ5, Pseudomonas mendocina HZ1 and Pseudomonas pseudoalcaligenes WH3 were positively hybridized with both of the probes. Agrobacterium radiobacter HY17, Corynebacterium sp. HY12, YZ and Pseudomonas sp. HY11 had Eco RI fragments hybridized with the K. pneumoniae nifHDKYE ' gene probe. An Eco RI fragment of total DNA from Bacillus megaterium YY4 was positively hybridized to the A. brasilense nifH gene probe. No hybridization sign was found in the total DNA fragments from Alcaligenes cupidus YY6 and Corynebacterium sp. NC11 hybridized with either of the gene probes. The data provide the number and size of EcoRI fragments of the total DNA hybridized with the nif gene probes for these strains of rarely studied species, suggesting additional evidence for N2 fixing and nif gene diversity of N2-fixing bacteria in rice fields along the Yangtze River Plain.

  8. Temporal and spatial distribution of Cronobacter isolates in a milk powder processing plant determined by pulsed-field gel electrophoresis.

    PubMed

    Hein, Ingeborg; Gadzov, Boris; Schoder, Dagmar; Foissy, Helmut; Malorny, Burkhard; Wagner, Martin

    2009-03-01

    A milk powder processing line was sampled for the presence of Enterobacteriaceae and the opportunistic neonatal pathogen Cronobacter at six different sampling sites during an 11-month period. The highest number of Enterobacteriaceae-positive samples was recovered from the raw milk concentrate before pasteurization (78.2%) and from nonproduct samples of the processing line (86.5%), which included swabs from the drying tower and screw conveyers, swabs from the explosion chamber, waste water after the automated cleaning-in-place procedure, air filter cut-outs, and floor samples underneath the outlet of the packaging machine. The prepackaged and packaged final product was contaminated at a rate of 6.6% and 7.1%, respectively. The prevalence of Cronobacter in the prefinal product and the prepackaged and packaged final product was 14.3%, 3.8%, and 2.1%, respectively. Pulsed-field gel electrophoresis (PFGE) analysis of 133 Cronobacter isolates yielded 40 different PFGE profiles. Long-term persistence in the processing line of some of these PFGE profiles was observed. Comparison of the PFGE profiles recovered at different sampling sites revealed the supply air as a potential source for extrinsic Cronobacter contamination. In addition, recovery of the same PFGE profiles before and after CIP events followed by heat treatment indicated the inefficiency of these hygiene measures to completely eliminate Cronobacter from all areas of the processing line. This information provides an essential basis for developing control and prevention strategies concerning this opportunistic pathogen.

  9. Low Frequency Electromagnetic Field Conditioning Protects against I/R Injury and Contractile Dysfunction in the Isolated Rat Heart.

    PubMed

    Bialy, Dariusz; Wawrzynska, Magdalena; Bil-Lula, Iwona; Krzywonos-Zawadzka, Anna; Wozniak, Mieczyslaw; Cadete, Virgilio J J; Sawicki, Grzegorz

    2015-01-01

    Low frequency electromagnetic field (LF-EMF) decreases the formation of reactive oxygen species, which are key mediators of ischemia/reperfusion (I/R) injury. Therefore, we hypothesized that the LF-EMF protects contractility of hearts subjected to I/R injury. Isolated rat hearts were subjected to 20 min of global no-flow ischemia, followed by 30 min reperfusion, in the presence or absence of LF-EMF. Coronary flow, heart rate, left ventricular developed pressure (LVDP), and rate pressure product (RPP) were determined for evaluation of heart mechanical function. The activity of cardiac matrix metalloproteinase-2 (MMP-2) and the contents of coronary effluent troponin I (TnI) and interleukin-6 (IL-6) were measured as markers of heart injury. LF-EMF prevented decreased RPP in I/R hearts, while having no effect on coronary flow. In addition, hearts subjected to I/R exhibited significantly increased LVDP when subjected to LF-EMF. Although TnI and IL-6 levels were increased in I/R hearts, their levels returned to baseline aerobic levels in I/R hearts subjected to LF-EMF. The reduced activity of MMP-2 in I/R hearts was reversed in hearts subjected to LF-EMF. The data presented here indicate that acute exposure to LF-EMF protects mechanical function of I/R hearts and reduces I/R injury.

  10. Low Frequency Electromagnetic Field Conditioning Protects against I/R Injury and Contractile Dysfunction in the Isolated Rat Heart

    PubMed Central

    Bialy, Dariusz; Wawrzynska, Magdalena; Bil-Lula, Iwona; Krzywonos-Zawadzka, Anna; Wozniak, Mieczyslaw; Cadete, Virgilio J. J.

    2015-01-01

    Low frequency electromagnetic field (LF-EMF) decreases the formation of reactive oxygen species, which are key mediators of ischemia/reperfusion (I/R) injury. Therefore, we hypothesized that the LF-EMF protects contractility of hearts subjected to I/R injury. Isolated rat hearts were subjected to 20 min of global no-flow ischemia, followed by 30 min reperfusion, in the presence or absence of LF-EMF. Coronary flow, heart rate, left ventricular developed pressure (LVDP), and rate pressure product (RPP) were determined for evaluation of heart mechanical function. The activity of cardiac matrix metalloproteinase-2 (MMP-2) and the contents of coronary effluent troponin I (TnI) and interleukin-6 (IL-6) were measured as markers of heart injury. LF-EMF prevented decreased RPP in I/R hearts, while having no effect on coronary flow. In addition, hearts subjected to I/R exhibited significantly increased LVDP when subjected to LF-EMF. Although TnI and IL-6 levels were increased in I/R hearts, their levels returned to baseline aerobic levels in I/R hearts subjected to LF-EMF. The reduced activity of MMP-2 in I/R hearts was reversed in hearts subjected to LF-EMF. The data presented here indicate that acute exposure to LF-EMF protects mechanical function of I/R hearts and reduces I/R injury. PMID:25961016

  11. Isolation of a thermophilic and halophilic tyrosol-degrading Geobacillus from a Tunisian high-temperature oil field.

    PubMed

    Chamkha, Mohamed; Mnif, Sami; Sayadi, Sami

    2008-06-01

    An aerobic, thermophilic, halotolerant and Gram-positive bacterium, designated strain C5, was isolated from a high-temperature oil field, located in Sfax, Tunisia, after enrichment on tyrosol. Strain C5 grew between 25 and 70 degrees C and optimally at 50 degrees C. It grew in the presence of 0-12% (w/v) NaCl, with optimum growth at 3% (w/v) NaCl. Strain C5 was able to degrade tyrosol aerobically, in the presence of 30 g L(-1) NaCl and under warm conditions (55 degrees C). The degradation of tyrosol proceeded via p-hydroxyphenylacetic and 3,4-dihydroxyphenylacetic acids. The products were confirmed by HPLC and GC-MS analyses. Strain C5 was also found to degrde a wide range of other aromatic compounds, including benzoic, p-hydroxybenzoic, protocatechuic, vanillic, p-hydroxyphenylacetic, 3,4-dihydroxyphenylacetic, cinnamic and ferulic acids, phenol and m-cresol. Moreover, strain C5 was grown on diesel and crude oil as sole carbon and energy sources. Strain C5 was also able to utilize several carbohydrates. Phenotypic characteristics and phylogenetic analysis of the 16S rRNA gene sequence of strain C5 revealed that it was related to members of the genus Geobacillus, being most closely related to the type strain of G. pallidus (99% sequence similarity). In addition, we report on growth of the type strain of G. pallidus on different aromatic compounds and hydrocarbons.

  12. Isolation and characterization of Klebsiella oxytoca strain degrading crude oil from a Tunisian off-shore oil field.

    PubMed

    Chamkha, Mohamed; Trabelsi, Yosra; Mnif, Sami; Sayadi, Sami

    2011-12-01

    A facultatively anaerobic, Gram-negative, mesophilic, moderately halotolerant, non-motile, and non-sporulated bacterium, designated strain BSC5 was isolated from an off-shore "Sercina" oil field, located near the Kerkennah island, Tunisia. Yeast extract was not required for growth. Phenotypic characteristics and phylogenetic analysis of the 16S rRNA gene sequence of strain BSC5 revealed that it was related to members of the genus Klebsiella, being most closely related to the type strain of K. oxytoca (99% sequence similarity). Strain BSC5 was capable of using aerobically the crude oil as substrate growth. The growth of strain BSC5 on crude oil was followed by measuring the OD(600 nm) and by enumeration of viable cells at different culture's time. GC-MS analysis showed that strain BSC5 was capable of degrading a wide range of aliphatic hydrocarbons from C(13) to C(30) . The biodegradation rate for n -alkanes reached 44% and 75%, after 20 and 45 days of incubation, respectively. Addition of the synthetic surfactant, Tween 80, accelerated the crude oil degradation. The biodegradation rate for n -alkanes reached 61% and 98%, after 20 and 45 days of incubation, respectively. Moreover, three aromatic compounds, p -hydroxybenzoate, protocatechuate and gentisate, were metabolized completely by strain BSC5 after 24 h, under aerobic conditions.

  13. Comparison of pulsed-field gel electrophoresis & repetitive sequence-based PCR methods for molecular epidemiological studies of Escherichia coli clinical isolates

    PubMed Central

    Bae, Il Kwon; Kim, Juwon; Sun, Je Young Hannah; Jeong, Seok Hoon; Kim, Yong-Rok; Wang, Kang-Kyun; Lee, Kyungwon

    2014-01-01

    Background & objectives: PFGE, rep-PCR, and MLST are widely used to identify related bacterial isolates and determine epidemiologic associations during outbreaks. This study was performed to compare the ability of repetitive sequence-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE) to determine the genetic relationships among Escherichia coli isolates assigned to various sequence types (STs) by two multilocus sequence typing (MLST) schemes. Methods: A total of 41 extended-spectrum β-lactamase- (ESBL-) and/or AmpC β-lactamase-producing E. coli clinical isolates were included in this study. MLST experiments were performed following the Achtman's MLST scheme and the Whittam's MLST scheme, respectively. Rep-PCR experiments were performed using the DiversiLab system. PFGE experiments were also performed. Results: A comparison of the two MLST methods demonstrated that these two schemes yielded compatible results. PFGE correctly segregated E. coli isolates belonging to different STs as different types, but did not group E. coli isolates belonging to the same ST in the same group. Rep-PCR accurately grouped E. coli isolates belonging to the same ST together, but this method demonstrated limited ability to discriminate between E. coli isolates belonging to different STs. Interpretation & conclusions: These results suggest that PFGE would be more effective when investigating outbreaks in a limited space, such as a specialty hospital or an intensive care unit, whereas rep-PCR should be used for nationwide or worldwide epidemiology studies. PMID:25579152

  14. Complete genome sequence of Cupriavidus basilensis 4G11, isolated from the Oak Ridge Field Research Center site

    SciTech Connect

    Ray, Jayashree; Waters, R. Jordan; Skerker, Jeffrey M.; Kuehl, Jennifer V.; Price, Morgan N.; Huang, Jiawen; Chakraborty, Romy; Arkin, Adam P.; Deutschbauer, Adam

    2015-05-14

    Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field Research Center (FRC) site. Here, we report the complete genome sequence and annotation of Cupriavidus basilensis 4G11. The genome contains 8,421,483 bp, 7,661 predicted protein-coding genes, and a total GC content of 64.4%.

  15. Detection of a Bacteriophage Gene Encoding a Mu-like Portal Protein in Haemophilus parasuis Reference Strains and Field Isolates by Nested Polymerase Chain Reaction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A nested PCR assay was developed to determine the presence of a gene encoding a bacteriophage Mu-like portal protein, gp29, in 15 reference strains and 31 field isolates of Haemophilus parasuis. Specific primers, based on the gene’s sequence, were utilized. A majority of the virulent reference strai...

  16. Complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from lettuce (Lactuca sativa) originating from a conventional field in Norway.

    PubMed

    Dees, Merete Wiken; Brurberg, May Bente; Lysøe, Erik

    2016-12-01

    Here, we present the 3,795,952 bp complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from conventionally grown lettuce (Lactuca sativa) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017580.

  17. Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China)

    PubMed Central

    Poltaraus, Andrey B.; Sokolova, Diyana S.; Grouzdev, Denis S.; Ivanov, Timophey M.; Malakho, Sophia G.; Korshunova, Alena V.; Rozanov, Aleksey S.; Tourova, Tatiyana P.

    2016-01-01

    The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus. PMID:27284131

  18. Draft Genome Sequence of Rhodococcus rhodochrous Strain KG-21, a Soil Isolate from Oil Fields of Krishna-Godavari Basin, India.

    PubMed

    Dawar, Chhavi; Aggarwal, Ramesh K

    2015-10-15

    Here, we present the 6.1-Mb draft genome sequence of Rhodococcus rhodochrous strain KG-21, a soil isolate from the oil fields of Krishna-Godavari Basin in Andhra Pradesh, India. This genomic resource may help in the identification of the gene(s) involved in hydrocarbon degradation and their possible deployment for bioremediation.

  19. Virus isolation vs RT-PCR: which method is more successful in detecting VHSV and IHNV in fish tissue sampled under field conditions?

    PubMed

    Knüsel, R; Bergmann, S M; Einer-Jensen, K; Casey, J; Segner, H; Wahli, T

    2007-09-01

    This study compared the results of reverse transcription-polymerase chain reaction (RT-PCR) and traditional virus isolation on cell culture in detection of viral haemorrhagic septicaemia virus (VHSV) and infectious haematopoietic necrosis virus (IHNV). RT-PCR was used for 172 tissue sample pools (total of 859 fish) originating from a field survey on the occurrence of VHSV and IHNV in farmed and wild salmonids in Switzerland. These samples represented all sites with fish that were either identified as virus-positive by means of virus isolation (three sites, four positive tissue sample pools) and/or demonstrated positive anti-VHSV-antibody titres (83 sites, 121 positive blood samples) in a serum plaque neutralization test (SPNT). The RT-PCR technique confirmed the four VHSV-positive tissue sample pools detected by virus isolation and additionally identified one VHSV-positive sample that showed positive anti-VHSV-AB titres, but was negative in virus isolation. With IHNV, RT-PCR detected two positive samples not identified by virus isolation while in these fish the SPNT result had been questionable. One of the IHNV-positive samples represents the first detection of IHNV-RNA in wild brown trout in Switzerland. Compared to SPNT, the RT-PCR method detected, as with virus isolation, a much lower number of positive cases; reasons for this discrepancy are discussed. Our results indicate that RT-PCR can not only be successfully applied in field surveys, but may also be slightly more sensitive than virus isolation. However, in a titration experiment under laboratory conditions, the sensitivity of RT-PCR was not significantly higher when compared with virus isolation.

  20. The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome.

    PubMed

    Schneiker-Bekel, Susanne; Wibberg, Daniel; Bekel, Thomas; Blom, Jochen; Linke, Burkhard; Neuweger, Heiko; Stiens, Michael; Vorhölter, Frank-Jörg; Weidner, Stefan; Goesmann, Alexander; Pühler, Alfred; Schlüter, Andreas

    2011-08-20

    Isolates of the symbiotic nitrogen-fixing species Sinorhizobium meliloti usually contain a chromosome and two large megaplasmids encoding functions that are absolutely required for the specific interaction of the microsymbiont with corresponding host plants leading to an effective symbiosis. The complete genome sequence, including the megaplasmids pSmeSM11c (related to pSymA) and pSmeSM11d (related to pSymB), was established for the dominant, indigenous S. meliloti strain SM11 that had been isolated during a long-term field release experiment with genetically modified S. meliloti strains. The chromosome, the largest replicon of S. meliloti SM11, is 3,908,022bp in size and codes for 3785 predicted protein coding sequences. The size of megaplasmid pSmeSM11c is 1,633,319bp and it contains 1760 predicted protein coding sequences whereas megaplasmid pSmeSM11d is 1,632,395bp in size and comprises 1548 predicted coding sequences. The gene content of the SM11 chromosome is quite similar to that of the reference strain S. meliloti Rm1021. Comparison of pSmeSM11c to pSymA of the reference strain revealed that many gene regions of these replicons are variable, supporting the assessment that pSymA is a major hot-spot for intra-specific differentiation. Plasmids pSymA and pSmeSM11c both encode unique genes. Large gene regions of pSmeSM11c are closely related to corresponding parts of Sinorhizobium medicae WSM419 plasmids. Moreover, pSmeSM11c encodes further novel gene regions, e.g. additional plasmid survival genes (partition, mobilisation and conjugative transfer genes), acdS encoding 1-aminocyclopropane-1-carboxylate deaminase involved in modulation of the phytohormone ethylene level and genes having predicted functions in degradative capabilities, stress response, amino acid metabolism and associated pathways. In contrast to Rm1021 pSymA and pSmeSM11c, megaplasmid pSymB of strain Rm1021 and pSmeSM11d are highly conserved showing extensive synteny with only few rearrangements

  1. Speciation and strain-typing of Staphylococcus agnetis and Staphylococcus hyicus isolated from bovine milk using a novel multiplex PCR and pulsed-field gel electrophoresis.

    PubMed

    Adkins, P R F; Middleton, J R; Calcutt, M J; Stewart, G C; Fox, L K

    2017-03-22

    Staphylococcus hyicus and Staphylococcus agnetis are two coagulase variable staphylococcal species that can be isolated from bovine milk and are difficult to differentiate. The objectives of this study were to characterize isolates of bovine milk origin from a collection that had previously been characterized as coagulase positive S. hyicus based on phenotypic speciation methods and to develop a PCR-based method for differentiating S. hyicus, S. agnetis, and S. aureus. Isolates (n = 62) were selected from a previous study in which milk samples were collected from cows on 15 dairy herds. Isolates were coagulase tested and speciated using housekeeping gene sequencing. A multiplex PCR to differentiate S. hyicus, S. agnetis, and S. aureus was developed. Pulsed-field gel electrophoresis was conducted to strain type isolates. Based on gene sequencing, 44/62 of the isolates were determined to be either S. agnetis (n = 43) or S. hyicus (n = 1). Overall, 88% (37/42) of coagulase positive S. agnetis isolates were found to be coagulase positive at 4 hours. Herd-level prevalence of coagulase positive S. agnetis ranged from 0 to 2.17%. Strain-typing identified 23 different strains. Six strains were identified more than once and from multiple cows within the herd. Three strains were isolated from cows at more than one time point, with 41-264 days between samplings. These data suggest that S. agnetis is likely more prevalent on dairy farms than S. hyicus Also, some S. agnetis isolates in this study appeared to be contagious and associated with persistent infections.

  2. Diversity of pulsed-field gel electrophoresis pulsotypes, serovars, and antibiotic resistance among Salmonella isolates from wild amphibians and reptiles in the California Central Coast.

    PubMed

    Gorski, Lisa; Jay-Russell, Michele T; Liang, Anita S; Walker, Samarpita; Bengson, Yingjia; Govoni, Jessica; Mandrell, Robert E

    2013-06-01

    A survey of cold-blooded vertebrates and associated surface waters in a produce-growing region on the Central California Coast was done between May and September 2011 to determine the diversity of Salmonella. Samples from 460 amphibians and reptiles and 119 water samples were collected and cultured for Salmonella. Animals sampled were frogs (n=331), lizards (n=59), newts (n=5), salamanders (n=6), snakes (n=39), and toads (n=20). Salmonella was isolated from 37 individual animals, including frogs, lizards, snakes, and toads. Snakes were the most likely to contain Salmonella, with 59% testing positive followed by 15.3% of lizards, 5% of toads, and 1.2% of frogs. Fifteen water samples (12.6%) were positive. Twenty-two different serovars were identified, and the majority of isolates were S. enterica subsp. IIIb, with subsp. I, II, and IIIa also found. The serovar isolated most frequently was S. enterica subsp. IIIb 16:z₁₀:e,n,x,z₁₅, from snakes and frogs in five different locations. S. enterica subsp. I serovar Typhimurium and the monophasic I 6,8:d:- were isolated from water, and subspecies I Duisburg and its variants were found in animals and water. Some samples contained more than one type of Salmonella. Analysis of pulsed-field gel electrophoresis pulsotypes indicated that some strains persisted in animals and water collected from the same location. Sixty-six isolates displayed antibiotic resistance, with 27 isolates resistant to more than one antibiotic, including a subspecies IIIb isolate from snake having resistance to five different antibiotics. Twenty-three isolates were resistant to more than one class of antibiotic, and six isolates were resistant to three classes. While these subspecies of IIIa and IIIb cause fewer instances of human illness, they may serve as reservoirs of antibiotic resistance, determinants in the environment, and be sources of contamination of leafy greens associated with product recalls.

  3. Generation of isolated attosecond pulses in the far field by spatial filtering with an intense few-cycle mid-infrared laser

    SciTech Connect

    Jin Cheng; Le, Anh-Thu; Trallero-Herrero, Carlos A.; Lin, C. D.

    2011-10-15

    We report theoretical calculations of high-order harmonic generation (HHG) of Xe with the inclusion of multielectron effects and macroscopic propagation of the fundamental and harmonic fields in an ionizing medium. By using the time-frequency analysis we show that the reshaping of the fundamental laser field is responsible for the continuum structure in the HHG spectra. We further suggest a method for obtaining an isolated attosecond pulse (IAP) by using a filter centered on axis to select the harmonics in the far field with different divergence. We also discuss the carrier-envelope-phase dependence of an IAP and the possibility to optimize the yield of the IAP. With intense few-cycle mid-infrared lasers, this offers a possible method for generating isolated attosecond pulses.

  4. Characterization of Fusarium isolates from asparagus fields in southwestern Ontario and influence of soil organic amendments on Fusarium crown and root rot.

    PubMed

    Borrego-Benjumea, Ana; Basallote-Ureba, María J; Melero-Vara, José M; Abbasi, Pervaiz A

    2014-04-01

    Fusarium crown and root rot (FCRR) of asparagus has a complex etiology with several soilborne Fusarium spp. as causal agents. Ninety-three Fusarium isolates, obtained from plant and soil samples collected from commercial asparagus fields in southwestern Ontario with a history of FCRR, were identified as Fusarium oxysporum (65.5%), F. proliferatum (18.3%), F. solani (6.4%), F. acuminatum (6.4%), and F. redolens (3.2%) based on morphological or cultural characteristics and polymerase chain reaction (PCR) analysis with species-specific primers. The intersimple-sequence repeat PCR analysis of the field isolates revealed considerable variability among the isolates belonging to different Fusarium spp. In the in vitro pathogenicity screening tests, 50% of the field isolates were pathogenic to asparagus, and 22% of the isolates caused the most severe symptoms on asparagus. The management of FCRR with soil organic amendments of pelleted poultry manure (PPM), olive residue compost, and fish emulsion was evaluated in a greenhouse using three asparagus cultivars of different susceptibility in soils infested with two of the pathogenic isolates (F. oxysporum Fo-1.5 and F. solani Fs-1.12). Lower FCRR symptom severity and higher plant weights were observed for most treatments on 'Jersey Giant' and 'Grande' but not on 'Mary Washington'. On all three cultivars, 1% PPM consistently reduced FCRR severity by 42 to 96% and increased plant weights by 77 to 152% compared with the Fusarium control treatment. Populations of Fusarium and total bacteria were enumerated after 1, 3, 7, and 14 days of soil amendment. In amended soils, the population of Fusarium spp. gradually decreased while the population of total culturable bacteria increased. These results indicate that soil organic amendments, especially PPM, can decrease disease severity and promote plant growth, possibly by decreasing pathogen population and enhancing bacterial activity in the soil.

  5. High genetic diversity of Enterococcus faecium and Enterococcus faecalis clinical isolates by pulsed-field gel electrophoresis and multilocus sequence typing from a hospital in Malaysia.

    PubMed

    Weng, Poh Leng; Ramli, Ramliza; Shamsudin, Mariana Nor; Cheah, Yoke-Kqueen; Hamat, Rukman Awang

    2013-01-01

    Little is known on the genetic relatedness and potential dissemination of particular enterococcal clones in Malaysia. We studied the antibiotic susceptibility profiles of Enterococcus faecium and Enterococcus faecalis and subjected them to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). E. faecium and E. faecalis displayed 27 and 30 pulsotypes, respectively, and 10 representative E. faecium and E. faecalis isolates (five each) yielded few different sequence types (STs): ST17 (2 isolates), ST78, ST203, and ST601 for E. faecium, and ST6, ST16, ST28, ST179, and ST399 for E. faecalis. Resistance to tazobactam-piperacillin and ampicillin amongst E. faecium isolates was highly observed as compared to E. faecalis isolates. All of the isolates were sensitive to vancomycin and teicoplanin. The presence of epidemic and nosocomial strains of selected E. faecium STs: 17, 78, and 203 and E. faecalis ST6 as well as high rates of resistance to multiple antibiotics amongst E. faecium isolates is of a particular concern.

  6. Role of real-time molecular typing in the surveillance of Campylobacter enteritis and comparison of pulsed-field gel electrophoresis profiles from chicken and human isolates.

    PubMed

    Michaud, Sophie; Ménard, Suzanne; Arbeit, Robert D

    2005-03-01

    The goal of the present study was to assess the contribution of real-time molecular typing, used alone or with clinical surveillance, to the prompt identification of clusters of Campylobacter enteritis. Potential poultry sources were sought by comparing the pulsed-field gel electrophoresis genotypes of human and fresh whole retail chicken isolates collected during the same study period. Among 183 human isolates, 82 (45%) had unique genotypes, 72 (39%) represented 26 clusters of 2 to 7 isolates each, and 29 (16%) represented three clusters of 8 to 11 isolates each. Molecular typing was useful for the confirmation of outbreaks suspected on the basis of epidemiological surveillance, but for most small clusters, no epidemiological link could be established. Thus, the added value of real-time molecular typing is questionable, since the numerous small clusters identified were of unclear public health significance. Among 177 chickens, 41 (23%) yielded campylobacter isolates; of these, 19 (46%) had genotypes similar to those of 41 (22%) human isolates. However, a temporal association was demonstrated in only a minority of cases, and most genotypes were present only in a single species, suggesting that sources other than chickens are important in human campylobacteriosis. Further investigation with samples from water and other possible environmental sources is needed to define the most efficient strategy for the application of molecular typing and identification of the source(s) of sporadic cases of campylobacteriosis.

  7. Marinitoga arctica sp. nov., a thermophilic, anaerobic heterotroph isolated from a Mid-Ocean Ridge vent field.

    PubMed

    Steinsbu, Bjørn O; Røyseth, Victoria; Thorseth, Ingunn H; Steen, Ida H

    2016-12-01

    A thermophilic, anaerobic, heterotrophic bacterium, designated 2PyrY55-1T, was isolated from the wall of an active hydrothermal white-smoker chimney in the Soria Moria vent field (71° N) at the Mohns Ridge in the Norwegian-Greenland Sea. Cells of the strain were Gram-negative, motile rods that possessed a polar flagellum and a sheath-like outer structure ('toga'). Growth was observed at 45-70 °C (optimum 65 °C), at pH 5.0-7.5 (optimum pH 5.5) and in 1.5-5.5 % (w/v) NaCl (optimum 2.5 %). The strain grew on pyruvate, complex proteinaceous substrates and various sugars. Cystine and elemental sulfur were used as electron acceptors, and sulfide was then produced. The G+C content of the genomic DNA was 27 mol% (Tm method). Cellular fatty acids included C16 : 0, C14 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 1ω9c, C18 : 1ω9c, C18 : 0, C18 : 1ω7c and C12 : 0. Phylogenetic analyses of the 16S rRNA gene showed that the strain belonged to the genus Marinitoga in the family Petrotogaceae. Based on the phylogenetic and chemotaxonomic data, strain 2PyrY55-1T (=DSM 29778T=JCM 30566T) is the type strain of a novel species of the genus Marinitoga, for which the name Marinitoga arctica sp. nov. is proposed.

  8. Inhibition of Plasmodium falciparum Field Isolates-Mediated Endothelial Cell Apoptosis by Fasudil: Therapeutic Implications for Severe Malaria

    PubMed Central

    Zang-Edou, Estelle S.; Bisvigou, Ulrick; Taoufiq, Zacharie; Lékoulou, Faustin; Lékana-Douki, Jean Bernard; Traoré, Yves; Mazier, Dominique; Touré-Ndouo, Fousseyni S.

    2010-01-01

    Plasmodium falciparum infection can abruptly progress to severe malaria, a life-threatening complication resulting from sequestration of parasitized red blood cells (PRBC) in the microvasculature of various organs such as the brain and lungs. PRBC adhesion can induce endothelial cell (EC) activation and apoptosis, thereby disrupting the blood-brain barrier. Moreover, hemozoin, the malarial pigment, induces the erythroid precursor apoptosis. Despite the current efficiency of antimalarial drugs in killing parasites, severe malaria still causes up to one million deaths every year. A new strategy targeting both parasite elimination and EC protection is urgently needed in the field. Recently, a rho-kinase inhibitior Fasudil, a drug already in clinical use in humans for cardio- and neuro-vascular diseases, was successfully tested on laboratory strains of P. falciparum to protect and to reverse damages of the endothelium. We therefore assessed herein whether Fasudil would have a similar efficiency on P. falciparum taken directly from malaria patients using contact and non-contact experiments. Seven (23.3%) of 30 PRBC preparations from different patients were apoptogenic, four (13.3%) acting by cytoadherence and three (10%) via soluble factors. None of the apoptogenic PRBC preparations used both mechanisms indicating a possible mutual exclusion of signal transduction ligand. Three PRBC preparations (42.9%) induced EC apoptosis by cytoadherence after 4 h of coculture (“rapid transducers”), and four (57.1%) after a minimum of 24 h (“slow transducers”). The intensity of apoptosis increased with time. Interestingly, Fasudil inhibited EC apoptosis mediated both by cell-cell contact and by soluble factors but did not affect PRBC cytoadherence. Fasudil was found to be able to prevent endothelium apoptosis from all the P. falciparum isolates tested. Our data provide evidence of the strong anti-apoptogenic effect of Fasudil and show that endothelial cell-P. falciparum

  9. Overexpression of ShCYP51B and ShatrD in Sclerotinia homoeocarpa isolates exhibiting practical field resistance to a demethylation inhibitor fungicide.

    PubMed

    Hulvey, Jon; Popko, James T; Sang, Hyunkyu; Berg, Andrew; Jung, Geunhwa

    2012-09-01

    We investigated genetic factors that govern the reduced propiconazole sensitivity of Sclerotinia homoeocarpa field isolates collected during a 2-year field efficacy study on dollar spot disease of turf in five New England sites. These isolates displayed a >50-fold range of in vitro sensitivity to a sterol demethylation inhibitor (DMI) fungicide, propiconazole, making them ideal for investigations of genetic mechanisms of reduced DMI sensitivity. The CYP51 gene homolog in S. homoeocarpa (ShCYP51B), encoding the enzyme target of DMIs, is likely a minor genetic factor for reduced propiconazole sensitivity, since there were no differences in constitutive relative expression (RE) values and only 2-fold-higher induced RE values for insensitive than for sensitive isolate groups. Next, we mined RNA-Seq transcriptome data for additional genetic factors and found evidence for the overexpression of a homolog of Botrytis cinerea atrD (BcatrD), ShatrD, a known efflux transporter of DMI fungicides. The ShatrD gene showed much higher constitutive and induced RE values for insensitive isolates. Several polymorphisms were found upstream of ShatrD but were not definitively linked to overexpression. The screening of constitutive RE values of ShCYP51B and ShatrD in isolates from two golf courses that exhibited practical field resistance to propiconazole uncovered evidence for significant population-specific overexpression of both genes. However, linear regression demonstrated that the RE of ShatrD displays a more significant relationship with propiconazole sensitivity than that of ShCYP51B. In summary, our results suggest that efflux is a major determinant of the reduced DMI sensitivity of S. homoeocarpa genotypes in New England, which may have implications for the emergence of practical field resistance in this important turfgrass pathogen.

  10. Neutralization serotypes of human immunodeficiency virus type 1 field isolates are not predicted by genetic subtype. The WHO Network for HIV Isolation and Characterization.

    PubMed Central

    Weber, J; Fenyö, E M; Beddows, S; Kaleebu, P; Björndal, A

    1996-01-01

    Human immunodeficiency virus type 1 (HIV-1) primary isolates from four geographical locations in Thailand, Brazil, Rwanda, and Uganda, representing genetic subtypes A, B, C, D, and E, were examined for autologous and heterologous neutralization by panels of human HIV+ polyclonal plasma. In independent linked experiments in three laboratories using diverse methodologies and common reagents, no defined pattern of genetic subtype-specific neutralization was observed. Most plasma tested were broadly cross-neutralizing across two or more genetic subtypes, although the titer of neutralization varied across a wide range. We conclude that the genetic subtypes of HIV-1 are not classical neutralization serotypes. PMID:8892904

  11. Detection of beta2 and major toxin genes by PCR in Clostridium perfringens field isolates of domestic animals suffering from enteritis or enterotoxaemia.

    PubMed

    Sting, Reinhard

    2009-01-01

    The production of Clostridium (C.) perfringens toxins in the intestine is an important cause of enteritis and enterotoxaemia in livestock. In the present study, the alpha toxin and the genes encoding beta2 and epsilon toxin could be frequently detected by means of phenotypical and PCR examinations in these bacteria. The C. perfringens isolates originated from 1213 field samples taken from diseased or perished livestock located in the north-eastern administrative districts of Baden-Württemberg (Germany) from 2005 to 2008. The beta2 toxin gene of C perfringens was detected in all animal species examined, comprising pigs, the small ruminants sheep and goats, cattle, horses, rabbits, alpacas and lamas, and fallow deer. Among all the animal species included in this study, pigs attracted attention by a high quota of 74.2% (610 of 822) cpb2-positive C. perfringens isolates in comparison to the other animal species tested, revealing a quota of 20.8% (72 of 346). Beta2 toxigenic isolates could be predominantly cultivated from the faeces of young piglets. The beta toxin gene was detected in isolates from piglets and small ruminants only, amounting to 82.5% (33 of 40) in piglets in combination with the cpb2 gene. In this context, cpb2/cpb-positive C. perfringens isolates of piglets could be clearly detected more often in the intestine of perished animals (18 of 158) than in faeces (15 of 629). Furthermore, cpb2-bearing C. perfringens isolates were detected in cattle, horses, rabbits, alpacas and lamas, and fallow deer to a notable degree. The detection of C. perfringens isolates carrying the epsilon toxin gene was restricted to sheep and goats. Of a total of 242 small ruminants that succumbed to sudden death, 71 (29.3%) harboured epsilon toxin-positive C. perfringens isolates in their intestines. These cases clustered seasonally in the second quarter (April, May, and June) of the year. Neither the isolates bearing the beta2 nor beta toxin gene nor those carrying the epsilon

  12. Molecular epidemiology of Salmonella spp. isolates from gulls, fish-meal factories, feed factories, animals and humans in Norway based on pulsed-field gel electrophoresis.

    PubMed Central

    Nesse, L. L.; Refsum, T.; Heir, E.; Nordby, K.; Vardund, T.; Holstad, G.

    2005-01-01

    The molecular epidemiology of 98 isolates of Salmonella serovar Agona (n = 27), S. Montevideo (n = 42) and S. Senftenberg (n = 29) from wild-living gulls, fish-meal factories, feed factories, humans and domestic animals was investigated using pulsed-field gel electrophoresis (PFGE) and computerized numerical analysis. Two of the S. Agona profiles were identified both in gulls and in two of the factories. In addition, one of these profiles was detected in two infected poultry farms. Two of the S. Montevideo profiles were also identified both in gulls and in two of the factories, and one of these profiles was observed in a human isolate. Four factories shared an identical S. Senftenberg profile. The S. Senftenberg profile found in gulls was not identified in any other source investigated. The presence of isolates with identical PFGE profiles indicates potential epidemiological links between different factories, as well as between gulls and factories. PMID:15724711

  13. Characterization of nosocomial Serratia marcescens isolates: comparison of Fourier-transform infrared spectroscopy with pulsed-field gel electrophoresis of genomic DNA fragments and multilocus enzyme electrophoresis.

    PubMed

    Irmscher, H M; Fischer, R; Beer, W; Seltmann, G

    1999-07-01

    A total of 66 Serratia marcescens isolates from 46 patients was investigated by macrorestriction using XbaI followed by pulsed-field gel electrophoresis. 7 restriction fragment patterns attributable to more than one patient and 9 individual patterns were identified. The isolates were additionally characterized by multilocus enzyme electrophoresis and Fourier-transform infrared spectroscopy. The macrorestriction patterns and the multilocus enzyme electrophoresis patterns corresponded fairly well while the classifications derived from these methods were not completely congruent. The grouping achieved by Fourier-transform infrared spectroscopy on the basis of high (> 1000) and moderately high heterogeneity values (300) was consistent with the macrorestriction results. Grouping on a lower heterogeneity level did not contribute to further discrimination. In general, Fourier-transform infrared spectroscopy was less discriminatory than the two other methods, but easier to perform. Therefore, laboratories equipped with the necessary devices may use it to rapidly select bacterial isolates for macrorestriction or other well established characterization procedures.

  14. Comparison of the sequence of the gene encoding African swine fever virus attachment protein p12 from field virus isolates and viruses passaged in tissue culture.

    PubMed Central

    Angulo, A; Viñuela, E; Alcamí, A

    1992-01-01

    Comparison of the amino acid sequence of the African swine fever virus attachment protein p12 from different field virus isolates, deduced from the nucleotide sequence of the gene, revealed a high degree of conservation. No mutations were found after adaptation to Vero cells, and a polypeptide with similar characteristics was present in an IBRS2-adapted virus. The sequence of the 5' flanking region was conserved among the isolates, whereas sequences downstream of the gene were highly variable in length and contained direct repeats in tandem that may account for the deletions found in different isolates. Protein p12 was synthesized in swine macrophages infected with all of the viruses tested. PMID:1583733

  15. Observations on macrolide resistance and susceptibility testing performance in field isolates collected from clinical bovine respiratory disease cases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this study were; first, to describe gamithromycin susceptibility of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni isolated from cattle diagnosed with bovine respiratory disease (BRD) and previously treated with either gamithromycin for control of BRD (mass me...

  16. A New Approach to Isolating External Magnetic Field Components in Spacecraft Measurements of the Earth's Magnetic Field Using Global Positioning System observables

    NASA Technical Reports Server (NTRS)

    Raymond, C.; Hajj, G.

    1994-01-01

    We review the problem of separating components of the magnetic field arising from sources in the Earth's core and lithosphere, from those contributions arising external to the Earth, namely ionospheric and magnetospheric fields, in spacecraft measurements of the Earth's magnetic field.

  17. Erythromycin resistance in italian isolates of Streptococcus pyogenes and correlations with pulsed-field gel electrophoresis analysis.

    PubMed

    Zampaloni, Claudia; Vitali, Luca A; Prenna, Manuela; Toscano, Maria A; Tempera, Gianna; Ripa, Sandro

    2002-01-01

    Erythromycin resistance among Streptococcus pyogenes strains has been reported in Italy at high rates during the last few years. A total of 152 erythromycin-resistant isolates of this species from southern Italian regions were characterized for the macrolide-resistance phenotype and screened by PCR for the corresponding genetic determinant. A close correlation was found between these phenotypic/genotypic data concerning macrolide resistance and results of Sma I macrorestriction fragment patterns (PFGE) analysis. In fact, the vast majority of the isolates assigned to individual PFGE classes mostly belonged to a single phenotype of macrolide resistance. All untypeable isolates belonged to the M phenotype. Twenty-two distinct PFGE types were recognized, of which 11 were recorded in only one isolate (one-strain type); about 50% of typeable isolates fell into five type clusters and 70% in seven. The increased erythromycin resistance among Italian isolates of S. pyogenes does not appear to be due to the spread of a single clone, but results indicate that the majority of group A streptococci examined are probably spread from a limited number of clones.

  18. Repression of flagella is a common trait in field isolates of Salmonella enterica serovar Dublin and is associated with invasive human infections.

    PubMed

    Yim, Lucía; Sasías, Sebastián; Martínez, Arací; Betancor, Laura; Estevez, Verónica; Scavone, Paola; Bielli, Alejandro; Sirok, Alfredo; Chabalgoity, José Alejandro

    2014-04-01

    The nontyphoidal Salmonella enterica serovar Dublin is adapted to cattle but infrequently infects humans, very often resulting in invasive infections with high levels of morbidity and mortality. A Salmonella-induced intestinal acute inflammatory response is postulated as a mechanism to prevent bacterial dissemination to systemic sites. In S. enterica serovar Typhimurium, flagella contribute to this response by providing motility and FliC-mediated activation of pattern recognition receptors. In this study, we found 4 Salmonella enterica isolates, with the antigenic formula 9,12:-:-, that, based on fliC sequence and multilocus sequence type (MLST) analyses, are aflagellate S. Dublin isolates. Interestingly, all were obtained from human bloodstream infections. Thus, we investigated the potential role of flagella in the unusual invasiveness exhibited by S. Dublin in humans by analyzing flagellation and proinflammatory properties of a collection of 10 S. Dublin human clinical isolates. We found that 4 of 7 blood isolates were aflagellate due to significantly reduced levels of fliC expression, whereas all 3 isolates from other sources were flagellated. Lack of flagella correlated with a reduced ability of triggering interleukin-8 (IL-8) and CCL20 chemokine expression in human intestinal Caco-2 cells and with reduced early inflammation in the ceca of streptomycin-pretreated C57/BL6 mice. These results indicate that flagella contribute to the host intestinal inflammatory response to Salmonella serovar Dublin and suggest that their absence may contribute to its systemic dissemination through dampening of the gut immune response. Analysis of FliC production in a collection of cattle isolates indicated that the aflagellate phenotype is widely distributed in field isolates of S. Dublin.

  19. Repression of Flagella Is a Common Trait in Field Isolates of Salmonella enterica Serovar Dublin and Is Associated with Invasive Human Infections

    PubMed Central

    Sasías, Sebastián; Martínez, Arací; Betancor, Laura; Estevez, Verónica; Scavone, Paola; Bielli, Alejandro; Sirok, Alfredo; Chabalgoity, José Alejandro

    2014-01-01

    The nontyphoidal Salmonella enterica serovar Dublin is adapted to cattle but infrequently infects humans, very often resulting in invasive infections with high levels of morbidity and mortality. A Salmonella-induced intestinal acute inflammatory response is postulated as a mechanism to prevent bacterial dissemination to systemic sites. In S. enterica serovar Typhimurium, flagella contribute to this response by providing motility and FliC-mediated activation of pattern recognition receptors. In this study, we found 4 Salmonella enterica isolates, with the antigenic formula 9,12:−:−, that, based on fliC sequence and multilocus sequence type (MLST) analyses, are aflagellate S. Dublin isolates. Interestingly, all were obtained from human bloodstream infections. Thus, we investigated the potential role of flagella in the unusual invasiveness exhibited by S. Dublin in humans by analyzing flagellation and proinflammatory properties of a collection of 10 S. Dublin human clinical isolates. We found that 4 of 7 blood isolates were aflagellate due to significantly reduced levels of fliC expression, whereas all 3 isolates from other sources were flagellated. Lack of flagella correlated with a reduced ability of triggering interleukin-8 (IL-8) and CCL20 chemokine expression in human intestinal Caco-2 cells and with reduced early inflammation in the ceca of streptomycin-pretreated C57/BL6 mice. These results indicate that flagella contribute to the host intestinal inflammatory response to Salmonella serovar Dublin and suggest that their absence may contribute to its systemic dissemination through dampening of the gut immune response. Analysis of FliC production in a collection of cattle isolates indicated that the aflagellate phenotype is widely distributed in field isolates of S. Dublin. PMID:24421045

  20. Sequence Variation in the T-Cell Epitopes of the Plasmodium falciparum Circumsporozoite Protein among Field Isolates Is Temporally Stable: a 5-Year Longitudinal Study in Southern Vietnam

    PubMed Central

    Jalloh, Amadu; van Thien, Huynh; Ferreira, Marcelo U.; Ohashi, Jun; Matsuoka, Hiroyuki; Kanbe, Toshio; Kikuchi, Akihiko; Kawamoto, Fumihiko

    2006-01-01

    In an effort to decipher the nature and extent of antigen polymorphisms of malaria parasites in a setting where malaria is hypomesoendemic, we conducted a 5-year longitudinal study (1998 to 2003) by sequencing the Th2R and Th3R epitopes of the circumsporozoite protein (CSP) of 142 Plasmodium falciparum field isolates from Bao Loc, Vietnam. Samples were collected during the high-transmission season, September through December 1998 (n = 43), as well as from July 2000 to August 2001 (n = 34), September 2001 to July 2002 (n = 33), and August 2002 to July 2003 (n = 32). Marked sequence diversity was noted during the high-transmission season in 1998, but no significant variation in allele frequencies was observed over the years (χ2 = 70.003, degrees of freedom = 57, P = 0.116). The apparent temporal stability in allele frequency observed in this Bao Loc malaria setting may suggest that polymorphism in the Th2R and Th3R epitopes is not maintained by frequency-dependent immune selection. By including 36 isolates from Flores Island, Indonesia, and 19 isolates from Thaton, Myanmar, we investigated geographical patterns of sequence polymorphism for these epitopes in Southeast Asia; among the characterized isolates, a globally distributed variant appears to be predominant in Vietnam (75 of 142 isolates, or 52.8%) as well as in Myanmar (15 of 19 isolates, or 78.9%) and Indonesia (31 of 36 isolates, or 86.1%). Further analyses involving worldwide CSP sequences revealed distinct regional patterns, a finding which, together with the unique mutations observed here, may suggest a possible role for host or local factors in the generation of sequence diversity in the T-cell epitopes of CSP. PMID:16597843

  1. Complete genome sequence of the biofilm-forming Microbacterium sp. strain BH-3-3-3, isolated from conventional field-grown lettuce (Lactuca sativa) in Norway.

    PubMed

    Dees, Merete Wiken; Brurberg, May Bente; Lysøe, Erik

    2017-03-01

    The genus Microbacterium contains bacteria that are ubiquitously distributed in various environments and includes plant-associated bacteria that are able to colonize tissue of agricultural crop plants. Here, we report the 3,508,491 bp complete genome sequence of Microbacterium sp. strain BH-3-3-3, isolated from conventionally grown lettuce (Lactuca sativa) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017674.

  2. Seven new ovine progressive pneumonia virus (OPPV) field isolates from Dubois Idaho sheep comprise part of OPPV clade II based on surface envelope glycoprotein (SU) sequences.

    PubMed

    Herrmann, Lynn M; Hötzel, Isidro; Cheevers, William P; On Top, Kathy Pretty; Lewis, Gregory S; Knowles, Donald P

    2004-06-15

    Seven new ovine progressive pneumonia virus (OPPV) field isolates were derived from colostrum and milk of 10 naturally OPPV-infected sheep from the US Sheep Experiment Station in Dubois, Idaho, USA. Sixteen sequences of the surface envelope glycoprotein (SU) from these seven Dubois OPPV field isolates and SU sequence from OPPV WLC1 were obtained, aligned with published SRLV SU sequences, and analyzed using phylogenetic analysis using parsimony (PAUP). Percent nucleotide identity in SU was greater than 95.8% among clones from individual Dubois OPPVs and ranged from 85.5 to 93.8% between different Dubois OPPV clones. SU sequences from Dubois OPPVs and WLC1 OPPV had significantly higher percent nucleotide identity to SU sequences from the North American OPPVs (85/34 and S93) than caprine-arthritis encephalitis virus (CAEVs) or MVVs. PAUP analysis also showed that SU sequences from the Dubois OPPVs and OPPV WLC1 grouped with other North American OPPVs (85/34 and S93) with a bootstrap value of 100 and formed one OPPV clade II group. In addition, Dubois and WLC1 SU amino acid sequences had significantly higher identity to SU sequences from North American OPPVs than CAEV or MVV. These data indicate that the seven new Dubois OPPV field isolates along with WLC1 OPPV are part of the OPPV clade II and are distinct from CAEVs and MVVs.

  3. In vitro susceptibility of Plasmodium falciparum Welch field isolates to infusions prepared from Artemisia annua L. cultivated in the Brazilian Amazon.

    PubMed

    Silva, Luiz Francisco Rocha e; Magalhães, Pedro Melillo de; Costa, Mônica Regina Farias; Alecrim, Maria das Graças Costa; Chaves, Francisco Célio Maia; Hidalgo, Ari de Freitas; Pohlit, Adrian Martin; Vieira, Pedro Paulo Ribeiro

    2012-11-01

    Artemisinin is the active antimalarial compound obtained from the leaves of Artemisia annua L. Artemisinin, and its semi-synthetic derivatives, are the main drugs used to treat multi-drug-resistant Plasmodium falciparum (one of the human malaria parasite species). The in vitro susceptibility of P. falciparum K1 and 3d7 strains and field isolates from the state of Amazonas, Brazil, to A. annua infusions (5 g dry leaves in 1 L of boiling water) and the drug standards chloroquine, quinine and artemisinin were evaluated. The A. annua used was cultivated in three Amazon ecosystems (várzea, terra preta de índio and terra firme) and in the city of Paulínia, state of São Paulo, Brazil. Artemisinin levels in the A. annua leaves used were 0.90-1.13% (m/m). The concentration of artemisinin in the infusions was 40-46 mg/L. Field P. falciparum isolates were resistant to chloroquine and sensitive to quinine and artemisinin. The average 50% inhibition concentration values for A. annua infusions against field isolates were 0.11-0.14 μL/mL (these infusions exhibited artemisinin concentrations of 4.7-5.6 ng/mL) and were active in vitro against P. falciparum due to their artemisinin concentration. No synergistic effect was observed for artemisinin in the infusions.

  4. Impact of experimental design on Drosophila sexual isolation studies: direct effects and comparison to field hybridization data.

    PubMed

    Coyne, Jerry A; Elwyn, Susannah; Rolán-Alvarez, Emilio

    2005-12-01

    Many studies of speciation rely critically on estimates of sexual isolation obtained in the laboratory. Here we examine the sensitivity of sexual isolation to alterations in experimental design and mating environment in two sister species of Drosophila, D. santomea and D. yakuba. We use a newly devised measure of mating frequencies that is able to disentangle sexual isolation from species differences in mating propensity. Variation in fly density, presence or absence of a quasi-natural environment, degree of starvation, and relative frequency of species had little or no effect on sexual isolation, but one factor did have a significant effect: the possibility of choice. Designs that allowed flies to choose between conspecific and heterospecific mates showed significantly more sexual isolation than other designs that did not allow choice. These experiments suggest that sexual isolation between these species (whose ranges overlap on the island of São Tomé) is due largely to discrimination against D. yakuba males by D. santomea females. This suggestion was confirmed by direct observations of mating behavior. Drosophila santomea males also court D. yakuba females less ardently than conspecific females, whereas neither males nor females of D. yakuba show strong mate discrimination. Thus, sexual isolation appears to be a result of evolutionary changes in the derived island endemic D. santomea. Surprisingly, as reported in a companion paper (Llopart et al. 2005), the genotypes of hybrids found in nature do not accord with expectations from these laboratory studies: all F1 hybrids in nature come from matings between D. santomea females and D. yakuba males, matings that occur only rarely in the laboratory.

  5. Characterization of the metacaspase 1 gene in Plasmodium vivax field isolates from southern Iran and Italian imported cases.

    PubMed

    Rezanezhad, H; Menegon, M; Sarkari, B; Hatam, G R; Severini, C

    2011-07-01

    Plasmodium vivax is still the more prevalent human Plasmodium outside Africa and despite this fact, there is still a deep lack of knowledge on its biology. Metacaspases are cysteine proteases related to metazoan caspases, involved in programmed cell death. Here, we have characterized the P. vivax metacaspase 1 gene in a total of 63 vivax isolates, 32 isolates collected in southern Iran and 31 Italian imported isolates originating from 12 different endemic countries. We have firstly identified DNA size polymorphism in P. vivax metacaspase 1 gene. A total of four different allelic sizes were found, resulting from the insertion of 1 to 4 tandem repeat units located within the intronic region of the P. vivax metacaspase 1. Similarly, we also have identified four distinct allelic types by using vivax merozoite surface protein-1 size polymorphism analysis.

  6. [Characterization of Shigella strains isolated in ankara, Turkey by antimicrobial resistance models, plasmid profile analysis and pulsed-field gel electrophoresis].

    PubMed

    Saran, Begüm; Erdem, Birsel; Tekeli, Fazıl Alper; Sahin, Fikret; Aysev, Ahmet Derya

    2013-01-01

    Shigella is one of the most important causative agents of diarrhea especially in childhood. Since man is the main reservoir of Shigella and human to human transmission is possible, Shigella can easily spread in public and cause outbreaks. In this study, a total of 60 Shigella strains isolated in Ankara, Turkey by years 2001, 2008 and 2009 were investigated by their antimicrobial susceptibility profiles, plasmid profile analysis (PPA) and pulsed-field gel electrophoresis (PFGE). For epidemiological investigation, the results obtained by antibiotic resistance typing (ART) which was the phenotyping method, was compared to the results of the genotyping methods which were PPA and PFGE. Of the isolates 49 (81.6%) were S.sonnei, 10 (16.6%) were S.flexneri and one was (1.6%) S.dysenteriae. Antimicrobial susceptibilities were evaluated by disc diffusion method and the highest resistance rates were found against trimethoprim/sulfamethoxazole (91.6%), followed by tetracycline (68.3%) and ampicillin (26.6%). Resistance against ampicillin, chloramphenicol and amoxycillin/clavulanic acid were found higher in S.flexneri isolates than S.sonnei (p< 0.001). All isolates were found to be susceptible to ciprofloxacin, gentamicin and ceftazidime. S.sonnei demonstrated 12 and S.flexneri demonstrated 4 antibiotic resistance models. All isolates were carrying plasmids with varying sizes and varying numbers between 1 to 7. S.sonnei isolates demonstrated 27 and S.flexneri isolates demonstrated 8 plasmid profiles. S.sonnei isolates were clustered in 4 patterns and S.flexneri were clustered in 5 patterns by PFGE. This method demonstrated obvious clonal similarity among S.sonnei strains isolated in Ankara and discriminative power (DP) was calculated as 0.26. PPA and ART demonstrated higher DP among S.sonnei strains (0.97 and 0.75, respectively). In this study gain or loss of instable genetic mobile elements were thought to be responsible for higher discriminative powers of PPA and ART methods

  7. Exploration of the susceptibility of AChE from the poultry red mite Dermanyssus gallinae (Acari: Mesostigmata) to organophosphates in field isolates from France.

    PubMed

    Roy, Lise; Chauve, Claude; Delaporte, Jean; Inizan, Gilbert; Buronfosse, Thierry

    2009-06-01

    The red fowl mite Dermanyssus gallinae (De Geer, 1778) is a hematophagous mite species, which is very commonly found in layer facilities in Europe. The economic and animal health impact of this parasite is quite important. In laying hen houses, organophosphates are almost the only legally usable chemicals. Detecting a target resistance can be useful in order to limit the emergence of resistant populations. The acetylcholinesterase (AChE) activity and the enzyme sensitivity to paraoxon was investigated in 39 field samples and compared to a susceptible reference strain (SSK). Insensitivity factor values (expressed as IC50 ratio) obtained from field isolates compared to SSK revealed some polymorphism but not exceeding a 6-fold difference. The kinetic characteristics of AChE from some field samples showed some difference in KM values for acetylthiocholine and inhibition kinetics performed with diethyl paraoxon exhibited a 5.5-fold difference in the bimolecular rate constant in one field isolate. Taken together, these data suggested that differences in AChE susceptibility to organophosphates may exist in D. gallinae but no resistant population was found.

  8. Analysis of von Willebrand factor A domain-related protein (WARP) polymorphism in temperate and tropical Plasmodium vivax field isolates

    PubMed Central

    Gholizadeh, Saber; Djadid, Navid Dinparast; Basseri, Hamid Reza; Zakeri, Sedigheh; Ladoni, Hossein

    2009-01-01

    Background The identification of key molecules is crucial for designing transmission-blocking vaccines (TBVs), among those ookinete micronemal proteins are candidate as a general class of malaria transmission-blocking targets. Here, the sequence analysis of an extra-cellular malaria protein expressed in ookinetes, named von Willebrand factor A domain-related protein (WARP), is reported in 91 Plasmodium vivax isolates circulating in different regions of Iran. Methods Clinical isolates were collected from north temperate and southern tropical regions in Iran. Primers have been designed based on P. vivax sequence (ctg_6991) which amplified a fragment of about 1044 bp with no size variation. Direct sequencing of PCR products was used to determine polymorphism and further bioinformatics analysis in P. vivax sexual stage antigen, pvwarp. Results Amplified pvwarp gene showed 886 bp in size, with no intron. BLAST analysis showed a similarity of 98–100% to P. vivax Sal-I strain; however, Iranian isolates had 2 bp mismatches in 247 and 531 positions that were non-synonymous substitution [T (ACT) to A (GCT) and R (AGA) to S (AGT)] in comparison with the Sal-I sequence. Conclusion This study presents the first large-scale survey on pvwarp polymorphism in the world, which provides baseline data for developing WARP-based TBV against both temperate and tropical P. vivax isolates. PMID:19549316

  9. Three-Dimensional MHD Simulation of FTEs Produced by Merging at an Isolated Point in a Sheared Magnetic Field Configuration

    NASA Technical Reports Server (NTRS)

    Santos, J. C.; Sibeck, D. G.; Buchner, J.; Gonzalez, W. D.; Ferreira, J. L.

    2014-01-01

    We present predictions for the evolution of FTEs generated by localized bursts of reconnection on a planar magnetopause that separates a magnetosheath region of high densities and weak magnetic field from a magnetospheric region of low densities and strong magnetic field. The magnetic fields present a shear angle of 105 degrees. Reconnection forms a pair of FTEs each crossing the magnetopause in the field reversal region and bulging into the magnetosphere and magnetosheath. At their initial stage they can be characterized as flux tubes since the newly reconnected magnetic field lines are not twisted. Reconnection launches Alfvenic perturbations that propagate along the FTEs generating high-speed jets, which move the pair of FTEs in opposite directions. As the FTE moves, it displaces the ambient magnetic field and plasma producing bipolar magnetic field and plasma velocity signatures normal to the nominal magnetopause in the regions surrounding the FTE. The combination of the ambient plasma with the FTE flows generates a vortical velocity pattern around the reconnected field lines. During its evolution the FTE evolves to a flux rope configuration due to the twist of the magnetic field lines. The alfvenic perturbations propagate faster along the part of the FTE bulging into the magnetosphere than in the magnetosheath, and due to the differences between the plasma and magnetic field properties the perturbations have slightly different signatures in the two regions. As a consequence, the FTEs have different signatures depending on whether the satellite encounters the part bulging into the magnetosphere or into the magnetosheath.

  10. Molecular characterisation of Mycoplasma hyorhinis isolated from pigs using pulsed-field gel electrophoresis and 16S rRNA sequencing

    PubMed Central

    Yamaguti, Maurício; Oliveira, Rosângela C; Marques, Lucas M; Buzinhani, Melissa; Buim, Marcos R; Neto, Renata L; Guimarães, Ana Márcia S; Timenetsky, Jorge

    2015-01-01

    Economic loss in pig breeding is common due to respiratory disorders, and Mycoplasma hyopneumoniae and Mycoplasma hyorhinis, namely, are the most common infectious agents. The aim of this study is to recover these mollicutes and detect their genotypic variations by pulsed-field gel electrophoresis (PFGE) and sequencing the 16 s rRNA gene. One hundred and twenty-six swabs from tonsil and nasal mucus of pigs with respiratory disorders were analysed. A total of 78 lungs were sampled, as well as two trachea and two tonsils obtained from animals with respiratory disorder. A total of 59 isolates were obtained: 1 (1.70 per cent) of M hyopneumoniae, 2 (3.40 per cent) of Mycoplasma flocculare and 56 (94.90 per cent) of M hyorhinis. The PFGE for M hyorhinis showed 10 profiles with enzyme AvaI and 9 profiles with XhoI. A low polymorphism of the 16sRNS gene was detected in M hyorhinis isolates compared with the type strain in the GenBank. M hyorhinis isolates of different herds showed a large heterogenicity with enzymes AvaI and XhoI. The sequencing of the 16S rRNA gene allowed for analysing the interspecific and intraspecific variations of isolated mycoplasmas. PMID:26688737

  11. [Characterization of a Cl. Perfringens type D strain, isolated in the field and optimization of epsilon toxin biosynthesis in a cell culture].

    PubMed

    Maaroufi, A; Metoui, W; Rahmouni, S; Ghram, A

    2000-01-01

    A field strain of cl. perfringens, named Dt001, was isolated from kidney of ovine enterotoemia case. The isolate characterized as Cl. perfringens, type D was based on its cultural and biochemical characters and its factors of virulence. The strain was very toxinogenic and well adapted to culture conditions of biofermentation when the parameters related to ptt, incubation time, substrat ... were optimized. Thus, the use of carbon source as polymer (destrine), the continuous control of pH allowed improvement of the rate of biosynthesis of Epsilon toxine by 10 times. The study of the immunogenicity of the isolate showed that preparations of anacultures were more immunogenic then those of anatoxine type. The fact that the two forms of epsilon antigens (protoxin and active toxin) show similar immune response in rabbits, indicates that the proteolytic action of trypsin is limited only to the toxic sites and does not affect the immunogenic epsitopes of the toxin. It also suggests a molecular organization of epsilon toxin in which the immunogenic epsitopes and the toxin sites are apart. The biotechnological performances and the immunogenicity and toxinogenical of the Dt001 isolate are in favor of its possible use as a component of an inactivated vaccine against enterotoxenia.

  12. Molecular Typing of Fluoroquinolone-Resistant Campylobacter jejuni Isolated from Broilers in Japan Using Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis.

    PubMed

    Ozawa, Manao; Hiki, Mototaka; Kawanishi, Michiko; Abo, Hitoshi; Kojima, Akemi; Asai, Tetsuo; Hamamoto, Shuichi

    2016-01-01

    Fluoroquinolone-resistant Campylobacter jejuni isolates from broilers in Japan were characterized using multilocus sequence typing and pulsed-field gel electrophoresis (PFGE) in order to elucidate the genetic relationship between these strains. Forty-three of the isolates were classified into 20 sequence types and were clustered into 21 PFGE types with 70% similarity. The most dominant clonal complex (CC) was CC-21 (41.9%). Diverse PFGE patterns were observed within the same CC, but the combined analysis of PFGE type and CC revealed that the strains with the same combination were isolated from the same district or neighboring districts. On the other hand, strains with the same combination pattern were also isolated from geographically distant districts. Our results elucidate two possible reasons for the prevalence of fluoroquinolone-resistant C. jejuni among broiler farms: (1) the resistant C. jejuni is clonally disseminated within the limited area, and (2) susceptible C. jejuni acquired fluoroquinolone resistance during the use of fluoroquinolone on the farms.

  13. Isolation and pulsed-field gel electrophoresis typing of Listeria monocytogenes from modified atmosphere packaged fresh-cut vegetables collected in Ireland.

    PubMed

    Francis, Gillian A; O'Beirne, David

    2006-10-01

    The incidence of Listeria monocytogenes in modified atmosphere packaged fresh-cut fruits and vegetables from chill cabinets of a supermarket in Ireland was investigated over a 2-year period. Overall, 9.58% of fresh-cut produce was contaminated with Listeria spp. Various species of Listeria were isolated from samples, including L. monocytogenes, L. seeligeri, L. innocua, L. welshimeri, and L. ivanovii. No fruit samples contained detectable L. monocytogenes. Overall, a total of 21 L. monocytogenes isolates (2.9% of samples) were recovered from a range of products, including dry coleslaw mix (80% shredded cabbage and 20% shredded carrot), bean sprouts, and leafy vegetables such iceberg, romaine, and radicchio lettuce and mixed salad leaves (curly endive, escarole, and radicchio leaves). Dry coleslaw mix appeared to have the highest incidence of Listeria contamination (20%) compared with other products. Listeria contamination was more frequent (P < 0.05) during the summer and autumn months than during the winter and spring months. The 21 L. monocytogenes isolates were subsequently subtyped by genomic macrorestriction techniques using ApaI with pulsed-field gel electrophoresis (PFGE). PFGE of digested DNA produced bands of 79 to 518 kb. Four PFGE profiles were identified, and approximately 50% of the isolates were associated with profile 1. This study indicates that fresh-cut vegetables packaged under a modified atmosphere can support growth of numerous species of Listeria, including L. monocytogenes.

  14. A single isolated sub-50 attosecond pulse generation with a two-color laser field by a frequency-chirping technique

    NASA Astrophysics Data System (ADS)

    Zhao, Kun; Chu, Tianshu

    2011-07-01

    We discuss the possibility of using the frequency-chirping technique to shorten the duration of the generated single attosecond pulse (SAP) by a two-color laser field of 800 and 1600 nm with few-cycle pulses. By adopting various combinations of the two frequency-chirped laser fields in our numerical simulation of ionizing He atom, we demonstrate that the best possible condition to obtain the shortest SAP is using the same chirping in both the fundamental and the half-harmonic laser fields without any phase effect and any delay time. There is a maximum increment of about 40 eV in the bandwidth of the XUV super-continuum in the cutoff (the second plateau) region. A single isolated attosecond pulse of 48 as can be generated that is further reduced to 9.7 as by phase compensation.

  15. Efficacy of a commercial canarypox vaccine for protecting Hawai'i 'Amakihi from field isolates of avipoxvirus

    USGS Publications Warehouse

    Atkinson, Carter T.; Wiegand, Kimberly C.; Triglia, Dennis; Jarvi, Susan I.

    2010-01-01

    At least three variants of avian pox virus are present in Hawai’i - Fowlpox from domestic poultry and a group of genetically distinct viruses that cluster within two clades (Pox Variant 1 and Pox Variant 2) that are most similar to Canarypox based on DNA sequence of the virus 4b core protein gene. We tested whether Hawai’i ‘Amakihi can be protected from wild virus isolates with an attenuated live Canarypox vaccine that is closely related to isolates that cluster within clade 1 (Pox Variant 1) based on sequence of the attenuated Canarypox virus 4b core protein. Thirty-one (31) Hawai`i ‘Amakihi (Hemignathus virens) with no prior physical evidence of pox infection were collected on Mauna Kea from xeric, high elevation habitats with low pox prevalence and randomly divided into two groups. One group of 16 was vaccinated with Poximmune C® while the other group received a sham vaccination with virus diluent. Four of 15 (27%) vaccinated birds developed potentially life-threatening disseminated lesions or lesions of unusually long duration, while one bird never developed a vaccine-associated lesion or “take”. After vaccine-associated lesions healed, vaccinated birds were randomly divided into three groups of five and challenged with either a wild isolate of Fowlpox, a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 1 (Pox Variant 1) or a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 2 (Pox Variant 2). Similarly, three random groups of five unvaccinated ‘Amakihi were challenged with the same virus isolates. Vaccinated and unvaccinated ‘Amakihi challenged with Fowlpox had transient infections with no clinical signs of infection. Mortality in vaccinated ‘Amakihi that were challenged with Pox Variant 1 and Pox Variant 2 ranged from 0% (0/5) for Pox Variant 1 to 60% (3/5) for Pox Variant 2. Mortality in unvaccinated ‘Amakihi ranged from 40% (2/5) for Pox Variant 1 to 100% (5/5) for Pox Variant 2. While the vaccine provided some

  16. A predication model for combustion modes of the scramjet-powered aerospace vehicle based on the nonlinear features of the isolator flow field

    NASA Astrophysics Data System (ADS)

    Yang, Qingchun; Wang, Hongxin; Chetehouna, Khaled; Gascoin, Nicolas

    2017-01-01

    The supersonic combustion ramjet (scramjet) engine remains the most promising airbreathing engine cycle for hypersonic flight, particularly the high-performance dual-mode scramjet in the range of flight Mach number from 4 to 7, because it can operates under different combustion modes. Isolator is a very key component of the dual-mode scramjet engine. In this paper, nonlinear characteristics of combustion mode transition is theoretically analyzed. The discontinuous sudden changes of static pressure and Mach number are obtained as the mode transition occurs, which emphasizing the importance of predication and control of combustion modes. In this paper, a predication model of different combustion modes is developed based on these these nonlinear features in the isolator flow field. it can provide a valuable reference for control system design of the scramjet-powered aerospace vehicle.

  17. Electric field control of magnetic states in isolated and dipole-coupled FeGa nanomagnets delineated on a PMN-PT substrate

    NASA Astrophysics Data System (ADS)

    Ahmad, Hasnain; Atulasimha, Jayasimha; Bandyopadhyay, Supriyo

    2015-10-01

    We report observation of a ‘non-volatile’ converse magneto-electric effect in elliptical FeGa nanomagnets delineated on a piezoelectric PMN-PT substrate. The nanomagnets are first magnetized with a magnetic field directed along their nominal major axes. Subsequent application of a strong electric field across the piezoelectric substrate generates strain in the substrate, which is partially transferred to the nanomagnets and rotates the magnetizations of some of them away from their initial orientations. The rotated magnetizations remain in their new orientations after the field is removed, resulting in ‘non-volatility’. In isolated nanomagnets, the magnetization rotates by \\lt 90^\\circ upon application of the electric field, but in a dipole-coupled pair consisting of one ‘hard’ and one ‘soft’ nanomagnet, which are both initially magnetized in the same direction by the magnetic field, the soft nanomagnet’s magnetization rotates by \\gt 90^\\circ upon application of the electric field because of the dipole influence of the hard nanomagnet. This effect can be utilized for a nanomagnetic NOT logic gate.

  18. Electric field control of magnetic states in isolated and dipole-coupled FeGa nanomagnets delineated on a PMN-PT substrate.

    PubMed

    Ahmad, Hasnain; Atulasimha, Jayasimha; Bandyopadhyay, Supriyo

    2015-10-09

    We report observation of a 'non-volatile' converse magneto-electric effect in elliptical FeGa nanomagnets delineated on a piezoelectric PMN-PT substrate. The nanomagnets are first magnetized with a magnetic field directed along their nominal major axes. Subsequent application of a strong electric field across the piezoelectric substrate generates strain in the substrate, which is partially transferred to the nanomagnets and rotates the magnetizations of some of them away from their initial orientations. The rotated magnetizations remain in their new orientations after the field is removed, resulting in 'non-volatility'. In isolated nanomagnets, the magnetization rotates by <90° upon application of the electric field, but in a dipole-coupled pair consisting of one 'hard' and one 'soft' nanomagnet, which are both initially magnetized in the same direction by the magnetic field, the soft nanomagnet's magnetization rotates by [Formula: see text] upon application of the electric field because of the dipole influence of the hard nanomagnet. This effect can be utilized for a nanomagnetic NOT logic gate.

  19. Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence

    PubMed Central

    de la Fuente, José; Díez-Delgado, Iratxe; Contreras, Marinela; Vicente, Joaquín; Cabezas-Cruz, Alejandro; Tobes, Raquel; Manrique, Marina; López, Vladimir; Romero, Beatriz; Bezos, Javier; Dominguez, Lucas; Sevilla, Iker A.; Garrido, Joseba M.; Juste, Ramón; Madico, Guillermo; Jones-López, Edward; Gortazar, Christian

    2015-01-01

    Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to

  20. In vitro susceptibilities of caprine Mycoplasma agalactiae field isolates to six antimicrobial agents using the E test methodology.

    PubMed

    Filioussis, George; Petridou, Evanthia; Giadinis, Nektarios D; Kritas, Spyridon K

    2014-12-01

    The minimum inhibitory concentrations (MICs) of enrofloxacin, ciprofloxacin, spectinomycin, tetracycline, spiramycin and erythromycin against 30 caprine Greek isolates of Mycoplasma agalactiae were determined using E test methodology. The E test strips were placed on Eaton's agar medium without antimicrobials and phenol red. MICs were then read by determining where the growth inhibition zone intersected with the MIC scale on the strip. An MIC value of 8 µg/mL was considered as a guide to mycoplasma resistance. All isolates were sensitive to fluoroquinolones (MIC50, 0.19 g/mL; MIC90, 0.38 µg/mL; highest MIC, 0.5 µg/mL), spectinomycin (MIC50, 0.5 µg/mL; MIC90, 1 µg/mL; highest MIC, 1 µg/mL), and spiramycin (MIC50, 1 µg/mL; MIC90, 1.5 µg/mL; highest MIC, 2 µg/mL). Two strains exhibited resistance to tetracycline (MIC 32 µg/mL) but these were not found to carry any of the tet(M), tet(O), and tet(S) resistance genes. Finally all isolates expressed resistance to erythromycin (MIC50, 128 µg/mL; MIC90, >256 µg/mL).

  1. Evaluation of the protective efficacy of the anticoccidial vaccine Coccivac-B in broilers, when challenged with Egyptian field isolates of E. tenella.

    PubMed

    Awad, Asharaf M; El-Nahas, Abeer F; Abu-Akkada, Somaia S

    2013-01-01

    The present study was performed to explore the efficacy of the commercial anticoccidial vaccine (Coccivac B®) in broiler chickens using five field strains of Eimeria tenella that were isolated from five provinces in Egypt. This study also analyzed the ITS-1-rDNA sequence of these five strains and its corresponding sequence in the vaccine. In a floor pen experiment, 216 one-day-old commercial broiler chicks were classified into vaccinated and non-vaccinated groups. Each main group was classified into six subgroups. The chicks were challenged on the 28th day of age with 10(4) sporulated oocysts of one of the five field strains of E. tenella. Our results indicated that Coccivac B® produced variable degrees of protection in the birds infected with the five different strains of E. tenella. Aligning the ITS-1 sequences from the five strains with the ITS-1 sequence of E. tenella from the vaccine revealed 96 % sequence similarity with the Kafer El-Sheikh strain, 94 % with the Gharbia strain, 90 % with the Alexandria strain, and 78 % with the Matrouh and Behera strains. While interesting, these similarity values were not useful for predicting the protection conferred by the vaccine against the five field isolates. However, based on the data reported here, we can conclude that Coccivac B® produced variable degrees of protection in the birds infected with the five different strains of E. tenella.

  2. Compact optical isolator.

    PubMed

    Sansalone, F J

    1971-10-01

    This paper describes a compact Faraday rotation isolator using terbium aluminum garnet (TAG) as the Faraday rotation material and small high field permanent magnets made of copper-rare earth alloys. The nominal isolation is 26 dB with a 0.4-dB forward loss. The present isolator can be adjusted to provide effective isolation from 4880 A to 5145 A. Details of the design, fabrication, and performance of the isolator are presented.

  3. Emergence of a mutL mutation causing multilocus sequence typing-pulsed-field gel electrophoresis discrepancy among Pseudomonas aeruginosa isolates from a cystic fibrosis patient.

    PubMed

    García-Castillo, María; Máiz, Luis; Morosini, María-Isabel; Rodríguez-Baños, Mercedes; Suarez, Lucrecia; Fernández-Olmos, Ana; Baquero, Fernando; Cantón, Rafael; del Campo, Rosa

    2012-05-01

    A multilocus sequence type (MLST) shift (from ST242 to ST996) was detected in Pseudomonas aeruginosa isolates with a uniform pulsed-field gel electrophoresis (PFGE) pattern obtained from a chronically colonized patient. MLST mutational change involved the mutL gene with the consequent emergence of a hypermutable phenotype. This observation challenges the required neutrality of mutL as an appropriate marker in MLST and alerts researchers to the limitations of MLST-only-based population studies in chronic infections under constant antibiotic selective pressure.

  4. Video camera log used for water isolation in the Main Body B pool, Elk Hills field, Kern Co., California -- Water and oil identification

    SciTech Connect

    Starcher, M.G.; Murphy, J.R.; Alexander, P.D.; Whittaker, J.L.

    1995-12-31

    The Main Body B reservoir in the Elk Hills Field is a peripherally waterflooded, +400 ft thick series of layered, turbidite Stevens sands. Permeability variation between layers adversely affects the vertical sweep, resulting in production from lower permeability oil sands dominated by production from higher permeability sands. This paper discusses the unique use of various tools to identify water zones to isolate and oil zones to stimulate. Tools used to identify water and oil entry are discussed with respect to their capabilities of identifying oil and water entry into the wellbore.

  5. Emergence of a mutL Mutation Causing Multilocus Sequence Typing–Pulsed-Field Gel Electrophoresis Discrepancy among Pseudomonas aeruginosa Isolates from a Cystic Fibrosis Patient

    PubMed Central

    García-Castillo, María; Máiz, Luis; Morosini, María-Isabel; Rodríguez-Baños, Mercedes; Suarez, Lucrecia; Fernández-Olmos, Ana; Baquero, Fernando; Cantón, Rafael

    2012-01-01

    A multilocus sequence type (MLST) shift (from ST242 to ST996) was detected in Pseudomonas aeruginosa isolates with a uniform pulsed-field gel electrophoresis (PFGE) pattern obtained from a chronically colonized patient. MLST mutational change involved the mutL gene with the consequent emergence of a hypermutable phenotype. This observation challenges the required neutrality of mutL as an appropriate marker in MLST and alerts researchers to the limitations of MLST-only-based population studies in chronic infections under constant antibiotic selective pressure. PMID:22322352

  6. An improved protocol for the preparation and restriction enzyme digestion of pulsed-field gel electrophoresis agarose plugs for the analysis of Legionella isolates.

    PubMed

    Chang, Bin; Amemura-Maekawa, Junko; Watanabe, Haruo

    2009-01-01

    Pulsed-field gel electrophoresis (PFGE), which determines the genomic relatedness of isolates, is currently used for the epidemiological investigation of infectious agents such as bacteria. In particular, this method has been used for the epidemiological investigation of Legionella outbreaks. However, it takes 4 days to complete a Legionella-PFGE analysis. Due to partial digestion and DNA damage, the reproducibility of the obtained fragment digestion patterns is poor for this pathogen. In this study, we report an improved protocol that takes only 2 days to complete and that allows clear discrimination of the restriction profile with higher reproducibility than that previously achieved.

  7. Anti-Kibble-Zurek Behavior in Crossing the Quantum Critical Point of a Thermally Isolated System Driven by a Noisy Control Field.

    PubMed

    Dutta, Anirban; Rahmani, Armin; Del Campo, Adolfo

    2016-08-19

    We show that a thermally isolated system driven across a quantum phase transition by a noisy control field exhibits anti-Kibble-Zurek behavior, whereby slower driving results in higher excitations. We characterize the density of excitations as a function of the ramping rate and the noise strength. The optimal driving time to minimize excitations is shown to scale as a universal power law of the noise strength. Our findings reveal the limitations of adiabatic protocols such as quantum annealing and demonstrate the universality of the optimal ramping rate.

  8. Genotypic variations in field isolates of Theileria species infecting giraffes (Giraffa camelopardalis tippelskirchi and Giraffa camelopardalis reticulata) in Kenya.

    PubMed

    Githaka, Naftaly; Konnai, Satoru; Skilton, Robert; Kariuki, Edward; Kanduma, Esther; Murata, Shiro; Ohashi, Kazuhiko

    2013-10-01

    Recently, mortalities among giraffes, attributed to infection with unique species of piroplasms were reported in South Africa. Although haemoparasites are known to occur in giraffes of Kenya, the prevalence, genetic diversity and pathogenicity of these parasites have not been investigated. In this study, blood samples from 13 giraffes in Kenya were investigated microscopically and genomic DNA extracted. PCR amplicons of the hyper-variable region 4 (V4) of Theileria spp. small subunit ribosomal RNA (18S rRNA) gene were hybridized to a panel of genus- and species-specific oligonucleotide probes by reverse line blot (RLB). Two newly designed oligonucleotide probes specific for previously identified Theileria spp. of giraffes found single infections in eight of the specimens and mixed infections in the remaining five samples. Partial 18S rRNA genes were successfully amplified from 9 samples and the PCR amplicons were cloned. A total of 28 plasmid clones representing the Kenyan isolates were analyzed in the present study and compared with those of closely-related organisms retrieved from GenBank. In agreement with RLB results, the nucleotide sequence alignment indicated the presence of mixed infections in the giraffes. In addition, sequence alignment with the obtained 18S rRNA gene sequences revealed extensive microheterogeneities within and between isolates, characterized by indels in the V4 regions and point mutations outside this region. Phylogeny with 18S rRNA gene sequences from the detected parasites and those of related organisms places Theileria of giraffes into two major groups, within which are numerous clades that include the isolates reported in South Africa. Collectively, these data suggest the existence of at least two distinct Theileria species among giraffes, and extensive genetic diversity within the two parasite groups.

  9. In vitro susceptibilities of field isolates of Mycoplasma agalactiae to oxytetracycline, tylosin, enrofloxacin, spiramycin and lincomycin-spectinomycin.

    PubMed

    Loria, G R; Sammartino, C; Nicholas, R A J; Ayling, R D

    2003-08-01

    The minimum inhibitory concentrations (MICs) of tetracycline, enrofloxacin, tylosin, spiramycin and a lincomycin:spectinomycin 1:2 combination, against 24 Sicilian isolates of Mycoplasma agalactiae, the causative organism of contagious agalactia were determined in vitro by a broth dilution method. Enrofloxacin was the most effective antimicrobial in vitro with a range of MIC values from 0.125 to 0.500 microg/ml and an MIC(50) of 0.203 and MIC(90) of 0.365 microg/ml. Using the MIC(50) and MIC(90) values the remaining four antimicrobials are ranked in order of in vitro effectiveness as follows: tylosin (MIC(50)0.292; MIC(90)0.525 microg/ml) was slightly more effective than tetracycline (MIC(50)0.296; MIC(90)0.533 microg/ml), followed by lincomycin:spectinomycin (MIC(50)0.521; MIC(90)0.938 microg/ml) and spiramycin (MIC(50)1.583; MIC(90)2.850 microg/ml). MIC values above 1.000 microg/ml were obtained using tetracycline, tylosin and spiramycin for some M. agalactiae isolates.

  10. Analysis of the Genome of a Korean Isolate of the Pieris rapae Granulovirus Enabled by Its Separation from Total Host Genomic DNA by Pulse-Field Electrophoresis

    PubMed Central

    Jo, Yong Hun; Patnaik, Bharat Bhusan; Kang, Se Won; Chae, Sung-Hwa; Oh, Seunghan; Kim, Dong Hyun; Noh, Mi Young; Seo, Gi Won; Jeong, Heon Cheon; Noh, Ju Young; Jeong, Ji Eun; Hwang, Hee Ju; Ko, Kisung; Han, Yeon Soo; Lee, Yong Seok

    2013-01-01

    Background Most traditional genome sequencing projects involving viruses include the culture and purification of the virus particles. However, purification of virions may yield insufficient material for traditional sequencing. The electrophoretic method described here provides a strategy whereby the genomic DNA of the Korean isolate of Pieris rapae granulovirus (PiraGV-K) could be recovered in sufficient amounts for sequencing by purifying it directly from total host DNA by pulse-field gel electrophoresis (PFGE). Methodology/Principal Findings The total genomic DNA of infected P. rapae was embedded in agarose plugs, treated with restriction nuclease and methylase, and then PFGE was used to separate PiraGV-K DNA from the DNA of P. rapae, followed by mapping of fosmid clones of the purified viral DNA. The double-stranded circular genome of PiraGV-K was found to encode 120 open reading frames (ORFs), which covered 92% of the sequence. BLAST and ORF arrangement showed the presence of 78 homologs to other genes in the database. The mean overall amino acid identity of PiraGV-K ORFs was highest with the Chinese isolate of PiraGV (∼99%), followed up with Choristoneura occidentalis ORFs at 58%. PiraGV-K ORFs were grouped, according to function, into 10 genes involved in transcription, 11 involved in replication, 25 structural protein genes, and 15 auxiliary genes. Genes for Chitinase (ORF 10) and cathepsin (ORF 11), involved in the liquefaction of the host, were found in the genome. Conclusions/Significance The recovery of PiraGV-K DNA genome by pulse-field electrophoretic separation from host genomic DNA had several advantages, compared with its isolation from particles harvested as virions or inclusions from the P. rapae host. We have sequenced and analyzed the 108,658 bp PiraGV-K genome purified by the electrophoretic method. The method appears to be generally applicable to the analysis of genomes of large viruses. PMID:24391907

  11. Geometric Morphometrics of Nine Field Isolates of Aedes aegypti with Different Resistance Levels to Lambda-Cyhalothrin and Relative Fitness of One Artificially Selected for Resistance

    PubMed Central

    Jaramillo-O., Nicolás; Fonseca-González, Idalyd; Chaverra-Rodríguez, Duverney

    2014-01-01

    Aedes aegypti, a mosquito closely associated with humans, is the principal vector of dengue virus which currently infects about 400 million people worldwide. Because there is no way to prevent infection, public health policies focus on vector control; but insecticide-resistance threatens them. However, most insecticide-resistant mosquito populations exhibit fitness costs in absence of insecticides, although these costs vary. Research on components of fitness that vary with insecticide-resistance can help to develop policies for effective integrated management and control. We investigated the relationships in wing size, wing shape, and natural resistance levels to lambda-cyhalothrin of nine field isolates. Also we chose one of these isolates to select in lab for resistance to the insecticide. The main life-traits parameters were assessed to investigate the possible fitness cost and its association with wing size and shape. We found that wing shape, more than wing size, was strongly correlated with resistance levels to lambda-cyhalothrin in field isolates, but founder effects of culture in the laboratory seem to change wing shape (and also wing size) more easily than artificial selection for resistance to that insecticide. Moreover, significant fitness costs were observed in response to insecticide-resistance as proved by the diminished fecundity and survival of females in the selected line and the reversion to susceptibility in 20 generations of the non-selected line. As a practical consequence, we think, mosquito control programs could benefit from this knowledge in implementing efficient strategies to prevent the evolution of resistance. In particular, the knowledge of reversion to susceptibility is important because it can help in planning better strategies of insecticide use to keep useful the few insecticide-molecules currently available. PMID:24801598

  12. Geometric morphometrics of nine field isolates of Aedes aegypti with different resistance levels to lambda-cyhalothrin and relative fitness of one artificially selected for resistance.

    PubMed

    Jaramillo-O, Nicolás; Fonseca-González, Idalyd; Chaverra-Rodríguez, Duverney

    2014-01-01

    Aedes aegypti, a mosquito closely associated with humans, is the principal vector of dengue virus which currently infects about 400 million people worldwide. Because there is no way to prevent infection, public health policies focus on vector control; but insecticide-resistance threatens them. However, most insecticide-resistant mosquito populations exhibit fitness costs in absence of insecticides, although these costs vary. Research on components of fitness that vary with insecticide-resistance can help to develop policies for effective integrated management and control. We investigated the relationships in wing size, wing shape, and natural resistance levels to lambda-cyhalothrin of nine field isolates. Also we chose one of these isolates to select in lab for resistance to the insecticide. The main life-traits parameters were assessed to investigate the possible fitness cost and its association with wing size and shape. We found that wing shape, more than wing size, was strongly correlated with resistance levels to lambda-cyhalothrin in field isolates, but founder effects of culture in the laboratory seem to change wing shape (and also wing size) more easily than artificial selection for resistance to that insecticide. Moreover, significant fitness costs were observed in response to insecticide-resistance as proved by the diminished fecundity and survival of females in the selected line and the reversion to susceptibility in 20 generations of the non-selected line. As a practical consequence, we think, mosquito control programs could benefit from this knowledge in implementing efficient strategies to prevent the evolution of resistance. In particular, the knowledge of reversion to susceptibility is important because it can help in planning better strategies of insecticide use to keep useful the few insecticide-molecules currently available.

  13. Comparison of Haemophilus parasuis reference strains and field isolates by using random amplified polymorphic DNA and protein profiles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Haemophilus parasuis is the causative agent of Glässer’s disease and is a pathogen of swine in high-health status herds. Reports on serotyping of field strains from outbreaks describe that approximately 30% of them are nontypable and therefore cannot be traced. Molecular typing methods have been use...

  14. Observations and simulations of the wind structure in the boundary layer around an isolated mountain during the MATERHORN field experiment

    NASA Astrophysics Data System (ADS)

    De Wekker, S.; Liu, Y.; Knievel, J. C.; Pal, S.; Emmitt, G. D.

    2013-12-01

    We investigate atmospheric boundary layer structure and dynamics during an intensive observational period of the Mountain Terrain Atmospheric Modeling and Observations (MATERHORN) Program at Dugway Proving Ground (an army test range in Utah, USA) in Fall 2012. We use high-resolution data from an airborne Doppler lidar that reveal the interaction of the synoptic flows with the evolution of slope and valley flows around an isolated mountain of a horizontal and vertical scale of about 10 km and 1 km, respectively. The measurements at high spatiotemporal resolution allow a thorough evaluation of the Four-Dimensional Weather System (4DWX), a state-of-the-art meteorological analysis, forecast, and decision-support system which is used operationally at Dugway Proving Ground. We also perform very large eddy simulations using 4DWX to investigate in more detail the turbulent structures and their impact on flow dynamics in the convective boundary layer.

  15. Field application of the Numobag as a portable disposable isolation unit and for treating chemical, radiological or biologically induced wounds.

    SciTech Connect

    Miller, Keith A.; Felton, Robert; Vaughan, Courtenay Thomas

    2005-04-01

    Numotech Inc. has developed the Numobag{trademark}, a disposable, lightweight, wound healing device which produces Topical Hyperbaric Oxygen Therapy (THOT). The Numobag{trademark} is cost effective and has been clinically validated to heal large skin lesions rapidly and has proven to arrest wound advancement from several insidious forms of biological attack including dermal anthrax, small pox, necrotizing fasciitis etc. The Numobag{trademark} can treat mass casualties wounded by chemical/radiological burns or damaging biological exposures. The Numobag{trademark} can be a frontline tool as an isolation unit, reducing cross-contamination and infection of medical personnel. The heightened oxygen content kills organisms on the skin and in the wound, avoids expensive hospital trash disposal procedures, and helps the flesh heal. The Numobag{trademark} requires high purity oxygen. Numotech Inc. is teaming with Sandia National Laboratories and Spektr Conversion in Russia to develop a cost effective, portable, low power oxygen generator.

  16. Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field.

    PubMed

    Mochimaru, Hanako; Tamaki, Hideyuki; Katayama, Taiki; Imachi, Hiroyuki; Sakata, Susumu; Kamagata, Yoichi

    2016-11-01

    A mesophilic, hydrogenotrophic methanogen, designated strain MobHT, was isolated from sediments derived from deep sedimentary, natural-gas-bearing aquifers in Japan. Strain MobHT utilized H2/CO2 or formate, but not ethanol, 1-propanol, 2-propanol, 2-butanol or cyclopentanol, for growth and methane production. In addition, acetate and tungsten were required for growth. Yeast extract stimulated the growth, but was not required. The cells were weakly motile with multiple flagella, presented as a curved-rod-shaped (0.8×2.0 µm) and occurred singly or in pairs. Strain MobHT grew at 15-40 °C (optimum 35 °C) and at pH 5.9-7.9 (optimum pH 7.0-7.5). The sodium chloride range for growth was 0-5.8 % (optimum 2 %). The G+C content of the genomic DNA was 37.6 mol%. In the phylogenetic tree based on the 16S rRNA gene sequences, strain MobHT clustered together with Methanomicrobium mobile (95.4 % in sequence similarity), and formed a distinct clade from Methanolacinia petrolearia SEBR 4847T (95.6 %) and Methanolacinia paynteri G-2000T (95.4 %). The two species of the genus Methanolacinia utilized 2-propanol, whereas strain MobHT and Methanomicrobium mobile, the sole species of the genus Methanomicrobium, do not. Based on phenotypic and phylogenetic features, we propose a novel species for the isolate with the name, Methanomicrobiumantiquum sp. nov. The type strain is MobHT (=DSM 21220T=NBRC 104160T).

  17. Enhanced Emission from Single Isolated Gold Quantum Dots Investigated Using Two-Photon-Excited Fluorescence Near-Field Scanning Optical Microscopy.

    PubMed

    Abeyasinghe, Neranga; Kumar, Santosh; Sun, Kai; Mansfield, John F; Jin, Rongchao; Goodson, Theodore

    2016-12-21

    New approaches in molecular nanoscopy are greatly desired for interrogation of biological, organic, and inorganic objects with sizes below the diffraction limit. Our current work investigates emergent monolayer-protected gold quantum dots (nanoclusters, NCs) composed of 25 Au atoms by utilizing two-photon-excited fluorescence (TPEF) near-field scanning optical microscopy (NSOM) at single NC concentrations. Here, we demonstrate an approach to synthesize and isolate single NCs on solid glass substrates. Subsequent investigation of the NCs using TPEF NSOM reveals that, even when they are separated by distances of several tens of nanometers, we can excite and interrogate single NCs individually. Interestingly, we observe an enhanced two-photon absorption (TPA) cross section for single Au25 NCs that can be attributed to few-atom local field effects and to local field-induced microscopic cascading, indicating their potential for use in ultrasensitive sensing, disease diagnostics, cancer cell therapy, and molecular computers. Finally, we report room-temperature aperture-based TPEF NSOM imaging of these NCs for the first time at 30 nm point resolution, which is a ∼5-fold improvement compared to the previous best result for the same technique. This report unveils the unique combination of an unusually large TPA cross section and the high photostability of Au NCs to (non-destructively) investigate stable isolated single NCs using TPEF NSOM. This is the first reported optical study of monolayer-protected single quantum clusters, opening some very promising opportunities in spectroscopy of nanosized objects, bioimaging, ultrasensitive sensing, molecular computers, and high-density data storage.

  18. Virulence of Mexican isolates of entomopathogenic fungi upon Rhipicephalus-Boophilus microplus larvae and the efficacy of conidia formulations to reduce larval tick density under field conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The first objective was laboratory evaluation of the virulence of 53 Mexican isolates of fungi against larvae of Rhipicephalus (Boophilus) microplus. Thirty three isolates of Metarhizium anisopliae var. anisopliae (Metschnickoff) Sorokin (Hypocreales: Clavicipitaceae) and 20 isolates of Isaria (Paec...

  19. Microbial diversity in Los Azufres geothermal field (Michoacán, Mexico) and isolation of representative sulfate and sulfur reducers.

    PubMed

    Brito, Elcia M S; Villegas-Negrete, Norberto; Sotelo-González, Irene A; Caretta, César A; Goñi-Urriza, Marisol; Gassie, Claire; Hakil, Florence; Colin, Yannick; Duran, Robert; Gutiérrez-Corona, Felix; Piñón-Castillo, Hilda A; Cuevas-Rodríguez, Germán; Malm, Olaf; Torres, João P M; Fahy, Anne; Reyna-López, Georgina E; Guyoneaud, Rémy

    2014-03-01

    Los Azufres spa consists of a hydrothermal spring system in the Mexican Volcanic Axis. Five samples (two microbial mats, two mud pools and one cenote water), characterized by high acidity (pH between 1 and 3) and temperatures varying from 27 to 87 °C, were investigated for their microbial diversity by Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and 16S rRNA gene library analyses. These data are the first to describe microbial diversity from Los Azufres geothermal belt. The data obtained from both approaches suggested a low bacterial diversity in all five samples. Despite their proximity, the sampling points differed by their physico-chemical conditions (mainly temperature and matrix type) and thus exhibited different dominant bacterial populations: anoxygenic phototrophs related to the genus Rhodobacter in the biomats, colorless sulfur oxidizers Acidithiobacillus sp. in the warm mud and water samples, and Lyzobacter sp.-related populations in the hot mud sample (87 °C). Molecular data also allowed the detection of sulfate and sulfur reducers related to Thermodesulfobium and Desulfurella genera. Several strains affiliated to both genera were enriched or isolated from the mesophilic mud sample. A feature common to all samples was the dominance of bacteria involved in sulfur and iron biogeochemical cycles (Rhodobacter, Acidithiobacillus, Thiomonas, Desulfurella and Thermodesulfobium genera).

  20. In-vitro sensitivity of Pakistani Leishmania tropica field isolate against buparvaquone in comparison to standard anti-leishmanial drugs.

    PubMed

    Jamal, Qaisar; Khan, Nazma Habib; Wahid, Sobia; Awan, Mahwish Mustafa; Sutherland, Colin; Shah, Akram

    2015-07-01

    In this study, in vitro anti-leishmanial activity of buparvaquone was evaluated against promastigotes and intracellular amastigotes of Pakistani Leishmania tropica isolate KWH23 in relation to the current standard chemotherapy for leishmaniasis (sodium stibogluconate, sodium stibogluconate, amphotericin B and miltefosine). For buparvaquone, mean % inhibition in intracellular amastigotes at four different concentrations (1.35 µM, 0.51 µM, 0.17 µM and 0.057 µM) was 78%, 44%, 20% and 14% respectively, whereas, against promastigotes it was 89%, 77%, 45% and 35% respectively. IC50 values calculated to estimate the anti-leishmanial activity of buparvaquone against intra-cellular amastigotes and promastigotes was 0.53 µM (95% C.I. = 0.32-0.89) and 0.15 µM (95% C.I. = 0.01-1.84) respectively. Amphotericin B was the most potent in-vitro drug tested, with an IC50 of 0.075 µM (95% C.I. = 0.006-0.907) against promastigotes, and 0.065 µM (95% C.I. = 0.048-0.089) against intra-cellular amastigotes. Amphotericin B was more cytotoxic against THP1 cells, with an IC50 of 0.15 µM (95% C.I. = 0.01-0.95) and an apparent in-vitro therapeutic index of 2.0, than was buparvaquone, with an IC50 of 12.03 µM (95% C.I. = 5.36-26.96) against THP1 cells and a therapeutic index of 80.2. The study proposes that buparvaquone may be further investigated as a candidate drug for treatment of cutaneous leishmaniasis.

  1. Reproductive isolation revealed in preliminary crossbreeding experiments using field collected Triatoma dimidiata (Hemiptera: Reduviidae) from three ITS–2 defined groups

    PubMed Central

    García, Mauricio; Menes, Marianela; Dorn, Patricia L.; Monroy, Carlota; Richards, Bethany; Panzera, Francisco; Bustamante, Dulce María

    2013-01-01

    Triatoma dimidiata, a Chagas disease vector distributed in Mexico, Central America, Colombia, Venezuela, Peru and Ecuador, has been studied using genetic markers and four groups have been defined by ITS–2 sequences: 1A, 1B, 2 and 3. To gather evidence on the divergence and reproductive isolation among T. dimidiata ITS–2 groups, we carried out 15 crossbreeding experiments with field–collected sylvan and domestic T. dimidiata from Guatemala where three groups are found: 1A, 2 and 3. Reciprocal crosses between individuals from groups 1A and 2, and a cross between group 2 individuals from different habitats, produced an average 129.78±42.29 eggs with hatching success ranging from 31.6% to 90.1%. The offspring of these crosses reached the adult stage, and crosses between F1 insects produced eggs. These results suggest that there are no pre– or post– zygotic reproductive barriers between groups 1A and 2, or within group 2. Crosses between group 3 females and males from groups 1A or 2 produced on average 85.67±30.26 eggs and none of them hatched. These results support the existence of pre– zygotic barriers between T. dimidiata group 3 and groups 1A and 2. The group 3 individuals were collected in sylvatic environments in Yaxha, Peten, Guatemala. Previously, distinct chromosomal characteristics (cytotype 3) were described in individuals from this population. Based on this evidence we suggest that this population is divergent at the species level from other T. dimidiata populations. PMID:24041592

  2. Prevalence of Clostridium botulinum in Finnish Trout Farms: Pulsed-Field Gel Electrophoresis Typing Reveals Extensive Genetic Diversity among Type E Isolates

    PubMed Central

    Hielm, Sebastian; Björkroth, Johanna; Hyytiä, Eija; Korkeala, Hannu

    1998-01-01

    The distribution of Clostridium botulinum serotypes A, B, E, and F in Finnish trout farms was examined. A total of 333 samples were tested with a neurotoxin-specific PCR assay. C. botulinum type E was found in 68% of the farm sediment samples, in 15% of the fish intestinal samples, and in 5% of the fish skin samples. No other serotypes were found. The spore counts determined by the most-probable-number method were considerably higher for the sediments than for the fish intestines and skin; the average values were 2,020, 166, and 310 C. botulinum type E spores kg−1, respectively. The contamination rates in traditional freshwater ponds and marine net cages were high, but in concrete ponds equipped with sediment suction devices the contamination rates were significantly lower. Pulsed-field gel electrophoresis (PFGE) typing of 42 isolates obtained in this survey and 12 North American reference strains generated 28 pulsotypes upon visual inspection, suggesting that there was extensive genetic diversity and that the discriminatory power of PFGE typing in C. botulinum type E was high. A numerical analysis of SmaI-XmaI macrorestriction profiles confirmed these findings, as it divided the 54 isolates into 15 clusters at a similarity level of 76%. For this material, this level of similarity corresponded to a three-band difference in the macrorestriction profiles, which indicated that there is no genotypic proof of a close epidemiological relationship among the clusters. PMID:9797260

  3. Virulence patterns and long-range genetic mapping of extraintestinal Escherichia coli K1, K5, and K100 isolates: use of pulsed-field gel electrophoresis.

    PubMed Central

    Ott, M; Bender, L; Blum, G; Schmittroth, M; Achtman, M; Tschäpe, H; Hacker, J

    1991-01-01

    A total of 127 extraintestinal Escherichia coli strains of the capsule serotypes K1, K5, and K100 from human and animal sources were analyzed for DNA sequences specific for the genes for various adhesins (P fimbriae [pap] and P-related sequences [prs], S fimbriae [sfa]/F1C fimbriae [foc], and type I fimbriae [fim]), aerobactin (aer), and hemolysin (hly). The expression of corresponding virulence factors was also tested. Twenty-four selected strains were analyzed by long-range DNA mapping to evaluate their genetic relationships. DNA sequences for the adhesins were often found in strains not expressing them, while strains with hemolysin and aerobactin genes usually did express them. Different isolates of the same serotype often expressed different virulence patterns. The use of virulence-associated gene probes for Southern hybridization with genomic DNA fragments separated by pulsed-field gel electrophoresis revealed that a highly heterogeneous restriction fragment length and hybridization pattern existed even within strains of the same serotype. Long-range DNA mapping is therefore useful for the evaluation of genetic relatedness among individual isolates and facilitates the performance of precise molecular epidemiology. Images PMID:1677349

  4. Listeria monocytogenes biofilm-associated protein (BapL) may contribute to surface attachment of L. monocytogenes but is absent from many field isolates.

    PubMed

    Jordan, Suzanne J; Perni, Stefano; Glenn, Sarah; Fernandes, Isabel; Barbosa, Manuela; Sol, Manuela; Tenreiro, Rogerio P; Chambel, Lelia; Barata, Belarmino; Zilhao, Isabel; Aldsworth, Timothy G; Adriao, Andreia; Faleiro, M Leonor; Shama, Gilbert; Andrew, Peter W

    2008-09-01

    Listeria monocytogenes is a food-borne pathogen capable of adhering to a range of surfaces utilized within the food industry, including stainless steel. The factors required for the attachment of this ubiquitous organism to abiotic surfaces are still relatively unknown. In silico analysis of the L. monocytogenes EGD genome identified a putative cell wall-anchored protein (Lmo0435 [BapL]), which had similarity to proteins involved in biofilm formation by staphylococci. An insertion mutation was constructed in L. monocytogenes to determine the influence of this protein on attachment to abiotic surfaces. The results show that the protein may contribute to the surface adherence of strains that possess BapL, but it is not an essential requirement for all L. monocytogenes strains. Several BapL-negative field isolates demonstrated an ability to adhere to abiotic surfaces equivalent to that of BapL-positive strains. BapL is not required for the virulence of L. monocytogenes in mice.

  5. Investigation of porous silica nanostructures in diatoms isolated from Kurichi and Sulur lakes of Coimbatore, India using field emission scanning electron microscopy.

    PubMed

    N, Seethalakshmi; R, Selvakumar

    2015-12-01

    Diatoms are unicellular algae that possess cell wall made of silica. These diatoms play a pivotal role in synthesis of variety of silica nanostructures and have adorning morphology in nature. In the present study, we have used field emission scanning electron microscopy (FE-SEM) to investigate their morphological features like pore size, shape, and porous pattern in various diatoms isolated from Kurichi and Sulur fresh water lakes, Coimbatore, Tamil Nadu, India. Diatoms were identified as Nitzschia sp., Cyclotella meneghiniana, Coscinodiscus sp. and Cyclotella atomus based on their morphological features. The arrangement of porous nanostructures in these diatoms have been characterized. The change in the nanostructures present in the diatoms have been correlated to the contamination of water bodies.

  6. Changes in cell death of peripheral blood lymphocytes isolated from children with acute lymphoblastic leukemia upon stimulation with 7 Hz, 30 mT pulsed electromagnetic field.

    PubMed

    Kaszuba-Zwoińska, Jolanta; Ćwiklińska, Magdalena; Balwierz, Walentyna; Chorobik, Paulina; Nowak, Bernadeta; Wójcik-Piotrowicz, Karolina; Ziomber, Agata; Malina-Novak, Kinga; Zaraska, Wiesław; Thor, Piotr J

    2015-03-01

    Pulsed electromagnetic field (PEMF) influenced the viability of proliferating in vitro peripheral blood mononuclear cells (PBMCs) isolated from Crohn's disease patients as well as acute myeloblastic leukemia (AML) patients by induction of cell death, but did not cause any vital changes in cells from healthy donors. Experiments with lymphoid U937 and monocytic MonoMac6 cell lines have shown a protective effect of PEMF on the death process in cells treated with death inducers. The aim of the current study was to investigate the influence of PEMF on native proliferating leukocytes originating from newly diagnosed acute lymphoblastic leukemia (ALL) patients. The effects of exposure to PEMF were studied in PBMCs from 20 children with ALL. PBMCs were stimulated with three doses of PEMF (7 Hz, 30 mT) for 4 h each with 24 h intervals. After the last stimulation, the cells were double stained with annexin V and propidium iodide dye to estimate viability by flow cytometric analysis. The results indicated an increase of annexin V positive as well as double stained annexin V and propidium iodide positive cells after exposure to threefold PEMF stimulation. A low-frequency pulsed electromagnetic field induces cell death in native proliferating cells isolated from ALL patients. The increased vulnerability of proliferating PBMCs to PEMF-induced interactions may be potentially applied in the therapy of ALL. The analysis of expression of apoptosis-related genes revealed changes in mRNA of some genes engaged in the intrinsic apoptotic pathway belonging to the Bcl-2 family and the pathway with apoptosis-inducing factor (AIF) abundance upon PEMF stimulation of PBMCs.

  7. Characteristics of resistance to Bacillus thuringiensis toxin Cry2Ab in a strain of Helicoverpa punctigera (Lepidoptera: Noctuidae) isolated from a field population.

    PubMed

    Downes, S; Parker, T L; Mahon, R J

    2010-12-01

    In 1996, the Australian cotton industry adopted Ingard that expresses the Bacillus thuringiensis (Bt) toxin gene cry1Ac and was planted at a cap of 30%. In 2004-2005, Bollgard II, which expresses cry1Ac and cry2Ab, replaced Ingard in Australia, and subsequently has made up >80% of the area planted to cotton, Gossypium hirsutum L. The Australian target species Helicoverpa armigera (Hübner) and Helicoverpa punctigera (Wallengren) are innately moderately tolerant to Bt toxins, but the absence of a history of insecticide resistance indicates that the latter species is less likely to develop resistance to Bt cotton. From 2002-2003 to 2006-2007, F2 screens were deployed to detect resistance to CrylAc or Cry2Ab in natural populations of H. punctigera. Alleles that conferred an advantage against CrylAc were not detected, but those that conferred resistance to Cry2Ab were present at a frequency of 0.0018 (n = 2,192 alleles). Importantly, the first isolation of Cry2Ab resistance in H. punctigera occurred before significant opportunities to develop resistance in response to Bollgard II. We established a colony (designated Hp4-13) consisting of homozygous resistant individuals and examined their characteristics through comparison with individuals from a Bt-susceptible laboratory colony. Through specific crosses and bioassays, we established that the resistance present in Hp4-13 is due to a single autosomal gene. The resistance is fully recessive. Homozygotes are able to survive a dose of Cry2Ab toxin that is 15 times the reported concentration in field grown Bollgard II in Australia (500 microg/ml) and are fully susceptible to Cry1Ac and to the Bt product DiPel. These characteristics are the same as those described for the first Cry2Ab resistant strain of H. armigera isolated from a field population in Australia.

  8. Flavobacterium panaciterrae sp. nov., a β-glucosidase producing bacterium with ginsenoside-converting activity isolated from the soil of a ginseng field.

    PubMed

    Jin, Yan; Kim, Yeon-Ju; Hoang, Van-An; Young Jung, Sun; Nguyen, Ngoc-Lan; Woo Min, Jin; Wang, Chao; Yang, Deok-Chun

    2014-01-01

    The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain DCY69(T) is JX233806. A Gram-reaction-negative, oxidase- and catalase-positive, non-gliding motile strain, designated strain DCY69(T), was isolated from the soil of a ginseng field in the Republic of Korea. Colonies of strain DCY69(T) were circular, 0.5-1.5 mm diameter, yellow, and convex on an R2A agar plate after 2 days. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DCY69(T) belonged to the genus Flavobacterium with 90.5-98.3% gene sequence similarity. The major predominant quinone was MK-6. The major cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH and summed feature 3 (containing C16:1ω7c and/or C16:1ω6c). The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and unidentified polar lipids (L1, L2). The genomic DNA G+C content of strain DCY69(T) was 35.0mol%. The strain DCY69(T) transformed ginsenoside Rb1 into Rd and F2. Based on the polyphasic taxonomic data, strain DCY69(T) is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium panaciterrae sp. nov. is proposed. The type strain is DCY69(T)(= KCTC 32392(T) = JCM 19161(T)), isolated from the soil of a ginseng field in the Republic of Korea.

  9. Microbial Corrosion in Linepipe Steel Under the Influence of a Sulfate-Reducing Consortium Isolated from an Oil Field

    NASA Astrophysics Data System (ADS)

    AlAbbas, Faisal M.; Williamson, Charles; Bhola, Shaily M.; Spear, John R.; Olson, David L.; Mishra, Brajendra; Kakpovbia, Anthony E.

    2013-11-01

    This work investigates microbiologically influenced corrosion of API 5L X52 linepipe steel by a sulfate-reducing bacteria (SRB) consortium. The SRB consortium used in this study was cultivated from a sour oil well in Louisiana, USA. 16S rRNA gene sequence analysis indicated that the mixed bacterial consortium contained three phylotypes: members of Proteobacteria ( Desulfomicrobium sp.), Firmicutes ( Clostridium sp.), and Bacteroidetes ( Anaerophaga sp.). The biofilm and the pits that developed with time were characterized using field emission scanning electron microscopy (FE-SEM). In addition, electrochemical impedance spectroscopy (EIS), linear polarization resistance (LPR) and open circuit potential (OCP) were used to analyze the corrosion behavior. Through circuit modeling, EIS results were used to interpret the physicoelectric interactions between the electrode, biofilm and solution interfaces. The results confirmed that extensive localized corrosion activity of SRB is due to a formed biofilm in conjunction with a porous iron sulfide layer on the metal surface. X-ray diffraction (XRD) revealed semiconductive corrosion products predominantly composed of a mixture of siderite (FeCO3), iron sulfide (Fe x S y ), and iron (III) oxide-hydroxide (FeOOH) constituents in the corrosion products for the system exposed to the SRB consortium.

  10. Anaerobic thermophilic bacteria isolated from a Venezuelan oil field and its potential use in microbial improved oil recovery

    SciTech Connect

    Trebbau, G.; Fernandez, B.; Marin, A.

    1995-12-31

    The objective of this work is to determine the ability of indigenous bacteria from a Venezuelan oil field to grow under reservoir conditions inside a porous media, and to produce metabolites capable of recovering residual crude oil. For this purpose, samples of formation waters from a central-eastern Venezuelan oil reservoir were enriched with different carbon sources and a mineral basal media. Formation water was used as a source of trace metals. The enrichments obtained were incubated at reservoir temperature (71{degrees}C), reservoir pressure (1,200 psi), and under anaerobic conditions for both outside and inside porous media (Berea core). Growth and metabolic activity was followed outside porous media by measuring absorbance at 660 nm, increases in pressure, and decreases in pH. Inside porous media bacterial activity was determined by visual examination of the produced waters (gas bubbles and bacterial cells). All the carbohydrates tested outside porous media showed good growth at reservoir conditions. The pH was lowered, gases such as CO{sub 2} and CH{sub 4} were identified by GC. Surface tension was lowered in some enrichments by 30% when compared to controls. Growth was decreased inside porous media, but gases were produced and helped displace oil. In addition, 10% residual oil was recovered from the Berea core. Mathematical modeling was applied to the laboratory coreflood experiment to evaluate the reproducibility of the results obtained.

  11. Are isolated wetlands isolated?

    USGS Publications Warehouse

    Smith, Loren M.; Euliss, Ned H.; Haukos, David A.

    2011-01-01

    While federal regulations during the past 10 years have treated isolated wetlands as unconnected to aquatic resources protected by the Clean Water Act, they provide critical ecosystem services to society that extend well beyond their wetland boundaries. The authors offer well-documented examples from the scientific literature on some of the ecosystem services provided by isolated wetlands to society and other ecosystems.

  12. Breast Field Cancerization: Isolation and Comparison of Telomerase-Expressing Cells in Tumor and Tumor Adjacent, Histologically Normal Breast Tissue

    PubMed Central

    Trujillo, Kristina A.; Hines, William C.; Vargas, Keith M.; Jones, Anna C.; Joste, Nancy E.; Bisoffi, Marco; Griffith, Jeffrey K.

    2011-01-01

    Telomerase stabilizes chromosomes by maintaining telomere length, immortalizes mammalian cells, and is expressed in more than 90% of human tumors. However, the expression of human telomerase reverse transcriptase (hTERT) is not restricted to tumor cells. We have previously shown that a subpopulation of human mammary epithelial cells (HMEC) in tumor-adjacent, histologically normal (TAHN) breast tissues expresses hTERT mRNA at levels comparable with levels in breast tumors. In the current study, we first validated a reporter for measuring levels of hTERT promoter activity in early-passage HMECs and then used this reporter to compare hTERT promoter activity in HMECs derived from tumor and paired TAHN tissues 1, 3, and 5 cm from the tumor (TAHN-1, TAHN-3, and TAHN-5, respectively). Cell sorting, quantitative real-time PCR, and microarray analyses showed that the 10% of HMECs with the highest hTERT promoter activity in both tumor and TAHN-1 tissues contain more than 95% of hTERT mRNA and overexpress many genes involved in cell cycle and mitosis. The percentage of HMECs within this subpopulation showing high hTERT promoter activity was significantly reduced or absent in TAHN-3 and TAHN-5 tissues. We conclude that the field of normal tissue proximal to the breast tumors contains a population of HMECs similar in hTERT expression levels and in gene expression to the HMECs within the tumor mass and that this population is significantly reduced in tissues more distal to the tumor. PMID:21775421

  13. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site

    PubMed Central

    Butler, Jessica E; He, Qiang; Nevin, Kelly P; He, Zhili; Zhou, Jizhong; Lovley, Derek R

    2007-01-01

    Background Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known. Results The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold induced during benzoate oxidation

  14. The stellar mass-halo mass relation of isolated field dwarfs: a critical test of ΛCDM at the edge of galaxy formation

    NASA Astrophysics Data System (ADS)

    Read, J. I.; Iorio, G.; Agertz, O.; Fraternali, F.

    2017-01-01

    We fit the rotation curves of isolated dwarf galaxies to directly measure the stellar mass-halo mass relation (M★ - M200) over the mass range 5 {×} 10^5 ≲ M_{*} / M_⊙ ≲ 108. By accounting for cusp-core transformations due to stellar feedback, we find a monotonic relation with little scatter. Such monotonicity implies that abundance matching should yield a similar M★ - M200 if the cosmological model is correct. Using the `field galaxy' stellar mass function from the Sloan Digital Sky Survey (SDSS) and the halo mass function from the Λ Cold Dark Matter Bolshoi simulation, we find remarkable agreement between the two. This holds down to M200 ˜ 5 × 109 M⊙, and to M200 ˜ 5 × 108 M⊙ if we assume a power law extrapolation of the SDSS stellar mass function below M★ ˜ 107 M⊙. However, if instead of SDSS we use the stellar mass function of nearby galaxy groups, then the agreement is poor. This occurs because the group stellar mass function is shallower than that of the field below M★ ˜ 109 M⊙, recovering the familiar `missing satellites' and `too big to fail' problems. Our result demonstrates that both problems are confined to group environments and must, therefore, owe to `galaxy formation physics' rather than exotic cosmology. Finally, we repeat our analysis for a Λ Warm Dark Matter cosmology, finding that it fails at 68% confidence for a thermal relic mass of mWDM < 1.25 keV, and mWDM < 2 keV if we use the power law extrapolation of SDSS. We conclude by making a number of predictions for future surveys based on these results.

  15. WIPP site and vicinity geological field trip. A report of a field trip to the proposed Waste Isolation Pilot Plant project in Southeastern New Mexico, June 16 to 18, 1980

    SciTech Connect

    Chaturvedi, L

    1980-10-01

    The Environmental Evaluation Group is conducting an assessment of the radiological health risks to people from the Waste Isolation Pilot Plant. As a part of this work, EEG is making an effort to improve the understanding of those geological issues concerning the WIPP site which may affect the radiological consequences of the proposed repository. One of the important geological issues to be resolved is the timing and the nature of the dissolution processes which may have affected the WIPP site. EEG organized a two-day conference of geological scientists, on January 17-18, 1980. On the basis of the January conference and the June field trip, EEG has formed the following conclusions: (1) it has not been clearly established that the site or the surrounding area has been attacked by deep dissolution to render it unsuitable for the nuclear waste pilot repository; (2) the existence of an isolated breccia pipe at the site unaccompanied by a deep dissolution wedge, is a very remote possibility; (3) more specific information about the origin and the nature of the brine reservoirs is needed. An important question that should be resolved is whether each encounter with artesian brine represents a separate pocket or whether these occurrences are interconnected; (4) Anderson has postulated a major tectonic fault or a fracture system at the Basin margin along the San Simon Swale; (5) the area in the northern part of the WIPP site, identified from geophysical and bore hole data as the disturbed zone, should be further investigated to cleary understand the nature and significance of this structural anomaly; and (6) a major drawback encountered during the discussions of geological issues related to the WIPP site is the absence of published material that brings together all the known information related to a particular issue.

  16. Isolation and Identification of Post-Transcriptional Gene Silencing-Related Micro-RNAs by Functionalized Silicon Nanowire Field-effect Transistor

    NASA Astrophysics Data System (ADS)

    Chen, Kuan-I.; Pan, Chien-Yuan; Li, Keng-Hui; Huang, Ying-Chih; Lu, Chia-Wei; Tang, Chuan-Yi; Su, Ya-Wen; Tseng, Ling-Wei; Tseng, Kun-Chang; Lin, Chi-Yun; Chen, Chii-Dong; Lin, Shih-Shun; Chen, Yit-Tsong

    2015-11-01

    Many transcribed RNAs are non-coding RNAs, including microRNAs (miRNAs), which bind to complementary sequences on messenger RNAs to regulate the translation efficacy. Therefore, identifying the miRNAs expressed in cells/organisms aids in understanding genetic control in cells/organisms. In this report, we determined the binding of oligonucleotides to a receptor-modified silicon nanowire field-effect transistor (SiNW-FET) by monitoring the changes in conductance of the SiNW-FET. We first modified a SiNW-FET with a DNA probe to directly and selectively detect the complementary miRNA in cell lysates. This SiNW-FET device has 7-fold higher sensitivity than reverse transcription-quantitative polymerase chain reaction in detecting the corresponding miRNA. Next, we anchored viral p19 proteins, which bind the double-strand small RNAs (ds-sRNAs), on the SiNW-FET. By perfusing the device with synthesized ds-sRNAs of different pairing statuses, the dissociation constants revealed that the nucleotides at the 3‧-overhangs and pairings at the terminus are important for the interactions. After perfusing the total RNA mixture extracted from Nicotiana benthamiana across the device, this device could enrich the ds-sRNAs for sequence analysis. Finally, this bionanoelectronic SiNW-FET, which is able to isolate and identify the interacting protein-RNA, adds an additional tool in genomic technology for the future study of direct biomolecular interactions.

  17. Construction of infectious cDNA clone derived from a classical swine fever virus field isolate in BAC vector using in vitro overlap extension PCR and recombination.

    PubMed

    Kamboj, Aman; Saini, Mohini; Rajan, Lekshmi S; Patel, Chhabi Lal; Chaturvedi, V K; Gupta, Praveen K

    2015-12-15

    To develop reverse genetics system of RNA viruses, cloning of full-length viral genome is required which is often challenging due to many steps involved. In this study, we report cloning of full-length cDNA from an Indian field isolate (CSFV/IVRI/VB-131) of classical swine fever virus (CSFV) using in vitro overlap extension PCR and recombination which drastically reduced the number of cloning steps. The genome of CSFV was amplified in six overlapping cDNA fragments, linked by overlap extension PCR and cloned in a bacterial artificial chromosome (BAC) vector using in vitro recombination method to generate full-length cDNA clone. The full-length CSFV cDNA clone was found stable in E. coli Stellar and DH10B cells. The full-length RNA was transcribed in vitro using T7 RNA polymerase and transfected in PK15 cells using Neon-tip electroporator to rescue infectious CSFV. The progeny CSFV was propagated in PK15 cells and found indistinguishable from the parent virus. The expression of CSFV proteins were detected in cytoplasm of PK15 cells infected with progeny CSFV at 72 h post-infection. We concluded that the in vitro overlap extension PCR and recombination method is useful to construct stable full-length cDNA clone of RNA virus in BAC vector.

  18. Isolated thallus-associated compounds from the macroalga Fucus vesiculosus mediate bacterial surface colonization in the field similar to that on the natural alga.

    PubMed

    Lachnit, Tim; Wahl, Martin; Harder, Tilmann

    2010-01-01

    This study investigated whether surface-associated compounds isolated from the macroalga Fucus vesiculosus had the potential to mediate microbial and/or macrobial epibiosis similar to that on the natural alga. To selectively yield thallus-associated compounds and avoid contamination by intracellular algal compounds, cell lysis was monitored by surface microscopy of algal cells and chemical profiling of algal surface extracts by coupled gas chromatography mass spectroscopy. The optimized extraction resulted in polar and non-polar algal surface extracts. The non-polar surface extract was immobilized in hydrogel, the polar surface extract was homogeneously perfused through the gel to ensure a temporally constant delivery of polar extract components. During a 7 day field trial, bacterial biofilms were formed on control gels and gels featuring polar and/or non-polar extract components. PERMANOVA revealed that bacterial community profiles on controls and on gels featuring polar or non-polar extract were significantly different from the profile on F. vesiculosus, while the profile on the gels bearing both polar and non-polar extracts was not. Moreover, the polar surface extracts inhibited the settlement of barnacle cyprids. Considering the pronounced effects of bacterial biofilms on invertebrate larval settlement, these results suggest that algal surface chemistry affects macrofouling not only directly but also indirectly, via its control of biofilm formation and composition.

  19. Biodegradation of alachlor in liquid and soil cultures under variable carbon and nitrogen sources by bacterial consortium isolated from corn field soil

    PubMed Central

    2013-01-01

    Alachlor, an aniline herbicide widely used in corn production, is frequently detected in water resources. The main objectives of this research were focused on isolating bacterial consortium capable of alachlor biodegradation, assessing the effects of carbon and nitrogen sources on alachlor biodegradation and evaluating the feasibility of using bacterial consortium in soil culture. Kavar corn field soil with a long history of alachlor application in Fars province of Iran has been explored for their potential of alachlor biodegradation. The influence of different carbon compounds (glucose, sodium citrate, sucrose, starch and the combination of these compounds), the effect of nitrogen sources (ammonium nitrate and urea) and different pH (5.5-8.5) on alachlor removal efficiency by the bacterial consortium in liquid culture were investigated. After a multi-step enrichment program 100 days of acclimation, a culture with the high capability of alachlor degradation was obtained (63%). Glucose and sodium citrate had the highest alachlor reduction rate (85%). Alachlor reduction rate increased more rapidly by the addition of ammonium nitrate (94%) compare to urea. Based on the data obtained in the present study, pH of 7.5 is optimal for alachlor biodegradation. After 30 days of incubation, the percent of alachlor reduction were significantly enhanced in the inoculated soils (74%) as compared to uninoculated control soils (17.67%) at the soil moisture content of 25%. In conclusion, bioaugmentation of soil with bacterial consortium may enhance the rate of alachlor degradation in a polluted soil. PMID:23452801

  20. Overview of the data-acquisition system (including shielding, isolation and grounding) on the Beta II field-reversed plasma-gun experiment

    SciTech Connect

    Bell, H.H. Jr.

    1981-07-01

    Computer-supported acquisition, analysis, and storage of mirror fusion experimental data requires the solution of several problems. The data must be gathered with a minimum amount of noise, and transients must be excluded from the computer so that it can function properly. On Beta II (which was an experiment to produce field-reversed plasma rings from a coaxial plasma gun) the diagnostic system was planned to provide the shielding and isolation necessary to solve these two problems. The Beta II system has been in operation for about two years and provides 300-channel capacity, CAMAC interfaced, to a Hewlett Packard 21MX computer. The system routinely handles signals ranging from 1 mV to 50 kV, with bandwidths from .05 Hz to 10 MHz. The data are captured by transient recorders during a shot, then transferred to the computer. The computer stores the data on disc for immediate processing and on tape for long-term storage. Processed data from any number of channels (usually 20 to 30) is plotted between shots for immediate review. The rest of the data is processed and plotted during off hours.

  1. Genetic characterization of porcine epidemic diarrhea virus in Korea from 1998 to 2013.

    PubMed

    Kim, Seong-Hee; Lee, Jung-Min; Jung, Jongsun; Kim, In-Joong; Hyun, Bang-Hun; Kim, Hyun-Il; Park, Choi-Kyu; Oem, Jae-Ku; Kim, Yeon-Hee; Lee, Myoung-Heon; Lee, Kyoung-Ki

    2015-04-01

    The number of porcine epidemic diarrhea (PED) cases has increased over the past 20 years in Korea, with a major outbreak in 2013. A total of 27 Korean strains from 1998 to 2013 were analyzed (excluding the noncoding regions) and divided into two groups for comparison of the spike (S), ORF3, envelope (E), membrane (M), and nucleocapsid (N) genes with those of reference strains, vaccine strains, and previously identified strains based on phylogenetic analysis. Analysis of the selection patterns of PEDV isolated in Korea indicated positive selection of nine nonsynonymous sites in the S and N proteins and negative selection at 97 sites for all of the proteins. Interestingly, eight nonsynonymous mutations in S showed no significant pattern change over the 15-year period, and one of eight mutation sites was found only in IC05TK, GN05DJ, and KNU0802 in the epidemic years 2005 and 2008. These eight mutations were also present during the epidemic years in China. Furthermore, of the signs of positive selection in the S protein, the conservative substitutions were more frequent than radical substitutions in PEDVs, suggesting that the evolution of Korean strains has been slow. Serological cross-reactivity was detected between three field PEDVs and two vaccine strains, with different serum neutralization titers. In conclusion, although Korean PEDVs have been evolving slowly, their diverse antigenicity and genetics imply that multilateral efforts to prevent future PED outbreaks are required.

  2. Molecular identification and genetic diversity of open reading frame 7 field isolated porcine reproductive and respiratory syndrome in North Sumatera, Indonesia, in the period of 2008-2014

    PubMed Central

    Faisal, Faisal; Widayanti, Rini; Haryanto, Aris; Tabu, Charles Rangga

    2015-01-01

    Aim: Molecular identification and genetic diversity of open reading frame 7 (ORF7) of field isolated porcine reproductive and respiratory syndrome virus (PRRSV) in North Sumatera, Indonesia, in the period of 2008-2014. Materials and Methods: A total of 47 PRRSV samples were collected from the death case of pigs. The samples were collected from different districts in the period of 2008-2014 from North Sumatera province. Two pairs of primer were designed to amplify ORF7 of Type 1 and 2 PRRSV based on the sequence of reference viruses VR2332 and Lelystad. Viral RNAs were extracted from samples using PureLink™ micro-to-Midi total RNA purification system (Invitrogen). To amplify the ORF7 of PRRSV, the synthesis cDNA and DNA amplification were performed by reverse transcription polymerase chain reaction (RT-PCR) and nested PCR method. Then the DNA sequencing of PCR products and phylogenetic analysis were accomplished by molecular evolutionary genetics analysis version 6.0 software program. Results: RT-: PCR and nested PCR used in this study had successfully detected of 18 samples positive PRRS virus with the amplification products at 703bp and 508bp, respectively. Sequencing of the ORF7 shows that 18 PRRS viruses isolated from North Sumatera belonged to North American (NA). JXA1 Like and classic NA type viruses. Several mutations were detected, particularly in the area of nuclear localization signal (NLS1) and in NLS2. In the local viruses, which were related closed to JXA1 virus; there are two differences in amino acids in position 12 and 43 of ORF7. Our tested viruses showed that the amino acid positions 12 and 43 are Asparagine and Arginine, while the reference virus (VR2332, Lelystad, and JXA1) occupied both by Lysine. Based on differences in two amino acids at position 12 and 43 showed that viruses from North Sumatera has its own uniqueness and related closed to highly pathogenic PRRS (HP-PRRS) virus (JXA1). Conclusion: The results demonstrated that North Sumatera

  3. In vitro antibiotic susceptibility of Dutch Mycoplasma synoviae field isolates originating from joint lesions and the respiratory tract of commercial poultry.

    PubMed

    Landman, W J M; Mevius, D J; Veldman, K T; Feberwee, A

    2008-08-01

    The in vitro susceptibility of 17 Dutch Mycoplasma synoviae isolates from commercial poultry to enrofloxacin, difloxacin, doxycycline, tylosin and tilmicosin was examined. Three isolates originated from joint lesions and 14 were from the respiratory tract. The type strain M. synoviae WVU 1853 was included as a control strain. Antibiotic susceptibility was tested quantitatively using the broth microdilution test. Based on initial and final minimum inhibitory concentration values, all tested isolates were susceptible to doxycycline, tylosin and tilmicosin. Two isolates from the respiratory tract were resistant to enrofloxacin and showed intermediate resistance to difloxacin.

  4. Transmission blocking activity of Azadirachta indica and Guiera senegalensis extracts on the sporogonic development of Plasmodium falciparum field isolates in Anopheles coluzzii mosquitoes

    PubMed Central

    2014-01-01

    Background Targeting the stages of the malaria parasites responsible for transmission from the human host to the mosquito vector is a key pharmacological strategy for malaria control. Research efforts to identify compounds that are active against these stages have significantly increased in recent years. However, at present, only two drugs are available, namely primaquine and artesunate, which reportedly act on late stage gametocytes. Methods In this study, we assessed the antiplasmodial effects of 5 extracts obtained from the neem tree Azadirachta indica and Guiera senegalensis against the early vector stages of Plasmodium falciparum, using field isolates. In an ex vivo assay gametocytaemic blood was supplemented with the plant extracts and offered to Anopheles coluzzii females by membrane feeding. Transmission blocking activity was evaluated by assessing oocyst prevalence and density on the mosquito midguts. Results Initial screening of the 5 plant extracts at 250 ppm revealed transmission blocking activity in two neem preparations. Up to a concentration of 70 ppm the commercial extract NeemAzal® completely blocked transmission and at 60 ppm mosquitoes of 4 out of 5 replicate groups remained uninfected. Mosquitoes fed on the ethyl acetate phase of neem leaves at 250 ppm showed a reduction in oocyst prevalence of 59.0% (CI95 12.0 - 79.0; p < 10-4) and in oocyst density of 90.5% (CI95 86.0 - 93.5; p < 10-4 ), while the ethanol extract from the same plant part did not exhibit any activity. No evidence of transmission blocking activity was found using G. senegalensis ethyl acetate extract from stem galls. Conclusions The results of this study highlight the potential of antimalarial plants for the discovery of novel transmission blocking molecules, and open up the potential of developing standardized transmission blocking herbal formulations as malaria control tools to complement currently used antimalarial drugs and combination treatments. PMID:24735564

  5. Rapid real-time PCR methods to distinguish Salmonella Enteritidis wildtype field isolates from vaccine strains Salmovac SE/Gallivac SE and AviPro SALMONELLA VAC E.

    PubMed

    Maurischat, Sven; Szabo, Istvan; Baumann, Beatrice; Malorny, Burkhard

    2015-05-01

    Salmonella enterica serovar Enteritidis is a major non-typhoid Salmonella serovar causing human salmonellosis mainly associated with the consumption of poultry and products thereof. To reduce infections in poultry, S. Enteritidis live vaccine strains AviPro SALMONELLA VAC E and Salmovac SE/Gallivac SE have been licensed and used in several countries worldwide. To definitively diagnose a S. Enteritidis contamination in vaccinated herds a reliable and fast method for the differentiation between vaccine and wildtype field isolates is required. In this study, we developed and validated real-time PCR (qPCR) assays to distinguish those variants genetically. Suitable target sequences were identified by whole genome sequencing (WGS) using the Illumina MiSeq system. SNP regions in kdpA and nhaA proved to be most useful for differentiation of AviPro SALMONELLA VAC E and Salmovac SE/Gallivac SE, respectively, from wildtype strains. For each vaccine strain one TaqMan-qPCR assay and one alternative approach using High Resolution Melting (HRM) analysis was designed. All 30 Salmovac SE and 7 AviPro SALMONELLA VAC E vaccine strain reisolates tested were correctly identified by both approaches (100% inclusivity). Furthermore, all 137 (TaqMan) and 97 (HRM) Salmonella non-vaccine and related Enterobacteriaceae strains tested were excluded (100% exclusivity). The analytical detection limits were determined to be approx. 10(2) genome copies/reaction for the TaqMan and 10(4) genome copies/reaction for the HRM approach. The real-time PCR assays proved to be a reliable and fast alternative to the cultural vaccine strain identification tests helping decision makers in control measurements to take action within a shorter period of time.

  6. Analysis of genetic and molecular identity among field isolates of the rice blast fungus with an international differential system, rep-PCR and DNA sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Pi-ta gene deployed in the Southern US rice germplasm is effective in preventing the infection by strains of Magnaporthe oryzae isolates that carry the avirulence gene AVR-Pita1. In the present study, a total of 169 isolates from rice (Oryza sativa) cultivars, with and without Pi-ta, were analyz...

  7. Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales.

    PubMed

    Sakai, Sanae; Ehara, Masayuki; Tseng, I-Cheng; Yamaguchi, Takashi; Bräuer, Suzanna L; Cadillo-Quiroz, Hinsby; Zinder, Stephen H; Imachi, Hiroyuki

    2012-06-01

    A novel mesophilic, hydrogenotrophic methanogen, designated strain TNR(T), was isolated from an anaerobic, propionate-degradation enrichment culture that was originally established from a rice field soil sample from Taiwan. Cells were non-motile rods, 2.0-6.5 µm long by 0.3 µm wide. Filamentous (up to about 100 µm) and coccoid (about 1 µm in diameter) cells were also observed in cultures in the late exponential phase of growth. Strain TNR(T) grew at 20-40 °C (optimally at 37 °C), at pH 6.5-7.4 (optimally at pH 7.0) and in the presence of 0-25 g NaCl l(-1) (optimally at 0 g NaCl l(-1)). The strain utilized H(2)/CO(2) and formate for growth and produced methane. The G+C content of the genomic DNA was 56.4 mol%. Based on sequences of both the 16S rRNA gene and the methanogen-specific marker gene mcrA, strain TNR(T) was related most closely to Methanolinea tarda NOBI-1(T); levels of sequence similarities were 94.8 and 86.4 %, respectively. The 16S rRNA gene sequence similarity indicates that strain TNR(T) and M. tarda NOBI-1(T) represent different species within the same genus. This is supported by shared phenotypic properties, including substrate usage and cell morphology, and differences in growth temperature. Based on these genetic and phenotypic properties, strain TNR(T) is considered to represent a novel species of the genus Methanolinea, for which the name Methanolinea mesophila sp. nov. is proposed; the type strain is TNR(T) ( = NBRC 105659(T) = DSM 23604(T)). In addition, we also suggest family status for the E1/E2 group within the order Methanomicrobiales, for which the name Methanoregulaceae fam. nov. is proposed; the type genus of family is Methanoregula.

  8. Flavobacterium oryzae sp. nov., isolated from a flooded rice field, and emended descriptions of Flavobacterium flevense, Flavobacterium yonginense and Flavobacterium myungsuense.

    PubMed

    Chen, Wen-Ming; Chen, Jhen-Ci; Sheu, Shih-Yi

    2014-11-01

    A bacterial strain, designated Jyi-05(T), was isolated from a flooded rice field and characterized using a polyphasic taxonomic approach. Cells of strain Jyi-05(T) were Gram-stain-negative, strictly aerobic, bright-yellow-pigmented rods that were motile by gliding. Growth occurred at 10-30 °C (optimum 30 °C), at pH 6.5-7.5 (optimum pH 7.0) and with 0-2% (w/v) NaCl (optimum 1%, w/v, NaCl). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Jyi-05(T) belonged to the genus Flavobacterium and was most closely related to Flavobacterium flevense DSM 1076(T) with sequence similarity of 97.6%. Strain Jyi-05(T) contained iso-C(15:0) (16.6%), anteiso-C(15:0) (10.8%), summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c; 10.3%), iso-C((17:0) 3-OH (9.2%), C(16:0) (7.3%) and iso-C(15:0) 3-OH (7.2%) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized aminophospholipids and phospholipids. The major polyamine was homospermidine. The genomic DNA G+C content of strain Jyi-05(T) was 34.2 mol%. The DNA-DNA relatedness of strain Jyi-05(T) with respect to recognized species of the genus Flavobacterium was less than 70%. On the basis of the phylogenetic inference and phenotypic data, strain Jyi-05(T) should be classified as a novel species, for which the name Flavobacterium oryzae sp. nov. is proposed. The type strain is Jyi-05(T) ( = BCRC 80522(T) =LMG 27292(T) =KCTC 32240(T)). Emended descriptions of Flavobacterium flevense, Flavobacterium yonginense and Flavobacterium myungsuense are also presented.

  9. Evidence for high genetic diversity of NAD1 and COX1 mitochondrial haplotypes among triclabendazole resistant and susceptible populations and field isolates of Fasciola hepatica (liver fluke) in Australia.

    PubMed

    Elliott, T; Muller, A; Brockwell, Y; Murphy, N; Grillo, V; Toet, H M; Anderson, G; Sangster, N; Spithill, T W

    2014-02-24

    In recent years, the global incidence of Fasciola hepatica (liver fluke) infections exhibiting resistance to triclabendazole (TCBZ) has increased, resulting in increased economic losses for livestock producers and threatening future control. The development of TCBZ resistance and the worldwide discovery of F. hepatica population diversity has emphasized the need to further understand the genetic structure of drug susceptible and resistant Fasciola populations within Australia. In this study, the genetic diversity of liver flukes was estimated by sequencing mitochondrial DNA (mtDNA) encoding the NAD1 (530 bp) and COX1 (420 bp) genes of 208 liver flukes (F. hepatica) collected from three populations: field isolates obtained from abattoirs from New South Wales (NSW) and Victoria (Vic); three TCBZ-resistant fluke populations from NSW and Victoria; and the well-established TCBZ-susceptible Sunny Corner laboratory isolate. Overall nucleotide diversity for all flukes analysed of 0.00516 and 0.00336 was estimated for the NAD1 and COX1 genes respectively. Eighteen distinct haplotypes were established for the NAD1 gene and six haplotypes for the COX1 gene, resulting in haplotype diversity levels of 0.832 and 0.482, respectively. One field isolate showed a similar low level of haplotype diversity as seen in the Sunny Corner laboratory isolate. Analysis of TCBZ-resistant infrapopulations from 3 individual cattle grazing one property revealed considerable sequence parasite diversity between cattle. Analysis of parasite TCBZ-resistant infrapopulations from sheep and cattle revealed haplotypes unique to each host, but no significant difference between parasite populations. Fst analysis of fluke populations revealed little differentiation between the resistant and field populations. This study has revealed a high level of diversity in field and drug resistant flukes in South-Eastern Australia.

  10. Characterizations of purple non-sulfur bacteria isolated from paddy fields, and identification of strains with potential for plant growth-promotion, greenhouse gas mitigation and heavy metal bioremediation.

    PubMed

    Sakpirom, Jakkapan; Kantachote, Duangporn; Nunkaew, Tomorn; Khan, Eakalak

    2017-04-01

    This study was aimed at selecting purple non-sulfur bacteria (PNSB) isolated from various paddy fields, including Cd- and Zn-contaminated paddy fields, based on their biofertilizer properties. Among 235 PNSB isolates, strain TN110 was most effective in plant growth-promoting substance (PGPS) production, releasing 3.2 mg/L of [Formula: see text] , 4.11 mg/L of 5-aminolevulinic acid (ALA) and 3.62 mg/L of indole-3-acetic acid (IAA), and reducing methane emission up to 80%. This strain had nifH, vnfG and anfG, which are the Mo, V and Fe nitrogenase genes encoded for key enzymes in nitrogen fixation under different conditions. This strain provided 84% and 55% removal of Cd and Zn, respectively. Another isolate, TN414, not only produced PGPS (1.30 mg/L of [Formula: see text] , 0.94 mg/L of ALA and 0.65 mg/L of IAA), but was also efficient in removing both Cd and Zn at 72% and 74%, respectively. Based on 16S rDNA sequencing, strain TN110 was identified as Rhodopseudomonas palustris, while strain TN414 was Rubrivivax gelatinosus. A combination of TN110 and TN414 could potentially provide a biofertilizer, which is a greener alternative to commercial/chemical fertilizers and an agent for bioremediation of heavy metals and greenhouse gas mitigation in paddy fields.

  11. Plasmodium falciparum: in vitro activity of sulfadoxine and dapsone in field isolates from Kenya: point mutations in dihydropteroate synthase may not be the only determinants in sulfa resistance.

    PubMed

    Mberu, Edward K; Nzila, Alexis M; Nduati, Eunice; Ross, Amanda; Monks, Stephanie M; Kokwaro, Gilbert O; Watkins, William M; Hopkins Sibley, Carol

    2002-01-01

    We have determined the relationship between point mutations in the gene that encodes the sulfa target, dihydropteroate synthase (DHPS) and the chemosensitivity profile to sulfadoxine and dapsone in 67 isolates from Kilifi, Kenya. We assessed the presence of mutations at codons 436, 437, 540, 581, and 613 of dhps. The results showed that the dhps genotype had a strong influence on the sensitivity to sulfadoxine and dapsone, but that the correlation was far from perfect. Eleven isolates carried a wild-type dhps allele, but were resistant to sulfadoxine (IC(50) values >10 microg/ml), and 4/28 isolates were classed as sensitive to sulfadoxine (IC(50) values <10 microg/ml), but carried a triple mutant (436/437/613) allele of dhps. These data show that in low folate medium in vitro, the dhps genotype alone did not account completely for sulfadoxine or dapsone resistance; other factors such as the utilisation of exogenous folate must also be considered.

  12. Direct comparison of the histidine-rich protein-2 enzyme-linked immunosorbent assay (HRP-2 ELISA) and malaria SYBR green I fluorescence (MSF) drug sensitivity tests in Plasmodium falciparum reference clones and fresh ex vivo field isolates from Cambodia

    PubMed Central

    2013-01-01

    MSF assay, when evaluating ex vivo Cambodian isolates. Reduced sensitivity of the MSF assay is likely due to an interference of WBCs in clinical samples. Conclusions For clinical samples not depleted of WBCs, HRP-2 ELISA is superior to the MSF assay at evaluating fresh P. falciparum field isolates with low parasitaemia (<0.2%) generally observed in Southeast Asia. PMID:23849006

  13. Isolations of Jamestown Canyon virus (Bunyaviridae: Orthobunyavirus) from field-collected mosquitoes (Diptera: Culicidae) in Connecticut, USA: a ten-year analysis, 1997-2006.

    PubMed

    Andreadis, Theodore G; Anderson, John F; Armstrong, Philip M; Main, Andrew J

    2008-04-01

    Jamestown Canyon virus (JCV) (Bunyaviridae: Orthobunyavirus) is a mosquito-borne zoonosis belonging to the California serogroup. It has a wide geographic distribution, occurring throughout much of temperate North America. White-tailed deer, Odocoileus virginianus are the principal amplification hosts, and boreal Aedes and Ochlerotatus mosquitoes are the primary vectors. A 10-year study was undertaken to identify potential mosquito vectors in Connecticut, quantify seasonal prevalence rates of infection, and define the geographic distribution of JCV in the state as a function of land use and white-tailed deer populations, which have increased substantially over this period. Jamestown Canyon virus was isolated from 22 mosquito species. Five of them, Ochlerotatus canadensis, Oc. cantator, Anopheles punctipennis, Coquillettidia perturbans, and Oc. abserratus were incriminated as the most likely vectors, based on yearly isolation frequencies and the spatial geographic distribution of infected mosquitoes. Jamestown Canyon virus was isolated from Oc. canadensis more consistently and from a greater range of collection sites than any other species. Frequent virus isolations were also made from Aedes cinereus, Aedes vexans, and Oc. sticticus, and new North American isolation records were established for Anopheles walkeri, Culex restuans, Culiseta morsitans, Oc. sticticus, Oc. taeniorhynchus, and Psorophora ferox. Other species from which JCV was isolated included C. melanura, Oc. aurifer, Oc. communis, Oc. excrucians, Oc. provocans, Oc. sollicitans, Oc. stimulans, Oc. triseriatus, and Oc. trivittatus. Jamestown Canyon virus was widely distributed throughout Connecticut and found to consistently circulate in a diverse array of mosquito vectors. Infected mosquitoes were collected from June through September, and peak infection rates paralleled mosquito abundance from mid-June through mid-July. Infection rates in mosquitoes were consistent from year to year, and overall virus

  14. Mariprofundus micogutta sp. nov., a novel iron-oxidizing zetaproteobacterium isolated from a deep-sea hydrothermal field at the Bayonnaise knoll of the Izu-Ogasawara arc, and a description of Mariprofundales ord. nov. and Zetaproteobacteria classis nov.

    PubMed

    Makita, Hiroko; Tanaka, Emiko; Mitsunobu, Satoshi; Miyazaki, Masayuki; Nunoura, Takuro; Uematsu, Katsuyuki; Takaki, Yoshihiro; Nishi, Shinro; Shimamura, Shigeru; Takai, Ken

    2017-03-01

    A novel iron-oxidizing chemolithoautotrophic bacterium, strain ET2(T), was isolated from a deep-sea sediment in a hydrothermal field of the Bayonnaise knoll of the Izu-Ogasawara arc. Cells were bean-shaped, curved short rods. Growth was observed at a temperature range of 15-30 °C (optimum 25 °C, doubling time 24 h) and a pH range of 5.8-7.0 (optimum pH 6.4) in the presence of NaCl at a range of 1.0-4.0 % (optimum 2.75 %). The isolate was a microaerophilic, strict chemolithoautotroph capable of growing using ferrous iron and molecular oxygen (O2) as the sole electron donor and acceptor, respectively; carbon dioxide as the sole carbon source; and either ammonium or nitrate as the sole nitrogen source. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the new isolate was related to the only previously isolated Mariprofundus species, M. ferrooxydans. Although relatively high 16S rRNA gene similarity (95 %) was found between the new isolate and M. ferrooxydans, the isolate was distinct in terms of cellular fatty acid composition, genomic DNA G+C content and cell morphology. Furthermore, genomic comparison between ET2(T) and M. ferrooxydans PV-1 indicated that the genomic dissimilarity of these strains met the standard for species-level differentiation. On the basis of its physiological and molecular characteristics, strain ET2(T) (= KCTC 15556(T) = JCM 30585 (T)) represents a novel species of Mariprofundus, for which the name Mariprofundus micogutta is proposed. We also propose the subordinate taxa Mariprofundales ord. nov. and Zetaproteobacteria classis nov. in the phylum Proteobacteria.

  15. Pathogenicity of entomopathogenic fungi Metarhizium anisopliae and Beauveria bassiana (Hypocreales: Clavicipitaceae) isolates to the adult pea leafminer (Diptera: Agromyzidae) and prospects of an autoinoculation device for infection in the field.

    PubMed

    Migiro, L N; Maniania, N K; Chabi-Olaye, A; Vandenberg, J

    2010-04-01

    Seventeen isolates of Metarhizium anisopliae (Metschnikoff) Sorokin and three isolates of Beauveria bassiana (Balsamo) Vuillemin (Hypocreales: Clavicipitaceae) were evaluated for their pathogenicity to the adult pea leafminer, Liriomyza huidobrensis (Blanchard) (Diptera: Agromyzidae), in the laboratory. Flies were contaminated with dry conidia through a velvet material wrapped around the inner side of a cylindrical plastic tube. All the isolates were pathogenic to the pea leafminer, causing mortality between 40 and 100% at 5 d after exposure. The lethal time for 50% mortality (LT(50)) ranged from 2.6 to 5.4 d, whereas the LT(90) values varied between 3.2 and 9.1 d depending on the isolate. An autoinoculation device was evaluated in cage field experiments using only one of the virulent isolates, M. anisopliae ICIPE 20. The device was loaded with 2-3 g of dry conidia. Mortality of up to 100% was observed in flies captured from fungus-treated cages held under laboratory conditions. The average number of spores picked up by a single fly visiting the device increased with days after inoculation. One day after the inoculation, adults picked up an average of 4.1 +/- 0.7 x 10(5) conidia and 39.6 +/- 4.0 x 10(5) conidia 5 d after inoculation. Depending on the sampling date, the LT(50) varied between 1.8 and 3.4 d. Results indicate that some isolates of B. bassiana and M. anisopliae are highly pathogenic to L. huidobrensis, suggesting a potential for their use in the control of this pest. They also suggest the possibility of L. huidobrensis suppression with fungi using an autoinoculation device.

  16. Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus.

    PubMed

    Servín-Garcidueñas, Luis E; Rogel, Marco A; Ormeño-Orrillo, Ernesto; Zayas-Del Moral, Alejandra; Sánchez, Federico; Martínez-Romero, Esperanza

    2016-03-17

    We present the complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001, a nitrogen-fixing bacterium isolated from nodules of Phaseolus microcarpus. Strain CCGE-LA001 represents the first sequenced bradyrhizobial strain obtained from a wild Phaseolus sp. Its genome revealed a large and novel symbiotic island.

  17. Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus

    PubMed Central

    Servín-Garcidueñas, Luis E.; Rogel, Marco A.; Ormeño-Orrillo, Ernesto; Zayas-del Moral, Alejandra; Sánchez, Federico

    2016-01-01

    We present the complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001, a nitrogen-fixing bacterium isolated from nodules of Phaseolus microcarpus. Strain CCGE-LA001 represents the first sequenced bradyrhizobial strain obtained from a wild Phaseolus sp. Its genome revealed a large and novel symbiotic island. PMID:26988045

  18. Identification of a predominant multilocus sequence type, pulsed-field gel electrophoresis cluster, and novel staphylococcal chromosomal cassette in clinical isolates of mecA-containing, methicillin-resistant Staphylococcus pseudintermedius.

    PubMed

    Black, C C; Solyman, S M; Eberlein, L C; Bemis, D A; Woron, A M; Kania, S A

    2009-11-18

    Methicillin resistance encoded by the mecA gene is increasingly observed in Staphylococcus pseudintermedius. Little is known about the population genetics of veterinary staphylococci bearing methicillin resistance. The aim of this study was to determine the relatedness of resistant bacteria and to compare them with methicillin-susceptible isolates. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) fragment profiling were performed on methicillin-resistant S. pseudintermedius (MRSP) and methicillin-susceptible S. pseudintermedius (MSSP) isolates obtained from canine samples submitted to the veterinary teaching hospital bacteriology service between 2006 and 2008. Multilocus sequence typing detected 20 different sequence types, 16 of which were not previously described. Methicillin-resistant isolates were predominantly ST 68, possessed the Staphylococcus aureus-associated staphylococcal chromosomal cassette mec (SCCmec) type V(T) and fell within the largest PFGE cluster; whereas methicillin-susceptible strains were more genetically diverse. This suggests that most methicillin resistance within the population of isolates tested originated from a single source which has persisted and expanded for several years.

  19. Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov.

    PubMed

    Kawaichi, Satoshi; Ito, Norihiro; Kamikawa, Ryoma; Sugawara, Tatsuya; Yoshida, Takashi; Sako, Yoshihiko

    2013-08-01

    A novel thermophilic, chemoheterotrophic, Gram-negative-staining, multicellular filamentous bacterium, designated strain 110S(T), was isolated from an iron-rich coastal hydrothermal field in Japan. The isolate is facultatively aerobic and chemoheterotrophic. Phylogenetic analysis using 16S rRNA gene sequences nested strain 110S(T) in a novel class-level clone cluster of the phylum 'Chloroflexi'. The isolate grows by dissimilatory iron- and nitrate-reduction under anaerobic conditions, which is the first report of these abilities in the phylum 'Chloroflexi'. The organism is capable of growth with oxygen, ferric iron and nitrate as a possible electron acceptor, has a wide range of growth temperatures, and tolerates higher NaCl concentrations for growth compared to the other isolates in the phylum. Using phenotypic and phylogenetic data, strain 110S(T) (= JCM 17282(T) = NBRC 107679(T) = DSM 23922(T) = KCTC 23289(T) = ATCC BAA-2145(T)) is proposed as the type strain of a novel species in a new genus, Ardenticatena maritima gen. nov., sp. nov. In addition, as strain 110S(T) apparently constitutes a new class of the phylum 'Chloroflexi' with other related uncultivated clone sequences, we propose Ardenticatenia classis nov. and the subordinate taxa Ardenticatenales ord. nov. and Ardenticatenaceae fam. nov.

  20. Sequence variation of the glycoprotein gene identifies three distinct lineages within field isolates of viral hemorrhagic septicemia virus, a fish rhabdovirus

    USGS Publications Warehouse

    Benmansour, A.; Bascuro, B.; Monnier, A.F.; Vende, P.; Winton, J.R.; de Kinkelin, P.

    1997-01-01

    To evaluate the genetic diversity of viral haemorrhagic septicaemia virus (VHSV), the sequence of the glycoprotein genes (G) of 11 North American and European isolates were determined. Comparison with the G protein of representative members of the family Rhabdoviridae suggested that VHSV was a different virus species from infectious haemorrhagic necrosis virus (IHNV) and Hirame rhabdovirus (HIRRV). At a higher taxonomic level, VHSV, IHNV and HIRRV formed a group which was genetically closest to the genus Lyssavirus. Compared with each other, the G genes of VHSV displayed a dissimilar overall genetic diversity which correlated with differences in geographical origin. The multiple sequence alignment of the complete G protein, showed that the divergent positions were not uniformly distributed along the sequence. A central region (amino acid position 245-300) accumulated substitutions and appeared to be highly variable. The genetic heterogeneity within a single isolate was high, with an apparent internal mutation frequency of 1.2 x 10(-3) per nucleotide site, attesting the quasispecies nature of the viral population. The phylogeny separated VHSV strains according to the major geographical area of isolation: genotype I for continental Europe, genotype II for the British Isles, and genotype III for North America. Isolates from continental Europe exhibited the highest genetic variability, with sub-groups correlated partially with the serological classification. Neither neutralizing polyclonal sera, nor monoclonal antibodies, were able to discriminate between the genotypes. The overall structure of the phylogenetic tree suggests that VHSV genetic diversity and evolution fit within the model of random change and positive selection operating on quasispecies.

  1. Genetic diversity and effect of temperature and pH on the growth of Macrophomina phaseolina isolates from sunflower fields in Hungary.

    PubMed

    Csöndes, Izabella; Cseh, András; Taller, János; Poczai, Péter

    2012-03-01

    The effects of temperature and pH on the growth of 45 Hungarian Macrophomina phaseolina isolates from different locations and hosts were compared on the basis of their genetic diversity. One Spanish and two Serbian isolates were also included in the experiment. The most favourable temperature regimes for the development of the isolates ranged between 25 and 35 °C. The optimal pH for the pathogen varied between 4.0 and 6.0, but growth was observed on potato dextrose agar even at pH values of 3.0, 7.0 and 8.0. RAPD analysis with 13 different primer pairs generated 148 unambiguous bands. RFLP analysis involving 8 different restriction endonucleases was performed on a 1550 bp fragment of the rDNA region containing internal transcribed spacers (ITS1, ITS2), the 5.8S rDNA and part of the 25S rDNA. The greatest genetic distance values were obtained for three isolates, two from Hungary and one from Spain, which had similar values, but were quite distinct from all the others. A strong positive correlation was observed between the genetic distances and the growth parameters measured at various temperatures, and between the geographical data and the growth data sets at different pH values, but the correlation was less strong in the latter case. While Hungarian M. phaseolina populations are thought to reproduce clonally, the present results indicate the coexistence of different haplotypes in this area, and besides the geographical dominance of a given haplotype it was found that a closer genetic relationship might exist between spatially distinct haplotypes.

  2. Sequence variation of the glycoprotein gene identifies three distinct lineages within field isolates of viral haemorrhagic septicaemia virus, a fish rhabdovirus.

    PubMed

    Benmansour, A; Basurco, B; Monnier, A F; Vende, P; Winton, J R; de Kinkelin, P

    1997-11-01

    To evaluate the genetic diversity of viral haemorrhagic septicaemia virus (VHSV), the sequence of the glycoprotein genes (G) of 11 North American and European isolates were determined. Comparison with the G protein of representative members of the family Rhabdoviridae suggested that VHSV was a different virus species from infectious haemorrhagic necrosis virus (IHNV) and Hirame rhabdovirus (HIRRV). At a higher taxonomic level, VHSV, IHNV and HIRRV formed a group which was genetically closest to the genus Lyssavirus. Compared with each other, the G genes of VHSV displayed a dissimilar overall genetic diversity which correlated with differences in geographical origin. The multiple sequence alignment of the complete G protein, showed that the divergent positions were not uniformly distributed along the sequence. A central region (amino acid position 245-300) accumulated substitutions and appeared to be highly variable. The genetic heterogeneity within a single isolate was high, with an apparent internal mutation frequency of 1.2 x 10(-3) per nucleotide site, attesting the quasispecies nature of the viral population. The phylogeny separated VHSV strains according to the major geographical area of isolation: genotype I for continental Europe, genotype II for the British Isles, and genotype III for North America. Isolates from continental Europe exhibited the highest genetic variability, with sub-groups correlated partially with the serological classification. Neither neutralizing polyclonal sera, nor monoclonal antibodies, were able to discriminate between the genotypes. The overall structure of the phylogenetic tree suggests that VHSV genetic diversity and evolution fit within the model of random change and positive selection operating on quasispecies.

  3. Failed detection of Bovine viral diarrhea virus 2 subgenotype a (BVDV-2a) by direct fluorescent antibody test on tissue samples due to reduced reactivity of field isolates to raw anti-BVDV antibody.

    PubMed

    Yan, Lifang; Pace, Lanny W; Baughman, Brittany; Wilson, Floyd D; Zhang, Shuping; Zhang, Michael Z

    2016-03-01

    Bovine viral diarrhea virus 1 (BVDV-1) is associated with mild or subclinical infections, whereas BVDV-2 is frequently implicated in outbreaks of severe thrombocytopenia and acute fatal disease. In the present study, the carcass of a beef breed cow and tissue samples of a beef calf were received for laboratory diagnosis. Both animals exhibited severe clinical signs compatible with thrombocytopenia or hemorrhagic syndrome. Direct fluorescent antibody test (DFAT) failed to detect BVDV antigen in the tissue specimens of both cases. However, immunohistochemistry (IHC) revealed the presence of BVDV antigen in oral and esophageal mucosa and Peyer patches of the beef breed cow. Real-time reverse transcription polymerase chain reaction (real-time RT-PCR) detected BVDV-2 in selected tissues of both animals. Subsequently, BVDV was isolated from both cases and subjected to genetic and serologic characterizations. Mutations in the 5'-untranslated genomic region (5'-UTR) primer and probe binding sites and the E2 gene were associated with reduced efficiency of an established real-time RT-PCR assay and amino acid alterations in the E2 glycoprotein, respectively. Both viral isolates were classified by real-time RT-PCR and phylogenetic analysis as BVDV-2 subgenotype a. Unlike BVDV reference strains Singer and 125c, the isolates cross-reacted with anti-BVDV-1 and anti-BVDV-2 reference sera, indicating antigenic variations in field isolates. The isolates also showed reduced reactivity to porcine anti-BVDV antiserum (the raw serum used to produce BVDV DFA conjugate). In summary, data from the present investigation indicated that genetic and antigenic variations affected the performance of detection assays, especially DFAT, highlighting the need for regular evaluation and modification of BVDV tests.

  4. Characterization of epidemiologically unrelated Acinetobacter baumannii isolates from four continents by use of multilocus sequence typing, pulsed-field gel electrophoresis, and sequence-based typing of bla(OXA-51-like) genes.

    PubMed

    Hamouda, Ahmed; Evans, Benjamin A; Towner, Kevin J; Amyes, Sebastian G B

    2010-07-01

    This study used a diverse collection of epidemiologically unrelated Acinetobacter baumannii isolates to compare the robustness of a multilocus sequence typing (MLST) scheme, based on conserved regions of seven housekeeping genes, gltA, gdhB, recA, cpn60, rpoD, gyrB, and gpi, with that of sequence-based typing of bla(OXA-51-like) genes (SBT-bla(OXA-51-like) genes). The data obtained by analysis of MLST and SBT-bla(OXA-51-like) genes were compared to the data generated by pulsed-field gel electrophoresis (PFGE). The topologies of the phylogenetic trees generated for the gyrB and gpi genes showed evidence of recombination and were inconsistent with those of the trees generated for the other five genes. MLST identified 24 sequence types (STs), of which 19 were novel, and 5 novel alleles. Clonality was demonstrated by eBURST analysis and standardized index of association values of >1 (P < 0.001). MLST data revealed that all isolates harboring the major bla(OXA-51-like) alleles OXA-66, OXA-69, and OXA-71 fell within the three major European clonal lineages. However, the MLST data were not always in concordance with the PFGE data, and some isolates containing the same bla(OXA-51-like) allele demonstrated <50% relatedness by PFGE. It was concluded that the gyrB and gpi genes are not good candidates for use in MLST analysis and that a SBT-bla(OXA-51-like) gene scheme produced results comparable to those produced by MLST for the identification of the major epidemic lineages, with the advantage of having a significantly reduced sequencing cost and time. It is proposed that studies of A. baumannii epidemiology could involve initial screening of bla(OXA-51-like) alleles to identify isolates belonging to major epidemic lineages, followed by MLST analysis to categorize isolates from common lineages, with PFGE being reserved for fine-scale typing.

  5. Genetic manipulation of porcine epidemic diarrhoea virus recovered from a full-length infectious cDNA clone.

    PubMed

    Jengarn, Juggragarn; Wongthida, Phonphimon; Wanasen, Nanchaya; Frantz, Phanramphoei Namprachan; Wanitchang, Asawin; Jongkaewwattana, Anan

    2015-08-01

    Porcine epidemic diarrhoea virus (PEDV) causes acute diarrhoea and dehydration in swine of all ages, with significant mortality in neonatal pigs. The recent rise of PEDV outbreaks in Asia and North America warrants an urgent search for effective vaccines. However, PEDV vaccine research has been hampered by difficulties in isolating and propagating the virus in mammalian cells, thereby complicating the recovery of infectious PEDV using a full-length infectious clone. Here, we engineered VeroE6 cells to stably express porcine aminopeptidase N (pAPN) and used them as a platform to obtain a high-growth variant of PEDV, termed PEDVAVCT12. Subsequently, the full-length cDNA clone was constructed by assembling contiguous cDNA fragments encompassing the complete genome of PEDVAVCT12 in a bacterial artificial chromosome. Infectious PEDV could be recovered, and the rescued virus displayed phenotypic properties identical to the parental virus. Interestingly, we found that PEDVAVCT12 contained a C-terminal deletion of the spike gene, resulting in disruption of the ORF3 start codon. When a functional ORF3 gene was restored, the recombinant virus could not be rescued, suggesting that ORF3 could suppress PEDV replication in vitro. In addition, a high-growth and genetically stable recombinant PEDV expressing a foreign protein could be rescued by replacing the ORF3 gene with the mCherry gene. Together, the results of this study provide a means to generate genetically defined PEDV as a promising vaccine candidate.

  6. Determination of selected pesticides in water samples adjacent to agricultural fields and removal of organophosphorus insecticide chlorpyrifos using soil bacterial isolates

    NASA Astrophysics Data System (ADS)

    Hossain, M. S.; Chowdhury, M. Alamgir Zaman; Pramanik, Md. Kamruzzaman; Rahman, M. A.; Fakhruddin, A. N. M.; Alam, M. Khorshed

    2015-06-01

    The use of pesticide for crops leads to serious environmental pollution, therefore, it is essential to monitor and develop approaches to remove pesticide from contaminated environment. In this study, water samples were collected to monitor pesticide residues, and degradation of chlorpyrifos was also performed using soil bacteria. Identification of pesticide residues and determination of their levels were performed by high-performance liquid chromatography with photodiode array detector. Among 12 samples, 10 samples were found contaminated with pesticides. Chlorpyrifos was detected in four tested samples and concentrations ranged from 3.27 to 9.31 μg/l whereas fenitrothion ranging from (Below Detection Limit, <0.1 μg/l) to 33.41 μg/l in the tested samples. Parathion was found in two tested samples at the concentration of 0.73 and 6.23 μg/l. None of the tested samples was found contaminated with Methoxychlor, DDT and Ethion. Three soil bacterial isolates, Pseudomonas peli BG1, Burkholderia caryophylli BG4 and Brevundimonas diminuta PD6 degraded chlorpyrifos completely in 8, 10 and 10 days, respectively, when 20 mg/l chlorpyrifos was supplied as sole source of carbon. Whereas, BG1, BG4 and PD6 took 14, 16 and 16 days, respectively, for complete removal of 50 mg/l chlorpyrifos. Chlorpyrifos degradation rates were found maximum by all three isolates at 2nd day of incubation for both tested concentrations. The results of the present study suggest the need for regular monitoring of pesticide residues in water, to protect the aquatic environment. Chlorpyrifos degrading bacterial isolates can be used to clean up environmental samples contaminated with the organophosphate pesticides.

  7. Comparison of Danish isolates of Salmonella enterica serovar enteritidis PT9a and PT11 from hedgehogs (Erinaceus europaeus) and humans by plasmid profiling and pulsed-field gel electrophoresis.

    PubMed

    Nauerby, B; Pedersen, K; Dietz, H H; Madsen, M

    2000-10-01

    During the years 1994 to 1998, 10 strains of Salmonella enterica serovar Enteritidis phage type 11 (PT11) and 6 PT9a strains were isolated from Danish hedgehogs, together with 7 strains that did not yield phage susceptibility patterns conforming with any known phage type (routine dilution no conformity [RDNC]). From 1995 to 1998, five Danish patients were reported infected with serovar Enteritidis PT11 and two with PT9a. All serovar Enteritidis PT11, PT9a, and RDNC isolates from hedgehogs and humans were analyzed by pulsed-field gel electrophoresis (PFGE), plasmid profiling, and restriction fragment length polymorphism (RFLP) of plasmids. By use of S1 nuclease and HindIII, the PT11 and PT9a isolates had identical plasmid profiles and RFLP patterns, which differed from the RDNC profiles. The PFGE profiles were identical for all serovar Enteritidis PT11 and PT9a strains from hedgehogs, four of five human strains of serovar Enteritidis PT11, and two human strains of serovar Enteritidis PT9a, irrespective of restriction enzyme, whereas the last human strain deviated slightly when NotI was used but not when XbaI or SpeI was used. The results indicate that serovar Enteritidis PT9a and PT11 are closely related and that PT11 and PT9a from Danish hedgehogs and humans belong to the same clonal lineage.

  8. Genetic Diversity of Food-Isolated Salmonella Strains through Pulsed Field Gel Electrophoresis (PFGE) and Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR)

    PubMed Central

    Fendri, Imen; Ben Hassena, Amal; Grosset, Noel; Barkallah, Mohamed; Khannous, Lamia; Chuat, Victoria; Gautier, Michel; Gdoura, Radhouane

    2013-01-01

    All over the world, the incidence of Salmonella spp contamination on different food sources like broilers, clams and cow milk has increased rapidly in recent years. The multifaceted properties of Salomnella serovars allow the microorganism to grow and multiply in various food matrices, even under adverse conditions. Therefore, methods are needed to detect and trace this pathogen along the entire food supply network. In the present work, PFGE and ERIC-PCR were used to subtype 45 Salmonella isolates belonging to different serovars and derived from different food origins. Among these isolates, S. Enteritidis and S. Kentucky were found to be the most predominant serovars. The Discrimination Index obtained by ERIC-PCR (0.85) was slightly below the acceptable confidence value. The best discriminatory ability was observed when PFGE typing method was used alone (DI = 0.94) or combined with ERIC-PCR (DI = 0.93). A wide variety of profiles was observed between the different serovars using PFGE or/and ERIC-PCR. This diversity is particularly important when the sample origins are varied and even within the same sampling origin. PMID:24312546

  9. Characterization of two recent Japanese field isolates of canine distemper virus and examination of the avirulent strain utility as an attenuated vaccine.

    PubMed

    Takenaka, Akiko; Yoneda, Misako; Seki, Takahiro; Uema, Masashi; Kooriyama, Takanori; Nishi, Toshiya; Fujita, Kentaro; Miura, Ryuichi; Tsukiyama-Kohara, Kyoko; Sato, Hiroki; Kai, Chieko

    2014-12-05

    Recently, several new strains of canine distemper virus (CDV) have been isolated in Japan. To investigate their pathogenesis in dogs, the Yanaka and Bunkyo-K strains were investigated by infecting dogs and determining clinical signs, amount of virus, and antibody responses. The Yanaka strain is avirulent and induced an antibody response. The Bunkyo-K strain induced typical CDV clinical signs in infected dogs and virulence was enhanced by brain passage. Molecular and phylogenetic analyses of H genes demonstrated the Bunkyo-K strains were of a different lineage from Asia-1 group including the Yanaka strain and Asia-2 group that contain recent Japanese isolates, which were recently identified as major prevalent strains worldwide but distinct from old vaccine strains. Based on these data, we tested the ability of the Yanaka strain for vaccination. Inoculation with the Yanaka strain efficiently induced CDV neutralizing antibodies with no clinical signs, and the protection effects against challenge with either old virulent strain or Bunkyo-K strain were equal or greater when compared with vaccination by an original vaccine strain. Thus, the Yanaka strain is a potential vaccine candidate against recent prevalent CDV strains.

  10. Candidate isolated neutron stars and other optically blank x-ray fields identified from the rosat all-sky and sloan digital sky surveys

    SciTech Connect

    Agueros, Marcel A.; Anderson, Scott F.; Margon, Bruce; Haberl, Frank; Voges, Wolfgang; Annis, James; Schneider, Donald P.; Brinkmann, Jonathan; /Apache Point Observ.

    2005-11-01

    Only seven radio-quiet isolated neutron stars (INSs) emitting thermal X rays are known, a sample that has yet to definitively address such fundamental issues as the equation of state of degenerate neutron matter. We describe a selection algorithm based on a cross-correlation of the ROSAT All-Sky Survey (RASS) and the Sloan Digital Sky Survey (SDSS) that identifies X-ray error circles devoid of plausible optical counterparts to the SDSS g {approx} 22 magnitudes limit. We quantitatively characterize these error circles as optically blank; they may host INSs or other similarly exotic X-ray sources such as radio-quiet BL Lacs, obscured AGN, etc. Our search is an order of magnitude more selective than previous searches for optically blank RASS error circles, and excludes the 99.9% of error circles that contain more common X-ray-emitting subclasses. We find 11 candidates, nine of which are new. While our search is designed to find the best INS candidates and not to produce a complete list of INSs in the RASS, it is reassuring that our number of candidates is consistent with predictions from INS population models. Further X-ray observations will obtain pinpoint positions and determine whether these sources are entirely optically blank at g {approx} 22, supporting the presence of likely isolated neutron stars and perhaps enabling detailed follow-up studies of neutron star physics.

  11. Evaluation of two singleplex reverse transcription-Insulated isothermal PCR tests and a duplex real-time RT-PCR test for the detection of porcine epidemic diarrhea virus and porcine deltacoronavirus.

    PubMed

    Zhang, Jianqiang; Tsai, Yun-Long; Lee, Pei-Yu Alison; Chen, Qi; Zhang, Yan; Chiang, Cheng-Jen; Shen, Yu-Han; Li, Fu-Chun; Chang, Hsiao-Fen Grace; Gauger, Phillip C; Harmon, Karen M; Wang, Hwa-Tang Thomas

    2016-08-01

    Recent outbreaks of porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) in multiple countries have caused significant economic losses and remain a serious challenge to the swine industry. Rapid diagnosis is critical for the implementation of efficient control strategies before and during PEDV and PDCoV outbreaks. Insulated isothermal PCR (iiPCR) on the portable POCKIT™ device is user friendly for on-site pathogen detection. In the present study, a singleplex PEDV RT-iiPCR, a singleplex PDCoV RT-iiPCR, and a duplex PEDV/PDCoV real-time RT-PCR (rRT-PCR) commercial reagents targeting the M gene were compared to an N gene-based PEDV rRT-PCR and an M gene-based PDCoV rRT-PCR that were previously published and used as reference PCRs. All PCR assays were highly specific and did not cross react with other porcine enteric pathogens. Analytical sensitivities of the PEDV RT-iiPCR, PDCoV RT-iiPCR and duplex PEDV/PDCoV rRT-PCR were determined using in vitro transcribed RNA as well as viral RNA extracted from ten-fold serial dilutions of PEDV and PDCoV cell culture isolates. Performance of each PCR assay was further evaluated using 170 clinical samples (86 fecal swabs, 24 feces, 19 intestines, and 41 oral fluids). Compared to the reference PEDV rRT-PCR, the sensitivity, specificity and accuracy of the PEDV RT-iiPCR were 97.73%, 98.78%, and 98.24%, respectively, and those of the duplex PEDV/PDCoV rRT-PCR were 98.86%, 96.34%, and 97.65%, respectively. Compared to the reference PDCoV rRT-PCR, the sensitivity, specificity and accuracy of the PDCoV RT-iiPCR were 100%, 100%, and 100%, respectively, and those of the PEDV/PDCoV duplex rRT-PCR were 96.34%, 100%, and 98.24%, respectively. Overall, all three new PCR assays were comparable to the reference rRT-PCRs for detection of PEDV and/or PDCoV. The PEDV and PDCoV RT-iiPCRs are potentially useful tools for on-site detection and the duplex PEDV/PDCoV rRT-PCR provides a convenient method to simultaneously detect

  12. Comparison of Molecular and Biological Characteristics of a Modified Live Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Vaccine (Ingelvac PRRS MLV), the Parent Strain of the Vaccine (ATCC VR2332), ATCC VR2385, and Two Recent Field Isolates of PRRSV

    PubMed Central

    Opriessnig, T.; Halbur, P. G.; Yoon, K.-J.; Pogranichniy, R. M.; Harmon, K. M.; Evans, R.; Key, K. F.; Pallares, F. J.; Thomas, P.; Meng, X. J.

    2002-01-01

    The objectives of this study were to compare the molecular and biological characteristics of recent porcine reproductive and respiratory syndrome virus (PRRSV) field isolates to those of a modified live virus (MLV) PRRS vaccine and its parent strain. One hundred seventeen, 4-week-old pigs were randomly assigned to six groups. Group 1 (n = 20) served as sham-inoculated negative controls, group 2 (n = 19) was inoculated with Ingelvac PRRS MLV vaccine, group 3 (n = 20) was inoculated with the parent strain of the vaccine (ATCC VR2332), group 4 (n = 19) was inoculated with vaccine-like PRRSV field isolate 98-38803, group 5 (n = 19) was inoculated with PRRSV field isolate 98-37120, and group 6 (n = 20) was inoculated with known high-virulence PRRSV isolate ATCC VR2385. The levels of severity of gross lung lesions (0 to 100%) among the groups were significantly different at both 10 (P < 0.0001) and 28 days postinoculation (p.i.) (P = 0.002). At 10 days p.i., VR2332 (26.5% ± 4.64%) and VR2385 (36.4% ± 6.51%) induced gross lesions of significantly greater severity than 98-38803 (0.0% ± 0.0%), 98-37120 (0.8% ± 0.42%), Ingelvac PRRS MLV (0.9% ± 0.46%), and negative controls (2.3% ± 1.26%). At 28 days p.i., 98-37120 (17.2% ± 6.51%) induced gross lesions of significantly greater severity than any of the other viruses. Analyses of the microscopic-interstitial-pneumonia-lesion scores (0 to 6) revealed that VR2332 (2.9 ± 0.23) and VR2385 (3.1 ± 0.35) induced significantly more severe lesions at 10 days p.i. At 28 days p.i., VR2385 (2.5 ± 0.27), VR2332 (2.3 ± 0.21), 98-38803 (2.6 ± 0.29), and 98-37120 (3.0 ± 0.41) induced significantly more severe lesions than Ingelvac PRRS MLV (0.7 ± 0.17) and controls (0.7 ± 0.15). The molecular analyses and biological characterizations suggest that the vaccine-like isolate 98-38803 (99.5% amino acid homology based on the ORF5 gene) induces microscopic pneumonia lesions similar in type to, but different in severity and time of

  13. Epidemiological typing of isolates from an outbreak of infection with multidrug-resistant Enterobacter cloacae by repetitive extragenic palindromic unit b1-primed PCR and pulsed-field gel electrophoresis.

    PubMed Central

    Shi, Z Y; Liu, P Y; Lau, Y J; Lin, Y H; Hu, B S

    1996-01-01

    An outbreak of multidrug-resistant Enterobacter cloacae infection lasted for 4 months in a neonatal intensive care unit (NICU). Forty-six isolates from the NICU and 20 epidemiologically unrelated strains were characterized by pulsed-field gel electrophoresis (PFGE) and repetitive extragenic palindromic unit b1-primed PCR (REPUb1-PCR) typing. The PFGE patterns after XbaI restriction of the bacterial DNA were analyzed by computer software (Gelcompar) using the UPGMA (unweighted pair group method with arithmetic averages) clustering method and the Dice coefficient. The 46 isolates from the NICU were classified by PFGE typing into five clusters: A (further classified into 7 subtypes, A1 to A7), B, C, D, and E. This outbreak was attributed to multiple genetically related strains of cluster A which had a similarity of 85.8% +/- 4.6%. The minor band differences among strains of cluster A were probably due to minor genetic mutations. The type A1 and A3 strains were isolated from the clinical specimens of patients and hands of nurses. It was probable that these outbreak strains were transmitted among patients via the hands of personnel. REPUb1-PCR typing of the 46 isolates also demonstrated five types, in agreement with results obtained by the PFGE technique, but could not detect the minor mutations among the cluster A strains. Twenty epidemiologically unrelated strains were well distinguished by both PFGE and REPUb1-PCR typing. We conclude that PFGE is a highly discriminatory but time-consuming method for epidemiological typing of E. cloacae and that REPUb1-PCR is a more rapid method with good reproducibility and discriminatory power comparable to that of PFGE. PMID:8897183

  14. US variant porcine epidemic diarrhea virus: histological lesions and genetic characterization.

    PubMed

    Wang, Leyi; Hayes, Jeff; Byrum, Beverly; Zhang, Yan

    2016-08-01

    Porcine epidemic diarrhea virus (PEDV) was first recognized in pigs in the United States (US) in May 2013. Since then, the virus has spread to over 30 states and caused significant economic losses in the US swine industry due to the high mortality in newborn piglets less than 2 weeks of age. A mild-variant strain OH851 of PEDV in the US was first reported in January 2014. Here, we report histological changes in the small intestines of five piglets infected with the variant strain OH851 of PEDV. The lesions observed were milder, compared to the US classical strain of PEDV. Our study, for the first time, reports the histological lesions caused by the variant PEDV OH851 strain from a field case. In addition, genomic characterization demonstrated that US variant PEDV is more closely related to European-like strains in the first 1170 nt of the 5' spike gene but to US classical PEDV strains in the remaining genome, suggesting that the variant PEDV strain may derive from a recombinant event between the US classical and European-like PEDV strains.

  15. Ex Vivo Drug Sensitivity Profiles of Plasmodium falciparum Field Isolates from Cambodia and Thailand, 2005 to 2010, Determined by a Histidine-Rich Protein-2 Assay

    DTIC Science & Technology

    2012-06-13

    hydrochlor- ide (MQ), quinine sulfate hydrate (QN) artesunate (AS), dihydroartemisinin (DHA), lumefantrine (LUM) and piperaquine (PPQ). CQ, MQ, QN and PPQ...within previ- ously validated criteria were cleared to be sent to the field. Out of range lots were destroyed. Drug plating consistency and stability ...the assessment of the response of Plasmodium falciparum to chloroquine, mefloquine, quinine , amodiaquine, sulfadoxine/pyrimethamine, and artemisinin

  16. Negotiating the radiologically isolated syndrome.

    PubMed

    Cummings, A; Chataway, J

    2014-10-01

    Multiple sclerosis, always challenging, hands down a particular gauntlet with the concept of the radiologically isolated syndrome. This article discusses what it is, recent developments in the field and how these patients should be managed.

  17. Radioactive waste isolation in salt: geochemistry of brine in rock salt in temperature gradients and gamma-radiation fields - a selective annotated bibliography

    SciTech Connect

    Hull, A.B.; Williams, L.B.

    1985-07-01

    Evaluation of the extensive research concerning brine geochemistry and transport is critically important to successful exploitation of a salt formation for isolating high-level radioactive waste. This annotated bibliography has been compiled from documents considered to provide classic background material on the interactions between brine and rock salt, as well as the most important results from more recent research. Each summary elucidates the information or data most pertinent to situations encountered in siting, constructing, and operating a mined repository in salt for high-level radioactive waste. The research topics covered include the basic geology, depositional environment, mineralogy, and structure of evaporite and domal salts, as well as fluid inclusions, brine chemistry, thermal and gamma-radiation effects, radionuclide migration, and thermodynamic properties of salts and brines. 4 figs., 6 tabs.

  18. Offset trench isolation

    NASA Astrophysics Data System (ADS)

    Roth, S. S.; Cooper, K. J.; Ray, W.; Kirsch, H. C.; Grove, Charlotte

    1994-08-01

    Feasibility of a new, recessed isolation technique that utilizes an offset, shallow trench in combination with thermal oxidation for achieving near zero final encroachment with excellent planarity is demonstrated. Etch of the shallow trench is offset from the original hardmask by an oxide sidewall spacer. After trench etch, HF is used to remove the hardmask oxide and sidewall spacers and to form a cavity which is self-aligned to the nitride edge. Exposed silicon regions are then reoxidized and encapsulated with polysilicon. Field oxide is then grown. The final field oxide profile exhibits steep sidewall angles without inducing substrate defects as evidenced by low diode leakage. Other isolation sensitive device parametrics such as gate oxide quality and metal oxide semiconductor field effect transistor threshold voltage stability are presented and exhibit good characteristics.

  19. Efficacy and transmissibility of Newcastle disease I-2 vaccine strain against a field isolate of virulent ND virus (JF820294.1) in village chicken.

    PubMed

    Habibi, Hassan; Nili, Hassan; Asasi, Kramat; Mosleh, Najmeh; Firouzi, Sobhan; Mohammadi, Mitra

    2015-01-01

    This study was conducted to assess efficacy of heat-stable I-2 vaccine against Newcastle diseases in vaccinated and vaccinated in contact birds group following challenge against virulent Newcastle disease (ND) virus in village chicken. Also, to assess whether birds that have been exposed to vaccine virus-shedding, birds were protected against mortality and clinical signs after infection with a virulent strain of the ND virus (NDV). One hundred fifty one-day-old native chickens were divided into seven groups (4 experimental groups of 30 birds/group and 3 control groups (unvaccinated unchallenged, challenged, and just vaccinated). Birds in experimental groups were vaccinated either via drinking water or as food carrier with thermostable I-2 vaccine and then challenged with virulent isolate of NDV (JF820294.1), and eight birds were added as in-contact birds to vaccinated groups. Following challenge, seven extra birds were added to each group as in contact with vaccinated and challenged birds. Survival rate, clinical signs, necropsy finding, and mean antibody titer were evaluated in different experimental and control groups. Birds vaccinated via drinking water showed 100% survival rate. However, birds vaccinated with food carrier vaccine showed less than 50% survival rate. Based on the results obtained from this study, it can be recommended that I-2 vaccination via drinking water can effectively prevent ND in village chicken, since I-2 strain has been able to transmit to non-vaccinated-sensitive birds more effectively than velogenic NDV.

  20. Multiple strain infections and high genotypic diversity among Mycobacterium avium subsp. paratuberculosis field isolates from diseased wild and domestic ruminant species in the eastern Alpine region of Austria.

    PubMed

    Gerritsmann, H; Stalder, G L; Spergser, J; Hoelzl, F; Deutz, A; Kuebber-Heiss, A; Walzer, C; Smith, S

    2014-01-01

    Johne's disease, or paratuberculosis, is a chronic fatal ruminant gastroenteritis caused by Mycobacterium avium subspecies paratuberculosis (MAP) whose foodborne zoonotic potential and association with Crohn's disease are still under debate. The disease is widespread but its epidemiology and epizootiology remains elusive. Wildlife is suspected to play a major role. After a surge in MAP seroprevalence in Austrian cattle, paratuberculosis was declared a notifiable disease in Austria in 2006. At the same time a rise in MAP cases in wild ruminant populations in the Austrian province of Styria was reported. All five autochthonous ruminants were affected. Genetic analysis of isolates, yielded numerous genotypes (>15) and several multiple strain infections (15%) across host species. Identical MIRU-VNTR profiles were identified in different species and sampling locations. On the other hand varying MIRU-VNTR profiles were revealed at the same location and in conspecifics. Our data, taken together with earlier epidemiological studies on MAP and other mycobacteria, raised concerns about the organisms' ecology. Constraints regarding in vitro culture of this highly fastidious organism potentially bias our current understanding of its epidemiology. We suggest that MAP infections could be polyclonal and question the informative value of genotyping a single MAP colony derived from a single specimen for epidemiological analysis of MAP.

  1. Final Scientific Report: Bacterial Nanowires and Extracellular Electron Transfer to Heavy Metals and Radionuclides by Bacterial Isolates from DOE Field Research Centers

    SciTech Connect

    Nealson, Kenneth

    2016-12-20

    This proposal involved the study of bacteria capable of transferring electrons from the bacterial cells to electron acceptors located outside the cell. These could be either insoluble minerals that were transformed into soluble products upon the addition of electrons, or they could be soluble salts like uranium or chromium, that become insoluble upon the addition of electrons. This process is called extracellular electron transport or EET, and can be done directly by cellular contact, or via conductive appendages called bacterial nanowires. In this work we examined a number of different bacteria for their ability to perform EET, and also looked at their ability to produce conductive nanowires that can be used for EET at a distance away from the EET-capable cells. In the work, new bacteria were isolated, new abilities of EET were examined, and many new methods were developed, and carefully described in the literature. These studies set the stage for future work dealing with the bioremediation of toxic metals like uranium and chromium. They also point out that EET (and conductive nanowires) are far more common that had been appreciated, and may be involved with energy transfer not only in sediments, but in symbioses between different bacteria, and in symbiosis/pathogenesis between bacteria and higher organisms.

  2. Charge trapping and de-trapping in isolated CdSe/ZnS nanocrystals under an external electric field: indirect evidence for a permanent dipole moment.

    PubMed

    Zang, Huidong; Cristea, Mihail; Shen, Xuan; Liu, Mingzhao; Camino, Fernando; Cotlet, Mircea

    2015-09-28

    Single nanoparticle studies of charge trapping and de-trapping in core/shell CdSe/ZnS nanocrystals incorporated into an insulating matrix and subjected to an external electric field demonstrate the ability to reversibly modulate the exciton dynamics and photoluminescence blinking while providing indirect evidence for the existence of a permanent ground state dipole moment in such nanocrystals. A model assuming the presence of energetically deep charge traps physically aligned along the direction of the permanent dipole is proposed in order to explain the dynamics of nanocrystal blinking in the presence of a permanent dipole moment.

  3. Binding Site Alteration Is Responsible for Field-Isolated Resistance to Bacillus thuringiensis Cry2A Insecticidal Proteins in Two Helicoverpa Species

    PubMed Central

    Caccia, Silvia; Hernández-Rodríguez, Carmen Sara; Mahon, Rod J.; Downes, Sharon; James, William; Bautsoens, Nadine; Van Rie, Jeroen; Ferré, Juan

    2010-01-01

    Background Evolution of resistance by target pests is the main threat to the long-term efficacy of crops expressing Bacillus thuringiensis (Bt) insecticidal proteins. Cry2 proteins play a pivotal role in current Bt spray formulations and transgenic crops and they complement Cry1A proteins because of their different mode of action. Their presence is critical in the control of those lepidopteran species, such as Helicoverpa spp., which are not highly susceptible to Cry1A proteins. In Australia, a transgenic variety of cotton expressing Cry1Ac and Cry2Ab (Bollgard II) comprises at least 80% of the total cotton area. Prior to the widespread adoption of Bollgard II, the frequency of alleles conferring resistance to Cry2Ab in field populations of Helicoverpa armigera and Helicoverpa punctigera was significantly higher than anticipated. Colonies established from survivors of F2 screens against Cry2Ab are highly resistant to this toxin, but susceptible to Cry1Ac. Methodology/Principal Findings Bioassays performed with surface-treated artificial diet on neonates of H. armigera and H. punctigera showed that Cry2Ab resistant insects were cross-resistant to Cry2Ae while susceptible to Cry1Ab. Binding analyses with 125I-labeled Cry2Ab were performed with brush border membrane vesicles from midguts of Cry2Ab susceptible and resistant insects. The results of the binding analyses correlated with bioassay data and demonstrated that resistant insects exhibited greatly reduced binding of Cry2Ab toxin to midgut receptors, whereas no change in 125I-labeled-Cry1Ac binding was detected. As previously demonstrated for H. armigera, Cry2Ab binding sites in H. punctigera were shown to be shared by Cry2Ae, which explains why an alteration of the shared binding site would lead to cross-resistance between the two Cry2A toxins. Conclusion/Significance This is the first time that a mechanism of resistance to the Cry2 class of insecticidal proteins has been reported. Because we found the same

  4. Charge trapping and de-trapping in isolated CdSe/ZnS nanocrystals under an external electric field: Indirect evidence for a permanent dipole moment

    SciTech Connect

    Zang, Huidong; Cristea, Mihail; Shen, Xuan; Liu, Mingzhao; Camino, Fernando; Cotlet, Mircea

    2015-08-05

    Single nanoparticle studies of charge trapping and de-trapping in core/shell CdSe/ZnS nanocrystals incorporated into an insulating matrix and subjected to an external electric field demonstrate the ability to reversibly modulate the exciton dynamics and photoluminescence blinking while providing indirect evidence for the existence of a permanent ground state dipole moment in such nanocrystals. A model assuming the presence of energetically deep charge traps physically aligned along the direction of the permanent dipole is proposed in order to explain the dynamics of nanocrystal blinking in the presence of a permanent dipole moment.

  5. Flooded area and plant zonation in isolated wetlands in well fields in the Northern Tampa Bay Region, Florida, following reductions in groundwater-withdrawal rates

    USGS Publications Warehouse

    Haag, Kim H.; Pfeiffer, William R.

    2012-01-01

    WAP scores and weighted average scores for wetland vegetation were generally consistent with the results of the flooded area analysis. The WAP scores and weighted average scores were higher overall and did not decline with time at four wetlands in well fields (W-33, W-56, Starkey N, and Starkey 108) during the years following reductions in groundwater-withdrawal rates. These four wetlands also had increases in the extent and duration of the flooded area during the post-reduction period. Scores for trees were more consistent than scores for shrubs and groundcover. WAP scores remained relatively low or generally declined at five well-field wetlands (Q-1, W-17, W-41, Starkey D, and Starkey E) during the years following reductions in groundwater-withdrawal rates, and weighted average scores either declined over time or remained low. These five wetlands either did not have an increase in the extent and duration of the flooded area, or if there was an increase, it was small.

  6. Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the epsilon-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field.

    PubMed

    Takai, Ken; Nealson, Kenneth H; Horikoshi, Koki

    2004-01-01

    A novel thermophilic bacterium, strain EP1-55-1%T, was isolated from an in-situ colonization system deployed in a superheated, deep-sea, hydrothermal vent emission at the Kairei Field on the Central Indian Ridge in the Indian Ocean. The cells were highly motile rods, each possessing a single polar flagellum. Growth was observed between 35 and 65 degrees C (optimum temperature, 55 degrees C; 70 min doubling time) and between pH 4.9 and 7.2 (optimum, pH 5.9). The isolate was a microaerobic-to-anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Molecular oxygen, nitrate or elemental sulfur (S0) could serve as electron acceptors to support growth. The G+C content of the genomic DNA was 34.6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that strain EP1-55-1%T represents the first strain for which taxonomic properties have been characterized within the previously uncultivated phylogroup classified as belonging to the uncultivated epsilon-Proteobacteria group A; the name Hydrogenimonas thermophila gen. nov., sp. nov. is proposed, with strain EP1-55-1%T (=JCM 11971T=ATCC BAA-737T) as the type strain.

  7. Thioprofundum hispidum sp. nov., an obligately chemolithoautotrophic sulfur-oxidizing gammaproteobacterium isolated from the hydrothermal field on Suiyo Seamount, and proposal of Thioalkalispiraceae fam. nov. in the order Chromatiales.

    PubMed

    Mori, Koji; Suzuki, Ken-ichiro; Urabe, Tetsuro; Sugihara, Maki; Tanaka, Kenji; Hamada, Moriyuki; Hanada, Satoshi

    2011-10-01

    A novel mesophilic, facultatively anaerobic, sulfur-oxidizing bacterial strain, designated gps61(T), was isolated from a surface rock sample collected from the hydrothermal field of Suiyo Seamount on the Izu-Bonin Arc in the Western Pacific Ocean. Cells of the isolate were rod-shaped with a single sheathed polar flagellum. Neither extensive internal membranes nor storage materials were present in the cells. In a 20 % CO(2) atmosphere, strain gps61(T) grew using thiosulfate, sulfur or tetrathionate as electron donors and oxygen or nitrate as electron acceptors. Other substrates, including organic acids and sugars, did not support growth, indicating that strain gps61(T) was an obligate chemolithoautotroph. 16S rRNA gene sequence analysis revealed that strain gps61(T) was closely related to Thioprofundum lithotrophicum 106(T) (98.5 % sequence similarity) in the order Chromatiales. Phylogenetic trees grouped strain gps61(T) and Thioprofundum lithotrophicum in the same cluster along with Thioalkalispira microaerophila and Thiohalophilus thiocyanoxidans, but it was apparent from the analysis that the novel strain had definitely departed from the family lineage. On the basis of its phylogenetic position along with its morphological and physiological characteristics, strain gps61(T) ( = NBRC 101261(T)  = DSM 18546(T)) represents a novel species of the genus Thioprofundum, for which the name Thioprofundum hispidum sp. nov. is proposed. In addition, we propose a novel family name, Thioalkalispiraceae, in the order Chromatiales, to accommodate the genera Thioalkalispira, Thiohalophilus and Thioprofundum.

  8. Comparative field evaluation of the fluorescent-antibody test, virus isolation from tissue culture, and enzyme immunodiagnosis for rapid laboratory diagnosis of rabies.

    PubMed Central

    Bourhy, H; Rollin, P E; Vincent, J; Sureau, P

    1989-01-01

    The rabies tissue culture infection test (RTCIT) and rapid rabies enzyme immunodiagnosis (RREID) were compared to the fluorescent-antibody test (FAT) with field specimens. At the French National Reference Center for Rabies, 15,248 specimens were analyzed by FAT and RTCIT, and 2,290 of those specimens were also tested by RREID; 818 other specimens were tested by FAT and RREID in 12 laboratories located in Africa, Asia, and Latin America. The sensitivities and specificities of RREID and RTCIT were comparable. This study showed that both tests can be used as backup procedures to confirm FAT. RREID is also strongly recommended for epidemiological studies and for laboratories which are not equipped for performing FAT. PMID:2654181

  9. Microbial diversity in methanogenic hydrocarbon-degrading enrichment cultures isolated from a water-flooded oil reservoir (Dagang oil field, China)

    NASA Astrophysics Data System (ADS)

    Jiménez, Núria; Cai, Minmin; Straaten, Nontje; Yao, Jun; Richnow, Hans H.; Krüger, Martin

    2015-04-01

    Microbial transformation of oil to methane is one of the main degradation processes taking place in oil reservoirs, and it has important consequences as it negatively affects the quality and economic value of the oil. Nevertheless, methane could constitute a recovery method of carbon from exhausted reservoirs. Previous studies combining geochemical and isotopic analysis with molecular methods showed evidence for in situ methanogenic oil degradation in the Dagang oil field, China (Jiménez et al., 2012). However, the main key microbial players and the underlying mechanisms are still relatively unknown. In order to better characterize these processes and identify the main microorganisms involved, laboratory biodegradation experiments under methanogenic conditions were performed. Microcosms were inoculated with production and injection waters from the reservoir, and oil or 13C-labelled single hydrocarbons (e.g. n-hexadecane or 2-methylnaphthalene) were added as sole substrates. Indigenous microbiota were able to extensively degrade oil within months, depleting most of the n-alkanes in 200 days, and producing methane at a rate of 76 ± 6 µmol day-1 g-1 oil added. They could also produce heavy methane from 13C-labeled 2-methylnaphthalene, suggesting that further methanogenesis may occur from the aromatic and polyaromatic fractions of Dagang reservoir fluids. Microbial communities from oil and 2-methyl-naphthalene enrichment cultures were slightly different. Although, in both cases Deltaproteobacteria, mainly belonging to Syntrophobacterales (e.g. Syntrophobacter, Smithella or Syntrophus) and Clostridia, mostly Clostridiales, were among the most represented taxa, Gammaproteobacteria could be only identified in oil-degrading cultures. The proportion of Chloroflexi, exclusively belonging to Anaerolineales (e.g. Leptolinea, Bellilinea) was considerably higher in 2-methyl-naphthalene degrading cultures. Archaeal communities consisted almost exclusively of representatives of

  10. Field and laboratory investigations of coring-induced damage in core recovered from Marker Bed 139 at the waste isolation pilot plant underground facility

    SciTech Connect

    Holcomb, D.J.; Zeuch, D.H.; Morin, K.; Hardy, R.; Tormey, T.V.

    1995-09-01

    A combined laboratory and field investigation was carried out to determine the extent of coring-induced damage done to samples cored from Marker Bed 139 at the WIPP site. Coring-induced damage, if present, has the potential to significantly change the properties of the material used for laboratory testing relative to the in situ material properties, resulting in misleading conclusions. In particular, connected, crack-like damage could make the permeability of cored samples orders of magnitude greater than the in situ permeabilities. Our approach compared in situ velocity and resistivity measurements with laboratory measurements of the same properties. Differences between in situ and laboratory results could be attributed to differences in the porosity due to cracks. The question of the origin of the changes could not be answered directly from the results of the measurements. Pre-existing cracks, held closed by the in situ stress, could open when the core was cut free, or new cracks could be generated by coring-induced damage. We used core from closely spaced boreholes at three orientations (0{degree}, {plus_minus}45{degrees} relative to vertical) to address the origin of cracks. The absolute orientation of pre-existing cracks would be constant, independent of the borehole orientation. In contrast, cracks induced by coring were expected to show an orientation dependent on that of the source borehole.

  11. Study of the bioremediation of atrazine under variable carbon and nitrogen sources by mixed bacterial consortium isolated from corn field soil in Fars province of Iran.

    PubMed

    Dehghani, Mansooreh; Nasseri, Simin; Hashemi, Hassan

    2013-01-01

    Atrazine herbicide that is widely used in corn production is frequently detected in water resources. The main objectives of this research were focused on assessing the effects of carbon and nitrogen sources on atrazine biodegradation by mixed bacterial consortium and by evaluating the feasibility of using mixed bacterial consortium in soil culture. Shiraz corn field soil with a long history of atrazine application has been explored for their potential of atrazine biodegradation. The influence of different carbon compounds and the effect of nitrogen sources and a different pH (5.5-8.5) on atrazine removal efficiency by mixed bacterial consortium in liquid culture were investigated. Sodium citrate and sucrose had the highest atrazine biodegradation rate (87.22%) among different carbon sources. Atrazine biodegradation rate decreased more quickly by the addition of urea (26.76%) compared to ammonium nitrate. Based on the data obtained in this study, pH of 7.0 is optimum for atrazine biodegradation. After 30 days of incubation, the percent of atrazine reduction rates were significantly enhanced in the inoculated soils (60.5%) as compared to uninoculated control soils (12%) at the soil moisture content of 25%. In conclusion, bioaugmentation of soil with mixed bacterial consortium may enhance the rate of atrazine degradation in a highly polluted soil.

  12. Field evaluation of a cement-bentonite grout and a chlorosulfonated polyethylene fabric liner in hydrologically isolating low-level radioactive solid waste

    SciTech Connect

    Davis, E.C.; Spalding, B.P.

    1986-05-01

    Two engineered modifications, trench lining and grouting, have been demonstrated and evaluated. Reinforced chlorosulfonated polyethylene (Hypalon) fabric and a Portland cement-bentonite grout were selected for demonstration within a group of nine 28-m/sup 3/ experimental trenches containing compacted low-level waste generated at the Oak Ridge National Laboratory. Groundwater monitoring has shown that standing water is present in all nine experimental trenches (both treated and untreated); however, depth of water and water level fluctuation patterns differed according to trench treatment and were minimal in the case of the grouted trenches. Both water pump-in and water pump-out tests conducted on the lined trenches showed that the original goal of watertight liners was not achieved and that water was entering and leaving these trenches with each precipitation event. Water entering into the grouted trenches was inhibited by the cement-bentonite grout backfill, as reflected in the lower values of hydraulic conductivities that were measured in these three trenches compared with those in the three control (untreated) trenches. In examining engineering properties of the grout and liner material, it was found that no significant change in liner tensile strength or liner aging study, indicating that there were no short-term changes in these engineering properties with field weathering. Cover subsidence has not occurred over the grouted or control trenches, while 2 of the lined trenches have settled 7 to 10 cm (2 to 3% of the trench depth) in the first two years. Based on these treatment evaluation tests, the cement-bentonite grouted trenches appear to offer the highest level of water protection compared to the Hypalon lined and the control trenches.

  13. Steady compression characteristics of laminated MRE isolator

    NASA Astrophysics Data System (ADS)

    Wahab, N. A. A.; Mazlan, S. A.; Ubaidillah; Sharif, A. H. R.; Kamaruddin, S.

    2016-11-01

    This paper focused on an experimental setup on laminated magnetorheological elastomer (MRE) isolator under steady state compression test. An isotropic type natural rubber (NR) based MRE were fabricated and layered with a steel plate to form a multilayer sandwich structure adopted from the conventional laminated rubber bearing design. A set of static compression test was conducted to explore the potential of semi-active laminated MRE isolator in field-dependent stiffness properties. Stress versus strain relationship was assessed under different magnetic fields application. Based on the examination, the stress altered as the application of magnetic fields. Consequently, the effective stiffness of isolator also influenced by the magnetic fields induction. The experimental results show that the proposed laminated MRE isolator can effectively alter the compression stiffness up to the 14.56%. The preliminary results have confirmed the tunability of the semi-active laminated MRE isolator in which it would be beneficial for improving building isolator in general.

  14. Visible optical isolator using ZnSe.

    PubMed

    Wunderlich, J A; Deshazer, L G

    1977-06-01

    A compact Faraday effect optical isolator was constructed for visible wavelengths and tested at 5145 A. The nonreciprocal element of the isolator was polycrystalline zinc selenide placed in the magnetic field of a permanent magnet. For 5145 A the isolator had a 2.06-dB insertion loss and a 25.5-dB isolation. Indices of refraction and Verdet constants were measured for zinc selenide in the wavelengthregion from 4700 to 6300 A.

  15. Visible optical isolator using ZnSe

    NASA Technical Reports Server (NTRS)

    Wunderlich, J. A.; Deshazer, L. G.

    1977-01-01

    A compact Faraday effect optical isolator was constructed for visible wavelengths and tested at 5145 A. The nonreciprocal element of the isolator was polycrystalline zinc selenide placed in the magnetic field of a permanent magnet. For 5145 A the isolator had a 2.06-dB insertion loss and a 25.5-dB isolation. Indices of refraction and Verdet constants were measured for zinc selenide in the wavelength region from 4700 to 6300 A.

  16. Manipulation of isolated brain nerve terminals by an external magnetic field using D-mannose-coated γ-Fe2O3 nano-sized particles and assessment of their effects on glutamate transport

    PubMed Central

    Krisanova, Natalia; Borуsov, Arsenii; Sivko, Roman; Ostapchenko, Ludmila; Babic, Michal; Horak, Daniel

    2014-01-01

    Summary The manipulation of brain nerve terminals by an external magnetic field promises breakthroughs in nano-neurotechnology. D-Mannose-coated superparamagnetic nanoparticles were synthesized by coprecipitation of Fe(II) and Fe(III) salts followed by oxidation with sodium hypochlorite and addition of D-mannose. Effects of D-mannose-coated superparamagnetic maghemite (γ-Fe2O3) nanoparticles on key characteristics of the glutamatergic neurotransmission were analysed. Using radiolabeled L-[14C]glutamate, it was shown that D-mannose-coated γ-Fe2O3 nanoparticles did not affect high-affinity Na+-dependent uptake, tonic release and the extracellular level of L-[14C]glutamate in isolated rat brain nerve terminals (synaptosomes). Also, the membrane potential of synaptosomes and acidification of synaptic vesicles was not changed as a result of the application of D-mannose-coated γ-Fe2O3 nanoparticles. This was demonstrated with the potential-sensitive fluorescent dye rhodamine 6G and the pH-sensitive dye acridine orange. The study also focused on the analysis of the potential use of these nanoparticles for manipulation of nerve terminals by an external magnetic field. It was shown that more than 84.3 ± 5.0% of L-[14C]glutamate-loaded synaptosomes (1 mg of protein/mL) incubated for 5 min with D-mannose-coated γ-Fe2O3 nanoparticles (250 µg/mL) moved to an area, in which the magnet (250 mT, gradient 5.5 Т/m) was applied compared to 33.5 ± 3.0% of the control and 48.6 ± 3.0% of samples that were treated with uncoated nanoparticles. Therefore, isolated brain nerve terminals can be easily manipulated by an external magnetic field using D-mannose-coated γ-Fe2O3 nanoparticles, while the key characteristics of glutamatergic neurotransmission are not affected. In other words, functionally active synaptosomes labeled with D-mannose-coated γ-Fe2O3 nanoparticles were obtained. PMID:24991515

  17. Manipulation of isolated brain nerve terminals by an external magnetic field using D-mannose-coated γ-Fe2O3 nano-sized particles and assessment of their effects on glutamate transport.

    PubMed

    Borisova, Tatiana; Krisanova, Natalia; Borуsov, Arsenii; Sivko, Roman; Ostapchenko, Ludmila; Babic, Michal; Horak, Daniel

    2014-01-01

    The manipulation of brain nerve terminals by an external magnetic field promises breakthroughs in nano-neurotechnology. D-Mannose-coated superparamagnetic nanoparticles were synthesized by coprecipitation of Fe(II) and Fe(III) salts followed by oxidation with sodium hypochlorite and addition of D-mannose. Effects of D-mannose-coated superparamagnetic maghemite (γ-Fe2O3) nanoparticles on key characteristics of the glutamatergic neurotransmission were analysed. Using radiolabeled L-[(14)C]glutamate, it was shown that D-mannose-coated γ-Fe2O3 nanoparticles did not affect high-affinity Na(+)-dependent uptake, tonic release and the extracellular level of L-[(14)C]glutamate in isolated rat brain nerve terminals (synaptosomes). Also, the membrane potential of synaptosomes and acidification of synaptic vesicles was not changed as a result of the application of D-mannose-coated γ-Fe2O3 nanoparticles. This was demonstrated with the potential-sensitive fluorescent dye rhodamine 6G and the pH-sensitive dye acridine orange. The study also focused on the analysis of the potential use of these nanoparticles for manipulation of nerve terminals by an external magnetic field. It was shown that more than 84.3 ± 5.0% of L-[(14)C]glutamate-loaded synaptosomes (1 mg of protein/mL) incubated for 5 min with D-mannose-coated γ-Fe2O3 nanoparticles (250 µg/mL) moved to an area, in which the magnet (250 mT, gradient 5.5 Т/m) was applied compared to 33.5 ± 3.0% of the control and 48.6 ± 3.0% of samples that were treated with uncoated nanoparticles. Therefore, isolated brain nerve terminals can be easily manipulated by an external magnetic field using D-mannose-coated γ-Fe2O3 nanoparticles, while the key characteristics of glutamatergic neurotransmission are not affected. In other words, functionally active synaptosomes labeled with D-mannose-coated γ-Fe2O3 nanoparticles were obtained.

  18. Genetic characteristics of porcine epidemic diarrhea virus in Chinese mainland, revealing genetic markers of classical and variant virulent parental/attenuated strains.

    PubMed

    Chen, Fangzhou; Ku, Xugang; Li, Zhonghua; Memon, Atta Muhammad; Ye, Shiyi; Zhu, Yinxing; Zhou, Chunling; Yao, Li; Meng, Xianrong; He, Qigai

    2016-08-15

    Since October 2010, porcine epidemic diarrhea (PED) caused by variant porcine epidemic diarrhea virus (PEDV) has led great economic losses to the global pig industry, especially in China. To study the genetic characteristics of PEDV strains in Chinese mainland, a total of 603 clinical samples from nine provinces/districts of Chinese mainland from January 2014 to December 2015 were collected for RT-PCR detection and 1-1323bp of S gene of 91 isolates and ORF3 gene of 46 isolates were sequenced. The results showed that the variant PEDV were the dominant pathogens of viral diarrhea diseases in these areas. Six novel variant PEDV strains (FJAX1, FJAX2, HeNPDS1, HeNPDS2, HeNPY3, and HeNPY4) with two amino acids (aa) deletion at the 56-57 aa of S protein were identified. A total of 405 Chinese PEDV strains were subjected to phylogenetic and phylogeographic analysis. The results revealed that the subgroup Va in variant PEDV group were the dominant subgroup and the spread trend of variant PEDV strains seemed to be from the southeast coastal districts to other coastal districts and interior districts. The N-terminal of S gene (1-750bp), to some extent, could represent S1 or full length S gene for phylogenetic, similarity, antigen index, hydrophilicity plot, and differentiation analyses. The 404-472bp of S gene contained the three genetic markers, i.e., "TAA" insertion at 404-405bp, "ACAGGT" deletion at 430-435bp, and "ATA" deletion at 455-457bp can be used to differentiate the classical and variant virulent parental/attenuated PEDV strains and help us to learn the infectious and genetic characteristics of PEDV strains more convenient and cheaper. This study has important implication for understanding the infectious, genetic, and evolutionary aspects of PEDV strains in Chinese mainland.

  19. Rhabdothermus arcticus gen. nov., sp. nov., a member of the family Thermaceae isolated from a hydrothermal vent chimney in the Soria Moria vent field on the Arctic Mid-Ocean Ridge.

    PubMed

    Steinsbu, Bjørn O; Tindall, Brian J; Torsvik, Vigdis L; Thorseth, Ingunn H; Daae, Frida L; Pedersen, Rolf B

    2011-09-01

    A novel thermophilic member of the family Thermaceae, designated strain 2M70-1(T), was isolated from the wall of an active white smoker chimney collected in the Soria Moria vent field at 71 °N in the Norwegian-Greenland Sea. Cells of the strain were Gram-negative, non-motile rods. Growth was observed at 37-75 °C (optimum 65 °C), at pH 6-8 (optimum pH 7.3) and in 1-5 % (w/v) NaCl (optimum 2.5-3.5 %). The isolate was aerobic but could also grow anaerobically using nitrate or elemental sulfur as electron acceptors. The strain was obligately heterotrophic, growing on complex organic substrates like yeast extract, Casamino acids, tryptone and peptone. Pyruvate, acetate, butyrate, sucrose, rhamnose and maltodextrin were used as complementary substrates. The G+C content of the genomic DNA was 68 mol%. Cells possessed characteristic phospholipids and glycolipids. Major fatty acids constituted saturated and unsaturated iso-branched and saturated anteiso-branched forms. Menaquinone 8 was the sole respiratory lipoquinone. Phylogenetic analysis of 16S rRNA gene sequences placed the strain in the family Thermaceae in the phylum 'Deinococcus-Thermus', which is consistent with the chemotaxonomic data. On the basis of phenotypic and phylogenetic data, strain 2M70-1(T) ( = JCM 15963(T)  = DSM 22268(T)) represents the type strain of a novel species of a novel genus, for which the name Rhabdothermus arcticus gen. nov., sp. nov. is proposed.

  20. Characterisation of drug resistance of nosocomial ESBL-producing E. coli isolates obtained from a Turkish university hospital between 2009 and 2012 by pulsed field gel electrophoresis and antibiotic resistance tests.

    PubMed

    Karagöz, Alper; Sunnetcioglu, Mahmut; Ceylan, Mehmet Resat; Bayram, Yasemin; Yalcin, Gozde; Kocak, Nadir; Suvak, Burak; Andac, Cenk A

    2016-01-01

    In this study, drug resistance of 28 ESBL-producing Escherichia coli isolates obtained from 144 patients hospitalized at the Yüzüncüyil University Hospital at Van (YUH), Turkey, between 2009 and 2012 were characterized by pulsed field gel electrophoresis and antibiotic susceptibility tests. Antibiotic resistance profile was determined by Phoenix automated system (BD, USA). The ratio of ESBL-producing E. coli strains was determined to be 19.4% (28 out of 144 E. coli isolates). It was determined that the anaesthesiology, paediatrics and thoracic medicine intensive care units in YUH were cross-contaminated between 2009 and 2012 by ESBL-producing E. coli strains, which is a sign of nosocomial infection in YUH. Analysis of PFGE results gave rise to two main PFGE profiles, profile-A with four subprofiles and profile-B with three subprofiles, where profile-A predominates over profile-B (14%). Comparison of the antibiotic resistance profile with the PFGE profile yielded similarities while some differences also exist due to either identical restriction enzyme cutting sites with slightly different genetic sequences in between the cutting sites or newly formed restriction enzyme cutting sites that do not affect antibiotic resistance genes. Enterobacteriaceae, particularly E. coli, have developed resistance in YUH by producing ESBLs against oxyimino and non-oxyimino cephalosporins, and penicillin-type antibiotics. Therefore, more effective antibiotics such as cefoxitin or cefoperazone-sulbactam should be used for the treatment of future nosocomial infections in YUH while hospital staff should take care with hygiene, such as hand washing.

  1. Molecular characterization and phylogenetic analysis of new variants of the porcine epidemic diarrhea virus in Gansu, China in 2012.

    PubMed

    Tian, Yufei; Yu, Zhijun; Cheng, Kaihui; Liu, Yuxiu; Huang, Jing; Xin, Yue; Li, Yuanguo; Fan, Shengtao; Wang, Tiecheng; Huang, Geng; Feng, Na; Yang, Zhenguo; Yang, Songtao; Gao, Yuwei; Xia, Xianzhu

    2013-08-15

    Between January 2012 and March 2012, the infection rates of porcine epidemic diarrhea virus (PEDV) increased substantially in vaccinated swine herds in many porcine farms in Gansu Province, China. The spike (S) glycoprotein is an important determinant for PEDV biological properties. To determine the distribution profile of PEDV outbreak strains, we sequenced the full-length S gene of five samples from two farms where animals exhibited severe diarrhea and high mortality rates. Five new PEDV variants were identified, and the molecular diversity, phylogenetic relationships, and antigenicity analysis of Gansu field samples with other PEDV reference strains were investigated. A series of insertions, deletions, and mutations in the S gene was found in five PEDV variants compared with classical and vaccine strains. These mutations may provide stronger pathogenicity and antigenicity to the new PEDV variants that influenced the effectiveness of the CV777-based vaccine. Our results suggest that these new PEDV variant strains in Gansu Province might be from South Korean or South China, and the effectiveness of the CV777-based vaccine needs to be evaluated.

  2. SYMBIODINIUM ISOLATES FROM STONY CORAL: ISOLATION, GROWTH CHARACTERISTICS AND EFFECTS OF UV IRRADIATION

    EPA Science Inventory

    Symbiodinium spp. Isolates from Stony Coral: Isolation, Growth Characteristics and Effects of UV Irradiation (Abstract). J. Phycol. 37(3):42-43.

    Symbiodinium species were isolated from Montipora capitata, Acropora palmata and two field samples of Porites porites. Cultures ...

  3. Determination of the infectious titer and virulence of an original US porcine epidemic diarrhea virus PC22A strain.

    PubMed

    Liu, Xinsheng; Lin, Chun-Ming; Annamalai, Thavamathi; Gao, Xiang; Lu, Zhongyan; Esseili, Malak A; Jung, Kwonil; El-Tholoth, Mohamed; Saif, Linda J; Wang, Qiuhong

    2015-09-25

    The infectious dose of a virus pool of original US PEDV strain PC22A was determined in 4-day-old, cesarean-derived, colostrum-deprived (CDCD) piglets. The median pig diarrhea dose (PDD50) of the virus pool was determined as 7.35 log10 PDD50/mL, similar to the cell culture infectious titer, 7.75 log10 plaque-forming units (PFU)/mL. 100 PDD50 caused watery diarrhea in all conventional suckling piglets (n = 12) derived from a PEDV-naive sow, whereas 1000 and 10 000 PDD50 did not cause diarrhea in piglets derived from two PEDV-field exposed-recovered sows. This information is important for future PEDV challenge studies and validation of PEDV vaccines.

  4. Optical Isolators With Transverse Magnets

    NASA Technical Reports Server (NTRS)

    Fan, Yuan X.; Byer, Robert L.

    1991-01-01

    New design for isolator includes zigzag, forward-and-backward-pass beam path and use of transverse rather than longitudinal magnetic field. Design choices produce isolator with as large an aperture as desired using low-Verdet-constant glass rather than more expensive crystals. Uses commercially available permanent magnets in Faraday rotator. More compact and less expensive. Designed to transmit rectangular beam. Square cross section of beam extended to rectangular shape by increasing one dimension of glass without having to increase magnetic field. Potentially useful in laser systems involving slab lasers and amplifiers. Has applications to study of very-high-power lasers for fusion research.

  5. Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia

    PubMed Central

    Mei, Nan; Postec, Anne; Monnin, Christophe; Pelletier, Bernard; Payri, Claude E.; Ménez, Bénédicte; Frouin, Eléonore; Ollivier, Bernard; Erauso, Gaël; Quéméneur, Marianne

    2016-01-01

    High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e., high-pH, low-salt, mesothermic fluids). In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales) were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ. PMID:27625634

  6. Effects of Isolation by Continental Islands in the Seto Inland Sea, Japan, on Genetic Diversity of the Large Japanese Field Mouse, Apodemus speciosus (Rodentia: Muridae), Inferred from the Mitochondrial Dloop Region.

    PubMed

    Sato, Jun J; Tasaka, Yurina; Tasaka, Ryoya; Gunji, Kentaro; Yamamoto, Yuya; Takada, Yasushi; Uematsu, Yasushi; Sakai, Eiichi; Tateishi, Takashi; Yamaguchi, Yasunori

    2017-04-01

    To study the effects of post-glacial isolation by islands on population genetic diversity and differentiation of the large Japanese field mouse, Apodemus speciosus, we examined partial nucleotide sequences of the mitochondrial Dloop region (ca. 300 bp) in 231 individuals collected from islands in the Seto Inland Sea and adjacent regions on Honshu and Shikoku Islands in the western part of the Japanese archipelago. Molecular phylogenetic and network analyses showed that haplotypes in each island tended to form monophyletic groups, while those in Honshu and Shikoku (the major Japanese islands) showed scattered relationships and were connected with island haplotypes. These observations suggest that a set of Honshu and Shikoku haplotypes became the ancestral lineages of the island population. No gene flow was detected among island populations, indicating that independent evolution occurred on each island, without the influence of human activities, since the establishment of the islands in the Holocene. Population genetic diversities on each island were lower than those on Honshu and Shikoku. Comparison between genetic diversity and island area size showed positive correlations and supported the suggestion that genetic drift is a major factor that shaped the current haplotype constitution of the islands in the Seto Inland Sea.

  7. Tiamulin resistance in porcine Brachyspira pilosicoli isolates.

    PubMed

    Pringle, M; Landén, A; Franklin, A

    2006-02-01

    There are few studies on antimicrobial susceptibility of Brachyspira pilosicoli, therefore this study was performed to investigate the situation among isolates from pigs. The tiamulin and tylosin susceptibility was determined by broth dilution for 93 and 86 porcine B. pilosicoli isolates, respectively. The isolates came from clinical samples taken in Swedish pig herds during the years 2002 and 2003. The tylosin minimal inhibitory concentration (MIC) was >16 microg/ml for 50% (n=43) of the isolates tested. A tiamulin MIC >2 microg/ml was obtained for 14% (n=13) of the isolates and these were also tested against doxycycline, salinomycin, valnemulin, lincomycin and aivlosin. For these isolates the susceptibility to salinomycin and doxycycline was high but the MICs for aivlosin varied. The relationship between the 13 tiamulin resistant isolates was analyzed by pulsed-field gel electrophoresis (PFGE). Among the 13 isolates 10 different PFGE patterns were identified.

  8. Consistent force field modeling of matrix isolated molecules. V. Minimum energy path potential to the conformer conversion of 1,2-difluoroethane: Ar 364, ab initio calculation of electric multipole moments and electric polarization contribution to the conversion barrier

    NASA Astrophysics Data System (ADS)

    Gunde, R.; Ha, T.-K.; Günthard, H. H.

    1990-08-01

    In this paper results of consistent force field modeling (CFF) of the potential function to conversion of the gauche (g) to the trans (t) conformer of 1,2-difluoroethane (DFE) isolated in an argon matrix will be reported. Starting point are locally stable configurations gDFE:Ar 364 (defect GH1) and tDFE:Ar 364 (TH1) obtained in previous work from CFF modeling of a cube shaped Ar 364 fragment containing one DFE molecule in its center. Using the dihedral angle of DFE as an independent parameter the minimum energy path of the conversion process gDFE:Ar 364→tDFE:Ar 364 will be determined by CFF energy minimization. Determination of the minimum energy path is found to require large numbers of energy minimization steps and to lead to a rather complicated motion of the molecule with respect to the crystal fragment. Surprisingly the molecule-matrix interactions lead to a reduction of the g-t barrier by ≈500 cal/mol and to a stabilization of the trans species by ≈500 cal/mol. This finding is a consequence of a delicate interplay of matrix-molecule and matrix-matrix interactions. Calculation of the electric polarization energy (induced dipole-first-order polarization approximation) is based on extended ab initio calculations of dipole and quadrupole moments and a bond polarizability estimate of the first-order polarizability of DFE as a function of the internal rotation angle, on Fourier expansion of multipole components and use of symmetry for reduction of the order of the linear system defining the (self-consistent) induced dipole moments of all Ar atoms. Electric polarization is found to alter the potential function of the conversion process in a profound way: the g-t barrier and the t-g energy difference are increased to ≈3000 cal/mol and to ≈1500 cal/mol respectively (≈2500 and ≈530 cal/mol respectively for free DFE). Further applications of the technique developed in this work to related problems of matrix isolated molecules, e.g., vibrational matrix

  9. The rate of co-infection for piglet diarrhea viruses in China and the genetic characterization of porcine epidemic diarrhea virus and porcine kobuvirus.

    PubMed

    Zhao, Z-P; Yang, Z; Lin, W-D; Wang, W-Y; Yang, J; Jin, W-J; Qin, A-J

    2016-03-01

    Piglet diarrhea epidemics result in major economic losses for the swine industry. Four viruses are closely linked to porcine diarrhea: porcine kobuvirus (PKV), porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), and porcine rotavirus (PRoV). We have conducted an epidemiology study to determine the frequency of infection and co-infection with these viruses in China, and characterized the genetic variation of the isolated PEDV and PKV strains. Stool and intestinal samples (n = 314) were collected from piglets with diarrhea in China from years 2012 to 2014. RT-PCR was used to detect PKV, PEDV, TGEV, and PRoV. Phylogenetic relationships between reference strains and the isolated PEDV and PKV strains were determined based on the M and 3D gene sequence. The rates of infection with PKV, PEDV, TGEV and PRoV were 29.9%, 24.2%, 1.91%, and 0.31%, respectively. Co-infections with PKV and the other three viruses were very common. Co-infection of PKV and PEDV was detected in 15.0% (47/314) of the samples. Phylogenetic analysis of the PKV 3D gene indicated that there were some phylogenetic differences in the PKV strains across regions within China. However, according to the PEDV M gene, strains clustered into three groups and the primary group was distinct from the vaccine strain CV777. This study provides insights in to the prevalence of diarrhea viruses and their prevention and control in China.

  10. High-Voltage Isolation Transformer

    NASA Technical Reports Server (NTRS)

    Clatterbuck, C. H.; Ruitberg, A. P.

    1985-01-01

    Arcing and field-included surface erosion reduced by electrostatic shields around windings and ferromagnetic core of 80-kilovolt isolation transformer. Fabricated from high-resistivity polyurethane-based material brushed on critical surfaces, shields maintained at approximately half potential difference of windings.

  11. Beta adrenergic modulation of spontaneous microcontractions and electrical field-stimulated contractions in isolated strips of rat urinary bladder from normal animals and animals with partial bladder outflow obstruction.

    PubMed

    Gillespie, J I; Rouget, C; Palea, S; Granato, C; Korstanje, C

    2015-07-01

    Spontaneous microcontractions and electrical field stimulation (EFS)-evoked contractions in isolated rat bladder strips from normal and from 6 weeks partial bladder outflow obstruction (pBOO) animals were studied to identify the potential site of action for the β3-adrenoceptor (AR) agonist mirabegron in detrusor overactivity in rats. For this, effects of the β-AR agonist isoprenaline and mirabegron were tested in presence or absence of selective antagonists for β-AR subtypes, namely CGP-20712A for β1-AR, ICI-118,551 for β2-AR, and L-748,337 for β3-AR. In detrusor strips from both normal and obstructed animals, EFS-induced contractions were weakly affected by isoprenaline and even less so by mirabegron. In contrast, microcontraction activity was more potently reduced by isoprenaline (pIC50 7.3; Emax ±85 %), whereas mirabegron showed a small effect. In pBOO strips, concentration response curves for isoprenaline and mirabegron at inhibition of EFS and spontaneous microcontractions were similar to those in normal strips. Isoprenaline-induced inhibition of microcontractions and EFS was antagonized by the β1-AR antagonist, but not by the β2- and β3-AR antagonists. In the context of β3-AR-mediated bladder functions for mirabegron in other experiments, the current data question a role for effects at spontaneous microcontractions, or neurogenic detrusor stimulation in the mode of action for mirabegron in vivo, since functional bladder effects for mirabegron are reported to occur at much lower concentrations.

  12. Isolation and characterization of a heavy metal-resistant Burkholderia sp. from heavy metal-contaminated paddy field soil and its potential in promoting plant growth and heavy metal accumulation in metal-polluted soil.

    PubMed

    Jiang, Chun-yu; Sheng, Xia-fang; Qian, Meng; Wang, Qing-ya

    2008-05-01

    A heavy metal-resistant bacterial strain was isolated from heavy metal-contaminated soils and identified as Burkholderia sp. J62 based on the 16S rDNA gene sequence analysis. The heavy metal- and antibiotic resistance, heavy metal solubilization of the isolate were investigated. The isolate was also evaluated for promoting plant growth and Pb and Cd uptakes of the plants from heavy metal-contaminated soils in pot experiments. The isolate was found to exhibit different multiple heavy metal and antibiotic resistance characteristics. Atomic absorption spectrometer analysis showed increased bacterial solubilization of lead and cadmium in solution culture and in soils. The isolate produced indole acetic acid, siderophore and 1-aminocyclopropane-1-carboxylate deaminase. The isolate also solubilized inorganic phosphate. Inoculation with the isolate was found to significantly (p<0.05) increase the biomass of maize and tomato plants. Increase in tissue Pb and Cd contents varied from 38% to 192% and from 5% to 191% in inoculated plants growing in heavy metal-contaminated soils compared to the uninoculated control, respectively. These results show that heavy metal-solubilizing and plant growth promoting bacteria are important for plant growth and heavy metal uptake which may provide a new microbial enhanced-phytoremediation of metal-polluted soils.

  13. Isolated Northern Dunes

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site]

    Our topic for the weeks of April 4 and April 11 is dunes on Mars. We will look at the north polar sand sea and at isolated dune fields at lower latitudes. Sand seas on Earth are often called 'ergs,' an Arabic name for dune field. A sand sea differs from a dune field in two ways: 1) a sand sea has a large regional extent, and 2) the individual dunes are large in size and complex in form.

    This VIS image was taken at 81 degrees North latitude during Northern spring. In this region, the dunes are isolated from each other. The dunes are just starting to emerge from the winter frost covering appearing dark with bright crests. These dunes are located on top of ice.

    Image information: VIS instrument. Latitude 82.1, Longitude 191.3 East (168.7 West). 19 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  14. Isolated sleep paralysis

    MedlinePlus

    Sleep paralysis - isolated; Parasomnia - isolated sleep paralysis ... Episodes of isolated sleep paralysis last from a few seconds to 1 or 2 minutes. During these episodes the person is unable to move or ...

  15. Fasciola hepatica: Histology of the Reproductive Organs and Differential Effects of Triclabendazole on Drug-Sensitive and Drug-Resistant Fluke Isolates and on Flukes from Selected Field Cases.

    PubMed

    Hanna, Robert

    2015-06-26

    This review summarises the findings of a series of studies in which the histological changes, induced in the reproductive system of Fasciola hepatica following treatment of the ovine host with the anthelmintic triclabendazole (TCBZ), were examined. A detailed description of the normal macroscopic arrangement and histological features of the testes, ovary, vitelline tissue, Mehlis' gland and uterus is provided to aid recognition of the drug-induced lesions, and to provide a basic model to inform similar toxicological studies on F. hepatica in the future. The production of spermatozoa and egg components represents the main energy consuming activity of the adult fluke. Thus the reproductive organs, with their high turnover of cells and secretory products, are uniquely sensitive to metabolic inhibition and sub-cellular disorganisation induced by extraneous toxic compounds. The flukes chosen for study were derived from TCBZ-sensitive (TCBZ-S) and TCBZ-resistant (TCBZ-R) isolates, the status of which had previously been proven in controlled clinical trials. For comparison, flukes collected from flocks where TCBZ resistance had been diagnosed by coprological methods, and from a dairy farm with no history of TCBZ use, were also examined. The macroscopic arrangement of the reproductive system in flukes was studied using catechol/carmine stained whole mounts, and the histology of the main organs was examined using conventional haematoxylin-eosin stained sections. Validation of apoptosis in the fluke sections was carried out using an in situ hybridisation method designed to label endonuclease-induced DNA strand breaks. In TCBZ-S flukes exposed to TCBZ metabolites for 24-96 h in vivo, but not in TCBZ-R flukes, those tissues where active meiosis and/or mitosis occurred (testis, ovary, and vitelline follicles), were found to display progressive loss of cell content. This was due to apparent failure of cell division to keep pace with expulsion of the mature or effete products

  16. Fasciola hepatica: Histology of the Reproductive Organs and Differential Effects of Triclabendazole on Drug-Sensitive and Drug-Resistant Fluke Isolates and on Flukes from Selected Field Cases

    PubMed Central

    Hanna, Robert

    2015-01-01

    This review summarises the findings of a series of studies in which the histological changes, induced in the reproductive system of Fasciola hepatica following treatment of the ovine host with the anthelmintic triclabendazole (TCBZ), were examined. A detailed description of the normal macroscopic arrangement and histological features of the testes, ovary, vitelline tissue, Mehlis’ gland and uterus is provided to aid recognition of the drug-induced lesions, and to provide a basic model to inform similar toxicological studies on F. hepatica in the future. The production of spermatozoa and egg components represents the main energy consuming activity of the adult fluke. Thus the reproductive organs, with their high turnover of cells and secretory products, are uniquely sensitive to metabolic inhibition and sub-cellular disorganisation induced by extraneous toxic compounds. The flukes chosen for study were derived from TCBZ-sensitive (TCBZ-S) and TCBZ-resistant (TCBZ-R) isolates, the status of which had previously been proven in controlled clinical trials. For comparison, flukes collected from flocks where TCBZ resistance had been diagnosed by coprological methods, and from a dairy farm with no history of TCBZ use, were also examined. The macroscopic arrangement of the reproductive system in flukes was studied using catechol/carmine stained whole mounts, and the histology of the main organs was examined using conventional haematoxylin-eosin stained sections. Validation of apoptosis in the fluke sections was carried out using an in situ hybridisation method designed to label endonuclease-induced DNA strand breaks. In TCBZ-S flukes exposed to TCBZ metabolites for 24–96 h in vivo, but not in TCBZ-R flukes, those tissues where active meiosis and/or mitosis occurred (testis, ovary, and vitelline follicles), were found to display progressive loss of cell content. This was due to apparent failure of cell division to keep pace with expulsion of the mature or effete products

  17. Comparison of an enzyme-linked immunosorbent assay with serum neutralization test for serodiagnosis of porcine epidemic diarrhea virus infection.

    PubMed

    Oh, Jin Sik; Song, Dae Sub; Yang, Jeong Sun; Song, Ju Young; Moon, Hyoung Joon; Kim, Tae Yung; Park, Bong Kyun

    2005-12-01

    An indirect porcine epidemic diarrhea (PED) virus (PEDV) enzyme-linked immunosorbent assay (ELISA) was compared with the serum neutralization (SN) test by testing 46 samples from experimentally infected sows, 73 samples from naive sows, and 1,024 field sow samples from 48 commercial swine farms of undefined PED status. The SN test and the ELISA were performed using PEDV, KPEDV-9 strain. Viral proteins as a coating antigen of PEDV ELISA were extracted from the cytoplasm of PEDV-infected Vero cells using a non-ionic detergent, Triton X-100, and a simple protocol of PEDV ELISA was followed. The presence of antibodies in these experimental samples was confirmed by SN and ELISA in which the sensitivity of the ELISA was 89.1%, and the corresponding specificity was 94.5%. On testing 1,024 field samples, an overall agreement of 84.2% was generated between the SN and ELISA. This study demonstrates that the PEDV ELISA is a useful serodiagnostic screening test at herd level for detecting swine antibodies against PEDV.

  18. Magnetically coupled signal isolator

    NASA Technical Reports Server (NTRS)

    Black, Jr., William C. (Inventor); Hermann, Theodore M. (Inventor)

    2001-01-01

    A current determiner having an output at which representations of input currents are provided having an input conductor for the input current and a current sensor supported on a substrate electrically isolated from one another but with the sensor positioned in the magnetic fields arising about the input conductor due to any input currents. The sensor extends along the substrate in a direction primarily perpendicular to the extent of the input conductor and is formed of at least a pair of thin-film ferromagnetic layers separated by a non-magnetic conductive layer. The sensor can be electrically connected to electronic circuitry formed in the substrate including a nonlinearity adaptation circuit to provide representations of the input currents of increased accuracy despite nonlinearities in the current sensor, and can include further current sensors in bridge circuits.

  19. Isolation and molecular characterization of Banna virus from mosquitoes, Vietnam.

    PubMed

    Nabeshima, Takeshi; Thi Nga, Phan; Guillermo, Posadas; Parquet, Maria del Carmen; Yu, Fuxun; Thanh Thuy, Nguyen; Minh Trang, Bui; Tran Hien, Nguyen; Sinh Nam, Vu; Inoue, Shingo; Hasebe, Futoshi; Morita, Kouichi

    2008-08-01

    We isolated and characterized a Banna virus from mosquitoes in Vietnam; 5 strains were isolated from field-caught mosquitoes at various locations; Banna virus was previously isolated from encephalitis patients in Yunnan, China, in 1987. Together, these findings suggest widespread distribution of this virus throughout Southeast Asia.

  20. Investigation into the Role of Potentially Contaminated Feed as a Source of the First-Detected Outbreaks of Porcine Epidemic Diarrhea in Canada

    PubMed Central

    Pasick, J; Berhane, Y; Ojkic, D; Maxie, G; Embury-Hyatt, C; Swekla, K; Handel, K; Fairles, J; Alexandersen, S

    2014-01-01

    Summary In January 2014, approximately 9 months following the initial detection of porcine epidemic diarrhea (PED) in the USA, the first case of PED was confirmed in a swine herd in south-western Ontario. A follow-up epidemiological investigation carried out on the initial and 10 subsequent Ontario PED cases pointed to feed as a common risk factor. As a result, several lots of feed and spray-dried porcine plasma (SDPP) used as a feed supplement were tested for the presence of PEDV genome by real-time RT-PCR assay. Several of these tested positive, supporting the notion that contaminated feed may have been responsible for the introduction of PEDV into Canada. These findings led us to conduct a bioassay experiment in which three PEDV-positive SDPP samples (from a single lot) and two PEDV-positive feed samples supplemented with this SDPP were used to orally inoculate 3-week-old piglets. Although the feed-inoculated piglets did not show any significant excretion of PEDV, the SDPP-inoculated piglets shed PEDV at a relatively high level for ≥9 days. Despite the fact that the tested PEDV genome positive feed did not result in obvious piglet infection in our bioassay experiment, contaminated feed cannot be ruled out as a likely source of this introduction in the field where many other variables may play a contributing role. PMID:25098383

  1. Pharmacokinetics of tildipirosin in porcine plasma, lung tissue, and bronchial fluid and effects of test conditions on in vitro activity against reference strains and field isolates of Actinobacillus pleuropneumoniae.

    PubMed

    Rose, M; Menge, M; Bohland, C; Zschiesche, E; Wilhelm, C; Kilp, S; Metz, W; Allan, M; Röpke, R; Nürnberger, M

    2013-04-01

    The pharmacokinetics of tildipirosin (Zuprevo(®) 40 mg/mL solution for injection for pigs), a novel 16-membered-ring macrolide for the treatment for swine respiratory disease (SRD), was investigated in studies collecting blood plasma and postmortem samples of lung tissue and bronchial fluid (BF) from swine. In view of factors influencing the in vitro activity of macrolides, and for the interpretation of tildipirosin pharmacokinetics in relation to minimum inhibitory concentrations (MIC), additional experiments were conducted to study the effects of pH, carbon dioxide-enriched atmosphere, buffers, and serum on tildipirosin MICs for various reference strains and Actinobacillus (A.) pleuropneumoniae field isolates. After single intramuscular (i.m.) injection at 4 mg/kg body weight, maximum plasma concentration (Cmax) was 0.9 μg/mL observed within 23 min (Tmax ). Mean residence time from the time of dosing to the time of last measurable concentration (MRTlast) and terminal half-life (T1/2) both were about 4 days. A dose-response relationship with no significant sex effect is observed for area under the plasma concentration-time curve from time 0 to the last sampling time with a quantifiable drug concentration (AUClast) over the range of doses up to 6 mg/kg. However, linear dose proportionality could not be proven with statistical methods. The time-concentration profile of tildipirosin in BF and lung far exceeded that in blood plasma. In lung, tildipirosin concentrations reached 3.1 μg/g at 2 h, peaked at 4.3 μg/g at day 1, and slowly declined to 0.8 μg/g at day 17. In BF, tildipirosin levels were 14.3, 7.0, and 6.5 μg/g at days 5, 10, and 14. T1/2 in lung was ∼7 days. Tildipirosin is rapidly and extensively distributed to the respiratory tract followed by slow elimination. Culture media pH and carbon dioxide-enriched atmosphere (CO2 -EA) had a marked impact on in vitro activity of tildipirosin in reference strains of various rapidly growing aerobic and

  2. Noise cancellation in magnetoencephalography and electroencephalography with isolated reference sensors

    DOEpatents

    Kraus, Jr., Robert H.; Espy, Michelle A.; Matlachov, Andrei; Volegov, Petr

    2010-06-01

    An apparatus measures electromagnetic signals from a weak signal source. A plurality of primary sensors is placed in functional proximity to the weak signal source with an electromagnetic field isolation surface arranged adjacent the primary sensors and between the weak signal source and sources of ambient noise. A plurality of reference sensors is placed adjacent the electromagnetic field isolation surface and arranged between the electromagnetic isolation surface and sources of ambient noise.

  3. Psychopathology of social isolation

    PubMed Central

    Baek, Sang-Bin

    2014-01-01

    The most important defining factor of being human is the use of symbolic language. Language or communication problem occurs during the growth, the child will have a higher risk of social isolation and then the survival will be threatened constantly. Today, adolescents and youths are familiar with computer and smart-phone devices, and communication with others by these devices is easy than face-to-face communication. As adolescents and youths live in the comfortable and familiar cyber-world rather than actively participating real society, so they make social isolation. Extreme form of this isolation in adolescents and youths is so-called Socially Withdrawn Youth. In this study, the psychopathological factors inducing social isolation were discussed. Development stages of social isolation in relation with types of social isolation, Ego-syntonic isolation and Ego-dystonic isolation, were also considered. PMID:25061592

  4. Direct Comparison of the Histidine-rich Protein-2 Enzyme-linked Immunosorbent Assay (HRP-2 ELISA) and Malaria SYBR Green I Fluorescence (MSF) Drug Sensitivity Tests in Plasmodium falciparum Reference Clones and Fresh ex vivo Field Isolates from Cambodia

    DTIC Science & Technology

    2013-07-12

    parasitaemia detection for both methods was determined for reference clones and IEV isolates. Since human white blood cell (WBC) DNA in clinical samples is...that may reduce sensitivity of parasite detection [8]. Since 2004, Armed Forces Research Institute of Medical Sciences (AFRIMS) routinely applies the HRP...susceptibilities of P. falciparum la- boratory reference strains showed that the HRP-2 assay provides a similar limit of detection in either whole blood

  5. Comparative studies on the pathogenicity and tissue distribution of three virulence variants of classical swine fever virus, two field isolates and one vaccine strain, with special regard to immunohistochemical investigations

    PubMed Central

    Belák, Katinka; Koenen, Frank; Vanderhallen, Hans; Mittelholzer, Christian; Feliziani, Francesco; De Mia, Gian Mario; Belák, Sándor

    2008-01-01

    Background The aim of this study was to compare the tissue distribution and pathogenicity of three virulence variants of classical swine fever virus (CSFV) and to investigate the applicability of various conventional diagnostic procedures. Methods 64 pigs were divided into three groups and infected with the highly virulent isolate ISS/60, the moderately virulent isolate Wingene'93 and the live attenuated vaccine strain Riems, respectively. Clinical signs, gross and histopathological changes were compared in relation to time elapsed post infection. Virus spread in various organs was followed by virus isolation, by immunohistochemistry, applying monoclonal antibodies in a two-step method and by in situ hybridisation using a digoxigenin-labelled riboprobe. Results The tissue distribution data are discussed in details, analyzing the results of the various diagnostic approaches. The comparative studies revealed remarkable differences in the onset of clinical signs as well as in the development of the macro- and microscopical changes, and in the tissue distribution of CSFV in the three experimental groups. Conclusion The present study demonstrates that in the case of highly and moderately virulent virus variants the virulence does not affect the pattern of the viral spread, however, it influences the outcome, the duration and the intensity of the disease. Immunohistochemistry has the advantage to allow the rapid detection and localisation of the virus, especially in cases of early infection, when clinical signs are still absent. Compared to virus isolation, the advantage of this method is that no cell culture facilities are required. Thus, immunohistochemistry provides simple and sensitive tools for the prompt detection of newly emerging variants of CSFV, including the viruses of very mild virulence. PMID:18775072

  6. Isolation in Early Childhood.

    ERIC Educational Resources Information Center

    Rogers, Sinclair

    This paper presents information on isolated children and describes a study being undertaken to examine the role of isolation in reported cases of child abuse and neglect. The effects of extreme isolation on language and psychological development are emphasized. The importance of early socialization is seen in relation to normal development.…

  7. Polarization proximity effect in isolator crystal pairs.

    PubMed

    Linzon, Y; Ferrera, M; Razzari, L; Pignolet, A; Morandotti, R

    2008-12-01

    We experimentally study the polarization dynamics (orientation and ellipticity) of near-infrared light transmitted through magneto-optical yttrium iron garnet isolator crystal pairs using a modified balanced detection scheme. When the pair separation is in the submillimeter range, we observed a proximity effect in which the saturation field is reduced by up to 20%. One-dimensional calculations suggest that the proximity effect originates from magnetostatic interactions between the dipole moments of the isolator crystals.

  8. Optical isolator using two tandem phase modulators.

    PubMed

    Doerr, Christopher R; Dupuis, Nicolas; Zhang, Liming

    2011-11-01

    We propose and demonstrate an integrated optical isolator in InP using two phase modulators in series. The phase modulators are driven with a single-frequency signal in quadrature. Theoretically there is no effect on the forward signal, and the carrier of the backward signal can be eliminated, the energy distributed to other frequencies. We achieve a carrier isolation of 11 dB and an excess insertion loss of 2.3 dB. Such an isolator can be monolithically integrated with a laser without extra materials or magnetic fields.

  9. Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas.

    PubMed

    Mori, Koji; Suzuki, Ken-ichiro; Yamaguchi, Kaoru; Urabe, Tetsuro; Hanada, Satoshi

    2015-01-01

    A novel, obligately chemolithoautotrophic, sulfur-oxidizing bacterial strain, designated strain gps52(T), was isolated from a rock sample collected near the hydrothermal vents of the Suiyo Seamount in the Pacific Ocean. The cells possessed a Gram-stain-negative-type cell wall and contained menaquinone-8(H4) and menaquinone-9(H4) as respiratory quinones, and C16 : 1ω7c, C16 : 0 and C18 : 1ω7c as major cellular fatty acids. Neither storage compounds nor extensive internal membranes were observed in the cells. Strain gps52(T) grew using carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as electron acceptor. Optimal growth was observed at 32 °C, pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain gps52(T) belongs to the family Ectothiorhodospiraceae and is different from any other known bacteria, with sequence similarities of less than 93 %. Based on phenotypic and phylogenetic findings, the isolate is considered to represent a novel genus and species in the family Ectothiorhodospiraceae, and the name Thiogranum longum gen. nov., sp. nov. is proposed. The type strain is gps52(T) ( = NBRC 101260(T) = DSM 19610(T)). An emended description of the genus Thiohalomonas is also proposed.

  10. Module isolation devices

    DOEpatents

    Carolan, Michael Francis; Cooke, John Albert; Buzinski, Michael David

    2010-04-27

    A gas flow isolation device includes a gas flow isolation valve movable from an opened condition to a closed condition. The module isolation valve in one embodiment includes a rupture disk in flow communication with a flow of gas when the module isolation valve is in an opened condition. The rupture disk ruptures when a predetermined pressure differential occurs across it causing the isolation valve to close. In one embodiment the valve is mechanically linked to the rupture disk to maintain the valve in an opened condition when the rupture disk is intact, and which permits the valve to move into a closed condition when the rupture disk ruptures. In another embodiment a crushable member maintains the valve in an open condition, and the flow of gas passed the valve upon rupturing of the rupture disk compresses the crushable member to close the isolation valve.

  11. Mutation and premating isolation

    NASA Technical Reports Server (NTRS)

    Woodruff, R. C.; Thompson, J. N. Jr

    2002-01-01

    While premating isolation might be traceable to different genetic mechanisms in different species, evidence supports the idea that as few as one or two genes may often be sufficient to initiate isolation. Thus, new mutation can theoretically play a key role in the process. But it has long been thought that a new isolation mutation would fail, because there would be no other individuals for the isolation-mutation-carrier to mate with. We now realize that premeiotic mutations are very common and will yield a cluster of progeny carrying the same new mutant allele. In this paper, we discuss the evidence for genetically simple premating isolation barriers and the role that clusters of an isolation mutation may play in initiating allopatric, and even sympatric, species divisions.

  12. Mutation and premating isolation.

    PubMed

    Woodruff, R C; Thompson, J N

    2002-11-01

    While premating isolation might be traceable to different genetic mechanisms in different species, evidence supports the idea that as few as one or two genes may often be sufficient to initiate isolation. Thus, new mutation can theoretically play a key role in the process. But it has long been thought that a new isolation mutation would fail, because there would be no other individuals for the isolation-mutation-carrier to mate with. We now realize that premeiotic mutations are very common and will yield a cluster of progeny carrying the same new mutant allele. In this paper, we discuss the evidence for genetically simple premating isolation barriers and the role that clusters of an isolation mutation may play in initiating allopatric, and even sympatric, species divisions.

  13. High temperature behavior of multi-region direct current current-voltage spectroscopy and relationship with shallow-trench-isolation-based high-voltage laterally diffused metal-oxide-semiconductor field-effect-transistors reliability

    NASA Astrophysics Data System (ADS)

    He, Yandong; Zhang, Ganggang; Zhang, Xing

    2014-01-01

    With the process compatibility with the mainstream standard complementary metal-oxide-semiconductor (CMOS), shallow trench isolation (STI) based laterally diffused metal-oxide-semiconductor (LDMOS) devices have become popular for its better tradeoff between breakdown voltage and performance, especially for smart power applications. A multi-region direct current current-voltage (MR-DCIV) technique with spectroscopic features was demonstrated to map the interface state generation in the channel, accumulation and STI drift regions. High temperature behavior of MR-DCIV spectroscopy was analyzed and a physical model was verified. Degradation of STI-based LDMOS transistors under high temperature reverse bias (HTRB) stress is experimentally studied by MR-DCIV spectroscopy. The impact of interface state location on device electrical characteristics was investigated. Our results show that the major contribution to HTRB degradation, in term of the on-resistance degradation, was attributed to interface state generation under STI drift region.

  14. Listeria fleischmannii sp. nov., isolated from cheese.

    PubMed

    Bertsch, David; Rau, Jörg; Eugster, Marcel R; Haug, Martina C; Lawson, Paul A; Lacroix, Christophe; Meile, Leo

    2013-02-01

    A study was performed on three isolates (LU2006-1(T), LU2006-2 and LU2006-3), which were sampled independently from cheese in western Switzerland in 2006, as well as a fourth isolate (A11-3426), which was detected in 2011, using a polyphasic approach. The isolates could all be assigned to the genus Listeria but not to any known species. Phenotypic and chemotaxonomic data were compatible with the genus Listeria and phylogenetic analysis based on 16S rRNA gene sequences confirmed that the closest relationships were with members of this genus. However, DNA-DNA hybridization demonstrated that the isolates did not belong to any currently described species. Cell-wall-binding domains of Listeria monocytogenes bacteriophage endolysins were able to attach to the isolates, confirming their tight relatedness to the genus Listeria. Although PCR targeting the central portion of the flagellin gene flaA was positive, motility was not observed. The four isolates could not be discriminated by Fourier transform infrared spectroscopy or pulsed-field gel electrophoresis. This suggests that they represent a single species, which seems to be adapted to the environment in a cheese-ripening cellar as it was re-isolated from the same type of Swiss cheese after more than 5 years. Conjugation experiments demonstrated that the isolates harbour a transferable resistance to clindamycin. The isolates did not exhibit haemolysis or show any indication of human pathogenicity or virulence. The four isolates are affiliated with the genus Listeria but can be differentiated from all described members of the genus Listeria and therefore they merit being classified as representatives of a novel species, for which we propose the name Listeria fleischmannii sp. nov.; the type strain is LU2006-1(T) ( = DSM 24998(T)  = LMG 26584(T)).

  15. Visual field

    MedlinePlus

    Perimetry; Tangent screen exam; Automated perimetry exam; Goldmann visual field exam; Humphrey visual field exam ... Confrontation visual field exam : This is a quick and basic check of the visual field. The health care provider ...

  16. Broadband optical isolator based on helical metamaterials.

    PubMed

    Cao, Hu; Yang, ZhenYu; Zhao, Ming; Wu, Lin; Zhang, Peng

    2015-05-01

    Based on helical metamaterials, a new broadband optical isolator with a triple-helix structure is proposed in this paper. The right-handed circularly polarized light can transmit through the isolator with its polarization unchanged. The reverse propagating light, which is caused by the reflection of the latter optical devices, is converted into left-handed circularly polarized light that is suppressed by the proposed isolator because of absorption. Our design has some unprecedented advantages such as broad frequency ranges and a compact structure; moreover, neither polarizers nor adscititious magnetic fields are required. Properties of the isolator are investigated using the finite-difference time-domain method, and this phenomenon is studied by the mechanism of helical antenna theory.

  17. A novel approach for the isolation of the sound and pseudo-sound contributions from near-field pressure fluctuation measurements: analysis of the hydroacoustic and hydrodynamic perturbation in a propeller-rudder system

    NASA Astrophysics Data System (ADS)

    Felli, Mario; Grizzi, Silvano; Falchi, Massimo

    2014-01-01

    The main scope of the present work is to investigate the mechanisms underlying the hydroacoustic and hydrodynamic perturbations in a rudder operating in the wake of a free running marine propeller. The study consisted of detailed near-field pressure fluctuation measurements which were acquired on the face and back surfaces of the rudder, at different deflection angles. To this aim, a novel wavelet-filtering procedure was applied to separate and analyze distinctly the acoustic and hydrodynamic components of the recorded near-field pressure signals. The filtering procedure undertakes the separation of intermittent pressure peaks induced by the passage of eddy structures, interpreted as pseudo-sound, from homogenous background fluctuations, interpreted as sound. The use of wavelet in the filtering procedure allows to overcome the limitations of the earlier attempts based on frequency (wave number) band-pass filtering, retrieving the overall frequency content of both the acoustic and the hydrodynamic components and returning them as independent signals in the time domain. Acoustic and hydrodynamic pressure distributions were decomposed harmonically and compared to the corresponding topologies of the vorticity field, derived from earlier LDV measurements performed by Felli and Falchi (Exp Fluids 51(5):1385-1402, 2011). The study highlighted that the acoustic perturbation is mainly correlated with the unsteady load variations of the rudder and to the shear layer fluctuations of the propeller streamtube. Conversely, the dynamics of the propeller tip and hub vortices underlies the hydrodynamic perturbation.

  18. Heterogeneity in pepper isolates of cucumber mosaic virus

    USGS Publications Warehouse

    Rodriguez-Alvarado, G.; Kurath, G.; Dodds, J.A.

    1995-01-01

    Twenty-four cucumber mosaic cucumovirus (CMV) field isolates from pepper crops in Cali-fornia were characterized and compared by nucleic acid hybridization subgrouping, virion electrophoresis, and biological effects in several hosts. Isolates, belonging to subgroup I or subgroup II, were found that induced severe symptoms in mechanically inoculated bell pep-pers. Only two isolates, both from subgroup II, were mild. A group of 19 isolates collected from a single field were all in subgroup II and appeared identical by virion electrophoresis, but they exhibited varying degrees of symptom severity in peppers. As a more detailed indicator of heterogeneity, these 19 isolates were examined by RNase protection assays to delect sequence variation in the coat protein gene region of their genomes. The patterns of bands observed were complex and a high degree of genomic heterogeneity was detected between isolates, with no apparent correlation to symptomatology in bell pepper.

  19. Positive isolation disconnect

    NASA Technical Reports Server (NTRS)

    Rosener, A. A.; Jonkoniec, T. G.

    1975-01-01

    A positive isolation disconnect was developed for component replacement in serviced liquid and gaseous spacecraft systems. Initially a survey of feasible concepts was made to determine the optimum method for fluid isolation, sealing techniques, coupling concepts, and foolproofing techniques. The top concepts were then further evaluated, including the fabrication of a semifunctional model. After all tradeoff analyses were made, a final configuration was designed and fabricated for development testing. This resulted in a 6.35 mm (1/4 inch) line and 12.7 mm (1/2 inch) line positive isolation disconnect, each unit consisting of two coupled disconnect halves, each capable of fluid isolation with essentially zero clearance between them for zero leakage upon disconnect half disengagement. An interlocking foolproofing technique was incorporated that prevents uncoupling of disconnect halves prior to fluid isolation.

  20. Fasciola hepatica: histological demonstration of apoptosis in the reproductive organs of flukes of triclabendazole-sensitive and triclabendazole-resistant isolates, and in field-derived flukes from triclabendazole-treated hosts, using in situ hybridisation to visualise endonuclease-generated DNA strand breaks.

    PubMed

    Hanna, R E B; Forster, F I; Brennan, G P; Fairweather, I

    2013-01-31

    Investigation of the triclabendazole (TCBZ) resistance status of populations of Fasciola hepatica in field cases of fasciolosis, where treatment failure has been reported, can be supported by histological examination of flukes collected from recently treated hosts. In TCBZ-sensitive flukes (TCBZ-S) exposed to TCBZ metabolites for 1-4days in vivo, but not in TCBZ-resistant flukes (TCBZ-R), morphological changes suggestive of apoptosis occur in cells undergoing meiosis or mitosis in the testis, ovary and vitelline follicles. In order to verify or refute the contention that efficacy of TCBZ treatment is associated with apoptosis in the reproductive organs of flukes, histological sections of TCBZ-S (Cullompton isolate) flukes and TCBZ-R (Sligo isolate) flukes were subjected to the TdT-mediated dUDP nick end labelling (TUNEL) in situ hybridisation method, a commercially available test specifically designed to label endonuclease-induced DNA strand breaks associated with apoptosis. Additionally, sections of in vivo-treated and untreated flukes originating from field outbreaks of suspected TCBZ-S and TCBZ-R fasciolosis were labelled by the TUNEL method. It was found that in treated TCBZ-S flukes, strong positive labelling indicating apoptosis was associated with morphologically abnormal cells undergoing mitosis or meiosis in the testis, ovary and vitelline follicles. Background labelling in the positive testis sections was attributed to heterophagy of cell debris by the sustentacular tissue. The triggering of apoptosis was probably related to failure of spindle formation at cell division, supporting the contention that TCBZ inhibits microtubule formation. In treated TCBZ-R (Sligo Type 1) flukes, and in treated flukes from field outbreaks of suspected TCBZ-R fasciolosis, no significant labelling was observed, while sections of fluke derived from a field case of fasciolosis where TCBZ resistance was not suspected were heavily labelled. Light labelling was associated with the

  1. Phage displayed peptide recognizing porcine aminopeptidase N is a potent small molecule inhibitor of PEDV entry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three phage-displayed peptides designated H, S and F that recognize porcine aminopeptidase N (pAPN), the cellular receptor of porcine transmissible gastroenteritis virus (TGEV) were able to inhibit cell infection by TGEV. These same peptides had no inhibitory effects on infection of Vero cells by po...

  2. Nanophotonics of isolated spherical particles

    NASA Astrophysics Data System (ADS)

    Geints, Yu. É.; Zemlyanov, A. A.; Panina, E. K.

    2010-09-01

    The problem of extreme focusing of an optical beam into the spatial region with wavelength dimensions is considered with the use of the special features of radiation interaction with isolated spherical particles. Results of numerical computations of the optical field intensity at the surface of silver particles of different radii upon exposure to laser radiation with different wavelengths are presented. It is demonstrated that the relative intensity of the plasmon optical field on the nanoparticle surface increases and the field focusing region decreases with increasing particle radius. Results of numerical computations illustrating the influence of the shell of composite nanoparticles comprising a dielectric core and a metal shell on the optical field intensity in the vicinity of the particle are presented. The problem of local optical foci of a transparent microparticle (photonic nanojets) is investigated. It is established that variation of the micron particle size, its optical properties, and laser radiation parameters allows the amplitude and spatial characteristics of the photonic nanojet region to be controlled efficiently.

  3. Isolated adipic aciduria.

    PubMed

    Hasbini, D A; Mikati, M A; Habbal, Z M

    2001-01-01

    Adipic acid can appear, in combination with other dicarboxylic acids, in the urine of patients in a number of underlying metabolic diseases. A child with seizures and mental retardation of unknown etiology who was found to have elevated isolated adipic aciduria on investigation for metabolic diseases is reported. A dietary artifact was suspected, and the adipic aciduria resolved after the child was kept on a specific restricted diet for 3 days. This is the third report of isolated adipic aciduria secondary to food. Findings confirm the previous reports of dietary origin of isolated adipic aciduria and should alert clinicians to such artifact before committing patients to unnecessary treatments.

  4. Fault detection and isolation

    NASA Technical Reports Server (NTRS)

    Bernath, Greg

    1994-01-01

    In order for a current satellite-based navigation system (such as the Global Positioning System, GPS) to meet integrity requirements, there must be a way of detecting erroneous measurements, without help from outside the system. This process is called Fault Detection and Isolation (FDI). Fault detection requires at least one redundant measurement, and can be done with a parity space algorithm. The best way around the fault isolation problem is not necessarily isolating the bad measurement, but finding a new combination of measurements which excludes it.

  5. Isolation of Chlamydomonas Flagella

    PubMed Central

    Craige, Branch; Brown, Jason M.; Witman, George B.

    2014-01-01

    A simple, scalable, and fast procedure for the isolation of Chlamydomonas flagella is described. Chlamydomonas can be synchronously deflagellated by treatment with chemicals, pH shock, or mechanical shear. The Basic Protocol describes the procedure for flagellar isolation using dibucaine to induce flagellar abscission; we also describe the pH shock method as an Alternate Protocol when flagellar regeneration is desirable. Sub-fractionation of the isolated flagella into axonemes and the membrane + matrix fraction is described in a Support Protocol. PMID:23728744

  6. Base isolation: Fresh insight

    SciTech Connect

    Shustov, V.

    1993-07-15

    The objective of the research is a further development of the engineering concept of seismic isolation. Neglecting the transient stage of seismic loading results in a widespread misjudgement: The force of resistance associated with velocity is mostly conceived as a source of damping vibrations, though it is an active force at the same time, during an earthquake type excitation. For very pliant systems such as base isolated structures with relatively low bearing stiffness and with artificially added heavy damping mechanism, the so called `damping`` force may occur even the main pushing force at an earthquake. Thus, one of the two basic pillars of the common seismic isolation philosophy, namely, the doctrine of usefulness and necessity of a strong damping mechanism, is turning out to be a self-deception, sometimes even jeopardizing the safety of structures and discrediting the very idea of seismic isolation. There is a way out: breaking with damping dependancy.

  7. Are Field OB Stars Alone?

    NASA Astrophysics Data System (ADS)

    Oey, Sally

    2005-07-01

    This SNAP program offers an inexpensive, simple program to search for low-mass companions of field OB stars. Do field OB stars exist in true isolation, as suggested by a recent Galactic study, or are they the tip of the iceberg on a small cluster of low-mass stars as predicted by the cluster mass function and stellar IMF? Short ACS/WFC V and I observations proposed here may easily resolve this issue for field OB stars in the Small Magellanic Cloud. Truly isolated OB stars represent a theoretical challenge and variation from clusters, in mode of star formation, and have important consequences for our understanding of the field stellar population in galaxies. Small clusters around the field OB stars, on the other hand, may confirm the universality of the stellar clustering law and IMF.

  8. Isolated sleep paralysis.

    PubMed

    Sawant, Neena S; Parkar, Shubhangi R; Tambe, Ravindra

    2005-10-01

    Sleep paralysis (SP) is a cardinal symptom of narcolepsy. However, little is available in the literature about isolated sleep paralysis. This report discusses the case of a patient with isolated sleep paralysis who progressed from mild to severe SP over 8 years. He also restarted drinking alcohol to be able to fall asleep and allay his anxiety symptoms. The patient was taught relaxation techniques and he showed complete remission of the symptoms of SP on follow up after 8 months.

  9. Flywheel vibration isolation test using a variable-damping isolator

    NASA Astrophysics Data System (ADS)

    Oh, Hyun-Ung; Taniwaki, Shigemune; Kinjyo, Naofumi; Izawa, Katsuhiko

    2006-04-01

    This study demonstrates the isolation performance of a variable-damping isolator using a bio-metal fiber (BMF) valve to enhance the pointing performance of observation satellites by isolating disturbances induced by reaction wheel assemblies. Vibration isolation tests of the variable-damping isolator were performed using an air-floating wheel disturbance detector to investigate whether the isolator can actually isolate flywheel vibration. In this paper, we first present a recently developed variable-damping isolator with low power consumption, and a reaction wheel disturbance detector, fabricated in a previous study, which detects low-frequency disturbances. Next, we describe the effectiveness of the variable-damping isolator based on flywheel vibration isolation test results.

  10. Isolation of Plasmodesmata.

    PubMed

    Faulkner, Christine; Bayer, Emmanuelle M F

    2017-01-01

    Plasmodesmata (PD) are plasma membrane lined pores that cross the plant cell wall and connect adjacent cells. Plasmodesmata are composed of elements of the endoplasmic reticulum, plasma membrane, cytosol, and cell wall and thus, as multicomposite structures that are embedded in the cell wall, they are notoriously difficult to isolate from whole plant tissue. However, understanding PD structure, function, and regulation necessitates identification of their molecular components and therefore proteomic and lipidomic analyses of PD fractions are an essential strategy for plasmodesmal biology. Here we outline a simple two-step purification procedure that allows isolation of PD-derived membranes from Arabidopsis suspension cells. The method involves isolation of purified cell wall fragments containing intact PD which is followed by enzymatic degradation of the cell wall to release the PD. This membrane-rich fraction can be subjected to protein and lipid extraction for molecular characterization of PD components. The first step of this procedure involves the isolation of cell wall fragments containing intact PD, free from contamination from other cellular compartments. Purified PD membranes are then released from the cell wall matrix by enzymatic degradation. Isolated PD membranes provide a suitable starting material for the analysis of PD-associated proteins and lipids.

  11. Influenza virus isolation.

    PubMed

    Krauss, Scott; Walker, David; Webster, Robert G

    2012-01-01

    The isolation of influenza viruses is important for the diagnosis of respiratory diseases in lower animals and humans, for the detection of the infecting agent in surveillance programs, and is an essential element in the development and production of vaccine. Since influenza is caused by a zoonotic virus it is necessary to do surveillance in the reservoir species (aquatic waterfowls), intermediate hosts (quails, pigs), and in affected mammals including humans. Two of the hemagglutinin (HA) subtypes of influenza A viruses (H5 and H7) can evolve into highly pathogenic (HP) strains for gallinaceous poultry; some HP H5 and H7 strains cause lethal infection of humans. In waterfowls, low pathogenic avian influenza (LPAI) isolates are obtained primarily from the cloaca (or feces); in domestic poultry, the virus is more often recovered from the respiratory tract than from cloacal samples; in mammals, the virus is most often isolated from the respiratory tract, and in cases of high pathogenic avian influenza (HPAI) from the blood and internal organs of infected birds. Virus isolation procedures are performed by inoculation of clinical specimens into embryonated eggs (primarily chicken eggs) or onto a variety of primary or continuous tissue culture systems. Successful isolation of influenza virus depends on the quality of the sample and matching the appropriate culture method to the sample type.

  12. Molecular variation of hop mosaic virus isolates.

    PubMed

    Poke, Fiona S; Crowle, Damian R; Whittock, Simon P; Wilson, Calum R

    2010-10-01

    Hop mosaic virus (HpMV), a member of the genus Carlavirus, is importance to hop production worldwide. We identified variation in nucleic and amino acid sequences among 23 HpMV isolates from Australia, the USA, the Czech Republic, South Africa and Japan using a 1,455-bp fragment covering the 3' end of the virus genome including ORFs 4, 5 and 6. Three clusters of two or more isolates were identified in phylogenies of the total nucleotide sequence and the coat protein (ORF5) amino acid sequence. Two of these clusters combined in analyses of ORF4 and ORF6 amino acid sequences. Isolates from within and outside of Australia were found in each cluster, indicating that sequence variation was not associated with geographic source. Monitoring of HpMV variants in the field and evaluation of the impact of variants on vector association, rate of spread, and hop yield and quality can now be undertaken.

  13. Low-loss, high-isolation, fiber-optic isolator

    NASA Technical Reports Server (NTRS)

    Lutes, George F. (Inventor)

    1988-01-01

    A low-loss, high-isolation, fiber-optic isolator for use in single-mode fiber systems utilizes a Faraday rotator and two polarizers, one at each end angularly oriented from each other at the angle of rotation for isolation, and two aspheric lens connectors to couple optical fibers to the Faraday isolator to reduce forward loss to about 2.5 dB and improve isolation to greater than 70 dB.

  14. Strain isolated ceramic coatings

    NASA Technical Reports Server (NTRS)

    Tolokan, R. P.; Brady, J. B.; Jarrabet, G. P.

    1985-01-01

    Plasma sprayed ceramic coatings are used in gas turbine engines to improve component temperature capability and cooling air efficiency. A compliant metal fiber strain isolator between a plasma sprayed ceramic coating and a metal substrate improves ceramic durability while allowing thicker coatings for better insulation. Development of strain isolated coatings has concentrated on design and fabrication of coatings and coating evaluation via thermal shock testing. In thermal shock testing, five types of failure are possible: buckling failure im compression on heat up, bimetal type failure, isothermal expansion mismatch failure, mudflat cracking during cool down, and long term fatigue. A primary failure mode for thermally cycled coatings is designated bimetal type failure. Bimetal failure is tensile failure in the ceramic near the ceramic-metal interface. One of the significant benefits of the strain isolator is an insulating layer protecting the metal substrate from heat deformation and thereby preventing bimetal type failure.

  15. Nucleic acid isolation process

    DOEpatents

    Longmire, Jonathan L.; Lewis, Annette K.; Hildebrand, Carl E.

    1990-01-01

    A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduce the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without affect on the protocol.

  16. Nucleic acid isolation

    DOEpatents

    Longmire, J.L.; Lewis, A.K.; Hildebrand, C.E.

    1988-01-21

    A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduces the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without effect on the protocol.

  17. Isolated ventricular noncompaction.

    PubMed

    Okçün Baniş; Tekin, Abdullah; Oz, Büge; Küçükoğlu, M Serdar

    2004-04-01

    Isolated ventricular noncompaction of myocardium is a rare congenital disease due to an arrest of myocardial morphogenesis during foetal development. It is characterized by a thin compacted epicardial and an extremely thickened endocardial layer with prominent trabeculations and deep intertrabecular recesses. The persistence of myocardial noncompaction is usually an associated anomaly in patients with congenital left or right ventricular outflow tract obstruction. However, isolated noncompaction of myocardium is not associated with any factors that would explain it apart from the foetal arrest of compaction of the ventricular myocardium. The disease results in systolic and diastolic ventricular dysfunction, systemic embolism and ventricular arrhythmias. We describe a case of isolated noncompaction of the ventricular myocardium in a 20-year-old man who presented initially with ventricular tachycardia.

  18. Fault detection and isolation

    NASA Technical Reports Server (NTRS)

    Bernath, Greg

    1993-01-01

    Erroneous measurements in multisensor navigation systems must be detected and isolated. A recursive estimator can find fast growing errors; a least squares batch estimator can find slow growing errors. This process is called fault detection. A protection radius can be calculated as a function of time for a given location. This protection radius can be used to guarantee the integrity of the navigation data. Fault isolation can be accomplished using either a snapshot method or by examining the history of the fault detection statistics.

  19. [Isolated anterior cervical hypertrichosis].

    PubMed

    Monteagudo, B; Cabanillas, M; de las Heras, C; Cacharrón, J M

    2009-01-01

    Anterior cervical hypertrichosis was described by Trattner and coworkers in 1991. It consists of a of hair at the anterior cervical level just above the laryngeal prominence. To date, only 28 cases of anterior cervical hypertrichosis have been reported. Although it is normally an isolated finding, it may be associated with mental retardation, hallux valgus, retinal disorders, other hair disorders, facial dysmorphism, or sensory and motor peripheral neuropathy. We report the case of a 27-year-old woman who presented with this condition as an isolated finding.

  20. Genetic analysis of Streptococcus suis isolates from wild rabbits.

    PubMed

    Sánchez del Rey, V; Fernández-Garayzábal, J F; Briones, V; Iriso, A; Domínguez, L; Gottschalk, M; Vela, A I

    2013-08-30

    This work aims to investigate the presence of Streptococcus suis in wild rabbits. A total of 65 S. suis isolates were recovered from 33.3% of the wild rabbits examined. Most isolates (86.2%) belong to genotype cps9. These isolates were further characterized by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and virulence genotyping. Overall, S. suis exhibited a low genetic diversity. Only 5 genetic profiles were obtained by PFGE and most isolates (71.4%) were included in two pulsotypes that were also widely distributed among the wild rabbit population. MLST analysis assigned all cps9 isolates into three new singlestones (ST216, ST217 and ST284), which were not genetically related to the European ST87 and Spanish ST61 widespread swine clones, indicating a different genetic background for the S. suis isolates from wild rabbits and pigs. Wild rabbit isolates exhibited the genotype mrp-/epf-/sly-, different from those showed by most of the swine S. suis isolates of the ST87 and ST61 clones. None of the S. suis isolated from wild rabbits exhibited the genotype cps2/mrp+/epf+/sly+ associated with human infections. These results indicate that S. suis isolates from wild rabbits are not genetically related with prevalent clones usually associated with infections in pigs or humans in Europe and do not exhibit either their virulence genotypes. Therefore, although wild rabbits could represent an unknown reservoir of this pathogen, they could not represent a potential risk for pigs or humans.

  1. Genetic characterization of Shigella flexneri isolates in Guizhou Province, China.

    PubMed

    Li, Shijun; Sun, Qiangzheng; Wei, Xiaoyu; Klena, John D; Wang, Jianping; Liu, Ying; Tian, Kecheng; Luo, Xia; Ye, Changyun; Xu, Jianguo; Wang, Dingming; Tang, Guangpeng

    2015-01-01

    Shigella flexneri is one of the major etiologic causes of shigellosis in Guizhou Province, China. However, the genetic characteristics of circulating isolates are unknown. Phenotypic and molecular profiles of 60 S. flexneri isolates recovered in Guizhou between 1972 to 1982 and 2008 to 2010 were determined. Nine serotypes (1a, 2a, 3a, 1b, 2b, X, Y, 4av and Yv) were identified. Multi-locus sequence typing differentiated the isolates into 20 sequence types (STs); 18 were novel. Four STs, ST 129, ST 100, ST 126 and ST 18, were most abundant, accounting for 65% of the isolates. Thirty-nine NotI-pulsed field gel electrophoresis patterns (pulsotypes, PTs) were observed; eight PTs were represented by more than one isolate with six isolates sharing the PT 13 profile. Multi-locus variable-nucleotide tandem-repeat analysis recognized 44 different types (MTs); seven MTs were represented by more than one isolate and MT 1 was most commonly encountered. Correlation between genetic relationships and serotypes was observed among the isolates studied; the majority of isolates belonging to the same serotype from different years clustered together based on the molecular data. These clustered isolates were also from similar geographical origins. These results enhance our understanding of genetic relationships between S. flexneri in Guizhou Province and can be used to help understand the changing etiology of shigellosis in China.

  2. Rare cell isolation and analysis in microfluidics

    PubMed Central

    Chen, Yuchao; Li, Peng; Huang, Po-Hsun; Xie, Yuliang; Mai, John D.; Wang, Lin; Nguyen, Nam-Trung; Huang, Tony Jun

    2014-01-01

    Rare cells are low-abundance cells in a much larger population of background cells. Conventional benchtop techniques have limited capabilities to isolate and analyze rare cells because of their generally low selectivity and significant sample loss. Recent rapid advances in microfluidics have been providing robust solutions to the challenges in the isolation and analysis of rare cells. In addition to the apparent performance enhancements resulting in higher efficiencies and sensitivity levels, microfluidics provides other advanced features such as simpler handling of small sample volumes and multiplexing capabilities for high-throughput processing. All of these advantages make microfluidics an excellent platform to deal with the transport, isolation, and analysis of rare cells. Various cellular biomarkers, including physical properties, dielectric properties, as well as immunoaffinities, have been explored for isolating rare cells. In this Focus article, we discuss the design considerations of representative microfluidic devices for rare cell isolation and analysis. Examples from recently published works are discussed to highlight the advantages and limitations of the different techniques. Various applications of these techniques are then introduced. Finally, a perspective on the development trends and promising research directions in this field are proposed. PMID:24406985

  3. Development and characterization of a magnetorheological elastomer based adaptive seismic isolator

    NASA Astrophysics Data System (ADS)

    Li, Yancheng; Li, Jianchun; Li, Weihua; Samali, Bijan

    2013-03-01

    One of the main shortcomings in current base isolation design/practice is lack of adaptability. As a result, a base isolation system that is effective for one type earthquake may become ineffective or may have adverse effect for other earthquakes. The vulnerability of traditional base isolation systems can be exaggerated by two types of earthquakes, i.e. near-field earthquakes and far-field earthquakes. This paper addresses the challenge facing current base isolation design/practice by proposing a new type of seismic isolator for the base isolation system, namely an adaptive seismic isolator. The novel adaptive seismic isolator utilizes magnetorheological elastomer (MRE) for its field-sensitive material property. Traditional seismic isolator design with a unique laminated structure of steel and MRE layers has been adopted in the novel MRE seismic isolator. To evaluate and characterize the behavior of the MRE seismic isolator, experimental testing was conducted on a shake table facility under harmonic cycling loading. Experimental results show that the proposed adaptive seismic isolator can successfully alter the lateral stiffness and damping force in real time up to 37% and 45% respectively. Based on the successful development of the novel adaptive seismic isolator, a discussion is also extended to the impact and potential applications of such a device in structural control applications in civil engineering.

  4. Active Inertial Vibration Isolators And Dampers

    NASA Technical Reports Server (NTRS)

    Laughlin, Darren; Blackburn, John; Smith, Dennis

    1994-01-01

    Report describes development of active inertial vibration isolators and dampers in which actuators electromagnet coils moving linearly within permanent magnetic fields in housings, somewhat as though massive, low-frequency voice coils in loudspeakers. Discusses principle of operation, electrical and mechanical considerations in design of actuators, characteristics of accelerometers, and frequency responses of control systems. Describes design and performance of one- and three-degree-of-freedom vibration-suppressing system based on concept.

  5. Isolation of Nuclei.

    PubMed

    Nabbi, Arash; Riabowol, Karl

    2015-08-03

    The isolation of nuclei is often the first step in studying processes such as nuclear-cytoplasmic shuttling, subcellular localization of proteins, and protein-chromatin or nuclear protein-protein interactions in response to diverse stimuli. Therefore, rapidly obtaining nuclei from cells with relatively high purity and minimal subcellular contamination, protein degradation, or postharvesting modification is highly desirable. Historically, the isolation of nuclei involved a homogenization step followed by centrifugation through high-density glycerol or sucrose. Although clean nuclei with little cytoplasmic contamination can be prepared using this method, it is typically time consuming and can allow protein degradation, protein modification, and leaching of components from the nuclei to occur. We have developed a rapid and simple fractionation method that is based on the selective dissolution of the cytoplasmic membrane (but not the nuclear membrane) using a low concentration of a nonionic detergent and rapid centrifugation steps. Here we describe important considerations when isolating nuclei from cells, introduce our rapid method, and compare this method to a more traditional protocol for isolating nuclei, noting the strengths and limitations of each approach.

  6. Broadband Faraday isolator.

    PubMed

    Berent, Michał; Rangelov, Andon A; Vitanov, Nikolay V

    2013-01-01

    Driving on an analogy with the technique of composite pulses in quantum physics, we theoretically propose a broadband Faraday rotator and thus a broadband optical isolator, which is composed of sequences of ordinary Faraday rotators and achromatic quarter-wave plates rotated at the predetermined angles.

  7. Biological Isolation Garment

    NASA Technical Reports Server (NTRS)

    1976-01-01

    A spinoff of astronaut's biological garment will allow hospital patients who are highly vulnerable to infection to leave their sterile habitats for several hours, carrying their germ free environment with them. Garments can be used in any of some 200 hospitals where isolation rooms are installed to treat leukemia.

  8. Biological isolation garment

    NASA Technical Reports Server (NTRS)

    Spross, F. R.

    1968-01-01

    Biological Isolation Garment /BIG/ is a one-piece loose fitting garment fabricated from a tightly woven, permeable, 100 percent-cotton fabric. Its headpiece, incorporates an integral oronsal respirator with 0.3-micron-particle filters, and a full width visor. All fabrication seams are sealed on the inside of the garment.

  9. Isolation rearing induced fear-like behavior without affecting learning abilities of Wistar rats.

    PubMed

    Molina-Hernandez, M; Tellez-Alcantara, P; Perez-Garcia, J

    2001-07-01

    1. Isolation-reared rats display fear-like behavior and depressive-like behavior in several behavioral tasks, suggesting that isolation rearing may model certain aspects of human psychopathologies. 2. After weaning (20 days old), male and female Wistar rats were isolation-reared during 20, 50 or 70 days. After that, they were tested in the elevated plus maze test, and in the open field test. Another group of isolation-reared rats (70 days of isolation) were tested in an auto-shaping task. 3. Isolation-reared rats displayed high levels of fear-like behavior in the elevated plus-maze test, and hyperlocomotion in the open field test. But, isolation-reared rats learned an auto-shaping task. 4. In conclusion, isolation rearing induced fear-like behavior, without affect learning abilities of rats.

  10. Genetic diversity of the VP1 gene of duck hepatitis virus type I (DHV-I) isolates from southeast China is related to isolate attenuation.

    PubMed

    Liu, Guangqing; Wang, Fei; Ni, Zheng; Yun, Tao; Yu, Bin; Huang, Jionggang; Chen, Jianping

    2008-10-01

    The complete sequence of an isolate (ZJ-V) of Duck hepatitis virus I (DHV-I), originally taken from the field in southeast China was determined. It was 7691 nucleotides long and had 5'- and 3'-terminal non-coding regions of 626 and 315 nucleotides, respectively. The poly(A) tail contained at least 22 residues and the single open reading frame encoded a polypeptide of 2249 amino acids. The VP1 gene was also sequenced from nine southeast China field isolates and three attenuated DHV-I vaccine strains. In phylogenetic analysis of the isolates and other published sequences, attenuated and tissue-adapted isolates (including ZJ-V) clustered as genotypes significantly different from the field isolates that had not been passaged in chicken/duck embryos. There were two consistent amino acid substitutions (E(129)-->V(129) and A(142)-->S(142)) between all the field isolates and all the tissue-adapted ones. The carboxyl terminal region was generally the most variable and here the four attenuated Chinese isolates showed six consistent differences from the field isolates (S(181)-->L(181), H(183)K(184)-->R(183)G(1841), N(193)-->D(193), E(205)-->K(205), R(217)-->K(217), N(235)-->D(235)). It seems likely that at least some of these differences result from mutations leading to isolate attenuation.

  11. Method for isolating nucleic acids

    SciTech Connect

    Hurt, Jr., Richard Ashley; Elias, Dwayne A.

    2015-09-29

    The current disclosure provides methods and kits for isolating nucleic acid from an environmental sample. The current methods and compositions further provide methods for isolating nucleic acids by reducing adsorption of nucleic acids by charged ions and particles within an environmental sample. The methods of the current disclosure provide methods for isolating nucleic acids by releasing adsorbed nucleic acids from charged particles during the nucleic acid isolation process. The current disclosure facilitates the isolation of nucleic acids of sufficient quality and quantity to enable one of ordinary skill in the art to utilize or analyze the isolated nucleic acids for a wide variety of applications including, sequencing or species population analysis.

  12. Characterization of Staphylococcus caprae Clinical Isolates Involved in Human Bone and Joint Infections, Compared with Goat Mastitis Isolates.

    PubMed

    d'Ersu, J; Aubin, G G; Mercier, P; Nicollet, P; Bémer, P; Corvec, S

    2016-01-01

    Staphylococcus caprae is an emerging microorganism in human bone and joint infections (BJI). The aim of this study is to describe the features of S. caprae isolates involved in BJI (H for human) compared with those of isolates recovered in goat mastitis (A for animal). Fourteen isolates of each origin were included. Identifications were performed using a Vitek 2 GP ID card, tuf gene sequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Vitek MS. Molecular typing was carried out using pulsed-field gel electrophoresis (PFGE) and DiversiLab technology. The crystal violet method was used to determine biofilm-forming ability. Virulence factors were searched by PCR. Vitek MS technology provides an accurate identification for the two types of isolates compared to that of gold-standard sequencing (sensitivity, 96.4%), whereas the Vitek 2 GP ID card was more effective for H isolates. Molecular typing methods revealed two distinct lineages corresponding to the origin despite few overlaps: H and A. In our experimental conditions, no significant difference was observed in biofilm production ability between H and A isolates. Nine isolates (5 H isolates and 4 A isolates) behaved as weak producers while one A isolate was a strong producer. Concerning virulence factors, the autolysin atlC and the serine aspartate adhesin (sdrZ) genes were detected in 24 isolates (86%), whereas the lipase gene was always detected, except in one H isolate (96%). The ica operon was present in 23 isolates (82%). Fibrinogen-binding (fbe) or collagen-binding (cna) genes were not detected by using primers designed for Staphylococcus aureus or Staphylococcus epidermidis, even in low stringency conditions. Although S. caprae probably remains underestimated in human infections, further studies are needed to better understand the evolution and the adaptation of this species to its host.

  13. Characterization of Staphylococcus caprae Clinical Isolates Involved in Human Bone and Joint Infections, Compared with Goat Mastitis Isolates

    PubMed Central

    d'Ersu, J.; Aubin, G. G.; Mercier, P.; Nicollet, P.; Bémer, P.

    2015-01-01

    Staphylococcus caprae is an emerging microorganism in human bone and joint infections (BJI). The aim of this study is to describe the features of S. caprae isolates involved in BJI (H for human) compared with those of isolates recovered in goat mastitis (A for animal). Fourteen isolates of each origin were included. Identifications were performed using a Vitek 2 GP ID card, tuf gene sequencing, and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) Vitek MS. Molecular typing was carried out using pulsed-field gel electrophoresis (PFGE) and DiversiLab technology. The crystal violet method was used to determine biofilm-forming ability. Virulence factors were searched by PCR. Vitek MS technology provides an accurate identification for the two types of isolates compared to that of gold-standard sequencing (sensitivity, 96.4%), whereas the Vitek 2 GP ID card was more effective for H isolates. Molecular typing methods revealed two distinct lineages corresponding to the origin despite few overlaps: H and A. In our experimental conditions, no significant difference was observed in biofilm production ability between H and A isolates. Nine isolates (5 H isolates and 4 A isolates) behaved as weak producers while one A isolate was a strong producer. Concerning virulence factors, the autolysin atlC and the serine aspartate adhesin (sdrZ) genes were detected in 24 isolates (86%), whereas the lipase gene was always detected, except in one H isolate (96%). The ica operon was present in 23 isolates (82%). Fibrinogen-binding (fbe) or collagen-binding (cna) genes were not detected by using primers designed for Staphylococcus aureus or Staphylococcus epidermidis, even in low stringency conditions. Although S. caprae probably remains underestimated in human infections, further studies are needed to better understand the evolution and the adaptation of this species to its host. PMID:26511738

  14. Pump isolation valve

    DOEpatents

    Kinney, Calvin L.; Wetherill, Todd M.

    1983-08-02

    The pump isolation valve provides a means by which the pump may be selectively isolated from the remainder of the coolant system while being compatible with the internal hydraulic arrangement of the pump during normal operation of the pump. The valve comprises a valve cylinder disposed around the pump and adjacent to the last pump diffuser with a turning vane attached to the lower end of the valve cylinder in a manner so as to hydraulically match with the discharge diffuser. The valve cylinder is connected to a drive means for sliding the valve cylinder relative to the diffuser support cylinder so as to block flow in either direction through the discharge diffuser when the valve is in the closed position and to aid in the flow of the coolant from the discharge diffuser by means of the turning vane when the valve is in the open position.

  15. Cycle isolation monitoring

    SciTech Connect

    Svensen, L.M. III; Zeigler, J.R.; Todd, F.D.; Alder, G.C.

    2009-07-15

    There are many factors to monitor in power plants, but one that is frequently overlooked is cycle isolation. Often this is an area where plant personnel can find 'low hanging fruit' with great return on investment, especially high energy valve leakage. This type of leakage leads to increased heat rate, potential valve damage and lost generation. The fundamental question to ask is 'What is 100 Btu/kW-hr of heat rate worth to your plant? On a 600 MW coal-fired power plant, a 1% leakage can lead to an 81 Btu/kW-hr impact on the main steam cycle and a 64 Btu/kW-hr impact on the hot reheat cycle. The article gives advice on methods to assist in detecting leaking valves and to monitor cycle isolation. A software product, TP. Plus-CIM was designed to estimate flow rates of potentially leaking valves.

  16. Bacillus odysseyi isolate

    NASA Technical Reports Server (NTRS)

    Venkateswaran, Kasthuri (Inventor); La Duc, Myron Thomas (Inventor)

    2007-01-01

    The present invention relates to discovery and isolation of a biologically pure culture of a Bacillus odysseyi isolate with high adherence and sterilization resistant properties. B. odysseyi is a round spore forming Bacillus species that produces an exosporium. This novel species has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA-DNA hybridization. According to the results of these analyses, this strain belongs to the genus Bacillus and the type strain is 34hs-1.sup.T (=ATCC PTA-4993.sup.T=NRRL B-30641.sup.T=NBRC 100172.sup.T). The GenBank accession number for the 16S rDNA sequence of strain 34hs-1.sup.T is AF526913.

  17. Ultrasonic thermometer isolation standoffs

    DOEpatents

    Arave, Alvin E.

    1977-01-01

    A method is provided for minimizing sticking of the transmission line to the protective sheath and preventing noise echoes from interfering with signal echoes in an improved high temperature ultrasonic thermometer which includes an ultrasonic transmission line surrounded by a protective sheath. Small isolation standoffs are mounted on the transmission line to minimize points of contact between the transmission line and the protective sheath, the isolation standoffs serving as discontinuities mounted on the transmission line at locations where a signal echo is desired or where an echo can be tolerated. Consequently any noise echo generated by the sticking of the standoff to the protective sheath only adds to the amplitude of the echo generated at the standoff and does not interfere with the other signal echoes.

  18. High voltage isolation transformer

    NASA Technical Reports Server (NTRS)

    Clatterbuck, C. H.; Ruitberg, A. P. (Inventor)

    1985-01-01

    A high voltage isolation transformer is provided with primary and secondary coils separated by discrete electrostatic shields from the surfaces of insulating spools on which the coils are wound. The electrostatic shields are formed by coatings of a compound with a low electrical conductivity which completely encase the coils and adhere to the surfaces of the insulating spools adjacent to the coils. Coatings of the compound also line axial bores of the spools, thereby forming electrostatic shields separating the spools from legs of a ferromagnetic core extending through the bores. The transformer is able to isolate a high constant potential applied to one of its coils, without the occurrence of sparking or corona, by coupling the coatings, lining the axial bores to the ferromagnetic core and by coupling one terminal of each coil to the respective coating encasing the coil.

  19. Neglected isolated scaphoid dislocation

    PubMed Central

    Baek, Jong-Ryoon; Cho, Seung Hyun; Lee, Yong Seuk; Roh, Young Hak

    2016-01-01

    The authors present a case of isolated scaphoid dislocation in a 40-year-old male that was undiagnosed for 2 months. The patient was treated by open reduction, Kirschner wire fixation, interosseous ligament repair using a suture anchor and Blatt's dorsal capsulodesis. At 6 years followup, his radiographs of wrist showed a normal carpal alignment with a scapholunate gap of 3 mm and no evidence of avascular necrosis (AVN) of the scaphoid. PMID:27904228

  20. Isolation of Human Basophils.

    PubMed

    Schroeder, John T; Bieneman, Anja P

    2016-02-02

    Isolating human basophils from blood has long been hampered by the fact that these granulocytes represent just 1% or less of the circulating leukocyte population. We describe herein laboratory protocols that have been refined over the past ∼25 years that now enable investigators to prepare basophils for use in a variety of assays to assess the in vitro biology of these immune cells, both in IgE -dependent and -independent responses.

  1. Mechanism of DMI resistance in field isolates of Cercospora beticola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leaf spot, caused by the fungus Cercospora beticola, is an endemic disease of sugarbeets in the North Dakota and Minnesota growing regions. Control measures against the fungus include resistant sugarbeet varieties and crop rotation, but the disease is managed effectively only when combined with tim...

  2. Diversity of field isolates of sinorhizobium meliloti nodulating alfalfa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Most alfalfa seed is treated with a rhizobial inoculant consisting of one or more strains of Sinorhizobium meliloti before planting to enhance nodulation of seedlings. However, little is known about the persistence of inoculated strains later in the season. There is also a paucity of information on ...

  3. Isolated persistent hypermethioninemia.

    PubMed Central

    Mudd, S H; Levy, H L; Tangerman, A; Boujet, C; Buist, N; Davidson-Mundt, A; Hudgins, L; Oyanagi, K; Nagao, M; Wilson, W G

    1995-01-01

    New information has been obtained on 30 patients with isolated persistent hypermethioninemia, most of them previously unreported. Biopsies to confirm the presumptive diagnosis of partially deficient activity of ATP: L-methionine S-adenosyltransferase (MAT; E.C.2.5.1.6) in liver were not performed on most of these patients. However, none showed the clinical findings or the extreme elevations of serum folate previously described in other patients with isolated hypermethioninemia considered not to have hepatic MAT deficiency. Patients ascertained on biochemical grounds had no neurological abnormalities, and 27/30 had IQs or Bayley development-index scores within normal limits or were judged to have normal mental development. Methionine transamination metabolites accumulated abnormally only when plasma methionine concentrations exceeded 300-350 microM and did so more markedly after 0.9 years of age. Data were obtained on urinary organic acids as well as plasma creatinine concentrations. Patterns of inheritance of isolated hypermethioninemia were variable. Considerations as to the optimal management of this group of patients are discussed. PMID:7573050

  4. Rapid, high efficiency isolation of pancreatic ß-cells

    PubMed Central

    Clardy, Susan M.; Mohan, James F.; Vinegoni, Claudio; Keliher, Edmund J.; Iwamoto, Yoshiko; Benoist, Christophe; Mathis, Diane; Weissleder, Ralph

    2015-01-01

    The ability to isolate pure pancreatic ß-cells would greatly aid multiple areas of diabetes research. We developed a fluorescent exendin-4-like neopeptide conjugate for the rapid purification and isolation of functional mouse pancreatic β-cells. By targeting the glucagon-like peptide-1 receptor with the fluorescent conjugate, β-cells could be quickly isolated by flow cytometry and were >99% insulin positive. These studies were confirmed by immunostaining, microscopy and gene expression profiling on isolated cells. Gene expression profiling studies of cytofluorometrically sorted β-cells from 4 and 12 week old NOD mice provided new insights into the genetic programs at play of different stages of type-1 diabetes development. The described isolation method should have broad applicability to the β-cell field. PMID:26330153

  5. Beetle diversity in fragmented thornscrub and isolated trees.

    PubMed

    Cuéllar-Rodríguez, G; Jurado, E; Flores, J

    2017-03-01

    Due to land use change mainly for induced agriculture, Tamaulipan thornscrubin northeast Mexico has been cleared and transformed into small patches of vegetation as small as isolated trees surrounded by agricultural fields. In this study, we explored how tree isolation or growing inside a fragment of remnant vegetation influence diversity of coleopterans in two plant species (Prosopis laevigata (Humb. &Bonpl.exWilld.) M.C. Johnst. (mesquite) and Ebenopsis ebano (Berl.) Barneby (Texas ebony). We found 72 coleopteran morphospecies; fifteen occurred mainly in remnant fragments and ten mainly in isolated trees. There were more insects under isolated mesquites than under those immersed in remnant fragments, while in Texas ebony the highest beetle density for isolated trees coincided with periods of bean and maize in surrounding agriculture.

  6. Development of an isolator working with magnetorheological elastomers and fluids

    NASA Astrophysics Data System (ADS)

    Sun, S. S.; Yang, J.; Li, W. H.; Du, H.; Alici, G.; Yan, T. H.; Nakano, Masami

    2017-01-01

    This paper reports an isolator whose damping and stiffness can be simultaneously controlled by magnetorheological (MR) fluids and MR elastomers. A hydraulically actuated MTS machine was used to test this variable stiffness and damping isolator after its prototype. The field-dependent responses including stiffness variability and damping variability, together with the amplitude-dependent response and frequency-dependent responses were separately tested and analyzed successively. The experimental results prove the successful implementation of the as-designed MRE-F isolator with obvious variable damping and stiffness. A new phenomenological model incorporating Bingham model and four-parameter model was developed to describe the dynamic properties of the isolator. The successful development, experimental testing, and modelling of this innovative variable stiffness and damping isolator make the concept of variable stiffness and damping become feasible.

  7. Hollow-cylinder waveguide isolators for use at millimeter wavelengths

    NASA Technical Reports Server (NTRS)

    Kanda, M.; May, W. G.

    1974-01-01

    The device considered in this study is a semiconductor waveguide isolator consisting of a hollow column of a semiconductor mounted coaxially in a circular waveguide in a longitudinal dc magnetic field. An elementary and physical analysis based on the excitation of plane waves in the guide and a more rigorous mode-matching analysis (MMA) are presented. These theoretical predictions are compared with experimental results for an InSb isolator at 94 GHz and 75 K.

  8. Field Trip.

    ERIC Educational Resources Information Center

    Sanders, Bill

    1993-01-01

    Reports the results of a field trip to measure the intensity of electromagnetic fields generated by electronic devices in the home, in cars, at work, outside, and in places people visit during the day. Found that a person gets more intense exposure while working at a computer than by living next to an electrical substation. (MDH)

  9. Methicillin-resistant staphylococci isolated from animals.

    PubMed

    van Duijkeren, E; Box, A T A; Heck, M E O C; Wannet, W J B; Fluit, A C

    2004-10-05

    Staphylococci isolated from animals (n=311) were screened for methicillin resistance by oxacillin agar screening. Oxacillin-resistant strains were tested for the presence of the mecA gene by PCR. Isolates were identified by standard techniques and 16S rDNA analysis, and their antimicrobial susceptibilities were tested using an agar diffusion method. MecA-positive strains were further analyzed using pulsed-field gel electrophoresis (PFGE). From 11 multidrug-resistant staphylococci, 6 were mecA-positive: 2 methicillin-resistant Staphylococcus aureus (MRSA) and 4 Staphylococcus haemolyticus. Screening of 300 staphylococci (100 S. aureus, 100 S. intermedius and 100 coagulase-negative staphylococci (CNS)) randomly chosen from the strain collection of the Veterinary Microbiological Diagnostic Center yielded five oxacillin-resistant coagulase-negative staphylococci, four of which were mecA-positive. PFGE showed that all mecA-positive staphylococci isolated from animals had distinct patterns. However, one MRSA isolated from a flank fistula of a dog showed homology to a human epidemic MRSA cluster, suggesting that transfer of MRSA between humans and dogs might occur.

  10. The NASA Langley Isolator Dynamics Research Lab

    NASA Technical Reports Server (NTRS)

    Middleton, Troy F.; Balla, Robert J.; Baurle, Robert A.; Humphreys, William M.; Wilson, Lloyd G.

    2010-01-01

    The Isolator Dynamics Research Lab (IDRL) is under construction at the NASA Langley Research Center in Hampton, Virginia. A unique test apparatus is being fabricated to support both wall and in-stream measurements for investigating the internal flow of a dual-mode scramjet isolator model. The test section is 24 inches long with a 1-inch by 2-inch cross sectional area and is supplied with unheated, dry air through a Mach 2.5 converging-diverging nozzle. The test section is being fabricated with two sets (glass and metallic) of interchangeable sidewalls to support flow visualization and laser-based measurement techniques as well as static pressure, wall temperature, and high frequency pressure measurements. During 2010, a CFD code validation experiment will be conducted in the lab in support of NASA s Fundamental Aerodynamics Program. This paper describes the mechanical design of the Isolator Dynamics Research Lab test apparatus and presents a summary of the measurement techniques planned for investigating the internal flow field of a scramjet isolator model.

  11. Geological problems in radioactive waste isolation

    SciTech Connect

    Witherspoon, P.A.

    1991-01-01

    The problem of isolating radioactive wastes from the biosphere presents specialists in the fields of earth sciences with some of the most complicated problems they have ever encountered. This is especially true for high level waste (HLW) which must be isolated in the underground and away from the biosphere for thousands of years. Essentially every country that is generating electricity in nuclear power plants is faced with the problem of isolating the radioactive wastes that are produced. The general consensus is that this can be accomplished by selecting an appropriate geologic setting and carefully designing the rock repository. Much new technology is being developed to solve the problems that have been raised and there is a continuing need to publish the results of new developments for the benefit of all concerned. The 28th International Geologic Congress that was held July 9--19, 1989 in Washington, DC provided an opportunity for earth scientists to gather for detailed discussions on these problems. Workshop W3B on the subject, Geological Problems in Radioactive Waste Isolation -- A World Wide Review'' was organized by Paul A Witherspoon and Ghislain de Marsily and convened July 15--16, 1989 Reports from 19 countries have been gathered for this publication. Individual papers have been cataloged separately.

  12. Isolation of Salmonella typhimurium from outbreak-associated cake mix.

    PubMed

    Zhang, Guodong; Ma, Li; Patel, Nehal; Swaminathan, Bala; Wedel, Stephanie; Doyle, Michael P

    2007-04-01

    During May and June of 2005, 26 persons in several states were infected by a single strain (isolates indistinguishable by pulsed-field gel electrophoresis) of Salmonella enterica serotype Typhimurium after eating cake batter ice cream. The cake mix used to prepare the cake batter in the ice cream was implicated by epidemiologic investigation as the source of Salmonella contamination. Initial tests did not detect Salmonella in cake mix collected during the outbreak investigation. The objective of this study was to evaluate different procedures to isolate Salmonella from the implicated cake mix, cake, and ice cream. All outbreak-associated food samples (14 samples) were collected during the outbreak investigation by health departments of several of the states involved. Different combinations of Salmonella isolation procedures, including sample size, preenrichment broth, enrichment broth, enrichment temperature, and isolation medium, were used. Salmonella Typhimurium was isolated from two cake mix samples; the food isolates were indistinguishable from the outbreak pattern by pulsed-field gel electrophoresis subtyping. Universal preenrichment broth was substantially better than was lactose broth for preenrichment, and tetrathionate broth was better than was Rappaport-Vassiliadis broth for isolating Salmonella from the two positive cake mix samples. Although more typical Salmonella colonies were observed on plates from enrichment cultures grown at 35 degrees C, more confirmed Salmonella isolates were obtained from plates of enrichment cultures grown at 42 degrees C. Brilliant green agar, xylose lysine tergitol 4 agar, xylose lysine desoxycholate agar, Hektoen enteric agar, and bismuth sulfite agar plates were equally effective in isolating Salmonella from cake mix. The best combination of preenrichment-enrichment conditions for isolating the outbreak strain of Salmonella was preenrichment of cake mix samples in universal preenrichment broth at 35 degrees C for 24 h

  13. Silicon ring isolators with bonded nonreciprocal magneto-optic garnets.

    PubMed

    Tien, Ming-Chun; Mizumoto, Tetsuya; Pintus, Paolo; Kromer, Herbert; Bowers, John E

    2011-06-06

    A ring isolator is demonstrated for the first time by directly bonding a cerium-substituted yttrium iron garnet (Ce:YIG) onto a silicon ring resonator using oxygen plasma enhanced bonding. The silicon waveguide is 600 nm wide and 295 nm thick with 500-nm-thick Ce:YIG on the top to have reasonable nonreciprocal effect and low optical loss. With a radial magnetic field applied to the ring isolator, it exhibits 9-dB isolation at resonance in the 1550 nm wavelength regime.

  14. Molecular Characterization of First Human Bartonella Strain Isolated in Italy

    PubMed Central

    Ciervo, Alessandra; Petrucca, Andrea; Ciarrocchi, Simonetta; Pinto, Antonella; Bonazzi, Lucio; Fabio, Anna; Farnetti, Enrico; Chomel, Bruno B.; Ciceroni, Lorenzo

    2001-01-01

    The aim of this study was to characterize a Bartonella strain (BA-1) isolated from a blood culture of an Italian, human immunodeficiency virus-positive patient with bacillary angiomatosis. We analyzed the isolate using molecular biology methods such as whole-cell fatty acid analysis, PCR-restriction fragment length polymorphism analysis, type-specific 16S rRNA PCRs, sequence analysis of the 16S rRNA, pulsed-field gel electrophoresis, and arbitrarily primed PCR. The BA-1 isolate turned out to be a Bartonella quintana strain, similar but not identical to B. quintana Oklahoma, which was used as a control strain. PMID:11724882

  15. [Isolated Ledderhose fibromatosis plantaris].

    PubMed

    Runkel, N; Göhring, U; Friedl, W; Roeren, T

    1993-07-01

    Plantar fibromatosis or Ledderhose syndrome has rarely been discussed in the medical literature. This clinical entity includes nodular Dupuytren-like indurations of the plantar aponeurosis. We present a case of a young man with isolated disease of his right foot and describe the clinical and pathomorphological features of this disease as well as its characteristic findings at magnetic resonance tomography. The therapy of choice is a subtotal resection of the plantar aponeurosis to prevent irreversible contractions of the toes. The prognosis following fascietomy is good.

  16. Highly isolated photodetectors

    SciTech Connect

    Bluzer, N.; Borsuk, G.M.; Kub, F.J.; Turley, A.P.

    1984-12-11

    An array of photodetectors is described incorporating a PNP vertical structure in a monosilicon substrate with individual photodetectors optically and electrically isolated from one another by open or oxide filled grooves. Both PN junctions of the PNP structure or originally reverse biased with one junction acting as the photodetector may operate in the forward biased photovoltaic mode with high radiant energy intensity. The minority carriers injected into the N region are absorbed by the other PN junction providing base-collector transistor action to prevent blooming.

  17. "Isolated" postinfectious myoclonus.

    PubMed Central

    Bhatia, K; Thompson, P D; Marsden, C D

    1992-01-01

    Two cases are reported who developed myoclonus as the only manifestation of a post-infectious syndrome without evidence of encephalitis or the opsoclonus-myoclonus syndrome. Case 1 had generalised myoclonus following an influenza-like illness, while case 2 had right upper limb segmental myoclonus following uncomplicated chicken pox. Neither had any localising neurological signs or abnormality on investigation. Both recovered completely within six months of the onset. Similar cases are reviewed from the literature and it is suggested that such cases be called "isolated" post-infectious myoclonus. PMID:1469409

  18. Comparative Proteome Analysis of Porcine Jejunum Tissues in Response to a Virulent Strain of Porcine Epidemic Diarrhea Virus and Its Attenuated Strain

    PubMed Central

    Li, Zhonghua; Chen, Fangzhou; Ye, Shiyi; Guo, Xiaozhen; Muhanmmad Memon, Atta; Wu, Meizhou; He, Qigai

    2016-01-01

    Porcine epidemic diarrhea virus (PEDV), a predominant cause of acute enteric infection, leads to severe dehydrating diarrhea and mortality in piglets all over the world. A virulent PEDV YN13 strain, isolated in our laboratory, was attenuated to yield an attenuated PEDV strain YN144. To better understand the pathogenesis mechanism and the virus-host interaction during infection with both PEDV YN13 and YN144 strains, a comparative proteomic analysis was carried out to investigate the proteomic changes produced in the primary target organ, using isobaric tags for relative and absolute quantitation (iTRAQ) labeling, followed by liquid chromatography tandem-mass spectrometry (LC-MS/MS). A total of 269 and 301 differently expressed proteins (DEPs) were identified in the jejunum tissues of the piglets inoculated with YN13 and YN144, respectively. Bioinformatics analysis revealed that these proteins were involved in stress responses, signal transduction, and the immune system. All of these involved interferon-stimulated genes (ISGs) which were up-regulated in jejunums by both of the PEDV-infected groups. Based on the comparative analysis, we proposed that different changes induced by YN13 and YN144 in heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), eukaryotic initiation factor 4G1 (eIF4G1), and some members in the heat shock protein (HSP) family, may be responsible for differences in their pathogenicity. PMID:27916855

  19. Investigation of mercury thruster isolators

    NASA Technical Reports Server (NTRS)

    Mantenieks, M. A.

    1973-01-01

    Mercury ion thruster isolator lifetime tests were performed using different isolator materials and geometries. Tests were performed with and without the flow of mercury through the isolators in an oil diffusion pumped vacuum facility and cryogenically pumped bell jar. The onset of leakage current in isolators occurred in time intervals ranging from a few hours to many hundreds of hours. In all cases, surface contamination was responsible for the onset of leakage current and subsequent isolator failure. Rate of increase of leakage current and the leakage current level increased approximately exponentially with isolator temperature. Careful attention to shielding techniques and the elimination of sources of metal oxides appear to have eliminated isolator failures as a thruster life limiting mechanism.

  20. Braking index of isolated pulsars

    NASA Astrophysics Data System (ADS)

    Hamil, O.; Stone, J. R.; Urbanec, M.; Urbancová, G.

    2015-03-01

    moment of inertia and other macroscopic properties of rotating neutron stars. The calculations are performed for fixed values of MB (as masses of isolated pulsars are not known) ranging from 1.0 - 2.2 M⊙ , and fixed magnetic dipole moment and inclination angle between the rotational and magnetic field axes. The results are used to solve for the value of the braking index as a function of frequency, and find the effect of the choice of the EoS, MB. The density profile of a star with a given MB is calculated to determine the transition between the crust and the core and used in estimation of the effect of core superfluidity on the braking index. Our results show conclusively that, within the model used in this work, any significant deviation of the braking index away from the value n =3 occurs at frequencies higher than about ten times the frequency of the slow rotating isolated pulsars most accurately measured to date. The rate of change of n with frequency is related to the softness of the EoS and the MB of the star as this controls the degree of departure from sphericity. Change in the moment of inertia in the MDR model alone, even with the more realistic features considered here, cannot explain the observational data on the braking index and other mechanisms have to be sought.

  1. Mechanical strain isolator mount

    NASA Technical Reports Server (NTRS)

    James, Gordon E. (Inventor)

    1991-01-01

    Certain devices such as optical instruments must preserve their alignmental integrity while being subjected to mechanical strain. A mechanical strain isolator mount is provided to preserve the alignmental integrity of an alignment sensitive instrument. An alignment sensitive instrument is mounted on a rectangular base. Flexural legs are connected at their proximal ends to the rectangular base. Flexural legs are also spaced parallel to the sides. Mounting pads are connected to the legs at the distal end and the mechanical strain isolator mount is attached to the substrate by means of threaded bolts. When a mounting pad and its respective leg is subjected to lateral strain in either the X or Y direction via the substrate, the respective leg relieves the strain by bending in the direction of the strain. An axial strain on a mounting pad in the Z direction is relieved by a rotational motion of the legs in the direction of the strain. When the substrate is stress free, the flexural legs return to their original condition and thus preserve the original alignment integrity of the alignment sensitive instrument.

  2. Recombinant Baculovirus Isolation.

    PubMed

    King, Linda A; Hitchman, Richard; Possee, Robert D

    2016-01-01

    Although there are several different methods available of making recombinant baculovirus expression vectors (reviewed in Chapter 3 ), all require a stage in which insect cells are transfected with either the virus genome alone (Bac-to-Bac(®) or BaculoDirect™, Invitrogen) or virus genome and transfer vector. In the latter case, this allows the natural process of homologous recombination to transfer the foreign gene, under control of the polyhedrin or other baculovirus gene promoter, from the transfer vector to the virus genome to create the recombinant virus. Previously, many methods required a plaque-assay to separate parental and recombinant virus prior to amplification and use of the recombinant virus. Fortunately, this step is no longer required for most systems currently available. This chapter provides an overview of the historical development of increasingly more efficient systems for the isolation of recombinant baculoviruses (Chapter 3 provides a full account of the different systems and transfer vectors available). The practical details cover: transfection of insect cells with either virus DNA or virus DNA and plasmid transfer vector; a reliable plaque-assay method that can be used to separate recombinant virus from parental (nonrecombinant) virus where this is necessary; methods for the small-scale amplification of recombinant virus; and subsequent titration by plaque-assay or real-time polymerase chain reaction (PCR). Methods unique to the Bac-to-Bac(®) system are also covered and include the transformation of bacterial cells and isolation of bacmid DNA ready for transfection of insect cells.

  3. Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea

    PubMed Central

    Lee, Dong Hwan; Kim, Jin-Beom; Lim, Jeong-A; Han, Sang-Wook; Heu, Sunggi

    2014-01-01

    The plant pathogenic bacterial genus Pectobacteirum consists of heterogeneous strains. The P. carotovorum species is a complex strain showing divergent characteristics, and a new subspecies named P. carotovorum subsp. brasiliensis has been identified recently. In this paper, we re-identified the P. carotovorum subsp. brasiliensis isolates from those classified under the subspecies carotovorum and newly isolated P. carotovorum subsp. brasiliensis strains. All isolates were able to produce plant cell-wall degrading enzymes such as pectate lyase, polygalacturonase, cellulase and protease. We used genetic and biochemical methods to examine the diversity of P. carotovorum subsp. brasiliensis isolates, and found genetic diversity within the brasiliensis subsp. isolates in Korea. The restriction fragment length polymorphism analysis based on the recA gene revealed a unique pattern for the brasiliensis subspecies. The Korean brasiliensis subsp. isolates were divided into four clades based on pulsed-field gel electrophoresis. However, correlations between clades and isolated hosts or year could not be found, suggesting that diverse brasiliensis subsp. isolates existed. PMID:25288994

  4. Gravitational anomaly and Hawking radiation near a weakly isolated horizon

    SciTech Connect

    Wu Xiaoning; Huang Chaoguang; Sun Jiarui

    2008-06-15

    Based on the idea of the work by Wilczek and his collaborators, we consider the gravitational anomaly near a weakly isolated horizon. We find that there exists a universal choice of tortoise coordinate for any weakly isolated horizon. Under this coordinate, the leading behavior of a quite arbitrary scalar field near a horizon is a 2-dimensional chiral scalar field. This means we can extend the idea of Wilczek and his collaborators to more general cases and show the relation between gravitational anomaly and Hawking radiation is a universal property of a black hole horizon.

  5. Isolation of attosecond pulses from the attosecond lighthouse

    NASA Astrophysics Data System (ADS)

    Hammond, TJ; Balogh, Emeric; Taec Kim, Kyung

    2017-01-01

    This paper proposes and verifies methods to improve the isolation of the attosecond pulses generated via the attosecond lighthouse technique in gases. We find that the converging fundamental field can compensate for the inherent diverging wavefront of the attosecond pulses, but is only valid over a limited portion of the spectrum and sacrifices the maximum attainable photon energy. We discuss two methods of manipulating the fundamental field to control the divergence of the attosecond pulses: the first method uses a perturbing beam that manipulates the wavefront, and the second method controls the fundamental dispersion. These methods improve the isolation of the attosecond pulses up to the cutoff photon energy.

  6. Gravitational anomaly and Hawking radiation near a weakly isolated horizon

    NASA Astrophysics Data System (ADS)

    Wu, Xiaoning; Huang, Chao-Guang; Sun, Jia-Rui

    2008-06-01

    Based on the idea of the work by Wilczek and his collaborators, we consider the gravitational anomaly near a weakly isolated horizon. We find that there exists a universal choice of tortoise coordinate for any weakly isolated horizon. Under this coordinate, the leading behavior of a quite arbitrary scalar field near a horizon is a 2-dimensional chiral scalar field. This means we can extend the idea of Wilczek and his collaborators to more general cases and show the relation between gravitational anomaly and Hawking radiation is a universal property of a black hole horizon.

  7. Characterisation of successive Acinetobacter baumannii isolates from a deceased haemophagocytic lymphohistiocytosis patient.

    PubMed

    Choi, Hyeon Jin; Kil, Min Cheol; Choi, Ji-Young; Kim, Sun Ju; Park, Ki-Sup; Kim, Yae-Jean; Ko, Kwan Soo

    2017-01-01

    In this study, 38 Acinetobacter baumannii isolates successively isolated from blood, skin swabs and tracheal aspirates from a single patient who died from haemophagocytic lymphohistiocytosis were investigated. The isolates were collected between March 2012 and August 2012. A. baumannii genotypes were determined by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). In vitro antimicrobial susceptibility testing was performed and colistin heteroresistance and persistence were evaluated. The structure of AbaR resistance islands was explored, and serum sensitivity was determined. Based on MLST analysis, all 38 A. baumannii isolates showed the same sequence type (ST138). However, PFGE analysis showed that isolates from blood samples belonged to different genotypes depending on the isolation time: whilst blood isolates obtained at the early stages showed restriction patterns similar to those of isolates from other sources, isolates obtained at later stages exhibited a distinct pattern. All isolates were resistant to imipenem, cefepime, ciprofloxacin and piperacillin/tazobactam. Five isolates from tracheal aspirates and one from a skin swab were resistant to polymyxins, and two isolates from skin swabs and one from another source were non-susceptible to tigecycline. All colistin-susceptible isolates showed heteroresistance to colistin, and four were persisters. Isolates from blood showed higher survival rates against human serum than those from other sources. This study shows that the patient was infected with more than one A. baumannii strain. Heteroresistance, persistence or evasion of the innate immune response may explain the failure of antimicrobial treatments in this patient.

  8. Stellar Clusterings around "Isolated" Massive YSOs in the LMC

    NASA Astrophysics Data System (ADS)

    Stephens, Ian W.; Gouliermis, Dimitrios; Looney, Leslie W.; Gruendl, Robert A.; Chu, You-Hua; Weisz, Daniel R.; Seale, Jonathan P.; Chen, C.-H. Rosie; Wong, Tony; Hughes, Annie; Pineda, Jorge L.; Ott, Jürgen; Muller, Erik

    2017-01-01

    Observations suggest that there is a significant fraction of O stars in the field of the Milky Way that appear to have formed in isolation or in low-mass clusters (<100 {M}ȯ ). The existence of these high-mass stars that apparently formed in the field challenges the generally accepted paradigm, which requires star formation to occur in clustered environments. In order to understand the physical conditions for the formation of these stars, it is necessary to observe isolated high-mass stars while they are still forming. With the Hubble Space Telescope, we observe the seven most isolated massive (>8 {M}ȯ ) young stellar objects (MYSOs) in the Large Magellanic Cloud. The observations show that while these MYSOs are remote from other MYSOs, OB associations, and even known giant molecular clouds, they are actually not isolated at all. Imaging reveals ∼100 to several hundred pre-main-sequence (PMS) stars in the vicinity of each MYSO. These previously undetected PMS stars form prominent compact clusters around the MYSOs, and in most cases they are also distributed sparsely across the observed regions. Contrary to what previous high-mass field star studies show, these observations suggest that high-mass stars may not be able to form in clusters with masses less than 100 {M}ȯ . If these MYSOs are indeed the best candidates for isolated high-mass star formation, then the lack of isolation is at odds with random sampling of the initial mass function. Moreover, while isolated MYSOs may not exist, we find evidence that isolated clusters containing O stars can exist, which in itself is rare.

  9. Flow Field Around a Hovering Rotor

    NASA Technical Reports Server (NTRS)

    Tung, C.; Low, S.

    1997-01-01

    A lifting surface hover code developed by the Analytical Method Inc. (AMI) was used to compute the average and unsteady velocity flow field of an isolated rotor without ground effect. The predicted velocity field compares well with experimental data obtained by hot-wire anemometry and by Laser Doppler Velocimetry. A subroutine 'DOWNWASH' was written to predict the velocity field at any given point in the wake for a given blade position.

  10. Isolated resonator gyroscope with isolation trimming using a secondary element

    NASA Technical Reports Server (NTRS)

    Challoner, A. Dorian (Inventor); Shcheglov, Kirill V. (Inventor)

    2006-01-01

    The present invention discloses a resonator gyroscope including an isolated resonator. One or more flexures support the isolated resonator and a baseplate is affixed to the resonator by the flexures. Drive and sense elements are affixed to the baseplate and used to excite the resonator and sense movement of the gyroscope. In addition, at least one secondary element (e.g., another electrode) is affixed to the baseplate and used for trimming isolation of the resonator. The resonator operates such that it transfers substantially no net momentum to the baseplate when the resonator is excited. Typically, the isolated resonator comprises a proof mass and a counterbalancing plate.

  11. Optical scattering from isolated metal nanoparticles and arrays.

    SciTech Connect

    Wurtz, G. A.; Im, J. S.; Gray, S. K.; Wiederrecht, G. P.; Chemistry

    2003-12-25

    Near-field scanning optical microscopy (NSOM) is used to explore the optical scattering from isolated metal nanoparticles (MNPs) and arrays of MNPs. The optical excitation source is an evanescent wave created through total internal reflection of a continuous wave laser beam at the sample-air interface. For optical excitation of isolated Ag and Au MNPs, experimental results show that the scattered light propagates into the far field at an angle of 19{sup o} from the substrate. Finite-difference time-domain (FDTD) calculations are used to study simpler but related metallic nanowire systems under evanescent wave excitation. The FDTD results are found to be similar to the experimental results, indicating the generality of the scattering phenomenon. NSOM characterization of plasmonic arrays that consist of closely spaced Ag MNPs are subsequently reported. Confined optical signals within the array are observed along with a reduction in the far-field scattered signal. Simultaneous collection of the atomic force microscopy signal and near-field signals also shows that the spatial distribution of the near-field is strongly modified in the arrays compared to isolated MNPs. FDTD studies on arrays of nanowires also show large differences from the isolated metal nanoparticle calculations, including a decrease in the forward scattered angle (with chain length) and diminished overall forward scattering.

  12. Material isolation enclosure

    DOEpatents

    Martell, C.J.; Dahlby, J.W.; Gallimore, B.F.; Comer, B.E.; Stone, W.A.; Carlson, D.O.

    1993-04-27

    An enclosure is described, similar to a glove box, for isolating materials from the atmosphere, yet allowing a technician to manipulate the materials and also apparatus which is located inside the enclosure. A portion of a wall of the enclosure is comprised of at least one flexible curtain. An opening defined by a frame is provided for the technician to insert his hands and forearms into the enclosure. The frame is movable in one plane, so that the technician has access to substantially all of the working interior of the enclosure. As the frame is moved by the technician, while he accomplishes work inside the enclosure, the curtain moves such that the only opening through the enclosure wall is the frame. In a preferred embodiment, where a negative pressure is maintained inside the enclosure, the frame is comprised of airfoils so that turbulence is reduced, thereby enhancing material retention within the box.

  13. Material isolation enclosure

    DOEpatents

    Martell, Calvin J.; Dahlby, Joel W.; Gallimore, Bradford F.; Comer, Bob E.; Stone, Water A.; Carlson, David O.

    1993-01-01

    An enclosure similar to a glovebox for isolating materials from the atmosphere, yet allowing a technician to manipulate the materials and also apparatus which is located inside the enclosure. A portion of a wall of the enclosure is comprised of at least one flexible curtain. An opening defined by a frame is provided for the technician to insert his hands and forearms into the enclosure. The frame is movable in one plane, so that the technician has access to substantially all of the working interior of the enclosure. As the frame is moved by the technician, while he accomplishes work inside the enclosure, the curtain moves such that the only opening through the enclosure wall is the frame. In a preferred embodiment, where a negative pressure is maintained inside the enclosure, the frame is comprised of airfoils so that turbulence is reduced, thereby enhancing material retention within the box.

  14. Isolation of chromaffin granules.

    PubMed

    Creutz, Carl E

    2010-09-01

    Adrenal medullary chromaffin granules (dense core secr