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Sample records for pedv field isolates

  1. Evaluation of humoral immune status in porcine epidemic diarrhea virus (PEDV) infected sows under field conditions.

    PubMed

    Ouyang, Kang; Shyu, Duan-Liang; Dhakal, Santosh; Hiremath, Jagadish; Binjawadagi, Basavaraj; Lakshmanappa, Yashavanth S; Guo, Rui; Ransburgh, Russell; Bondra, Kathryn M; Gauger, Phillip; Zhang, Jianqiang; Specht, Terry; Gilbertie, Aaron; Minton, William; Fang, Ying; Renukaradhya, Gourapura J

    2015-01-01

    Porcine epidemic diarrhea virus (PEDV) is an economically devastating enteric disease in the swine industry. The virus infects pigs of all ages, but it cause severe clinical disease in neonatal suckling pigs with up to 100% mortality. Currently, available vaccines are not completely effective and feedback methods utilizing PEDV infected material has variable success in preventing reinfection. Comprehensive information on the levels and duration of effector/memory IgA and IgG antibody secreting B cell response in the intestines and lymphoid organs of PEDV-infected sows, and their association with specific antibody levels in clinical samples such as plasma, oral fluid, and feces is important. Therefore, our goal in this study was to quantify PEDV specific IgA and IgG B cell responses in sows at approximately 1 and 6 months post-infection in commercial swine herds, including parity one and higher sows. Our data indicated that evaluation of both PEDV specific IgA and IgG antibody levels in the plasma and oral fluid (but not feces) samples is beneficial in disease diagnosis. PEDV specific B cell response in the intestine and spleen of infected sows decline by 6 months, and this associates with specific antibody levels in the plasma and oral fluid samples; but the virus neutralization titers in plasma remains high beyond 6 months post-infection. In conclusion, in sows infected with PEDV the presence of effector/memory B cell response and strong virus neutralization titers in plasma up to 6 months post-infection, suggests their potential to protect sows from reinfection and provide maternal immunity to neonates, but challenge studies are required to confirm such responses. PMID:26667229

  2. Wild boars harboring porcine epidemic diarrhea virus (PEDV) may play an important role as a PEDV reservoir.

    PubMed

    Lee, Dong Uk; Kwon, Taeyong; Je, Sang H; Yoo, Sung J; Seo, Sang Won; Sunwoo, Sun Young; Lyoo, Young S

    2016-08-30

    Porcine epidemic diarrhea virus (PEDV) is a burdensome pathogen in the swine industry. Wild boar population poses a high risk for reservoir of viral pathogen. Two hundred eighty seven samples from wild boar (Sus scrofa) collected in South Korea during 2010/11 were analyzed using RT-PCR, revealing a PEDV infection rate of 9.75% (28/287). PEDV positive samples were distributed throughout the mainland of South Korea, clustering at the northern border adjacent to the Demilitarized Zone (DMZ) and in mountainous regions. PEDV in wild boar was genetically similar to Chinese PEDV strains in phylogenetic investigations. Our results indicated that PEDV is circulating in the wild boar and provided a novel knowledge into epidemiology of PEDV infection. PMID:27527769

  3. 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...

  4. 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 ...

  5. Isolation and molecular characterization of porcine epidemic diarrhea viruses collected in Japan in 2014.

    PubMed

    Horie, Masayuki; Kabemura, Mitsue; Masatani, Tatsunori; Matsuu, Aya; Ozawa, Makoto

    2016-08-01

    Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED), which is threatening the swine industry all over the world. In Japan, although there were no reported PED cases from 2007 to 2012, a large-scale PED outbreak started in 2013, causing severe economic losses. Although several PEDV studies have been conducted in Japan, more PEDV isolates and sequence information are needed to understand the molecular biology and epidemiology of PEDV. Here, we isolated seven Japanese PEDV strains from intestinal tissue samples collected in 2014 and determined the spike gene sequences of 13 Japanese PEDV strains, including the above seven isolates. Phylogenetic analysis shows that all of the strains are genetically distinct from classical Japanese PEDV strains isolated prior to 2013 and can be classified into two different genotypes: 12 strains belong to the North American clade composed of recent highly pathogenic PEDV strains, and the remaining one strain belongs to the so-called insertion deletion (INDEL) clade. These data suggest multiple PEDV invasions from abroad to Japan. Notably, compared to classical Japanese strains, all of the recent Japanese strains have two amino acid substitutions in a known neutralizing epitope. In addition, one of the strains acquired an additional mutation in another neutralizing epitope that is highly conserved among PEDVs, including the classical and recent isolates. Our isolates and findings will be useful for future investigations aimed at understanding, controlling, and preventing PED. PMID:27224981

  6. 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 ...

  7. Transverse Magnetic Field Propellant Isolator

    NASA Technical Reports Server (NTRS)

    Foster, John E.

    2000-01-01

    An alternative high voltage isolator for electric propulsion and ground-based ion source applications has been designed and tested. This design employs a transverse magnetic field that increases the breakdown voltage. The design can greatly enhance the operating range of laboratory isolators used for high voltage applications.

  8. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China

    PubMed Central

    Lan, Xi

    2016-01-01

    Porcine kobuvirus (PKV) has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV), and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1%) samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8%) were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea. PMID:27294133

  9. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China.

    PubMed

    Wang, Chen; Lan, Xi; Yang, Bin

    2016-01-01

    Porcine kobuvirus (PKV) has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV), and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1%) samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8%) were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea. PMID:27294133

  10. Distinct Characteristics and Complex Evolution of PEDV Strains, North America, May 2013–February 2014

    PubMed Central

    Vlasova, Anastasia N.; Wang, Qiuhong; Culhane, Marie R.; Rossow, Kurt D.; Rovira, Albert; Collins, James; Saif, Linda J.

    2014-01-01

    Porcine epidemic diarrhea virus (PEDV), which emerged in the United States in 2013, has spread throughout North America. Limited availability of PEDV complete genomes worldwide has impeded our understanding of PEDV introduction into the United States. To determine the relationship between the North American strains and global emerging and historic PEDV strains, we sequenced and analyzed complete genomes of 74 strains from North America; the strains clustered into 2 distinct clades. Compared with the initially reported virulent US PEDV strains, 7 (9.7%) strains from 4 states contained insertions and deletions in the spike gene (S INDELs). These S INDEL strains share 99.8%–100% nt identity with each other and 96.2%–96.7% nt identity with the initial US strains. Furthermore, the S INDEL strains form a distinct cluster within North American clade II, sharing 98.6%–100% nt identity overall. In the United States, the S INDEL and original PEDV strains are co-circulating and could have been introduced simultaneously. PMID:25279722

  11. Porcine epidemic diarrhea virus (PEDV) co-infection induced chlamydial persistence/stress does not require viral replication

    PubMed Central

    Schoborg, Robert V.; Borel, Nicole

    2014-01-01

    Chlamydiae may exist at the site of infection in an alternative replicative form, called the aberrant body (AB). ABs are produced during a viable but non-infectious developmental state termed “persistence” or “chlamydial stress.” As persistent/stressed chlamydiae: (i) may contribute to chronic inflammation observed in diseases like trachoma; and (ii) are more resistant to current anti-chlamydial drugs of choice, it is critical to better understand this developmental stage. We previously demonstrated that porcine epidemic diarrhea virus (PEDV) co-infection induced Chlamydia pecorum persistence/stress in culture. One critical characteristic of persistence/stress is that the chlamydiae remain viable and can reenter the normal developmental cycle when the stressor is removed. Thus, we hypothesized that PEDV-induced persistence would be reversible if viral replication was inhibited. Therefore, we performed time course experiments in which Vero cells were C. pecorum/PEDV infected in the presence of cycloheximide (CHX), which inhibits viral but not chlamydial protein synthesis. CHX-exposure inhibited PEDV replication, but did not inhibit induction of C. pecorum persistence at 24 h post-PEDV infection, as indicated by AB formation and reduced production of infectious EBs. Interestingly, production of infectious EBs resumed when CHX-exposed, co-infected cells were incubated 48–72 h post-PEDV co-infection. These data demonstrate that PEDV co-infection-induced chlamydial persistence/stress is reversible and suggest that this induction (i) does not require viral replication in host cells; and (ii) does not require de novo host or viral protein synthesis. These data also suggest that viral binding and/or entry may be required for this effect. Because the PEDV host cell receptor (CD13 or aminopeptidase N) stimulates cellular signaling pathways in the absence of PEDV infection, we suspect that PEDV co-infection might alter CD13 function and induce the chlamydiae to

  12. 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...

  13. Manure-borne PEDv (porcine epidemic diarrhea virus) survival in soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The porcine epidemic diarrhea virus (PEDv) outbreak in the US has had a significant impact on swine production in recent years. Although strictly limited to pigs and hence poses no threat to other animals or humans, it is easily transmitted to suckling piglets where it causes nearly 100% mortality....

  14. 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

  15. 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...

  16. 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.

  17. 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.

  18. 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

    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

  19. 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

  20. Velocity field of isolated turbulent puffs

    NASA Astrophysics Data System (ADS)

    Ghaem-Maghami, E.; Johari, H.

    2010-11-01

    The velocity field of isolated turbulent puffs was measured using the particle image velocimetry technique and was compared with the steady jet flow field. Puffs were generated by injecting air through a 5 mm diameter nozzle into a flow chamber with a weak coflow. Isolated puffs with a Reynolds number of 5000 were examined in the range of 40-75 diameters downstream of the nozzle. The injection time was varied in order to assess the effects of injection volume and equivalent stroke ratio on the puff structure. The results from phase-locked measurements indicate that as the injection volume increased, puffs elongated in the axial direction and became similar to starting jets in the range considered. The largest scaled fluctuating velocities and turbulent shear stress within the puffs were twice the steady jet values. Inspection of the vorticity field revealed the presence of vorticity throughout the puff volume. Entrainment takes place on the portion of the puff closest to the nozzle and the entrainment rate is greater for the puffs with the smaller injection volume. This is consistent with the observations of rapid mixing and combustion of puffs in previous studies.

  1. Velocity Field of Isolated Turbulent Puffs

    NASA Astrophysics Data System (ADS)

    Ghaem-Maghami, Elham; Johari, Hamid

    2006-11-01

    The velocity field of isolated turbulent puffs was investigated by the PIV technique. Particular attention was paid to the entrainment pattern of isolated puffs. Puffs were generated by injecting seeded air through a 5 mm diameter nozzle into a flow chamber with a weak co-flow. Puffs with a Reynolds number of 5,000 were examined in the range of 35 -- 75 diameters downstream of the nozzle. The injection time was varied in order to assess the effect of injection volume and impulse on the puff structure. The results indicate that as the injection volume increased, puffs elongated in the axial direction. The largest mean and fluctuating velocities were within the central portion of the puff. The maximum turbulent shear stress within the puff was as much as 2.5 times the steady jet value. The vorticity field showed the presence of vorticity throughout the puff volume. The ratio of volume flow rate at the puff center to the steady jet volume flux at the same location was largest for the smallest injection volume. The majority of entrainment into the puff occurs below the puff center while the puff cap pushes out into surrounding fluid.

  2. 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.

  3. Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus.

    PubMed

    Zhu, Yu; Wang, Gui-Hua; Cui, Yu-Dong; Cui, Shang-Jin

    2016-09-01

    Porcine epidemic diarrhea virus (PEDV) can cause serious disease and even death in neonatal piglets, resulting in serious damage to the swine industry worldwide. Open reading frame 3 (ORF3) is the only accessory gene in the PEDV genome. Previous studies have indicated that PEDV vaccine strains have a partial deletion in ORF3. In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The PCR products of field strains and attenuated strains were 264 bp and 215 bp in length, respectively. The sensitivity and specificity of this assay were also assessed. The nanoparticle-assisted RT-PCR assay was 10-100 times more sensitive than the conventional RT-PCR assay, with no cross-reactions when amplifying porcine pseudorabies virus (PRV), porcine circovirus type 2 (PCV2), classical swine fever virus (CSFV), porcine parvovirus (PPV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine rotavirus (RV), and porcine transmissible gastroenteritis virus (TGEV). The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection. PMID:27287433

  4. Phylogenetic and antigenic characterization of newly isolated porcine epidemic diarrhea viruses in Japan.

    PubMed

    Islam, Md Taimur; Kubota, Tomoe; Ujike, Makoto; Yahara, Yoshiriro; Taguchi, Fumihiro

    2016-08-15

    To evaluate the mechanism by which a large outbreak of porcine epidemic diarrhea (PED) occurred in Japan, where the majority of sows are vaccinated, we isolated two new strains of PED virus (PEDV) from the intestines of piglets and found that they showed greater similarity to US isolates (group II PEDV) than to the Japanese vaccine strain (group I PEDV). We compared the antigenicity of the vaccine type strain and newly isolated strains by means of a neutralization test using sera from a number of pigs from various farms; the results revealed that they are antigenically similar. This is the first report of the similarity of group I and II viruses using sera from individual pigs vaccinated with group I virus. These data suggest that the large outbreak of PED in Japan cannot be attributed to inefficient vaccination but may be due to the extremely high virulence of the newly appearing viruses. PMID:27292080

  5. 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. PMID:26602207

  6. Methanococcus thermolithotrophicus Isolated from North Sea Oil Field Reservoir Water

    PubMed Central

    Nilsen, R. K.; Torsvik, T.

    1996-01-01

    Methanococcus thermolithotrophicus ST22 was isolated from produced water of a North Sea oil field, on mineral medium with H(inf2)-CO(inf2) as the sole source of carbon and energy. The isolate grew at 17 to 62(deg)C, with an optimum at 60(deg)C. The pH range was 4.9 to 9.8, with optimal growth at pH 5.1 to 5.9; these characteristics reflected its habitat. Strain ST22 was quickly identified and distinguished from the type strain by immunoblotting. PMID:16535247

  7. 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). PMID:19084246

  8. Formation, evolution and properties of isolated field elliptical galaxies

    NASA Astrophysics Data System (ADS)

    Niemi, Sami-Matias; Heinämäki, Pekka; Nurmi, Pasi; Saar, Enn

    2010-06-01

    We study the properties, evolution and formation mechanisms of isolated field elliptical (IfE) galaxies. We create a `mock' catalogue of IfE galaxies from the Millennium Simulation Galaxy Catalogue, and trace their merging histories. The formation, identity and assembly redshifts of simulated isolated and non-isolated elliptical galaxies are studied and compared. Observational and numerical data are used to compare age, mass and the colour-magnitude relation. Our results, based on simulation data, show that almost 7 per cent of all elliptical galaxies brighter than -19mag in B band can be classified as IfE galaxies. Results also show that isolated elliptical galaxies have a rather flat luminosity function; a number density of ~3 × 10-6h3Mpc-3mag-1, throughout their B-band magnitudes. IfE galaxies show bluer colours than non-isolated elliptical galaxies and they appear younger, in a statistical sense, according to their mass-weighted age. IfE galaxies also form and assemble at lower redshifts compared to non-isolated elliptical galaxies. About 46 per cent of IfE galaxies have undergone at least one major merging event in their formation history, while the same fraction is only ~33 per cent for non-isolated ellipticals. Almost all (~98 per cent) isolated elliptical galaxies show merging activity during their evolution, pointing towards the importance of mergers in the formation of IfE galaxies. The mean time of the last major merging is at z ~ 0.6 or 6Gyr ago for isolated ellipticals, while non-isolated ellipticals experience their last major merging significantly earlier at z ~ 1.1 or 8Gyr ago. After inspecting merger trees of simulated IfE galaxies, we conclude that three different, yet typical, formation mechanisms can be identified: solitude, coupling and cannibalism. Our results also predict a previously unobserved population of blue, dim and light galaxies that fulfil observational criteria to be classified as IfE galaxies. This separate population comprises

  9. Expression and Purification of the scFv from Hybridoma Cells Secreting a Monoclonal Antibody Against S Protein of PEDV

    PubMed Central

    Zhu, Qinghe; Guo, Donghua; Feng, Li

    2013-01-01

    The variable regions of the heavy chain (VH) and light chain (VL) were amplified by RT-PCR from the hybridoma 6E6, which secretes the monoclonal antibody against PEDV S protein. The VL and VH amplicons were combined using SOE-PCR by a 12 amino acid flexible linker (SSGGGGSGGGGS), which produced the scFv gene (named scFv/6E6). After sequence analysis, the scFv/6E6 gene was cloned into the prokaryotic expression vector pGEX-6p-1 with a GST-tag. The recombinant scFv/6E6 protein was successfully expressed in recombinant Escherichia coli by IPTG induction. Moreover, the recombinant scFv/6E6 protein was purified from the inclusion body form by the gel-cutting measure followed by electroelution and dialysis. The recombinant scFv/6E6 protein reported here will provide some basis for further antiviral drug research based on the scFv molecule. PMID:23600505

  10. 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

    2014-11-01

    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. PMID:25278366

  11. Comprehensive antibiotic susceptibility profiling of Chilean Piscirickettsia salmonis field isolates.

    PubMed

    Henríquez, P; Kaiser, M; Bohle, H; Bustos, P; Mancilla, M

    2016-04-01

    Antibiotics have been extensively used against infections produced by Piscirickettsia salmonis, a fish pathogen and causative agent of piscirickettsiosis and one of the major concerns for the Chilean salmon industry. Therefore, the emergence of resistant phenotypes is to be expected. With the aim of obtaining a landscape of the antimicrobial resistance of P. salmonis in Chile, the susceptibility profiles for quinolones, florfenicol and oxytetracycline (OTC) of 292 field isolates derived from main rearing areas, different hosts and collected over 5 years were assessed. The results allowed for the determination of epidemiological cut-off values that were used to characterize the pathogen population. This work represents the first large-scale field study addressing the antimicrobial susceptibility of P. salmonis, providing evidence of the existence of resistant types with a high incidence of resistance to quinolones. Remarkably, despite the amounts and frequency of therapies, our results disclosed that the issue of resistance to florfenicol and OTC is still in the onset. PMID:26660665

  12. Isolation and characterization of a Korean porcine epidemic diarrhea virus strain KNU-141112.

    PubMed

    Lee, Sunhee; Kim, Youngnam; Lee, Changhee

    2015-10-01

    Severe outbreaks of porcine epidemic diarrhea virus (PEDV) have re-emerged in Korea and rapidly swept across the country, causing tremendous economic losses to producers and customers. Despite the availability of PEDV vaccines in the domestic market, the disease continues to plague the Korean pork industry, raising issues regarding their protective efficacy and new vaccine development. Therefore, PEDV isolation in cell culture is urgently needed to develop efficacious vaccines and diagnostic assays and to conduct further studies on the virus biology. In the present study, one Korean PEDV strain, KOR/KNU-141112/2014, was successfully isolated and serially propagated in Vero cells for over 30 passages. The in vitro and in vivo characteristics of the Korean PEDV isolate were investigated. Virus production in cell culture was confirmed by cytopathology, immunofluorescence, and real-time RT-PCR. The infectious virus titers of the viruses during the first 30 passages ranged from 10(5.1) to 10(8.2) TCID50 per ml. The inactivated KNU-141112 virus was found to mediate potent neutralizing antibody responses in immunized guinea pigs. Animal studies showed that KNU-141112 virus causes severe diarrhea and vomiting, fecal shedding, and acute atrophic enteritis, indicating that strain KNU-141112 is highly enteropathogenic in the natural host. In addition, the entire genomes or complete S genes of KNU-141112 viruses at selected cell culture passages were sequenced to assess the genetic stability and relatedness. Our genomic analyses indicated that the Korean isolate KNU-141112 is genetically stable during the first 30 passages in cell culture and is grouped within subgroup G2b together with the recent re-emergent Korean strains. PMID:26196056

  13. 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

  14. Incipient fault detection and isolation of sensors and field devices

    NASA Astrophysics Data System (ADS)

    Ferreira, Paulo Brasko

    The purpose of this research is to develop a robust fault detection and isolation method, for detecting faults in process sensors, actuators, controllers and other field devices. The approach to the solution to this problem is summarized below. A novel approach for the validation of control system components and sensors was developed in this research. The process is composed of detecting a system anomaly, isolating the faulty component (such as sensors, actuators, and controllers), computing its deviation from expected value for a given system's normal condition, and finally reconstructing its output when applicable. A variant of the Group Method of Data Handling (GMDH) was developed in this research for generating analytical redundancy from relationships among different system components. A rational function approximation was used for the data-driven modeling scheme. This analytical redundancy is necessary for detecting system anomalies and isolating faulty components. A rule-base expert system was developed in order to isolate the faulty component. The rule-based was established from model-simulated data. A fuzzy-logic estimator was implemented to compute the magnitude of the loop component fault so that the operator or the controller might take corrective actions. This latter engine allows the system to be operated in a normal condition until the next scheduled shutdown, even if a critical component were detected as degrading. The effectiveness of the method developed in this research was demonstrated through simulation and by implementation to an experimental control loop. The test loop consisted of a level control system, flow, pressure, level and temperature measuring sensors, motor-operated valves, and a pump. Commonly observed device faults were imposed in different system components such as pressure transmitters, pumps, and motor-operated valves. This research has resulted in a framework for system component failure detection and isolation, allowing easy

  15. Genomic Motifs as a Novel Indicator of the Relationship between Strains Isolated from the Epidemic of Porcine Epidemic Diarrhea in 2013-2014.

    PubMed

    Yamamoto, Takehisa; Suzuki, Tohru; Ohashi, Seiichi; Miyazaki, Ayako; Tsutsui, Toshiyuki

    2016-01-01

    Porcine epidemic diarrhea virus (PEDV) is a positive-sense RNA virus that causes infectious gastroenteritis in pigs. Following a PED outbreak that occurred in China in 2010, the disease was identified for the first time in the United States in April 2013, and was reported in many other countries worldwide from 2013 to 2014. As a novel approach to elucidate the epidemiological relationship between PEDV strains, we explored their genome sequences to identify the motifs that were shared within related strains. Of PED outbreaks reported in many countries during 2013-2014, 119 PEDV strains in Japan, USA, Canada, Mexico, Germany, and Korea were selected and used in this study. We developed a motif mining program, which aimed to identify a specific region of the genome that was exclusively shared by a group of PEDV strains. Eight motifs were identified (M1-M8) and they were observed in 41, 9, 18, 6, 10, 14, 2, and 2 strains, respectively. Motifs M1-M6 were shared by strains from more than two countries, and seemed to originate from one PEDV strain, Indiana12.83/USA/2013, among the 119 strains studied. BLAST search for motifs M1-M6 revealed that M3-M5 were almost identical to the strain ZMDZY identified in 2011 in China, while M1 and M2 were similar to other Chinese strains isolated in 2011-2012. Consequently, the PED outbreaks in these six countries may be closely related, and multiple transmissions of PEDV strains between these countries may have occurred during 2013-2014. Although tools such as phylogenetic tree analysis with whole genome sequences are increasingly applied to reveal the connection between isolates, its interpretation is sometimes inconclusive. Application of motifs as a tool to examine the whole genome sequences of causative agents will be more objective and will be an explicit indicator of their relationship. PMID:26808527

  16. Genomic Motifs as a Novel Indicator of the Relationship between Strains Isolated from the Epidemic of Porcine Epidemic Diarrhea in 2013-2014

    PubMed Central

    Yamamoto, Takehisa; Suzuki, Tohru; Ohashi, Seiichi; Miyazaki, Ayako; Tsutsui, Toshiyuki

    2016-01-01

    Porcine epidemic diarrhea virus (PEDV) is a positive-sense RNA virus that causes infectious gastroenteritis in pigs. Following a PED outbreak that occurred in China in 2010, the disease was identified for the first time in the United States in April 2013, and was reported in many other countries worldwide from 2013 to 2014. As a novel approach to elucidate the epidemiological relationship between PEDV strains, we explored their genome sequences to identify the motifs that were shared within related strains. Of PED outbreaks reported in many countries during 2013–2014, 119 PEDV strains in Japan, USA, Canada, Mexico, Germany, and Korea were selected and used in this study. We developed a motif mining program, which aimed to identify a specific region of the genome that was exclusively shared by a group of PEDV strains. Eight motifs were identified (M1–M8) and they were observed in 41, 9, 18, 6, 10, 14, 2, and 2 strains, respectively. Motifs M1–M6 were shared by strains from more than two countries, and seemed to originate from one PEDV strain, Indiana12.83/USA/2013, among the 119 strains studied. BLAST search for motifs M1–M6 revealed that M3–M5 were almost identical to the strain ZMDZY identified in 2011 in China, while M1 and M2 were similar to other Chinese strains isolated in 2011–2012. Consequently, the PED outbreaks in these six countries may be closely related, and multiple transmissions of PEDV strains between these countries may have occurred during 2013–2014. Although tools such as phylogenetic tree analysis with whole genome sequences are increasingly applied to reveal the connection between isolates, its interpretation is sometimes inconclusive. Application of motifs as a tool to examine the whole genome sequences of causative agents will be more objective and will be an explicit indicator of their relationship. PMID:26808527

  17. Molecular characterisation of virulence graded field isolates of myxoma virus

    PubMed Central

    2010-01-01

    Background Myxoma virus (MV) has been endemic in Europe since shortly after its deliberate release in France in 1952. While the emergence of more resistant hosts and more transmissible and attenuated virus is well documented, there have been relatively few studies focused on the sequence changes incurred by the virus as it has adapted to its new host. In order to identify regions of variability within the MV genome to be used for phylogenetic studies and to try to investigate causes of MV strain attenuation we have molecularly characterised nine strains of MV isolated in Spain between the years 1992 and 1995 from wide ranging geographic locations and which had been previously graded for virulence by experimental infection of rabbits. Results The findings reported here show the analysis of 16 genomic regions accounting for approximately 10% of the viral genomes. Of the 20 genes analysed 5 (M034L, M069L, M071L, M130R and M135R) were identical in all strains and 1 (M122R) contained only a single point mutation in an individual strain. Four genes (M002L/R, M009L, M036L and M017L) showed insertions or deletions that led to disruption of the ORFs. Conclusions The findings presented here provide valuable tools for strain differentiation and phylogenetic studies of MV isolates and some clues as to the reasons for virus attenuation in the field. PMID:20187925

  18. Molecular characterization of the Israeli B. bigemina vaccine strain and field isolates.

    PubMed

    Molad, T; Erster, O; Fleiderovitz, L; Roth, A; Leibovitz, B; Wolkomirsky, R; Mazuz, M L; Behar, A; Markovics, A

    2015-09-15

    The present study demonstrated the genetic character of the Israeli Babesia bigemina vaccine strain and field isolates, based on rap-1a and rap-1c gene sequences. The RAP-1a of blood-derived Israeli B. bigemina field isolates shared 100% amino acid sequence identity. However, comparison of RAP-1c from various Israeli B. bigemina field isolates revealed that the total sequence identity among the field isolates ranged from 98.2 to 100%. High identity was observed when RAP-1a sequences from the Israeli vaccine strain and field isolates were compared with RAP-1a from Egypt, Syria, Mexico and South Africa, while, the Israeli RAP-1c sequences showed the highest identity to the Mexican isolate JG-29 and to the PR isolate from Puerto-Rico. Based on sequence variations between the rap-1a of the vaccine strain and that of the field isolate, and between the rap-1c of the vaccine strain and that of the field isolates, nPCR-RFLP procedures were developed that enable, for the first time differentiation between the Israeli B. bigemina vaccine strain and field-infection isolates. These assays could serve as fast and sensitive methods for detection and differentiation between Israeli B. bigemina vaccine strains and field isolates, as well as for epidemiological investigations. PMID:26154404

  19. Concentration- and time-response characteristics of plaque isolates of Agrotis ipsilon multiple nucleopolyhedrovirus derived from a field isolate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plaque isolates derived from the Illinois field isolate of Agrotis ipsilon multiple nucleopolyhedrovirus are distinguished by the presence or absence of a small deletion in the baculovirus egt (ecdysteroid UDP-glucosyltransferase) coding sequence. Dose-response and time-response bioassays were perf...

  20. The first detection and full-length genome sequence of porcine deltacoronavirus isolated in Lao PDR.

    PubMed

    Lorsirigool, Athip; Saeng-Chuto, Kepalee; Temeeyasen, Gun; Madapong, Adthakorn; Tripipat, Thitima; Wegner, Matthew; Tuntituvanont, Angkana; Intrakamhaeng, Manakant; Nilubol, Dachrit

    2016-10-01

    Porcine deltacoronavirus (PDCoV) has been reported in many countries, including Hong Kong, the United States, South Korea, China and Thailand. In January 2016, clinical diarrhea similar to that of porcine epidemic diarrhea virus (PEDV) with a lower mortality rate was reported on a swine farm in Lao PDR. Intestine samples were collected from 3-day-old pigs with clinical diarrhea and assayed for the presence of swine enteric coronaviruses. The PCR results were positive for PDCoV but negative for PEDV and TGEV. A phylogenetic tree demonstrated that PDCoV from Lao PDR was grouped separately from PDCoV isolates from China and the USA, but was more closely related to the Chinese isolates than to the US isolates. The full-length genome sequence of the novel PDCoV isolate P1_16_BTL_0116 was determined. PMID:27424024

  1. 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...

  2. 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). PMID:26582085

  3. 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. PMID:19882104

  4. A New Record of Pseudallescheria boydii Isolated from Crop Field Soil in Korea

    PubMed Central

    Babu, A. Giridhar; Kim, Sang Woo; Yadhav, Dil Raj; Adhikari, Mahesh; Kim, Changmu; Lee, Hyang Burm

    2014-01-01

    Pseudallescheria boydii KNU13-2 was isolated from crop field soil and identified by analysis of internal transcribed spacer regions of rDNA and morphological characteristics. In the literature, P. boydii has been mentioned as a human pathogen. This is the first record of P. boydii isolated from crop field soil in Korea. PMID:25606013

  5. Drug responsiveness of field isolates of chicken Coccidia.

    PubMed

    Mathis, G F; McDougald, L R

    1982-01-01

    Coccidia were isolated from litter samples collected in poultry houses in Georgia and other southeastern states and from intestinal scrapings from chickens submitted to diagnostic laboratories. The most common species of coccidia encountered were E. tenella, E. acervulina, and E. maxima. Each of the 41 isolates was tested for sensitivity to eight commercial anticoccidial drugs. Most of the isolates were resistant to some of the drugs judged by the parameters of percent weight gain, percent lesion score reduction, and a sensitivity index score. There was a high frequency of resistance to clopidol, amprolium/ethopabate, nequinate, zoalene, and sulfaquinoxaline. A very small percentage of the isolates tested were resistant to nicarbazin, robenidine, or halofuginone. PMID:7088782

  6. 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). PMID:26739022

  7. 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.

  8. 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

  9. Characterization of isolates of meloidogyne from rice-wheat production fields in Nepal.

    PubMed

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

    2007-09-01

    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

  10. Studies of resistance to anticoccidials in Eimeria field isolates and pure Eimeria strains.

    PubMed

    Stephen, B; Rommel, M; Daugschies, A; Haberkorn, A

    1997-04-01

    Ten Eimeria field isolates from North Germany were studied in battery tests for sensitivity to selected anticoccidials. A high percentage of the Eimeria field isolates (9 out of 10) showed resistance to anticoccidials, mostly multiple resistance. Partial or complete resistance to maduramicin was found in 7 field isolates, to monensin in 6, to salinomycin in 5, to nicarbazin in 8, to halofuginone in 7, to robenidine and toltrazuril in 1, and to diclazuril in 2 field isolates. Multiple resistance had developed in 7 of the 10 isolates. Cross-resistance between maduramicin, monensin, and salinomycin occurred in 5 Eimeria isolates. One isolate showed cross-resistance between diclazuril and toltrazuril. From the resistant isolates 15 pure E. acerculina and 5 pure E. brunetti strains were obtained by single oocyst infections. Seven of the E. acerculina and 4 of the E. brunetti strains showed resistance or partial resistance that was also present in the original isolate. Ten of 11 resistant strains were multiply resistant. PMID:9187026

  11. 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. PMID:25749648

  12. Isolation and identification of gold nanoparticles synthesizing fungi from Indian Kolar Gold Field mine soil.

    PubMed

    Lakshmi, V Jhansi; Kannan, K P

    2016-07-01

    An indigenous fungal strain was isolated from Indian Kolar Gold Field mine soil. The isolate was heterothallic, branched septate, deeply floccose, fast-growing, dull green with white background conidial columnar mycelium from Aspergillus section Fumigati. Diverse metabolic patterns of the isolate exhibit high metal, thermal resistance which grews well from 28 ± 1 degrees C to 37 degrees C and pH concentration was significant on the growth of isolate. Phylogenetic analysis of 16srRNA β-Tubulin gene sequence established relationship among isolate and other taxa. Molecular identification and morphological features of fungal isolate were consistent with those of Neosartorya udagawae. Heterothallic N. udagawae FJ830683 strain was closely related to homothallic N. aureola EF661890. Fungal isolate extract synthesized narrow sized stable Gold nanoparticles (AuNPs). PMID:27498502

  13. A New Record of Volutella ciliata Isolated from Crop Field Soil in Korea

    PubMed Central

    Babu, Anam Giridhar; Kim, Sang Woo; Yadav, Dil Raj; Adhikari, Mahesh; Kim, Changmu; Lee, Hyang Burm

    2015-01-01

    During a survey of fungal species in South Korea, a species of Volutella ciliata was isolated and described based on the analysis of the internal transcribed spacer region of its rDNA and its morphological characteristics. This is the first record of Volutella ciliata isolated from crop field soil in Korea. PMID:25892918

  14. Flat Field Determinations Using AN Isolated Point Source

    NASA Astrophysics Data System (ADS)

    Bohlin, R. C.; Grogin, Norman

    2015-08-01

    The traditional method of measuring ACS flat fields (FF) involves a complicated analysis of multiple observations of a region of the 47 Tuc globular cluster at overlapping field positions. The analysis of the dithered 47 Tuc images suffers from source crowding and possible systematics related to the CTE correction and the high density of sources. New programs 13167 and 13602 avoid these problems by observing a single bright star at several locations around the field of view (FOV) in F435W and F814W. A discrepancy of ~3% with a 10σ level of significance exists between the two FF measurement techniques and is currently unexplained.

  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. Lack of an effect of static magnetic field on calcium efflux from isolated chick brains

    SciTech Connect

    Bellossi, A.

    1986-01-01

    /sup 45/Ca2+ efflux from neonatal isolated chick brains was measured. The brains were exposed to uniform or nonuniform static magnetic fields. The field intensity ranged from 200-900 mT. The exposure took place during incubation and/or when efflux was being measured. No difference appeared in the /sup 45/Ca2+ efflux between controls and exposed brains.

  17. Characterization of a Borna disease virus field isolate which shows efficient viral propagation and transmissibility.

    PubMed

    Watanabe, Yohei; Ibrahim, Madiha S; Hagiwara, Katsuro; Okamoto, Minoru; Kamitani, Wataru; Yanai, Hideyuki; Ohtaki, Naohiro; Hayashi, Yohei; Taniyama, Hiroyuki; Ikuta, Kazuyoshi; Tomonaga, Keizo

    2007-04-01

    To investigate the biological characteristics of field isolates of Borna disease virus (BDV), as well as to understand BDV infections outside endemic countries, we isolated the virus from brain samples of a heifer with Borna disease in Japan. We demonstrate that the brain lysate contained replication products of BDV and induced viral propagation in rat glioma cells, suggesting that a replication-competent BDV existed in the bovine brain. This field strain of BDV, named Bo/04w, showed efficient viral release and transmissibility and also displayed a distinct pattern of expression of viral phosphoprotein (P) during infection, as compared with laboratory-adapted BDV strains. Interestingly, we found the level of P to be significantly low in cells infected with Bo/04w, and the transcription of this isolate to be more efficient than that of laboratory strain of BDV. These results indicated that the field isolate may regulate the expression of P at an optimal level in infected cells. We also confirmed that Bo/04w maintains biological significance in neonatal gerbil brain. Sequencing revealed that despite the biological differences, the field isolate is closely related genetically to the laboratory strains of BDV. We discuss here the sequence similarities between BDV isolates from endemic and nonendemic countries. PMID:17306587

  18. Evidence of widespread natural recombination among field isolates of equine herpesvirus 4 but not among field isolates of equine herpesvirus 1.

    PubMed

    Vaz, P K; Horsington, J; Hartley, C A; Browning, G F; Ficorilli, N P; Studdert, M J; Gilkerson, J R; Devlin, J M

    2016-03-01

    Recombination in alphaherpesviruses allows evolution to occur in viruses that have an otherwise stable DNA genome with a low rate of nucleotide substitution. High-throughput sequencing of complete viral genomes has recently allowed natural (field) recombination to be studied in a number of different alphaherpesviruses, however, such studies have not been applied to equine herpesvirus 1 (EHV-1) or equine herpesvirus 4 (EHV-4). These two equine alphaherpesviruses are genetically similar, but differ in their pathogenesis and epidemiology. Both cause economically significant disease in horse populations worldwide. This study used high-throughput sequencing to determine the full genome sequences of EHV-1 and EHV-4 isolates (11 and 14 isolates, respectively) from Australian or New Zealand horses. These sequences were then analysed and examined for evidence of recombination. Evidence of widespread recombination was detected in the genomes of the EHV-4 isolates. Only one potential recombination event was detected in the genomes of the EHV-1 isolates, even when the genomes from an additional 11 international EHV-1 isolates were analysed. The results from this study reveal another fundamental difference between the biology of EHV-1 and EHV-4. The results may also be used to help inform the future safe use of attenuated equine herpesvirus vaccines. PMID:26691326

  19. Molecular Epidemiology of Mycobacterium tuberculosis Isolates in 100 Patients With Tuberculosis Using Pulsed Field Gel Electrophoresis

    PubMed Central

    Pooideh, Mohammad; Jabbarzadeh, Ismail; Ranjbar, Reza; Saifi, Mahnaz

    2015-01-01

    Background: Tuberculosis (TB) is a widespread infectious disease. Today, TB has created a public health crisis in the world. Genotyping of Mycobacterium tuberculosis isolates is useful for surveying the dynamics of TB infection, identifying new outbreaks, and preventing the disease. Different molecular methods for clustering of M. tuberculosis isolates have been used. Objectives: During a one year study of genotyping, 100 M. tuberculosis isolates from patients referred to Pasteur Institute of Iran were collected and their genotyping was accomplished using pulsed field gel electrophoresis (PFGE) method. Materials and Methods: Identification of all M. tuberculosis isolates was accomplished using standard biochemical and species-specific polymerase chain reaction (PCR) methods. Antibiotic susceptibility tests were performed using proportional method. After preparing PFGE plaques for each isolate of M. tuberculosis, XbaI restriction enzyme was applied for genome digestion. Finally, the digested DNA fragments were separated on 1% agarose gel and analyzed with GelCompar II software. Results: Genotyping of the studied isolates in comparison with the molecular weight marker revealed two common types; pulsotype A with 71 isolates and one multidrug resistant mycobacterium (MDR) case, and pulsotype B including 29 isolates and three MDR cases. No correlation between the antibiotypes and pulsotypes was observed. Conclusions: Molecular epidemiology studies of infectious diseases have been useful when bacterial isolates have been clustered in a period of time and in different geographical regions with variable antibiotic resistance patterns. In spite of high geographical differences and different antibiotic resistant patterns, low genetic diversity among the studied TB isolates may refer to the low rate of mutations in XbaI restriction sites in the mycobacterial genome. We also identified three MDR isolates in low-incidence pulsotype B, which could be disseminated and is highly

  20. Multilocus sequence typing scheme versus pulsed-field gel electrophoresis for typing Mycobacterium abscessus isolates.

    PubMed

    Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate; Leão, Sylvia Cardoso

    2014-08-01

    Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. PMID:24899019

  1. Multilocus Sequence Typing Scheme versus Pulsed-Field Gel Electrophoresis for Typing Mycobacterium abscessus Isolates

    PubMed Central

    Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate

    2014-01-01

    Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. PMID:24899019

  2. Bioinformatics insight into the spike glycoprotein gene of field porcine epidemic diarrhea strains during 2011-2013 in Guangdong, China.

    PubMed

    Hao, Jianwei; Xue, Chunyi; He, Liangliang; Wang, Yang; Cao, Yongchang

    2014-08-01

    Three strains of porcine epidemic diarrhea virus (PEDV) were isolated from dead or diseased pigs at different swine farms in Guangdong during 2011-2013, and their S genes were sequenced. In the same period, seven PEDV strains were also isolated in Guangdong by other laboratories. The spike sequences of 10 Guangdong isolates were compared with vaccine strains and reference pathogenic isolates using six bioinformatics tools. The results revealed that 10 Guangdong strains, excluding strain GDS03, had distinct characteristics in terms of primary structure, secondary structure, high-specificity N-glycosylation sites, potential phosphorylation sites, and palmitoylation sites. Phylogenetic analysis also confirmed these findings and revealed that all PEDV strains were clustered into three distinct groups. Ten Guangdong strains, not including GDS03, belong to Group 1, whereas four vaccine strains and GDS03 belong to Group 3, which is evolutionarily distant from Group 1. Alignment analysis of the neutralizing region amino acid sequences indicated that the amino acid substitutions of Y/D766S, T549S, and G594S that are present in the Guangdong strains, not including GDS03, were a sign of predominant genetic changes among the isolated strains. GDS03 is closely related to the 83P-5 vaccine strain, which suggests that it might represent re-isolation of the vaccine strain or vaccine variants. Taken together, these results indicate that there have been predominant new strains circulating in Guangdong from 2011 to 2013, and the circulating PEDV strains have a genetic composition that is distant from reference strains, especially the vaccine strains; however, the vaccinations might also provide some level of cross-protection, as there have been no changes in the neutralizing epitopes of SS2 and 2C10. This explains why there have been constant but infrequent outbreaks recently in comparison to late 2010 in which PEDV outbreaks were more frequent and severe. In addition, the USA

  3. 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.

  4. Intense Isolated Ultrashort Attosecond Pulse Generation in a Multi-Cycle Three-Colour Laser Field

    NASA Astrophysics Data System (ADS)

    Zhang, Gang-Tai

    2014-12-01

    An efficient method for generating an intense isolated ultrashort attosecond pulse is presented theoretically. By adding a 267 nm controlling pulse to a multi-cycle two-colour field, not only the spectral cutoff and the yields of the harmonic spectrum are evidently enhanced, but also the selection of the single quantum path is realised. Then a high-efficiency supercontinuum with a 504 eV bandwidth and smooth structure is obtained, which enables the production of an intense isolated 30 as pulse. In addition, the influences of the laser parameters on the supercontinuum and isolated attosecond pulse are investigated.

  5. Differentiation of field isolates and vaccine strains of infectious laryngotracheitis virus by DNA sequencing.

    PubMed

    Chacón, Jorge Luis; Ferreira, Antonio J Piantino

    2009-11-12

    Two different regions of the infected cell protein 4 (ICP4) gene of infectious laryngotracheitis virus (ILTV) were amplified and sequenced for characterization of field isolates and tissue culture-origin (TCO) and chicken embryo-origin (CEO) vaccine strains. Phylogenetic analysis of the two regions showed differences in nucleotide and amino acid sequences between field isolates and attenuated vaccines. The PCR-RFLP results were identical to those obtained by DNA sequencing and validated their use to differentiate ILTV strains. The approach using the sequencing of the two fragments of the ICP4 gene showed to be an efficient and practical procedure to differentiate between field isolates and vaccine strains of ILTV. PMID:19747995

  6. Molecular characterisation of Aspergillus flavus isolates from peanut fields in India using AFLP

    PubMed Central

    Singh, Diwakar; Radhakrishnan, T.; Kumar, Vinod; Bagwan, N.B.; Basu, M.S.; Dobaria, J.R.; Mishra, Gyan P.; Chanda, S.V.

    2015-01-01

    Aflatoxin contamination of peanut, due to infection by Aspergillus flavus, is a major problem of rain-fed agriculture in India. In the present study, molecular characterisation of 187 Aspergillus flavus isolates, which were sampled from the peanut fields of Gujarat state in India, was performed using AFLP markers. On a pooled cluster analysis, the markers could successfully discriminate among the ‘A’, ‘B’ and ‘G’ group A. flavus isolates. PCoA analysis also showed equivalent results to the cluster analysis. Most of the isolates from one district could be clustered together, which indicated genetic similarity among the isolates. Further, a lot of genetic variability was observed within a district and within a group. The results of AMOVA test revealed that the variance within a population (84%) was more than that between two populations (16%). The isolates, when tested by indirect competitive ELISA, showed about 68.5% of them to be atoxigenic. Composite analysis between the aflatoxin production and AFLP data was found to be ineffective in separating the isolate types by aflatoxigenicity. Certain unique fragments, with respect to individual isolates, were also identified that may be used for development of SCAR marker to aid in rapid and precise identification of isolates. PMID:26413047

  7. Pulsed-field gel electrophoresis for epidemiologic studies of Campylobacter hyointestinalis isolates.

    PubMed Central

    Salama, S M; Tabor, H; Richter, M; Taylor, D E

    1992-01-01

    Campylobacter hyointestinalis was isolated from five members of the same family who had previously consumed raw milk. Pulsed-field gel electrophoresis of genomic DNAs from the five strains, after digestion with restriction endonuclease SalI, revealed that three strains had identical genome patterns and therefore appeared to be related, whereas the other two had completely different genome patterns and appeared to be unrelated. We report here for the first time the isolation of C. hyointestinalis from family members who had consumed raw milk. Our study also demonstrates the usefulness of pulsed-field gel electrophoresis for epidemiologic studies of this unusual campylobacter. Images PMID:1500503

  8. Generation of an isolated few-attosecond pulse in optimized inhomogeneous two-color fields

    NASA Astrophysics Data System (ADS)

    Chou, Yi; Li, Peng-Cheng; Ho, Tak-San; Chu, Shih-I.

    2015-08-01

    We present a numerical study for optimization of ultrabroad supercontinuum spectrum by controlling the waveforms of laser fields, with the ultimate goal to generate isolated ultrashort attosecond pulses. Specifically, we extend a derivative-free nonconvex optimization algorithm for maximization of the supercontinnum power spectrum near the high-order harmonic generation (HHG) cutoff. It is found that optimally shaped inhomogeneous two-color mid-infrared laser fields can greatly enhance and extend the high-order harmonic generation plateau. Wavelet time-frequency analysis and classical simulations show that the superposition of resulting hydrogen HHG supercontinuum effectively gives rise to a robust isolated 5-as pulse.

  9. Porcine reproductive and respiratory syndrome virus field isolates differ in in vitro interferon phenotypes.

    PubMed

    Lee, Sang-Myeong; Schommer, Susan K; Kleiboeker, Steven B

    2004-12-01

    Type I interferons (IFN-alpha and -beta) play an important role in the innate host defense against viral infection by inducing antiviral responses. In addition to direct antiviral activities, type I IFN serves as an important link between the innate and adaptive immune response through multiple mechanisms. Therefore, the outcome of a viral infection can be affected by IFN induction and the IFN sensitivity of a virus. North American porcine reproductive and respiratory syndrome virus (PRRSV) field isolates were studied with regard to IFN-alpha sensitivity and induction in order to understand the role of type I IFN in PRRSV pathogenesis. PRRSV isolates were differentially sensitive to porcine recombinant IFN-alpha (rIFN-alpha) and varied in their ability to induce IFN-alpha in porcine alveolar macrophages (PAM) cultures as measured by a porcine IFN-alpha specific ELISA on cell culture supernatants. Fifty-two plaques were purified from three PRRSV isolates (numbers 3, 7, and 12) and tested for IFN sensitivity and IFN induction. Plaque-derived populations were composed of heterogeneous populations in terms of IFN-inducing capacity and sensitivity to rIFN-alpha. When macrophages infected with isolates 3, 7, or 12 were treated with polycytidylic acid (polyI:C), IFN-alpha production was enhanced. Cells infected with isolate 3 and treated with polyI:C showed the most consistent and strongest enhancement of IFN-alpha production. It was demonstrated that the relatively low concentrations of IFN-alpha produced by isolate 3 contributed to the enhanced IFN-alpha synthesis in response to polyI:C. Isolates 7 and 12 significantly suppressed the enhanced IFN-alpha production by isolate 3 in polyI:C treated cells. To determine if suppression was at the level of IFN-alpha transcription, quantitative RT-PCR was performed for IFN-alpha mRNA and compared to GAPDH and cyclophilin mRNA quantification. However, the relative number of IFN-alpha transcript copies did not correlate with IFN

  10. Phylogenetic analysis of bluetongue virus serotype 4 field isolates from Argentina.

    PubMed

    Legisa, D; Gonzalez, F; De Stefano, G; Pereda, A; Dus Santos, M J

    2013-03-01

    Bluetongue is an insect-transmitted viral disease of ruminant species, which represents a major barrier to the international trade of animals and their products. Bluetongue virus (BTV) has a genome composed of ten linear segments of dsRNA, which code for at least ten different viral proteins. In South America, serological evidence for the presence of BTV has been found in Peru, Argentina, Brazil, Ecuador and Chile. Brazil and Argentina are the only South American countries where BTV has been isolated. In Brazil, only one BTV isolate, serotype 12, has been reported, whereas in Argentina five BTV serotype 4 isolates have been obtained from cattle without clinical signs. Three of these five isolates were isolated during 1999-2001, whereas two of them were obtained as part of the present work. This study describes sequence comparisons and phylogenetic analyses of segment (Seg)-2, Seg-3, Seg-6, Seg-7 and Seg-10 of the first Argentinian field isolates of BTV. The analysis of Seg-2 and Seg-6 resulted in a single cluster of Argentinian sequences into the serotype 4 clade. In addition, the Argentinian sequences grouped within the nucleotype A clade, along with reference strains. The analysis of Seg-3, Seg-7 and Seg-10 showed that the Argentinian isolates grouped into the western topotype, indicating that the circulating virus had an African/European origin. Phylogenetic analysis revealed that the Argentinian sequences present a South American genetic identity, suggesting an independent lineage evolution. PMID:23152367

  11. Molecular epidemiologic analysis of Vibrio cholerae O1 isolates by pulsed-field gel electrophoresis.

    PubMed Central

    Mahalingam, S; Cheong, Y M; Kan, S; Yassin, R M; Vadivelu, J; Pang, T

    1994-01-01

    Isolates of Vibrio cholerae O1 El Tor from two well-defined cholera outbreaks in Malaysia were analyzed by using pulsed-field gel electrophoresis (PFGE). Isolates from sporadic cases occurring during the same time period were also studied. Digestion of chromosomal DNA from these isolates of V. cholerae O1 with restriction endonucleases NotI (5'-GCGGCCGC-3') and SfiI (5'-GGCCNNNN-3'), followed by PFGE, produced restriction endonuclease analysis (REA) patterns consisting of 13 to 24 bands (ranging in size from 46 to 398 kbp). Analysis of the REA patterns generated by PFGE after digestion with NotI and SfiI suggested the clonal nature and close genetic identity of the isolates obtained during each of the two outbreaks (Dice coefficient, 0.93 to 1.0). Although they had very similar REA patterns, the two outbreak clones were not identical. Isolates of V. cholerae O1 from sporadic cases, on the other hand, appeared to be much more heterogeneous (five different REA patterns detected in the five isolates tested; Dice coefficient, 0.31 to 0.81) than those obtained during the two outbreaks. We conclude that PFGE of V. cholerae O1 chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for molecular typing of V. cholerae isolates for epidemiological purposes. Images PMID:7883885

  12. Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein.

    PubMed

    Oh, Jongsuk; Lee, Kyung-Won; Choi, Hwan-Won; Lee, Changhee

    2014-11-01

    Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of swine. Acute PEDV outbreaks have continually emerged in most swine-producing Asian countries and, recently, in the United States, causing significant economic losses in the pig industry. The spike (S) protein of PEDV is a type 1 transmembrane envelope glycoprotein and consists of the S1 and S2 domains, which are responsible for virus binding and fusion, respectively. Since the S1 domain is involved in a specific high-affinity interaction with the cellular receptor and induction of neutralizing antibody in the natural host, it is a primary target for the development of effective vaccines against PEDV. In this study, a codon-optimized PEDV S1 gene containing amino acid residues 25-738 was synthesized based on a multiple alignment of the S amino acid sequences of PEDV field isolates and used to establish a stable porcine cell line constitutively expressing the PEDV S1 protein. The purified recombinant S1 protein was found to mediate highly potent antibody responses in immunized rabbits. The antibodies strongly recognized the recombinant S1 protein from cell lysates and supernatants of S1-expressing cells, whereas they bound weakly to the authentic S protein of PEDV vaccine strain SM98-1. Furthermore, a serum neutralization test revealed that the rabbit antisera completely inhibit infection of the PEDV vaccine strain at a serum dilution of 1:16. We then tested the ability of vaccination with the recombinant S1 protein to protect piglets against PEDV. Late-term pregnant sows were inoculated intramuscularly with the purified S1 protein, and the outcome was investigated in passively immunized suckling piglets after a virulent PEDV challenge. The results showed that vaccination with S1 protein efficiently protected neonatal piglets against PEDV. Our data suggest that the recombinant S1 protein shows potential as an effective and safe subunit vaccine for PED prevention. PMID:25008896

  13. Isolated attosecond pulse generation with the chirped two-color laser field

    NASA Astrophysics Data System (ADS)

    Tai, Huiqin; Li, Fang; Wang, Zhe

    2016-07-01

    We propose a scheme to generate isolated attosecond pulse using a linearly chirped two-color laser field, which includes a fundamental laser field and a weak infrared control laser field in the multicycle regime. The fundamental laser field consists of one linearly up-chirped and one linearly down-chirped pulses. The control pulse is chirped free. We compare the attosecond pulse generated in the chirped two-color field and the chirp-free field. It is found that an IAP can be generated even without carrier envelop phase stabilization in the chirped two-color laser field with a duration of 40 fs. We also discuss the influence of the relative intensity, relative phase, time delay, and chirping parameters on the generation of IAPs.

  14. 7 CFR 201.76 - Minimum Land, Isolation, Field, and Seed Standards.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Minimum Land, Isolation, Field, and Seed Standards. 201.76 Section 201.76 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) FEDERAL SEED ACT FEDERAL SEED ACT...

  15. Evaluation of Marek's disease field isolates by the "best fit" pathotyping assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although determination of pathotype is central to the study of Marek's disease field isolates, methods are not standardized and results from different laboratories may not compare well to the original Avian Disease and Oncology Laboratory (ADOL) assay. This study was designed to investigate the vali...

  16. In vitro antiviral activity of phlorotannins isolated from Ecklonia cava against porcine epidemic diarrhea coronavirus infection and hemagglutination.

    PubMed

    Kwon, Hyung-Jun; Ryu, Young Bae; Kim, Young-Min; Song, Naaleum; Kim, Cha Young; Rho, Mun-Chual; Jeong, Jae-Ho; Cho, Kyoung-Oh; Lee, Woo Song; Park, Su-Jin

    2013-08-01

    Despite the prepdominat agent causing severe entero-pathogenic diarrhea in swine, there are no effective therapeutical treatment of porcine epidemic diarrhea virus (PEDV). In this study, we evaluated the antiviral activity of five phlorotannins isolated from Ecklonia cava (E. cava) against PEDV. In vitro antiviral activity was tested using two different assay strategies: (1) blockage of the binding of virus to cells (simultaneous-treatment assay) and (2) inhibition of viral replication (post-treatment assay). In simultaneous-treatment assay, compounds 2-5 except compound 1 exhibited antiviral activities of a 50% inhibitory concentration (IC₅₀) with the ranging from 10.8 ± 1.4 to 22.5 ± 2.2 μM against PEDV. Compounds 1-5 were completely blocked binding of viral spike protein to sialic acids at less than 36.6 μM concentrations by hemagglutination inhibition. Moreover, compounds 4 and 5 of five phlorotannins inhibited viral replication with IC₅₀ values of 12.2 ± 2.8 and 14.6 ± 1.3 μM in the post-treatment assay, respectively. During virus replication steps, compounds 4 and 5 exhibited stronger inhibition of viral RNA and viral protein synthesis in late stages (18 and 24 h) than in early stages (6 and 12 h). Interestingly, compounds 4 and 5 inhibited both viral entry by hemagglutination inhibition and viral replication by inhibition of viral RNA and viral protein synthesis, but not viral protease. These results suggest that compounds isolated from E. cava have strong antiviral activity against PEDV, inhibiting viral entry and/or viral replication, and may be developed into natural therapeutic drugs against coronavirus infection. PMID:23746631

  17. 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.

  18. Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates from southern India.

    PubMed

    Gowda, Malali; Shirke, Meghana D; Mahesh, H B; Chandarana, Pinal; Rajamani, Anantharamanan; Chattoo, Bharat B

    2015-09-01

    The Indian subcontinent is the center of origin and diversity for rice (Oryza sativa L.). The O. sativa ssp. indica is a major food crop grown in India, which occupies the first and second position in area and production, respectively. Blast disease caused by Magnaporthe oryzae is a major constraint to rice production. Here, we report the analysis of genome architecture and sequence variation of two field isolates, B157 and MG01, of the blast fungus from southern India. The 40 Mb genome of B157 and 43 Mb genome of MG01 contained 11,344 and 11,733 predicted genes, respectively. Genomic comparisons unveiled a large set of SNPs and several isolate specific genes in the Indian blast isolates. Avr genes were analyzed in several sequenced Magnaporthe strains; this analysis revealed the presence of Avr-Pizt and Avr-Ace1 genes in all the sequenced isolates. Availability of whole genomes of field isolates from India will contribute to global efforts to understand genetic diversity of M. oryzae population and to track the emergence of virulent pathotypes. PMID:26484270

  19. Simulation of Intense Isolated Attosecond Pulse Generation with a Two-color Laser Field

    NASA Astrophysics Data System (ADS)

    Eilanlou, Abdolreza Amani; Ishikawa, Kenichi L.; Nabekawa, Yasuo; Takahashi, Hiroyuki; Midorikawa, Katsumi

    A numerical analysis by solving the time-dependent Schrödinger equation on a neon atom within the single-active electron approximation shows that a two-color laser field synthesized from a sub-12-fs fundamental field and a detuned second harmonic field with a wavelength shorter than 380nm is suitable for generating an intense isolated attosecond pulse (IAP). We have also investigated the effects of carrier-envelope phase variation on the obtained IAP and have compared the results to those obtained from a 5-fs fundamental field alone with the same peak field amplitude to show that a more intense IAP can be generated by the two-color laser field which is useful for nonlinear experiments in the extreme ultraviolet spectral range.

  20. Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

    PubMed Central

    Pestel-Caron, Martine; Graff, Gabriel; Berthelot, Gilles; Pons, Jean-Louis; Lemeland, Jean-François

    1999-01-01

    Genetic relationships among 46 isolates of Mycobacterium avium recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS1245 and IS1311. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of M. avium strains is high in a given community. Furthermore, this retrospective analysis of sporadic isolates allowed us (i) to suggest the existence of two remanent strains in our region, (ii) to raise the question of the possibility of nosocomial acquisition of M. avium strains, and (iii) to document laboratory contamination. The methods applied in the present study were found to be useful for the typing of M. avium isolates. In general, both methods yielded similar results for both related and unrelated isolates. However, the isolates in five of the six PCR clusters were distributed among two to three PFGE patterns, suggesting that this PCR-based method may have limitations for the analysis of strains with low insertion sequence copy numbers or for resolution of extended epidemiologic relationships. PMID:10405383

  1. 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

  2. Molecular Characterization of Acquired Enrofloxacin Resistance in Mycoplasma synoviae Field Isolates

    PubMed Central

    Gerchman, I.; Mikula, I.; Gobbo, F.; Catania, S.; Levisohn, S.

    2013-01-01

    The in vitro activity of enrofloxacin against 73 Mycoplasma synoviae field strains isolated in Israel and Europe was determined by broth microdilution. Decreased susceptibility to enrofloxacin was identified in 59% of strains, with the MICs ranging from 1 to >16 μg/ml. The estimated MIC50 and MIC90 values for enrofloxacin were 2 and 8 μg/ml, respectively. Moreover, this study showed that 92% of recent Israeli field isolates (2009 to 2011) of M. synoviae have MICs of ≥2 μg/ml to enrofloxacin. Comparison of the quinolone resistance-determining regions (QRDRs) in M. synoviae isolates revealed a clear correlation between the presence of one of the amino acid substitutions Asp79-Asn, Thr80-Ala/Ile, Ser81-Pro, and Asp84-Asn/Tyr/His of the ParC QRDR and decreased susceptibility to enrofloxacin (MIC, ≥1 μg/ml). Amino acid substitutions at positions GyrA 87, GyrB 401/402, and ParE 420/454 were also identified, but there was no clear-cut correlation with susceptibility to enrofloxacin. Comparison of vlhA molecular profiles revealed the presence of 9 different genotypes in the Israeli M. synoviae field isolates and 10 genotypes in the European isolates; only one vlhA genotype (type 4) was identified in both cohorts. Based on results of vlhA molecular typing, several mechanisms for emergence and dissemination of Israeli enrofloxacin-resistant M. synoviae isolates are suggested. PMID:23612192

  3. Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors

    PubMed Central

    2013-01-01

    Background Rice blast caused by the fungus Magnaporthe oryzae is an important disease in virtually every rice growing region of the world, which leads to significant annual decreases of grain quality and yield. To prevent disease, resistance genes in rice have been cloned and introduced into susceptible cultivars. However, introduced resistance can often be broken within few years of release, often due to mutation of cognate avirulence genes in fungal field populations. Results To better understand the pattern of mutation of M. oryzae field isolates under natural selection forces, we used a next generation sequencing approach to analyze the genomes of two field isolates FJ81278 and HN19311, as well as the transcriptome of FJ81278. By comparing the de novo genome assemblies of the two isolates against the finished reference strain 70–15, we identified extensive polymorphisms including unique genes, SNPs (single nucleotide polymorphism) and indels, structural variations, copy number variations, and loci under strong positive selection. The 1.75 MB of isolate-specific genome content carrying 118 novel genes from FJ81278, and 0.83 MB from HN19311 were also identified. By analyzing secreted proteins carrying polymorphisms, in total 256 candidate virulence effectors were found and 6 were chosen for functional characterization. Conclusions We provide results from genome comparison analysis showing extensive genome variation, and generated a list of M. oryzae candidate virulence effectors for functional characterization. PMID:24341723

  4. 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

  5. Trypanosoma (Herpetosoma) grosi: first isolation from Chinese striped field mouse (Apodemus agrarius).

    PubMed

    Guan, Guiquan; Niu, Qingli; Yang, Jifei; Li, Youquan; Gao, Jinliang; Luo, Jianxun; Yin, Hong

    2011-01-01

    A "lewisi-like" Trypanosoma parasite was isolated from the blood of Chinese striped field mice (Apodemus agrarius) trapped in the fields in the Gannan Tibet area, Gansu province, China. The parasite was successfully cultivated in vitro in HL-1 medium supplemented 20% fetal bovine serum (FBS). Full formed spheromastigote, metacyclic trypomastigote and trypomastigote structures were all visible in films made from the culture. A nucleotide fragment of 2159-bp length was amplified from genomic DNA of the parasite using specific primers for the 18S rRNA gene of trypanosomes. The alignment indicated that this parasite had higher identities with T. (Herpetosoma) grosi (more than 99.6%) than other Herpetosoma species (less than 98.5%), which suggest that the parasite should be classified as T. (Herpetosoma) grosi. This is the first time in China that an isolation of T. (Herpetosoma) grosi is reported although several strains of T. (Herpetosoma) lewisi have been isolated from rodents of family Muridae in various provinces. Thus, it was designated as T. (Herpetosoma) grosi Cha1 and deposited in the center of parasite strain collection and preservation in our laboratory for future study. In addition, this culture method will be used to isolate, maintain and study the long-term development of this parasite in vitro. PMID:21059401

  6. Comparison of field-collected ascovirus isolates by DNA hybridization, host range, and histopathology.

    PubMed

    Hamm, J J; Styer, E L; Federici, B A

    1998-09-01

    Six field-collected ascovirus isolates obtained from five noctuid species in the continental United States were compared with respect to the general relatedness of their DNA, host range, and histopathology. Two isolates were from Spodoptera frugiperda, and the other four were from Autographa precationis, Heliothis virescens, Helicoverpa zea, and Trichoplusia ni. DNA-DNA hybridization studies showed that the six isolates belonged to three distinct viral species, with the isolates from S. frugiperda composing one species, those from A. precationis and H. virescens a second species, and those from H. zea and T. ni a third species. The host range and histopathology of each isolate was studied in eight noctuid species, S. frugiperda, Spodoptera ornithogalli, Spodoptera exigua, Spodoptera eridania, H. virescens, H. zea, A. precationis, and Feltia subterranea. Though some variation existed between the different isolates of each viral species, distinct patterns were apparent for each. The viral species from S. frugiperda had a host range that was limited primarily to Spodoptera species and both isolates of this virus only replicated and caused significant pathology in the fat body, whereas the viral species from A. precationis and H. virescens had a much broader host range that included most of the species tested, but also had a tissue tropism primarily restricted to the fat body. The viral species from T. ni and H. zea readily infected all the hosts tested, where the principal site of replication and significant pathology was the epidermis. In many test hosts, however, this viral species also replicated and caused significant pathology in the tracheal epithelium and to a lesser extent in the fat body. Aside from contributing to knowledge of ascovirus biology, these studies indicate that DNA hybridization profiles combined with studies of host range and tissue tropism can be used as characters for defining ascovirus species. PMID:9709014

  7. On the Generation of Intense Isolated Attosecond Pulses by Many-Cycle Laser Fields

    NASA Astrophysics Data System (ADS)

    Tzallas, Paris; Skantzakis, Emmanouil; Kruse, Jann E.; Charalambidis, Dimitrios

    Real-time observation of ultrafast dynamics in all states of matter requires temporal resolution on the atomic unit of time (24.189 asec) (1 asec = 1{0}^{-18} s). Tools for tracking such ultrafast dynamics are ultrashort light pulses. During the last decade, continuous efforts in ultrashort pulse engineering led to the development of light pulses width duration close to the atomic unit of time. Attosecond (asec) pulses have been synthesized by broadband coherent extreme ultraviolet (XUV) radiation generated by the interaction of gases or solids with an intense IR fs pulse. Asec pulse trains can be generated when the medium interacts with many-cycle driving IR fs laser fields. In this case, a broadband XUV frequency comb is emitted from the medium. The Fourier synthesis of a part of the comb results in an asec pulse train. Isolated asec pulses are generated when the medium is forced to emit XUV radiation only during few cycles of the driving laser field. This leads to the emission of a broadband quasicontinuum XUV radiation. The Fourier synthesis of the continuum part of the spectrum results in an isolated asec pulse. For the realization of studies of ultrafast dynamics, intense asec pulses are preferable. If the pulses are intense enough to induce a nonlinear process in a target system, they can be used for ultrafast dynamic studies in an XUV pump-probe configuration. Although trains of intense asec pulses are commonly produced nowadays, the generation of intense isolated asec pulses remains a challenge. Here, we review a recently developed approach for the generation of intense asec pulses using high-peak-power many-cycle laser fields. The approach is based on controlling, with asec precession, the response of the atomic dipole to an external many-cycle driving field in such a way as to emit an isolated asec XUV burst. This approach has been implemented by using the inteferometric polarization gating (IPG) technique. The bandwidth of the generated XUV radiation is

  8. 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.

  9. How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

    PubMed

    Latorre-Margalef, Neus; Avril, Alexis; Tolf, Conny; Olsen, Björn; Waldenström, Jonas

    2016-02-01

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data. PMID:26655759

  10. How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

    PubMed Central

    Avril, Alexis; Tolf, Conny; Olsen, Björn

    2015-01-01

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data. PMID:26655759

  11. 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.

  12. Detection and Isolation Techniques for Methanogens from Microbial Mats (in the El Tatio Geyser Field, Chile)

    NASA Astrophysics Data System (ADS)

    Pearson, E. Z.; Franks, M. A.; Bennett, P.

    2010-12-01

    Isolating methanogenic archea from an extreme environment such as El Tatio (high altitude, arid climate) gives insight to the methanogenic taxas able to adapt and grow under extreme conditions. The hydrothermal waters at El Tatio geyser field demonstrate extreme geochemical conditions, with discharge water from springs and geysers at local boiling temperature (85° C) with high levels of arsenic and low DIC levels. Despite these challenges, many of El Tatio’s hundred plus hydrothermal features host extensive microbial mat communities, many showing evidence of methanogenesis. When trying to isolate methanogens unique to this area, various approaches and techniques were used. To detect the presence of methanogens in samples taken from the field, dissolved methane concentrations were determined via gas chromatography (GC) analysis. Samples were then selected for culturing and most probable number (MPN) enumeration, where growth was assessed using both methane production and observations of fluorescence under UV light. PCR was used to see if the archeal DNA was apparent directly from the field, and shotgun cloning was done to determine phylogenetic affiliation. Several culturing techniques were carried out in an attempt to isolate methanogens from samples that showed evidence of methanogenesis. The slant culturing method was used because of the increased surface area for colonization combined with the relative ease of keeping anaerobic. After a few weeks, when colonies were apparent, some were aseptically selected and inoculated to observe growth in a liquid media containing ampicillin to inhibit bacterial growth. Culturing techniques proved successful after inoculation, showing a slow growth of methanogens via GC and autofluorescence. Further PCR tests and subsequent sequencing were done to confirm and identify isolates.

  13. 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).

  14. Crystal field splitting on D<-->S transitions of atomic manganese isolated in solid krypton

    NASA Astrophysics Data System (ADS)

    Byrne, O.; Collier, M. A.; Ryan, M. C.; McCaffrey, J. G.

    2010-05-01

    Narrow excitation features present on the [Ar]3d64s1aD(J=9/2-1/2)6←[Ar]3d54s2aS1/26 transitions of manganese atoms isolated in solid Kr are analyzed within the framework of weak crystal field splitting. Use of the Wp optical lineshape function allowed identification of multiple zero-phonon lines for individual spin-orbit J states of the a aD6←aS6 transition recorded with laser-induced excitation spectroscopy. Excellent agreement exists between the predicted crystal field splitting patterns for the J levels of the aD6 state isolated in the «red» tetravacancy site of solid Kr. The tetrahedral crystal field of the «red» trapping site splits J >3/2 levels of the aDJ6 and aD7/24 states by approximately 30cm-1. This report represents the first definitive evidence of crystal field splitting, induced by the weak van der Waals interactions between a neutral metal atom and the rare gas atoms surrounding it in a well-defined solid-state site.

  15. 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. PMID:26831160

  16. 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.

  17. Phylogenetic and geographic analysis of fowl adenovirus field strains isolated from poultry in Poland.

    PubMed

    Niczyporuk, Jowita Samanta

    2016-01-01

    Fowl adenoviruses (FAdVs) are widely distributed in chickens in Poland and throughout the world. FAdV infections have been reported in the United States, Australia, Europe, and the Mediterranean basin. Detection of FAdVs strains is very important from the epidemiological point of view and for monitoring disease outbreaks and developing strategies for vaccine development. Several molecular epidemiology and phylogenetic studies have been performed, but the results obtained are still limited, because FAdV strains, even of the same serotype, have very diverse characteristics. Some strains are pathogenic and some are nonpathogenic. This report describes the successful isolation of 96 FAdV field strains from chickens in Poland. A PCR assay specific for the L1 loop region of the hexon gene was conducted, and the products were subjected to sequence analysis. The sequences were analysed using BLAST and Geneious 6.0 software and compared to adenovirus field and reference strain sequences from different parts of the world that are accessible in the NCBI GenBank database. The sequences of the adenovirus strains indicated that they belonged to five species, Fowl aviadenovirus A-E, represented by eight serotypes FAdV-1, FAdV-4, FAdV-5, FAdV-7, FAdV-8a, FAdV-8b, and FAdV-2/11 (FAdV-D). The relationships between FAdVs isolated in Poland and isolates from other regions of the world were determined. PMID:26446890

  18. 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. PMID:23102469

  19. Membrane solid-phase extraction: Field application for isolation of polycyclic aromatic hydrocarbons from water samples

    SciTech Connect

    Furlong, E.T.; Koleis, J.C.; Gates, P.M.

    1995-12-31

    Solid-phase extraction (SPE) membranes (M-SPE) were used to isolate microgram-per-liter to nanogram-per-liter quantities of polycyclic aromatic hydrocarbons (PAH) in 4- to 8-liter ground-water samples from a crude-oil-contaminated ground-water site near Bemidji, Minnesota. The M-SPE method was evaluated (1) under laboratory conditions using reagent water fortified with individual PAH at 1.23 micrograms per liter, and (2) at the Bemidji site. At the site, ground-water samples were processed and PAH isolated using a M-SPE system connected directly to the well pump. Following sample isolation, all M-SPE samples were extracted using dichloromethane and analyzed by gas chromatography-mass spectrometry with selected-ion monitoring. Operationally, the M-SPE method provided a simple means to isolate PAH on site at the wellhead, particularly for anoxic water samples. Acceptable recoveries, ranging from 56 to over 100 percent, were observed for lower molecular weight PAH (naphthalene to pyrene) using the M-SPE method. Recoveries using M-SPE were somewhat lower, but reproducible, for higher molecular weight PAH (chrysene to benzo[ghi]perylene), ranging from 18 to 56 percent. M-SPE provides the capability to collect and field isolate PAH from a sufficiently large number of samples to identify environmental chemical processes occurring at individual compound concentrations of 50 to 1,200 nanograms per liter. Using M-SPE, the potential for facilitated transport of PAH by in situ-derived dissolved organic carbon (DOC) was evaluated at the site. Plots comparing DOC and PAH concentrations indicate that PAH concentrations increase exponentially with linear increases in DOC concentrations.

  20. 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

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

    PubMed

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

    2015-09-01

    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

  2. Changes in Predominance of Pulsed-Field Gel Electrophoresis Profiles of Bordetella pertussis Isolates, United States, 2000-2012.

    PubMed

    Cassiday, Pamela K; Skoff, Tami H; Jawahir, Selina; Tondella, M Lucia

    2016-03-01

    To clarify the characteristics of circulating Bordetella pertussis isolates, we used pulsed-field gel electrophoresis (PFGE) to analyze 5,262 isolates collected in the United States during 2000-2012. We found 199 PFGE profiles; 5 profiles accounted for 72% of isolates. The most common profile, CDC013, accounted for 35%-46% of isolates tested from 2000-2009; however, the proportion of isolates of this profile rapidly decreased in 2010. Profile CDC237, first seen in 2009, increased rapidly and accounted for 29% of 2012 isolates. No location bias was observed among profiles during 2000-2010, but differences were observed among isolates from different states during 2012. Predominant profiles match those observed in recent European PFGE studies. PFGE profile changes are concurrent with other recent molecular changes in B. pertussis and may be contributing to the reemergence of pertussis in the United States. Continued PFGE monitoring is critical for understanding the changing epidemiology of pertussis. PMID:26886905

  3. Changes in Predominance of Pulsed-Field Gel Electrophoresis Profiles of Bordetella pertussis Isolates, United States, 2000–2012

    PubMed Central

    Skoff, Tami H.; Jawahir, Selina; Tondella, M. Lucia

    2016-01-01

    To clarify the characteristics of circulating Bordetella pertussis isolates, we used pulsed-field gel electrophoresis (PFGE) to analyze 5,262 isolates collected in the United States during 2000–2012. We found 199 PFGE profiles; 5 profiles accounted for 72% of isolates. The most common profile, CDC013, accounted for 35%–46% of isolates tested from 2000–2009; however, the proportion of isolates of this profile rapidly decreased in 2010. Profile CDC237, first seen in 2009, increased rapidly and accounted for 29% of 2012 isolates. No location bias was observed among profiles during 2000–2010, but differences were observed among isolates from different states during 2012. Predominant profiles match those observed in recent European PFGE studies. PFGE profile changes are concurrent with other recent molecular changes in B. pertussis and may be contributing to the reemergence of pertussis in the United States. Continued PFGE monitoring is critical for understanding the changing epidemiology of pertussis. PMID:26886905

  4. Characterization of Salmonella isolates from retail foods based on serotyping, pulse field gel electrophoresis, antibiotic resistance and other phenotypic properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sixteen Salmonella strains isolated from a variety of foods during 2000 and 2003, by the Florida State Department of Agriculture, were characterized by various genotypic and phenotypic tests. Among 16 isolates, 15 different serotypes were identified. Pulse-Field Gel Electrophoresis (PFGE) fingerpr...

  5. 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...

  6. 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...

  7. 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.

  8. 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.

  9. Sensitivity of Eimeria field isolates in the United States: responses of nicarbazin-containing anticoccidials.

    PubMed

    Bafundo, K W; Cervantes, H M; Mathis, G F

    2008-09-01

    A series of studies were conducted to assess the drug sensitivity of 26 coccidial field isolates to the anticoccidial effects of nicarbazin (NIC) and narasin + NIC (NAR + NIC). Isolates were collected from typical broiler farms in the United States from 2003 to 2006, propagated once in the absence of anticoccidial medication, and then used to inoculate broilers that were fed nonmedicated rations or those containing NIC 125 ppm or NAR + NIC 80 ppm. Results of these sensitivity trials indicated that 81% of these coccidial isolates were sensitive to the effects of NIC, but only 22% of these coccidia were controlled by NAR + NIC. Studies conducted to evaluate performance responses to these drugs demonstrated that birds fed NIC gained more weight and utilized feed more efficiently than those receiving NAR + NIC. The results of 2 floor pen tests, conducted to confirm the results of the above sensitivity trials, demonstrated that NIC provided a greater level of protection from coccidiosis than NAR + NIC. Lower lesion scores and improved performance were recorded for birds receiving NIC compared with NAR + NIC. Results of these studies revealed that changes in the susceptibility of Eimeria spp. to the activity of NAR + NIC are evident. These changes appear to be associated with the reduction in ionophore sensitivity that has been documented in most areas of the world. PMID:18753443

  10. Coherent control of broadband isolated attosecond pulses in a chirped two-color laser field

    SciTech Connect

    Zou Pu; Zeng Zhinan; Zheng Yinghui; Lu Yingying; Liu Peng; Li Ruxin; Xu Zhizhan

    2010-03-15

    A theoretical investigation is presented that uses a strong two-color laser field composed of a linearly chirped fundamental (900 nm) and its subharmonic (1800-nm) laser pulses to control coherently the broadband isolated attosecond pulses in high-order harmonic generations. After the subharmonic field is added, the intrinsic chirp of harmonic emission can be reduced significantly, and consequently, the temporal synchronization of harmonic emission with different photon energies at the level of the single-atom response can be realized. In addition, the scheme is robust against the carrier envelope phase variation to produce a twin pulse of stable sub-100-as duration, and the relative intensity of the twin pulses can be changed just by adjusting the relative time delay of the two driving pulses, which is of benefit in general pump-probe experiments.

  11. Evaluation of the in vitro activity of flumequine against field isolates of Brachyspira hyodysenteriae.

    PubMed

    Aller-Morán, Luis Miguel; Martínez-Lobo, Francisco Javier; Rubio, Pedro; Carvajal, Ana

    2015-12-01

    Flumequine is a quinolone derivative used in veterinary medicine to treat enteric infections, mainly those caused by Gram negative bacteria and also some Gram positive. Some recent reports by field practitioners have suggested that its use in swine dysentery outbreaks can minimize the impact of this disease. This study aims to evaluate the in vitro anti-Brachyspira hyodysenteriae activity of flumequine. Forty eight field isolates of the bacterium were evaluated using a microdilution test. The lack of colon bioavailability studies of flumequine in pigs makes it difficult to establish the true efficacy of this antibiotic for swine dysentery control. Nonetheless, the relatively high values of MIC50 (50 μg/mL) and MBC50 (50 μg/mL) obtained suggest poor activity against B. hyodysenteriae. Flumequine activity in swine dysentery outbreaks could be related to its activity against other bacteria, different from B. hyodysenteriae, engaged in swine dysentery pathogenesis. PMID:26679795

  12. Socially flexible female choice and premating isolation in field crickets (Teleogryllus spp.).

    PubMed

    Bailey, N W; Macleod, E

    2014-01-01

    Social influences on mate choice are predicted to influence evolutionary divergence of closely related taxa, because of the key role mate choice plays in reproductive isolation. However, it is unclear whether females choosing between heterospecific and conspecific male signals use previously experienced social information in the same manner or to the same extent that they do when discriminating among conspecific mates only. We tested this using two field cricket sister species (Teleogryllus oceanicus and Teleogryllus commodus), in which considerable information is known about the role of male calling song in premating isolation, in addition to the influence of acoustic experience on the development of reproductive traits. We manipulated the acoustic experience of replicate populations of both species and found, unexpectedly, that experience of male calling song during rearing did not change how accurate females were in choosing a conspecific over a heterospecific male song during playback trials. However, females with acoustic experience were considerably less responsive to male song compared with naïve females. Our results suggest that variation in the acoustic environment affects mate choice in both species, but that it may have a limited impact on premating isolation. The fact that social flexibility during interspecific mate discrimination does not appear to operate identically to that which occurs during conspecific mate discrimination highlights the importance of considering the context in which animals exercise socially flexible mating behaviours. We suggest an explanation for why social flexibility might be context dependent and discuss the consequences of such flexibility for the evolution of reproductive isolation. PMID:24330452

  13. 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 (13-30Hz) 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 (5-8Hz), alpha (8-12Hz), beta (13-30Hz), broadband gamma (50-200Hz), or high frequency oscillation (HFO, 250-350Hz) 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. PMID:26884091

  14. 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. PMID:26613662

  15. 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).

  16. Isolation and pathogenic analysis of virulent Marek's disease virus field strain in China.

    PubMed

    Cui, Ning; Su, Shuai; Sun, Peng; Zhang, Yankun; Han, Ni; Cui, Zhizhong

    2016-07-01

    Marek's disease (MD) has become increasingly common in China, resulting in considerable economic loss. The etiological agent is unclear. In this study, we isolated a field MD virus (MDV) strain, designated SX1301, from CVI988/Rispens-vaccinated chickens with tumors. Co-infection of avian leukosis virus, reticuloendotheliosis virus, and chicken infectious anemia virus was excluded by polymerase chain reaction, enzyme-linked immunosorbant assay, DNA blotting hybridization, and indirect immunofluorescence assay. As with most strains isolated in China, SX1301 had the same amino acid mutation of meq protein at positions 77(E), 80(Y), and 115(A) Animal experimental results showed development of lethal MD in 57% and MD tumor in 23% of the specific pathogen-free chickens inoculated with SX1301, with tumors mainly distributed in spleen, liver, and kidney. CVI988/Rispens protected 83% of chickens upon challenge with SX1301, with a mortality rate and tumor incidence of 10% and 7%, respectively. These results implicated SX1301 as a virulent MDV strain, with commercial MDV vaccine CVI988/Rispens unable to confer adequate protection against SX1301. There have been no reports of very virulent (vv) plus MDV in China, but frequently occurring virulent MDV may account for the repeated outbreaks of MD. Vaccines with greater efficacy are needed to protect against MDV. PMID:26976907

  17. The isolation of a field strain of Haemonchus contortus in Queensland showing multiple anthelmintic resistance.

    PubMed

    Green, P E; Forsyth, B A; Rowan, K J; Payne, G

    1981-02-01

    Following the apparent failure of levamisole to control infections of Haemonchus contortus in sheep at Lawes in south eastern Queensland, a strain of this parasite was isolated at the Animal Research Institute, Yeerongpilly. This strain was used to infect sheep at Yeerongpilly and the Merrindale Research Station, Victoria where four experiments to classify the resistance pattern of the parasite were carried out. Resistance to thiabendazole was first suspected in 1969, and these experiments confirmed that resistance to this drug was still present. They also showed that a strong degree of resistance had been developed to both levamisole and morantel tartrate. Other benzimidazole anthelmintics and also the organophosphorus compound naphthalophos were only moderately effective against the original isolate but rafoxanide, nitroxynil and phenothiazine were almost 100% effective. Other highly effective chemicals were disophenol and closantel. After passaging the strain for four generations with both levamisole and albendazole, resistance to both naphthalophos and the newer benzimidazole anthelmintics increased dramatically. This is the first report of a field strain of H. contortus exhibiting resistance to benzimidazole, non-benzimidazole and organophosphorus anthelmintics. PMID:7259650

  18. 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.

  19. 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.

  20. Optimization of infrared two-color multicycle field synthesis for intense-isolated-attosecond-pulse generation

    NASA Astrophysics Data System (ADS)

    Lan, Pengfei; Takahashi, Eiji J.; Midorikawa, Katsumi

    2010-11-01

    We present the optimization of the two-color synthesis method for generating an intense isolated attosecond pulse (IAP) in the multicycle regime. By mixing an infrared assistant pulse with a Ti:sapphire main pulse, we show that an IAP can be produced using a multicycle two-color pulse with a duration longer than 30 fs. We also discuss the influence of the carrier-envelope phase (CEP) and the relative intensity on the generation of IAPs. By optimizing the wavelength of the assistant field, IAP generation becomes insensitive to the CEP slip. Therefore, the optimized two-color method enables us to relax the requirements of pulse duration and easily produce the IAP with a conventional multicycle laser pulse. In addition, it enables us to markedly suppress the ionization of the harmonic medium. This is a major advantage for efficiently generating intense IAPs from a neutral medium by applying the appropriate phase-matching and energy-scaling techniques.

  1. Optimization of infrared two-color multicycle field synthesis for intense-isolated-attosecond-pulse generation

    SciTech Connect

    Lan Pengfei; Takahashi, Eiji J.; Midorikawa, Katsumi

    2010-11-15

    We present the optimization of the two-color synthesis method for generating an intense isolated attosecond pulse (IAP) in the multicycle regime. By mixing an infrared assistant pulse with a Ti:sapphire main pulse, we show that an IAP can be produced using a multicycle two-color pulse with a duration longer than 30 fs. We also discuss the influence of the carrier-envelope phase (CEP) and the relative intensity on the generation of IAPs. By optimizing the wavelength of the assistant field, IAP generation becomes insensitive to the CEP slip. Therefore, the optimized two-color method enables us to relax the requirements of pulse duration and easily produce the IAP with a conventional multicycle laser pulse. In addition, it enables us to markedly suppress the ionization of the harmonic medium. This is a major advantage for efficiently generating intense IAPs from a neutral medium by applying the appropriate phase-matching and energy-scaling techniques.

  2. 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

  3. 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.

  4. Chlorhexidine Digluconate Effects on Planktonic Growth and Biofilm Formation in Some Field Isolates of Animal Bacterial Pathogens

    PubMed Central

    Ebrahimi, Azizollah; Hemati, Majid; Habibian Dehkordi, Saeed; Bahadoran, Shahab; Khoshnood, Sheida; Khubani, Shahin; Dokht Faraj, Mahdi; Hakimi Alni, Reza

    2014-01-01

    Background: To study chlorhexidine digluconate disinfectant effects on planktonic growth and biofilm formation in some bacterial field isolates from animals. Objectives: The current study investigated chlorhexidine digluconate effects on planktonic growth and biofilm formation in some field isolates of veterinary bacterial pathogens. Materials and Methods: Forty clinical isolates of Escherichia coli, Salmonella serotypes, Staphylococcus. aureus and Streptococcus agalactiae (10 isolates for each) were examined for chlorhexidine digluconate effects on biofilm formation and planktonic growth using microtiter plates. In all of the examined strains in the presence of chlorhexidine digluconate, biofilm development and planktonic growth were affected at the same concentrations of the disinfectant. Results: Chlorhexidine digluconate inhibited the planktonic growth of different bacterial species at sub-MICs. But they were able to induce biofilm development of the E. coli, Salmonella spp., S. aureus and Str. agalactiae strains. Conclusions: Bacterial resistance against chlorhexidine is increasing. Sub-MIC doses of chlorhexidine digluconate can stimulate the formation of biofilm strains. PMID:24872940

  5. Faraday isolator based on a TSAG single crystal with compensation of thermally induced depolarization inside magnetic field

    NASA Astrophysics Data System (ADS)

    Snetkov, Ilya; Palashov, Oleg

    2015-04-01

    A Faraday isolator based on a terbium scandium aluminum garnet (TSAG) single crystal with compensation of thermally induced depolarization inside magnetic field was demonstrated. An isolation ratio of 32 dB at 350 W cw laser radiation power was achieved. Thermally induced depolarization and thermal lens were studied and compared with similar thermal effects arising in the widely used terbium gallium garnet crystal (TGG) for the first time.

  6. Isolation of marine bacteria with antimicrobial activities from cultured and field-collected soft corals.

    PubMed

    Chen, Yu-Hsin; Kuo, Jimmy; Sung, Ping-Jung; Chang, Yu-Chia; Lu, Mei-Chin; Wong, Tit-Yee; Liu, Jong-Kang; Weng, Ching-Feng; Twan, Wen-Hung; Kuo, Fu-Wen

    2012-12-01

    Bacteria associated with eight field-collected and five cultured soft corals of Briareum sp., Sinularia sp., Sarcophyton sp., Nephtheidae sp., and Lobophytum sp. were screened for their abilities in producing antimicrobial metabolites. Field-collected coral samples were collected from Nanwan Bay in southern Taiwan. Cultured corals were collected from the cultivating tank at National Museum of Marine Biology and Aquarium. A total of 1,526 and 1,138 culturable, heterotrophic bacteria were isolated from wild and cultured corals, respectively; seawater requirement and antimicrobial activity were then assessed. There is no significant difference between the ratio of seawater-requiring bacteria on the wild and cultured corals. The ratio of antibiotic-producing bacteria within the seawater-requiring bacteria did not differ between the corals. Nineteen bacterial strains that showed high antimicrobial activity were selected for 16S rDNA sequencing. Three strains could be assigned at the family level (Rhodobacteraceae). The remaining 16 strains belong to eight genera: Marinobacterium (2 strains), Pseudoalteromonas (1), Vibrio (5), Enterovibrio (1), Tateyamaria (1), Labrenzia (2), and Pseudovibrio (4). The crude extract from bacteria strains CGH2XX was found to have high cytotoxicity against the cancer cell line HL-60 (IC(50) = 0.94 μg/ml) and CCRF-CEM (IC(50) = 1.19 μg/ml). Our results demonstrate that the marine bacteria from corals have great potential in the discovery of useful medical molecules. PMID:22872580

  7. Excessive magnetic field flux density distribution from overhead isolated powerline conductors due to neutral line current.

    PubMed

    Netzer, Moshe

    2013-06-01

    Overhead isolated powerline conductors (hereinafter: "OIPLC") are the most compact form for distributing low voltage currents. From the known physics of magnetic field emission from 3-phase power lines, it is expected that excellent symmetry of the 120° shifted phase currents and where compact configuration of the 3-phase+neutral line exist, the phase current vectorial summation of the magnetic field flux density (MFFD) is expected to be extremely low. However, despite this estimation, an unexpectedly very high MFFD was found in at least three towns in Israel. This paper explains the reasons leading to high MFFD emissions from compact OIPLC and the proper technique to fix it. Analysis and measurement results had led to the failure hypothsis of neutral line poor connection design and poor grounding design of the HV-LV utility transformers. The paper elaborates on the low MFFD exposure level setup by the Israeli Environmental Protection Office which adopted a rather conservative precaution principal exposure level (2 mG averaged over 24 h). PMID:23675630

  8. Generation of isolated sub-40-attosecond pulse with a multicycle chirped laser and a static electric field

    NASA Astrophysics Data System (ADS)

    Mohebbi, Masoud

    2016-02-01

    We numerically investigate the high-order harmonic generation and isolated attosecond pulse generation in a waveform that linearly produced by chirped laser pulse, chirp-free laser pulse, and static electric field. When a chirp-free laser pulse is added to the produced field of the chirped driving pulse and the static electric field, the plateau harmonic yield is enhanced by two orders. The spectral modulation is also significantly decreased, and the bandwidth of XUV spectrum is further broadened. An intense and a clean isolated 38-as pulse can be produced from the intense broadband XUV supercontinuum. After proper phase compensation, an isolated sub-8-attosecond pulse can be obtained. Furthermore, quantum time-frequency analysis reveals that the selection of the short quantum path can be achieved in this scheme.

  9. Microscopic and biochemical evidence of differentially virulent field isolates of Diplocarpon rosae causing black spot disease of roses.

    PubMed

    Gachomo, Emma W; Kotchoni, Simeon O

    2010-01-01

    Black spot disease caused by Diplocarpon rosae is one of the most widespread diseases of roses that are very difficult to control due to the generative reproduction and complex genetic constitution of roses and up to now the control of black spot still requires intensive use of systemic fungicides. Here we report for the first time evidence of differentially virulent field isolates of D. rosae. Using a combination of fungal structures, disease symptoms and host cells protein expression pattern analysis we here provide direct biochemical evidence that tropical field isolates of D. rosae are more virulent and caused disease symptoms earlier than their temperate counterparts. The tropical fungal field isolates strongly induced an excessive accumulation of ROS and repressed activity of pathogenesis-related proteins such as peroxidases, chitinase and phenylalanine ammonia lyase compared to their temperate counterparts. These findings bring insights into a hidden pathogenic characteristic of tropical D. rosae field isolates compared to their temperate counterparts and open a novel dimension of parameters to be considered when controlling black spot disease of roses by fungicides in tropical versus temperate regions. Interestingly, we found that treatment of rose leaves with ROS (H2O2) prior to fungal inoculation promoted plant defense response regardless of the isolate virulence based on protein expression pattern analysis, suggesting that ROS (H2O2) can be efficiently incorporated into black spot disease management. PMID:20137960

  10. Epidemiological survey of porcine epidemic diarrhea virus in swine farms in Shanghai, China.

    PubMed

    Ge, Fei-Fei; Yang, De-Quan; Ju, Hou-Bin; Wang, Jian; Liu, Jian; Liu, Pei-Hong; Zhou, Jin-Ping

    2013-11-01

    An epidemiological survey of porcine diarrheal disease prevalence between September 2011 and January 2012 revealed that porcine epidemic diarrhea virus (PEDV) contributed to outbreaks of diarrhea in pig farms in Shanghai, China. The distribution profile of 10 PEDV strains revealed three distinct genotypes coexisting in the same pig farm. Two of the ten field strains that were isolated exhibited a distinct evolution from the others. In addition to PEDV, other enteric pathogens, including porcine kobuvirus, porcine teschovirus and Lawsonia intracellularis, were identified. PMID:23685898

  11. Use of two SPE-GC/MS methods for field isolation and quantitation of polycyclic aromatic hydrocarbons

    SciTech Connect

    Furlong, E.T.; Koleis, J.C.; Gates, P.M.

    1995-12-31

    Increasing sensitivity and subsequently improving method-detection limits for a variety of organic contaminant compounds is an ongoing effort in environmental analytical chemistry. Several field-deployable isolation techniques have been developed for concentrating hydrophobic organic contaminants from large (> 1 liter) volumes of aqueous samples. The capacity of large-volume solid-phase extraction (LV-SPE) was used as part of a simple, efficient, field-operable technique for isolating microgram-per-liter to nanogram-per-liter quantities of polycyclic aromatic hydrocarbons (PAH) in 4- to 8-liter ground-water samples from a petroleum- contaminated aquifer near Bemidji, Minn.

  12. Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil.

    PubMed

    Du, Juan; Ngo, Hien T T; Won, KyungHwa; Kim, Ki-Young; Jin, Feng-Xie; Yi, Tae-Hoo

    2015-08-01

    Strain THG-EP9T, a Gram-stain-negative, aerobic, motile, rod-shaped bacterium was isolated from field-grown eggplant (Solanum melongena) rhizosphere soil collected in Pyeongtaek, Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-EP9T had closest similarity with Chryseobacterium ginsenosidimutans THG 15T (97.3 % 16S rRNA gene sequence similarity), Chryseobacterium soldanellicola PSD1-4T (97.2%), Chryseobacterium zeae JM-1085T (97.2%) and Chryseobacterium indoltheticum LMG 4025T (96.8%). DNA-DNA hybridization showed 5.7% and 9.1% DNA reassociation with Chryseobacterium ginsenosidimutans KACC 14527T and Chryseobacterium soldanellicola KCTC 12382T, respectively. Chemotaxonomic data revealed that strain THG-EP9T possesses menaquinone-6 as the only respiratory quinone and iso-C15 : 0 (29.0%), C16 : 0 (12.5%) and iso-C17 : 0 3-OH (11.9 %) as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified glycolipids, six unidentified aminolipids and two unidentified polar lipids. The DNA G+C content was 35.3 mol%. These data corroborated the affiliation of strain THG-EP9T to the genus Chryseobacterium. Thus, the isolate represents a novel species of this genus, for which the name Chryseobacterium solani sp. nov. is proposed, with THG-EP9T ( = KACC 17652T = JCM 19456T) as the type strain. PMID:25878202

  13. The adipokine chemerin amplifies electrical field-stimulated contraction in the isolated rat superior mesenteric artery.

    PubMed

    Darios, Emma S; Winner, Brittany M; Charvat, Trevor; Krasinksi, Antoni; Punna, Sreenivas; Watts, Stephanie W

    2016-08-01

    The adipokine chemerin causes arterial contraction and is implicated in blood pressure regulation, especially in obese subjects with elevated levels of circulating chemerin. Because chemerin is expressed in the perivascular adipose tissue (PVAT) that surrounds the sympathetic innervation of the blood vessel, we tested the hypothesis that chemerin (endogenous and exogenous) amplifies the sympathetic nervous system in mediating electrical field-stimulated (EFS) contraction. The superior mesenteric artery, with or without PVAT and with endothelium and sympathetic nerve intact, was mounted into isolated tissue baths and used for isometric contraction and stimulation. Immunohistochemistry validated a robust expression of chemerin in the PVAT surrounding the superior mesenteric artery. EFS (0.3-20 Hz) caused a frequency-dependent contraction in isolated arteries that was reduced by the chemerin receptor ChemR23 antagonist CCX832 alone (100 nM; with, but not without, PVAT), but not by the inactive congener CCX826 (100 nM). Exogenous chemerin-9 (1 μM)-amplified EFS-induced contraction in arteries (with and without PVAT) was blocked by CCX832 and the α-adrenergic receptor antagonist prazosin. CCX832 did not directly inhibit, nor did chemerin directly amplify, norepinephrine-induced contraction. Whole mount immunohistochemical experiments support colocalization of ChemR23 with the sympathetic nerve marker tyrosine hydroxylase in superior mesenteric PVAT and, to a lesser extent, in arteries and veins. These studies support the idea that exogenous chemerin modifies sympathetic nerve-mediated contraction through ChemR23 and that ChemR23 may be endogenously activated. This is significant because of the well-appreciated role of the sympathetic nervous system in blood pressure control. PMID:27371688

  14. 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. PMID:26130517

  15. 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)). PMID:26452774

  16. 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). PMID:26827710

  17. Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field.

    PubMed

    Lee, Hye-Yeon; Liu, Qingmei; Kang, Myung-Suk; Kim, Soo-Ki; Lee, Soon-Youl; Im, Wan-Taek

    2016-05-01

    Two novel actinobacteria, designated strains Gsoil 097T and Gsoil 818T, isolated from soil of a ginseng field, South Korea, were characterized by a polyphasic approach to clarify their taxonomic positions. They were Gram-reaction-positive, aerobic, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Marmoricola and were related most closely to Marmicola solisilvae KIS18-7T (99.1 and 98.3 % similarity, respectively), Marmicola terrae JOS5-1T (97.9 and 97.9 %), Marmicola scoriae Sco-D01T (97.8 and 97.1 %) and Marmicola aequoreus SST-45T (97.5 and 97.0 %). The G+C content of the genomic DNA was 68.8 and 70.0 mol%, respectively. Both strains were characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and C17 : 1ω6c, C18 : 1ω9c, C18 : 0 10-methyl and iso-C16 : 0 as major fatty acids. These chemotaxonomic data supported the affiliation of both strains to the genus Marmoricola. However, levels of DNA-DNA relatedness between the two strains and closely related type strains of Marmoricola species were less than 30 %. Moreover, the results of physiological and biochemical tests allowed the phenotypic differentiation of strains Gsoil 097T and Gsoil 818T from other Marmoricola species with validly published names. Therefore, the two isolates represent two novel species, for which the names Marmoricola ginsengisoli sp. nov. (type strain Gsoil 097T = KACC 14267T = DSM 22772T) and Marmoricola pocheonensis sp. nov. (type strain Gsoil 818T = KACC 14275T = DSM 22773T) are proposed. PMID:26883120

  18. [Investigation of Salmonella serotype Enteritidis isolates by plasmid profile analysis and pulsed field gel electrophoresis].

    PubMed

    Us, Ebru; Erdem, Birsel; Tekeli, Alper; Gerçeker, Devran; Saran, Begüm; Bayramova, Mehseti; Sahin, Fikret

    2011-04-01

    In this study a total of 122 Salmonella serotype Enteritidis stock strains selected from the culture collection of Enterobacteriaceae Laboratory of Ankara University Faculty of Medicine, Department of Medical Microbiology, were investigated by plasmid profile analysis with the method defined by Kado and Liu and pulsed field gel electrophoresis (PFGE) according to World Health Organization protocols using SpeI and XbaI macrorestriction enzymes, for better understanding of the molecular epidemiology of S. Enteritidis. The study strains were selected from a collection of previously isolated epidemic (n= 13) and sporadic (n= 109) strains (103 stool, 16 blood and one each bile, urine and cerebrospinal fluid) obtained from 10 different cities after the year 2000. PFGE patterns were analyzed with Gene Directory software (Syngene, UK) and a similarity index was determined by using Dice coefficient and the unweighted pair group method with mathematical averaging (UPGMA). Plasmid-carrying 110 (90%) strains that harbored 1-4 plasmids with sizes ranging from 2.0 to 100 kb were separated into patterns more than 14 (p1-p14). A total of 85 (69.7%) isolates harbored the 57 kb plasmid solely or in combination with other plasmids. By PFGE, 11 distinct patterns were shown with each enzyme SpeI and XbaI. S. Enteritidis strains after digestion with macrorestriction enzyme SpeI generated 11 different PFGE patterns (A to K), whereas XbaI generated also 11 different PFGE patterns (a to k). PFGE pattern A consisted of 93 strains (76.2%) after digestion with macrorestriction enzyme SpeI, while PFGE pattern a consisted 53 (43.4%) and PFGE pattern b 42 strains (34.4%) after digestion with macrorestriction enzyme XbaI. Using two macrorestriction enzymes two PFGE cluster profiles Aa (50 strains, 40.9%) and Ab (42 strains, 34.4%) were found to be predominating among 17 different PFGE clusters. Our results confirmed the clonal nature of S. Enteritidis strains in Turkey. The use of two enzymes in

  19. 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...

  20. Role of naturally occurring genome segment reassortment in the pathogenicity of IBDV field isolates in Three-Yellow chickens.

    PubMed

    He, Xiumiao; Chen, Guo; Yang, Lin; Xuan, Jincai; Long, Han; Wei, Ping

    2016-01-01

    Reassortment among genome segments of infectious bursal disease virus (IBDV) field isolates was reported frequently worldwide, however the pathogenicity of the reassortant field IBDV is poorly understood. In this paper, a pathogenicity study on four representative IBDV field strains isolated from Southern China between 2005 and 2011 was conducted. Twenty-eight-day-old Three-Yellow chickens were divided into four groups and were inoculated intraocularly with one of the four field IBDV strains, namely NN1172, NN1005, GD10111 and JS7, respectively. The mortality and relative weight of bursa and thymus were subsequently determined in the acute phase of infection. In addition, B cells, T cells (CD4(+) and CD8(+)) and virus were quantified in the bursa of Fabricius and thymus, respectively, by flow cytometry and real-time reverse transcription-polymerase chain reaction. The results showed that isolate NN1172, of which parts of segment A and B encoding the hypervariable (v) region of viral protein (VP2) and VP1, respectively, derived from vvIBDV strains, showed the most severe pathogenicity, and caused the most severe bursal B cell depletion as well as CD4(+) and CD8(+) T cell infiltration in the bursa of Fabricius. However, the virus induced the strongest decrease in CD4(+) and CD8(+) T cells in the thymus and exhibited the most efficient viral replication in the target organs. Isolate NN1005, whose vVP2 derived from vvIBDV and VP1 from unidentified origin, exhibited relatively lower pathogenicity compared to NN1172. The other two isolates, JS7 and GD10111, of which the vVP2 derived from vvIBDV and intermediate IBDV, and VP1 from 002-73 and attenuated IBDV, respectively, showed the lowest level of virulence. Our results suggest that various IBDV field isolates with different natural segment reassortments exhibit differential pathogenicity after infection of commercial Three-Yellow chickens. PMID:27100151

  1. 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

  2. Field Studies Reveal Strong Postmating Isolation between Ecologically Divergent Butterfly Populations

    PubMed Central

    McBride, Carolyn S.; Singer, Michael C.

    2010-01-01

    Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive, intermediate phenotypes. This phenomenon, called extrinsic postzygotic isolation (EPI), is thought to play a critical role in the early stages of speciation. However, despite its intuitive appeal, we know surprisingly little about the strength and prevalence of EPI in nature, and even less about the specific phenotypes that tend to cause problems for hybrids. In this study, we searched for EPI among allopatric populations of the butterfly Euphydryas editha that have specialized on alternative host plants. These populations recall a situation thought typical of the very early stages of speciation. They lack consistent host-associated genetic differentiation at random nuclear loci and show no signs of reproductive incompatibility in the laboratory. However, they do differ consistently in diverse host-related traits. For each of these traits, we first asked whether hybrids between populations that use different hosts (different-host hybrids) were intermediate to parental populations and to hybrids between populations that use the same host (same-host hybrids). We then conducted field experiments to estimate the effects of intermediacy on fitness in nature. Our results revealed strong EPI under field conditions. Different-host hybrids exhibited an array of intermediate traits that were significantly maladaptive, including four behaviors. Intermediate foraging height slowed the growth of larvae, while intermediate oviposition preference, oviposition site height, and clutch size severely reduced the growth and survival of the offspring of adult females. We used our empirical data to construct a fitness surface on which different-host hybrids can be seen to fall in an adaptive valley between two peaks occupied by same-host hybrids. These findings demonstrate how ecological selection against hybrids can create a strong barrier to gene flow at the early

  3. Single-pinhole diffraction of few-cycle isolated attosecond pulses with a two-color field

    NASA Astrophysics Data System (ADS)

    Shaoyi, Wang; Dan, Han; Kegong, Dong; Yuchi, Wu; Fang, Tan; Bin, Zhu; Quanping, Fan; Leifeng, Cao; Yuqiu, Gu

    2016-03-01

    The spatio-temporal characterization of an isolated attosecond pulse is investigated theoretically in a two-color field. Our results show that a few-cycle isolated attosecond pulse with the center wavelength of 16 nm can be generated effectively by adding a weak controlling field. Using the split and delay units, the isolated attosecond pulse can be split to the two same ones, and then single-pinhole diffractive patterns of the two pulses with different delays can be achieved. The diffractive patterns depend severely on the periods of the attosecond pulses, which can be helpful to obtain temporal information of the coherent sources. Project supported by the National Science Instruments Major Project of China (Grant No. 2012YQ130125), the National Natural Science Foundation of China (Grant Nos. 11405159, 11375161, and 11174259), and the Science and Technology on Plasma Physics Laboratory at CAEP (Grant No. 9140C680302130C68242).

  4. Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field.

    PubMed

    Rahalkar, Monali C; Pandit, Pranitha S; Dhakephalkar, Prashant K; Pore, Soham; Arora, Preeti; Kapse, Neelam

    2016-04-01

    Flooded rice fields are important sources of atmospheric methane. Aerobic methanotrophs living in the vicinity of rice roots oxidize methane and act as environmental filters. Here, we present genome characteristics of a gammaproteobacterial methanotroph, isolate Sn10-6, which was isolated from a rice rhizosphere of a flooded field in India. Sn10-6 has been identified as a member of a putative novel genus and species within the family Methylococcaceae (Type I methanotrophs). The draft genome of Sn10-6 showed pathways for the following: methane oxidation, formaldehyde assimilation (RuMP), nitrogen fixation, conversion of nitrite to nitrous oxide, and other interesting genes including the ones responsible for survival in the rhizosphere environment. The majority of genes found in this genome were most similar to Methylovulum miyakonese which is a forest isolate. This draft genome provided insight into the physiology, ecology, and phylogeny of this gammaproteobacterial methanotroph. PMID:26547566

  5. 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)). PMID:27120464

  6. Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field.

    PubMed

    Geymonat, Estefanía; Ferrando, Lucía; Tarlera, Silvana E

    2011-11-01

    A novel methanotroph, designated strain E10(T), was isolated from a rice paddy field in Uruguay. Strain E10(T) grew on methane and methanol as sole carbon and energy sources. Cells were Gram-negative, non-motile, non-pigmented, slightly curved rods showing type I intracytoplasmic membranes arranged in stacks. The strain was neutrophilic and mesophilic; optimum growth occurred at 30-35 °C with no growth above 37 °C. The strain possessed only a particulate methane monooxygenase (pmoA). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the moderately thermophilic strains Methylocaldum szegediense OR2(T) (91.6 % sequence similarity) and Methylococcus capsulatus Bath (91.5 %). Comparative sequence analysis of pmoA genes also confirmed that strain E10(T) formed a new lineage among the genera Methylocaldum and Methylococcus with 89 and 84 % derived amino acid sequence identity to Methylococcus capsulatus Bath and Methylocaldum gracile VKM-14L(T), respectively. The DNA G+C content was 63.1 mol% and the major cellular fatty acid was C(16 :0) (62.05 %). Thus, strain E10(T) (=JCM 16910(T) = DSM 23452(T)) represents the type strain of a novel species within a new genus, for which the name Methylogaea oryzae gen. nov., sp. nov. is proposed. PMID:21131502

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

    DOE PAGESBeta

    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%.

  8. Pulsed Field Gel Electrophoresis along with Antimicrobial Resistance pattern of Salmonella serotypes isolated from broiler whole carcass rinses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pulsed field gel electrophoresis (PFGE) and antibiogram patterns have been used to evaluate the diversity within and between individual Salmonella serotypes. The objectives of the study were to evaluate the PFGE along with antimicrobial resistance patterns of Salmonella isolates originating from br...

  9. 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

  10. Understanding the molecular mechanism of instability of the avirulence gene AVR-Pita1 in field isolates of Maganporthe oryzae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The avirulence gene AVR-Pita1 in Magnaporthe oryzae triggers a resistance response in rice plants that contain the resistance gene Pi-ta. Understanding the evolution of the AVR-Pita1 gene in field isolates should benefit the deployment of Pi-ta for the control of rice blast disease. A total of 187 f...

  11. 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...

  12. Isolation of exotic Newcastle disease virus (ENDV) from field collected flies and experimental ENDV infections of three arthropod species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During the 2002 Exotic Newcastle Disease (END) outbreak in California arthropods were collected from two quarantined backyard poultry premises after removal of END virus infected birds. The END virus (ENDV) isolated from field collected pools of three fly species was found to have >98% homology by ...

  13. 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

  14. Improved protocol for isolation of Campylobacter spp. from retail broiler meat and use of pulsed field gel electrophoresis for the typing of isolates.

    PubMed

    Oyarzabal, Omar A; Williams, Aretha; Zhou, Ping; Samadpour, Mansour

    2013-10-01

    To improve the detection of Campylobacter spp. in retail broiler meat, a reference method (R subsamples) based on the enrichment of 25 g of meat in Bolton broth at 42°C under microaerobiosis was compared with an alternative method (A subsamples) consisting in the rinsing of meat samples for 30s in buffered peptone water with antimicrobials with incubation at 42°C under aerobiosis. One piece of meat (breasts, tenderloins and thighs) was rinse in experiment 1 (A1) and two pieces in experiment 2 (A2). Campylobacter spp. were isolated on agar plates and identified by PCR. Retail samples in Alabama had less prevalence (P ≤ 0.05) than samples in the state of Washington. The percentage of positive was higher (P ≤ 0.05) in A than in R subsamples and rinsing two pieces of meat yielded the highest percentage of positive subsamples. R subsamples showed variations in the prevalence by product. However, A subsamples had similar prevalence of positives among products compare to the result from reference method. More Campylobacter coli isolates were collected in A2 subsamples. Pulse field gel electrophoresis (PFGE) was used as subtyping method to study the genome similarity among the isolates from all methods. A larger diversity of isolates were detected by PFGE in A2 subsamples. Denaturing gradient gel electrophoresis analysis suggested that the initial bacterial populations of the meat samples impact the final bacterial profile after enrichment. Rinsing broiler meats was less time consuming, required less sample preparation and was more sensitive than the reference method for the isolation of naturally occurring Campylobacter spp. This new method could help with epidemiological and intervention studies to control Campylobacter spp. PMID:23545445

  15. Sensitivity of field isolates of Eimeria from two broiler complexes to anticoccidial drugs in the chicken.

    PubMed

    Chapman, H D; Hacker, A B

    1994-09-01

    The spectrum of resistance to seven currently used anticoccidial drugs in isolates of Eimeria obtained from farms two broiler complexes was examined. All isolates were resistant to monensin, salinomycin, and narasin. Lasalocid was more effective in controlling coccidiosis than the other ionophores, although most isolates were classified as resistant to the drug. The majority of isolates were sensitive or showed reduced sensitivity to robenidine, clopidol, and decoquinate. It was concluded that for drugs that have been used extensively (e.g., monensin and salinomycin), examination of isolates from one or two farms may give results applicable to the entire complex. For drugs that have been used infrequently, however (such as robenidine, clopidol, and decoquinate), examination of isolates from at least five farms would be desirable to establish the spectrum of drug sensitivity. PMID:7800639

  16. [The effect of ionophore anticoccidial agents on coccidia isolated in field conditions 1984-1985].

    PubMed

    Bedrník, P; Jurkovic, P; Firmanová, A; Kucera, J

    1987-12-01

    Out of six isolates of coccidia of the species Eimeria tenella, obtained in the years 1984 and 1985 on farms with a stationary occurrence of coccidiosis, five were found to have reduced sensitivity or resistance to monensin. Neither were these isolates sensitive to further monovalent ionophorous anticoccidials narasin and salinomycin. The bivalent ionophorous anticoccidial lasalocid controlled five isolates completely, but for one its effectiveness was reduced. An isolate obtained on a farm with long-term absence of coccidiosis was sensitive to all anticoccidial drugs. PMID:3127981

  17. Characterization of two Austrian porcine reproductive and respiratory syndrome virus (PRRSV) field isolates reveals relationship to East Asian strains.

    PubMed

    Sinn, Leonie J; Zieglowski, Leonie; Koinig, Hanna; Lamp, Benjamin; Jansko, Bettina; Mößlacher, Georg; Riedel, Christiane; Hennig-Pauka, Isabel; Rümenapf, Till

    2016-01-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) causes major problems for the swine industry worldwide. Due to Austria's central location in Europe, a large number of animals are transported through the country. However, little is known about current PRRSV strains and epidemiology. We determined full-length genome sequences of two Austrian field isolates (AUT13-883 and AUT14-440) from recent PRRSV outbreaks and of a related German isolate (GER09-613). Phylogenetic analysis revealed that the strains belong to European genotype 1 subtype 1 and form a cluster together with a South Korean strain. Remarkably, AUT14-440 infected the simian cell line MARC-145 without prior adaptation. In addition, this isolate showed exceptional deletions in nonstructural protein 2, in the overlapping region of glycoprotein 3 and 4 and in the 3' untranslated region. Both Austrian isolates caused similar lung lesions but only pigs infected with AUT14-440 developed clear clinical signs of infection. Taken together, the genetic and biological characterization of two novel Austrian PRRSV field isolates revealed similarities to East Asian strains. This stresses the necessity for a more detailed analysis of current PRRSV strains in Europe beyond the determination of short ORF5 and ORF7 sequences. PMID:26754154

  18. 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. PMID:25544307

  19. Genomic relatedness among Actinobacillus pleuropneumoniae field strains of sterotypes 1 and 5 isolated from healthy and diseased pigs.

    PubMed Central

    Chatellier, S; Harel, J; Dugourd, D; Chevallier, B; Kobisch, M; Gottschalk, M

    1999-01-01

    Forty-four Actinobacillus pleuropneumoniae isolates recovered from both healthy and diseased pigs were characterized by random amplified polymorphic DNA analysis (RAPD), pulsed field gel electrophoresis (PFGE) and apx toxin gene typing. Nine RAPD types and 14 PFGE patterns were identified. No common RAPD or PFGE patterns were found between strains of serotype 1 and those of serotype 5. The RAPD analysis indicated that the 15 serotype 1 strains isolated from diseased pigs were assigned to 4 RAPD types, with 66% of strains characterized by the same RAPD type. By contrast, the 5 strains of serotype 1 isolated from healthy carriers were dispersed in 4 RAPD types. These data suggest that the diversity of strains isolated from healthy pigs could be higher than that of strains recovered from diseased pigs. In addition, all serotype 5 strains exhibited a unique RAPD type. Unlike RAPD, PFGE analysis allowed discrimination among isolates of serotype 1 and among those of serotype 5. All but 3 isolates showed the same apx genotype as their respective serotype reference strain. These data indicate that RAPD analysis is a valuable rapid tool for routine subtyping of strains of serotype 1. For strains of serotype 5, a combination of several typing methods, such as PFGE and apx gene typing, is needed to provide useful information on the molecular epidemiology of swine pleuropneumonia. Images Figure 1. Figure 3. PMID:10480458

  20. Rice-Field Drowning-Associated Pneumonia in which Pseudomonas spp., Aspergillus fumigatus, and Cunninghamella sp. Are Isolated.

    PubMed

    Yamawaki, Satoshi; Nakashima, Kei; Suzuki, Fumi; Otsuki, Ayumu; Watanabe, Junko; Takai, Motohisa; Katsurada, Masahiro; Katsurada, Naoko; Ohkuni, Yoshihiro; Misawa, Masafumi; Kaneko, Norihiro; Otsuka, Yoshihito; Aoshima, Masahiro

    2016-01-01

    We herein report the case of an 84-year-old who developed pneumonia after drowning in a rice field. Besides Aspergillus fumigatus, many pathogens previously not reported in drowning-associated pneumonia (such as Pseudomonas fluorescens, Pseudomonas putida, Nocardia niigatensis, and Cunninghamella sp.) were isolated from his sputum. He received sulbactam/ampicillin, trimethoprim/sulfamethoxazole, voriconazole, levofloxacin and liposomal amphotericin B, but died due to respiratory failure. Because the patient had drowned in a contaminated stagnant rice field and had multiple lung cavities, zygomycosis was suspected. This report provides invaluable information for the consideration of zygomycosis after an individual drowning in a rice field, even in an immunocompetent patient. PMID:27041173

  1. [Radio Frequency Electromagnetic Field Effect on the State of Na+/Ca2+ Exchange in the Isolated Rat Heart].

    PubMed

    Alabovsky, V V; Kudryshov, Yu B; Vinokurov, A A; Bogacheva, E V; Maslov, O V; Perov, S Yu

    2016-01-01

    It has been shown that a single exposure to 171 MHz electromagnetic field with 180 V/m electric field strength and 0.04 mW/kg specific absorption rate significantly alters the Na+/Ca2+ exchange in the isolated rat heart. It is assumed that enhancement of the Na+/Ca2+ exchange towards removing Ca2+ from the cardiomyocytes electromagnetic field exposure is a result of Ca2+ extraction from the sarcoplasmic reticulum and the increase of its intracellular level. PMID:27534068

  2. Resistance to anticoccidial drugs of Dutch avian Eimeria spp. field isolates originating from 1996, 1999 and 2001.

    PubMed

    Peek, H W; Landman, W J M

    2003-08-01

    Fifteen Eimeria spp. field isolates sampled on Dutch broiler farms were subjected to an Anticoccidial Sensitivity Test (AST) in a battery cage study. Four isolates dated from 1996, another four from 1999 and the last seven isolates from 2001. The selected anticoccidial drugs were monensin, narasin, salinomycin, lasalocid, nicarbazin, diclazuril, halofuginone, maduramicin and meticlorpindol/methylbenzoquate. Maduramicin and halofuginone were not included in the ASTs of 1999 and 2001, while meticlorpindol/methylbenzoquate was not tested in 1996 and 1999. Eimeria acervulina present in each of the four 1996 field isolates showed resistance for almost all products tested except maduramicin (1/4) and salinomycin (114), which appeared to be reduced sensitive. In 1999 the same species presented a similar resistance pattern for most products, although reduced sensitivity occurred for salinomycin (1/4), and sensitivity was found for diclazuril (2/4), monensin (1/4) and narasin (1/4). In the year 2001 increased sensitivity to various products was found. Higher sensitivity was found for meticlorpindol/ methylbenzoquate (7/7) and salinomycin and narasin (both 4/7), followed by nicarbazin (3/7) and monensin (2/7). Reduced sensitivity was found for monensin (3/7), lasalocid (2/7), salinomycin and narasin (1/7). E. maxima was only found in one field isolate per year. The E. maxima from 1996 was resistant to all products except narasin (sensitive) and halofuginone (reduced sensitive). In 1999 this species was reduced sensitive to narasin and lasalocid, showing resistance for the other products. The strain originating from the 2001 isolate was reduced sensitive to most products except monensin and narasin (resistant). Full sensitivity was found for meticlorpindol/ methylbenzoquate. E. tenella was present in one isolate of 1996, two of 1999 and four isolates of 2001. The AST of 1996 showed reduced sensitivity for nicarbazin, and sensitive to narasin, maduramicin and halofuginone. All

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

    PubMed

    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

  4. 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

  5. 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

  6. Microbacterium oryzae sp. nov., an actinobacterium isolated from rice field soil.

    PubMed

    Kumari, Prabla; Bandyopadhyay, Saumya; Das, Subrata K

    2013-07-01

    A novel aerobic soil actinobacterium (strain MB10(T)) belonging to the genus Microbacterium was isolated from rice field soil samples collected from Jagatpur, Orissa, India. Cells were Gram-stain positive, short rod-shaped and motile. The strain was oxidase-negative and catalase-positive. Heterotrophic growth was observed at pH 5.0-11.0 and at 16-37 °C; optimum growth was observed at 28 °C and pH 7.0-9.0. The DNA G+C content was 71.6 mol%. Predominant cellular fatty acids of strain MB10(T) were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cell wall sugars were galactose, glucose and rhamnose. The major isoprenoid quinones were MK-9 (10 %), MK-10 (43 %) and MK-11 (36 %). The peptidoglycan represents the peptidoglycan type B2β. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and unknown glycolipids. 16S rRNA gene sequence identity revealed the strain MB10(T) clustered within the radiation of the genus Microbacterium and showed 99.2 % similarity with Microbacterium barkeri DSM 20145(T). However, DNA-DNA similarity study was 37.0 % with Microbacterium barkeri DSM 20145(T), the nearest phylogenetic relative. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA-DNA reassociation studies, it is proposed that strain MB10(T) represents a novel species of the genus Microbacterium, for which the name Microbacterium oryzae sp. nov. is proposed; the type strain is MB10(T) ( = JCM 16837(T) = DSM 23396(T)). PMID:23203624

  7. Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China.

    PubMed

    Zhang, Shi-Ying; Xiao, Wei; Xia, Yun-Sheng; Wang, Yong-Xia; Cui, Xiao-Long; Zhang, Nai-Ming

    2015-05-01

    A Gram-stain negative, aerobic, rod-shaped bacterial strain, YN2-31A(T), was isolated from rice-field soil, Taoyuan Village, Yunnan province of China. The bacterium was observed to grow at 20-45 °C (optimum 28 °C), at pH 5.0-10.0 (optimum 7.0), and in the presence of 0-2% (w/v) NaCl (optimum 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2-31A(T) is most closely related to Arenimonas daejeonensis DSM 18060(T) (96.1%), Arenimonas malthae DSM 21305(T) (95.9%), Arenimonas donghaensis DSM 18148(T) (95.1%), Arenimonas composti DSM 18010(T) (94.8%) and Arenimonas maotaiensis JCM 19710(T) (94.8%). The major cellular fatty acids (>10%) were found to be iso-C(18:1) ω9c, iso-C(15:0), Sum In Feature 3 (C(16:1) ω7c/C(16:1) ω6c), and C(16:0). The major ubiquinone was identified as Q-8 and the major cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The genomic DNA G+C content was determined to be 72.3 mol%. The results of the phylogenetic, genetic, phenotypic and chemotaxonomic analyses suggest that strain YN2-31A(T) represents a novel species of the genus Arenimonas, for which the name Arenimonas taoyuanensis sp. nov. is proposed. The type strain is YN2-31A(T) (=DSM 26777(T) = CCTCC AB2012964(T)). PMID:25731739

  8. Effects of transmural field stimulation in isolated muscle strips from rabbit sphincter of Oddi and duodenum.

    PubMed

    Elbrønd, H; Tøttrup, A; Virchenko, S; Forman, A

    1994-05-01

    The purpose of the study was to compare the effect of transmural field stimulation (TMS) on isolated smooth muscle strips from rabbit sphincter of Oddi (SO), duodenal circular layer (Dc) and duodenal longitudinal layer (D1). The strips were suspended in thermostatically controlled 5-ml organ baths containing Krebs solution constantly bubbled with 5% CO2 in O2. TMS was delivered through platinum electrodes (140 V, 0.4 ms, 5 s trains, 40 Hz). The TMS responses could be divided in two main responses: (1) contraction initiated after cessation of the stimulus train, preceded by an inhibitory phase during TMS ('off'); and (2) contraction initiated during TMS ('duration'). The 'duration' response was observed in one out of 20 strips in the SO and Dc compartments, whereas 11 D1 strips (55%) showed 'duration' responses (P < 0.001). Atropine (10(-6)) converted all 'duration' responses to an 'off' response preceded by an inhibitory phase during TMS and reduced the contractile amplitudes with 40-65%. L-NNA significantly increased the number of 'duration' responses in all types of muscle, and caused a 40% increase in D1 contractile amplitude. Inhibitory responses could not be removed by atropine, propranolol and phentolamine. The results suggest that the intrinsic innervation of SO and duodenal muscle consists of a mixture of excitatory, cholinergic and inhibitory NANC pathways. The latter may utilize, wholly or partly, NO or a related compound as transmitter. A relative dominance of excitatory, cholinergic responses was present in the D1 strips, whereas inhibitory responses were dominating in the SO and Dc strips. PMID:8048339

  9. Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field.

    PubMed

    Siddiqi, Muhammad Zubair; Im, Wan-Taek

    2016-08-01

    A Gram-staining-negative, non-spore-forming, non-flagellated, rod-shaped, catalase- and oxidase-negative bacterium, designated as Gsoil 193(T), was isolated from the soil of ginseng field in Pocheon province, South Korea. 16S rRNA gene sequence analysis showed that strain Gsoil 193(T) belonged to family Xanthomonadaceae and was most closely related to Lysobacter daecheongensis KCTC 12,600(T) (96.4 %), Lysobacter panaciterrae KCTC 12601(T) (96.3 %), Lysobacter dokdonensis DSM 17958(T) (96.3 %) and Lysobacter oligotrophicus JCM 18257(T) (95.6 %). Strain Gsoil 193(T) grew at temperatures between 20 and 30 °C with an optimum of 30 °C. The pH range for growth was 5-9 pH (optimum 6-7 pH). The predominant respiratory quinone was ubiquinone Q-8 and a fatty acid profile with iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17:1 ω9c/C16:0 10-methyl) as the major fatty acids supported the affiliation of strain Gsoil 193(T) to the genus Lysobacter. The genomic DNA G+C content was 64.8 mol %. On the basis of the genotypic analysis, physiological and chemotaxonomic results indicate that strain Gsoil 193(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter pocheonensis sp. nov. is proposed. The type strain is Gsoil 193(T) (= DSM 18338(T) = KCTC 12624(T)). PMID:27052400

  10. Combinations of Macrolide Resistance Determinants in Field Isolates of Mannheimia haemolytica and Pasteurella multocida▿

    PubMed Central

    Desmolaize, Benoit; Rose, Simon; Wilhelm, Cornelia; Warrass, Ralf; Douthwaite, Stephen

    2011-01-01

    Respiratory tract infections in cattle are commonly associated with the bacterial pathogens Mannheimia haemolytica and Pasteurella multocida. These infections can generally be successfully treated in the field with one of several groups of antibiotics, including macrolides. A few recent isolates of these species exhibit resistance to veterinary macrolides with phenotypes that fall into three distinct classes. The first class has type I macrolide, lincosamide, and streptogramin B antibiotic resistance and, consistent with this, the 23S rRNA nucleotide A2058 is monomethylated by the enzyme product of the erm(42) gene. The second class shows no lincosamide resistance and lacks erm(42) and concomitant 23S rRNA methylation. Sequencing of the genome of a representative strain from this class, P. multocida 3361, revealed macrolide efflux and phosphotransferase genes [respectively termed msr(E) and mph(E)] that are arranged in tandem and presumably expressed from the same promoter. The third class exhibits the most marked drug phenotype, with high resistance to all of the macrolides tested, and possesses all three resistance determinants. The combinations of erm(42), msr(E), and mph(E) are chromosomally encoded and intermingled with other exogenous genes, many of which appear to have been transferred from other members of the Pasteurellaceae. The presence of some of the exogenous genes explains recent reports of resistance to additional drug classes. We have expressed recombinant versions of the erm(42), msr(E), and mph(E) genes within an isogenic Escherichia coli background to assess their individually contributions to resistance. Our findings indicate what types of compounds might have driven the selection for these resistance determinants. PMID:21709086

  11. Kodamaea ohmeri isolates from patients in a university hospital: identification, antifungal susceptibility, and pulsed-field gel electrophoresis analysis.

    PubMed

    Lee, Jin Sol; Shin, Jong Hee; Kim, Mi-Na; Jung, Sook-In; Park, Kyung Hwa; Cho, Duck; Kee, Seung Jung; Shin, Myung Geun; Suh, Soon Pal; Ryang, Dong Wook

    2007-03-01

    Data on clinical isolates of Kodamaea (Pichia) ohmeri, an emerging fungal pathogen, are scarce. Over the past 5 years, we identified yeast isolates from nine patients with fungemia as K. ohmeri by using the API 20C system. Here, we reanalyzed these isolates first by sequencing the internal transcribed spacer 2 (ITS2) regions and then by growing the isolates on CHROMagar Candida medium and subjecting them to pulsed-field gel electrophoresis (PFGE). Based on their ITS2 sequences, six of the nine isolates were confirmed as K. ohmeri, while the others were identified as Candida haemulonii (n = 2) and Candida parapsilosis (n = 1). PFGE karyotyping of the K. ohmeri isolates revealed similar major bands, and their colonies showed a characteristic color change from pink to blue when grown on CHROMagar Candida medium for more than 48 h. For K. ohmeri, the ranges of MICs of fluconazole, voriconazole, caspofungin, and micafungin were 2 to 32 mug/ml, 0.03 to 0.5 mug/ml, 0.125 to 0.25 mug/ml, and 0.03 to 0.06 mug/ml, respectively. Restriction endonuclease analysis of genomic NotI-digested DNA (REAG-N) from isolates from different patients produced unique patterns, suggesting that the fungemia had occurred sporadically. This study determined that ITS2 sequence data, PFGE karyotypes, and CHROMagar Candida chromogenic culture medium are reliable diagnostic tools for identifying K. ohmeri while REAG-N is useful for genotyping the clinical isolates of K. ohmeri. PMID:17251396

  12. Epidemiologic analysis of sporadic Salmonella typhi isolates and those from outbreaks by pulsed-field gel electrophoresis.

    PubMed Central

    Thong, K L; Cheong, Y M; Puthucheary, S; Koh, C L; Pang, T

    1994-01-01

    Pulsed-field gel electrophoresis (PFGE) was used to compare and analyze 158 isolates of Salmonella typhi from five well-defined outbreaks of typhoid fever in Malaysia and also isolates involved in sporadic cases of typhoid fever occurring during the same period. Digestion of chromosomal DNAs from these S. typhi isolates with the restriction endonucleases XbaI (5'-TCTAGA-3'), SpeI (5'-ACTAGT-3'), and AvrII (5'-CCTAGG-3') and then PFGE produced restriction endonuclease analysis (REA) patterns consisting of 11 to 24 DNA fragments ranging in size from 20 to 630 kbp. Analysis of the REA patterns generated by PFGE after digestion with XbaI and SpeI indicated that the S. typhi isolates obtained from sporadic cases of infection were much more heterogeneous (at least 13 different REA patterns were detected; Dice coefficient, between 0.73 and 1.0) than those obtained during outbreaks of typhoid fever. The clonal nature and the close genetic identities of isolates from outbreaks in Alor Setar, Penang, Kota Kinabalu, Johor Bahru, and Kota Bahru were suggested by the fact that only a limited number of REA patterns, which mostly differed by only a single band, were detected (one to four patterns; Dice coefficient, between 0.82 and 1.0), although a different pattern was associated with each of these outbreaks. Comparison of REA patterns with ribotyping for 18 S. typhi isolates involved in sporadic cases of infection showed a good correlation, in that 72% of the isolates were in the same group. There was no clear correlation of phage types with a specific REA pattern. We conclude that PFGE of s. typhi chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for comparing and differentiating S. typhi isolates for epidemiological purposes. Images PMID:7914202

  13. 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

  14. Analysis of haemorrhagic septicaemia-causing isolates of Pasteurella multocida by ribotyping and field alternation gel electrophoresis (FAGE).

    PubMed

    Townsend, K M; Dawkins, H J; Papadimitriou, J M

    1997-10-16

    Ribotyping and field alternation gel electrophoresis (FAGE) were used to examine 19 Pasteurella multocida isolates, and to assess the ability of these techniques to differentiate P. multocida strains that cause haemorrhagic septicaemia (HS). Reproducible patterns were obtained from both methods, with FAGE demonstrating greater discriminatory power than ribotyping. FAGE analysis was particularly useful in distinguishing North American cultures originating from the 1922 Yellowstone National Park Buffalo 'B' strain, demonstrating the ability to detect genetic alterations induced by repeated subculture. A remarkable homogeneity was observed among Asian HS strains following ribotyping and FAGE analysis, with a clear distinction observed between virulent and avirulent HS isolates. This study has illustrated the value of genomic fingerprinting methods in distinguishing strains of similar serotype, and the capability of these methods to produce detailed characterisation of P. multocida isolates. PMID:9444075

  15. 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

  16. 7 CFR 201.76 - Minimum Land, Isolation, Field, and Seed Standards.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... varieties of dissimilar adaptation and establishment of the stand for the production of the Certified class... varieties of dissimilar adaptation. 4 Isolation between classes of the same variety may be reduced to...

  17. Quantitative Field Testing Rotylenchulus reniformis DNA from Metagenomic Samples Isolated Directly from Soil

    PubMed Central

    Showmaker, Kurt; Lawrence, Gary W.; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P.

    2011-01-01

    A quantitative PCR procedure targeting the β-tubulin gene determined the number of Rotylenchulus reniformis Linford & Oliveira 1940 in metagenomic DNA samples isolated from soil. Of note, this outcome was in the presence of other soil-dwelling plant parasitic nematodes including its sister genus Helicotylenchus Steiner, 1945. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from soil. PMID:22194958

  18. 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. PMID:21327574

  19. 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

    2014-03-01

    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. PMID:24412413

  20. 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

  1. Analysis of molecular epidemiology of Chilean Salmonella enterica serotype enteritidis isolates by pulsed-field gel electrophoresis and bacteriophage typing.

    PubMed

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

    2003-04-01

    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

  2. Comparison of in vitro activity of danofloxacin, florfenicol, oxytetracycline, spectinomycin and tilmicosin against recent field isolates of Mycoplasma bovis.

    PubMed

    Ayling, R D; Baker, S E; Peek, M L; Simon, A J; Nicholas, R A

    2000-06-24

    The minimum inhibitory concentrations (MICS) and minimum mycoplasmacidal concentrations (MMCs) of danofloxacin, florfenicol, oxytetracycline, spectinomycin and tilmicosin against 62 recent British field isolates of Mycoplasma bovis were determined in vitro by a broth microdilution method. The isolates were most susceptible todanofloxacin with MIC90 and MMC90 values of 0.5 microg/ml and 1.0 microg/ml, respectively. They were less susceptible to florfenicol with a MIC90 of 16 microg/ml and MMC90 of 32 microg/ml. Oxytetracycline and spectinomycin had only a limited effect against the majority of isolates tested with MIC50s of 32 microg/ml and 4 microg/ml, respectively and MIC90s of 64 microg/ml and more than 128 microg/ml, respectively. Nearly 20 per cent of the isolates were highly resistant to spectinomycin, and tilmicosin was ineffective, with 92 per cent of the isolates having MIC values of 128 microg/ml or greater. There was no evidence of resistance by M bovis to danofloxacin. PMID:10909906

  3. Generation of an extreme ultraviolet supercontinuum and isolated sub-50 as pulse in a two-colour laser field

    NASA Astrophysics Data System (ADS)

    Zhang, Gang-Tai; Liu, Xue-Shen

    2009-06-01

    We theoretically study high-order harmonic generation when a helium ion is exposed to a two-colour laser field, which is synthesized by a 5 fs/800 nm laser pulse and a 64 fs/2400 nm laser pulse. Our numerical results show that the harmonic spectrum exhibits an ultrabroad extreme ultraviolet supercontinuum when the initial state is prepared as a coherent superposition of the ground state and the first excited state. By superposing a series of properly selected harmonics, an isolated attosecond pulse with a duration of 47 as is obtained. Compared with the case of the ground state in a one-colour field, the intensity of this isolated attosecond pulse is six orders of magnitude higher. We also demonstrate these results in terms of the time-frequency analysis and the semiclassical three-step model.

  4. Saccharopolyspora subtropica sp. nov., a thermophilic actinomycete isolated from soil of a sugar cane field.

    PubMed

    Wu, Hao; Liu, Bin; Pan, Shangli

    2016-05-01

    A novel thermophilic actinomycete, designated strain T3T, was isolated from a soil sample of a sugar cane field. The strain grew at 25-60 °C (optimum 37-50 °C), at pH 6.0-11.0 (optimum 7.0-9.0) and with 0-12.0 % (w/v) NaCl (optimum 0-7 %). The aerial mycelium was white and the vegetative mycelium was colourless to pale yellow. The substrate mycelium fragmented into rod-shaped elements after 4-5 days at 50 °C. The aerial mycelium formed flexuous chains of 5-20 spores per chain; the oval-shaped spores had spiny surfaces and were non-motile. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars consisted of arabinose, galactose and ribose. The cellular fatty acid profile consisted mainly of anteiso-C17 : 0, iso-C17 : 0 and iso-C16 : 0. The quinone system was composed predominantly of MK-9(H4). The phospholipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine, phosphatidylmethylethanolamine and ninhydrin-positive glycophospholipids. The DNA G+C content of strain T3T was 71.3 mol%. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus Saccharopolyspora. In the 16S rRNA gene tree of Saccharopolyspora it formed a distinct phyletic line and was related most closely to Saccharopolyspora thermophila 216T. However, the phenotypic characteristics of strain T3T were significantly different from those of S. thermophila 216T and DNA-DNA hybridization revealed a low level of relatedness (28.6-32.3 %) between them. Based on the phenotypic and phylogenetic data, strain T3T represents a novel species in the genus Saccharopolyspora, for which the name Saccharopolyspora subtropica sp. nov. is proposed. The type strain is T3T ( = DSM 46801T = CGMCC 4.7206T). PMID:26882893

  5. Brachybacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Hoang, Van-An; Kim, Yeon-Ju; Nguyen, Ngoc-Lan; Yang, Deok-Chun

    2014-09-01

    A novel Gram-staining-positive, aerobic bacterium, designed DCY80(T), was isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence analysis revealed that strain DCY80(T) belonged to the genus Brachybacterium (95.8-98.2 % similarity) and was most closely related to Brachybacterium faecium DSM 4810(T) (98.2 %). Colonies were circular, entire, low-convex, opaque and 0.5-1.0 mm in diameter after growth for 2 days on TSA at 30 °C. Growth occurred at 4-34 °C (optimum, 25 °C), at pH 5.0-10.0 (optimum, pH 6.5-7.0) and in the presence of 0-7.0 % NaCl. Strain DCY80(T) produced siderophores and was sensitive to penicillin G, erythromycin, cefazolin, oleandomycin, ceftazidime, vancomycin, tetracycline, novobiocin, carbamicillin, rifampicin and neomycin. The DNA G+C content was 71.0 mol%. Levels of DNA-DNA relatedness between strain DCY80(T) and B. faecium DSM 4810(T), B. paraconglomeratum KCTC 9916(T), B. saurashtrense DSM 23186(T) and B. conglomeratum KCTC 9915(T) were 46.9±0.5, 28.9±0.6, 20.4±0.9 and 17.3±0.4 %, respectively. The cell-wall peptidoglycan of strain DCY80(T) contained meso-diaminopimelic acid as the diagnostic diamino acid. The menaquinones were MK-7 (85.8 %) and MK-8 (14.2 %). The major cellular fatty acids were anteiso-C15 : 0 (69.1 %) and anteiso-C17 : 0 (12.2 %). Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, two unidentified phospholipids and five unidentified polar lipids were found. On the basis of our phenotypic and genotypic analyses, strain DCY80(T) represents a novel species of the genus Brachybacterium, for which the name Brachybacterium ginsengisoli sp. nov. is proposed (type strain DCY80(T) = KCTC 29226(T) = JCM 19356(T)). PMID:24944333

  6. Central European Dobrava Hantavirus Isolate from a Striped Field Mouse (Apodemus agrarius)

    PubMed Central

    Klempa, Boris; Stanko, Michal; Labuda, Milan; Ulrich, Rainer; Meisel, Helga; Krüger, Detlev H.

    2005-01-01

    Dobrava virus (DOBV) is a hantavirus that causes hemorrhagic fever with renal syndrome (HFRS) in Europe. It is hosted by at least two rodent species, Apodemus flavicollis and A. agrarius. According to their natural hosts they form the distinct genetic lineages DOBV-Af and DOBV-Aa, respectively. We have now established a DOBV isolate named Slovakia (SK/Aa) from an A. agrarius animal captured in Slovakia. The complete S and M and partial L segment nucleotide sequences of the new isolate were determined. Phylogenetic analyses showed that the SK/Aa isolate clustered together with the other DOBV-Aa sequences amplified from A. agrarius before and can be taken as the representative of this genetic lineage. SK/Aa, in comparison with a DOBV-Af isolate, was used for serotyping neutralizing antibodies of HFRS patients in Central Europe. Most patients' sera exhibited a higher endpoint titer when probed with our new isolate, suggesting that DOBV-Aa strains are responsible for most of the DOBV-caused HFRS cases in this region. PMID:15956394

  7. Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing.

    PubMed

    Auburn, Sarah; Marfurt, Jutta; Maslen, Gareth; Campino, Susana; Ruano Rubio, Valentin; Manske, Magnus; Machunter, Barbara; Kenangalem, Enny; Noviyanti, Rintis; Trianty, Leily; Sebayang, Boni; Wirjanata, Grennady; Sriprawat, Kanlaya; Alcock, Daniel; Macinnis, Bronwyn; Miotto, Olivo; Clark, Taane G; Russell, Bruce; Anstey, Nicholas M; Nosten, François; Kwiatkowski, Dominic P; Price, Ric N

    2013-01-01

    Whole genome sequencing (WGS) of Plasmodium vivax is problematic due to the reliance on clinical isolates which are generally low in parasitaemia and sample volume. Furthermore, clinical isolates contain a significant contaminating background of host DNA which confounds efforts to map short read sequence of the target P. vivax DNA. Here, we discuss a methodology to significantly improve the success of P. vivax WGS on natural (non-adapted) patient isolates. Using 37 patient isolates from Indonesia, Thailand, and travellers, we assessed the application of CF11-based white blood cell filtration alone and in combination with short term ex vivo schizont maturation. Although CF11 filtration reduced human DNA contamination in 8 Indonesian isolates tested, additional short-term culture increased the P. vivax DNA yield from a median of 0.15 to 6.2 ng µl(-1) packed red blood cells (pRBCs) (p = 0.001) and reduced the human DNA percentage from a median of 33.9% to 6.22% (p = 0.008). Furthermore, post-CF11 and culture samples from Thailand gave a median P. vivax DNA yield of 2.34 ng µl(-1) pRBCs, and 2.65% human DNA. In 22 P. vivax patient isolates prepared with the 2-step method, we demonstrate high depth (median 654X coverage) and breadth (≥89%) of coverage on the Illumina GAII and HiSeq platforms. In contrast to the A+T-rich P. falciparum genome, negligible bias was observed in coverage depth between coding and non-coding regions of the P. vivax genome. This uniform coverage will greatly facilitate the detection of SNPs and copy number variants across the genome, enabling unbiased exploration of the natural diversity in P. vivax populations. PMID:23308154

  8. 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

  9. 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

    2012-07-01

    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

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

    PubMed Central

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

    2014-01-01

    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. PMID:24874680

  11. Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields.

    PubMed

    de Souza, Rocheli; Sant'Anna, Fernando Hayashi; Ambrosini, Adriana; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M P

    2015-01-01

    Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences. PMID:25838497

  12. Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields

    PubMed Central

    de Souza, Rocheli; Sant’Anna, Fernando Hayashi; Ambrosini, Adriana; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi

    2015-01-01

    Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences. PMID:25838497

  13. 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. PMID:25201253

  14. 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

  15. 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.

  16. 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. PMID:25514047

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

    PubMed Central

    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.

    2015-01-01

    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. PMID:25514047

  18. [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. PMID:1309137

  19. MAGNETIC FIELD IN THE ISOLATED MASSIVE DENSE CLUMP IRAS 20126+4104

    SciTech Connect

    Shinnaga, Hiroko; Phillips, Thomas G.; Novak, Giles; Vaillancourt, John E.; Machida, Masahiro N.; Kataoka, Akimasa; Tomisaka, Kohji; Davidson, Jacqueline; Houde, Martin; Dowell, C. Darren; Leeuw, Lerothodi

    2012-05-10

    We measured polarized dust emission at 350 {mu}m toward the high-mass star-forming massive dense clump IRAS 20126+4104 using the SHARC II Polarimeter, SHARP, at the Caltech Submillimeter Observatory. Most of the observed magnetic field vectors agree well with magnetic field vectors obtained from a numerical simulation for the case when the global magnetic field lines are inclined with respect to the rotation axis of the dense clump. The results of the numerical simulation show that rotation plays an important role on the evolution of the massive dense clump and its magnetic field. The direction of the cold CO 1-0 bipolar outflow is parallel to the observed magnetic field within the dense clump as well as the global magnetic field, as inferred from optical polarimetry data, indicating that the magnetic field also plays a critical role in an early stage of massive star formation. The large-scale Keplerian disk of the massive (proto)star rotates in an almost opposite sense to the clump's envelope. The observed magnetic field morphology and the counterrotating feature of the massive dense clump system provide hints to constrain the role of magnetic fields in the process of high-mass star formation.

  20. 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

  1. 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. PMID:26845339

  2. Characterization of western European field isolates and vaccine strains of avian infectious laryngotracheitis virus by restriction fragment length polymorphism and sequence analysis.

    PubMed

    Neff, C; Sudler, C; Hoop, R K

    2008-06-01

    Infectious laryngotracheitis is a dramatic disease of the upper respiratory tract in poultry caused by a herpesvirus. In this study we investigated the characteristics of western European field isolates of infectious laryngotracheitis virus (ILTV) to gain more information on their diversity. The examined 104 isolates, collected from acute outbreaks during the last 35 years, originated from eight different countries: Switzerland (48), Germany (21), Sweden (14), the United Kingdom (9), Italy (5), Belgium (4), Austria (2), and Norway (1). Two vaccines, a chicken embryo origin product and a tissue culture origin product, were included in the survey. Polymerase chain reaction (PCR) was performed to amplify a 2.1-kb DNA fragment of ILTV using primers generated for the thymidine kinase (TK) gene. After digestion of the resulting PCR products by restriction endonuclease HaeIII, restriction fragment length polymorphism analysis was carried out. PCR amplicons of three field isolates and both vaccine strains were selected for sequencing. Here 98 field isolates showed the same cleavage pattern and were identical to both vaccine strains (clone 1). They differed from five Swiss isolates with identical cleavage pattern (clone 2) and one Swedish isolate (clone 3). The present study demonstrated that at least three clones of ILTV have been circulating in western Europe during the last 35 years. The 104 isolates analyzed showed a high genetic similarity regarding the TK gene, and a large majority of the field isolates (98/104) were genetically related to the vaccine strains. PMID:18646457

  3. Bias field free tunability of microwave properties based on geometrically controlled isolated permalloy nanomagnets

    NASA Astrophysics Data System (ADS)

    Haldar, Arabinda; Adeyeye, Adekunle Olusola

    2016-04-01

    We have investigated the static and dynamic properties of two lithographically patterned bi-stable nanomagnets. Different ground magnetic states were realized using a simple in-plane field initialization technique. These states were directly imaged with magnetic force microscopy. Using the broadband ferromagnetic spectroscopy, we show that different magnetic ground states are associated with distinct microwave absorption spectra due to the variation of the internal magnetic field leading to large shift between the absorption spectra. Our experimental observations are in good agreement with micromagnetic simulations which also indicate the possibility of sub-ns switching between magnetic states using a rectangular pulse field.

  4. Generation of short and intense isolated Attosecond pulses by field-controlled excited states

    NASA Astrophysics Data System (ADS)

    Jooya, Hossein Z.; Li, Peng-Cheng; Liao, Sheng-Lun; Chu, Shih-I.

    2014-05-01

    A new mechanism for the coherent control of the generation of an isolated and ultrashort attosecond laser pulse with enhanced intensity is reported. Frequency and time delay of a weak high harmonics, added to a two color laser, are optimized to produce a 45 attosecond pulse with intensity of more than 70 times bigger than the original one. Resonance excitation and subsequent ionization are analyzed, along with electron trajectory investigation from wavelet time-frequency profile to explain the mechanism of the observed augmentation in this high-harmonic generation. This work is partially supported by DOE.

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

    PubMed

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

    2016-06-01

    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

  6. 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

  7. Genetic polymorphisms associated with sulphadoxine-pyrimethamine drug resistance among Plasmodium falciparum field isolates in malaria endemic areas of Assam

    PubMed Central

    Sharma, J; Dutta, P; Khan, SA; Soni, M; Dey, D; Mahanta, J

    2015-01-01

    Background: The emergence of antimalarial drug resistance malaria parasite is widespread in North eastern region of India. During January 2012-December 2013, we conducted active surveillance for detection of antifolate resistance-associated genetic polymorphisms in Plasmodium falciparum malaria parasite from different malaria endemic areas of Assam. Materials and Methods: A total of 281 field samples were collected from suspected malaria patients of which 106 malaria P. falciparum positive cases were detected in microscopic slide examination. A nested PCR was done for amplification of a 648 bp portion of the dhfr gene and 710 bp portion of the dhps gene. Results: Mutation analysis revealed existence of three different haplotypes of the P. falciparum dhfr gene of which ANRNI was highly prevalent (90%). Triple mutant haplotypes AIRNI (N51I + C59R + S108N) of the dhfr gene associated with pyrimethamine resistance were prevalent in Chirang district of Assam. Whereas, dhps mutation study revealed that triple mutant haplotype AGEAA (S436A + A437G + K540E) associated with Sulphadoxine resistance was found among 26% of P. falciparum field isolates. However, P. falciparum dhfr-dhps two locus mutation analysis showed that there were a total of nine dhfr-dhps genotypes. Conclusion: It was noticed that 93.62% (88/94) isolates had mutations in the sequences of both enzymes, which is an indication of prevalence of high grade of Sulphadoxine — pyrimethamine resistance in P. falciparum malaria parasites in Assam. PMID:25511211

  8. Efficacy of maduramicin against ionophore-tolerant field isolates of coccidia in broilers.

    PubMed

    McDougald, L R; Wang, G T; Kantor, S; Schenkel, R; Quarles, C

    1987-01-01

    Maduramicin ammonium was given at 2.5-8 ppm in the feed to broilers experimentally infected with coccidia recently isolated from broiler farms where ionophores had been used for several years. Infection pressure varied from mild to severe in five trials: mortality in unmedicated controls ranged from 0 to 59%, intestinal lesion scores were high, and weight gain was depressed by the infections. The cultures of Eimeria were partly resistant to ionophores: birds medicated with monensin at 100-121 ppm had only modest reductions in lesion scores and incomplete protection against weight loss or mortality. Control of infections by maduramicin was significant at 4 ppm but best at 5-7 ppm. Maduramicin was more effective than monensin or narasin, but about the same as salinomycin, in reducing lesions and mortality and in protecting performance. Maduramicin was well tolerated within the dose range of 5-7 ppm. PMID:3619823

  9. In vitro antibiotic susceptibility of field isolates of Mycoplasma synoviae in Argentina.

    PubMed

    Cerdá, R O; Giacoboni, G I; Xavier, J A; Sansalone, P L; Landoni, M F

    2002-01-01

    Minimum inhibitory concentrations (MICs) were determined in vitro for 7 antibiotics (aivlosin, enrofloxacine, tylosin, tiamulin, kitasamycin, chlortetracycline, and oxytetracycline) against eight recent local Argentinean isolates and two standard strains of Mycoplasma synoviae. Aivlosin (3-acetyl-4"-isovaleryl tylosin tartrate), tylosin, and tiamulin showed the lowest MICs with MIC90s of 0.006, 0.012, and 0.05 microg/ml, respectively. Except one strain that showed resistant values to chlortetracycline (> or = 12.5 microg/ml), all the analyzed strains were susceptible in different degrees to all the antibiotics tested. In this study, the improved activity of the tylosin-derived drug, aivlosin, was confirmed because it showed, in most strains, MIC values half those for tylosin. PMID:11922338

  10. Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001.

    PubMed

    Wang, Xiangru; Wei, Liuya; Wang, Bin; Zhang, Ruixuan; Liu, Canying; Bi, Dingren; Chen, Huanchun; Tan, Chen

    2016-01-01

    Avian pathogenic Escherichia coli is an important etiological agent of avian colibacillosis, which manifests as respiratory, hematogenous, meningitic, and enteric infections in poultry. It is also a potential zoonotic threat to human health. The diverse genomes of APEC strains largely hinder disease prevention and control measures. In the current study, pyrosequencing was used to analyze and characterize APEC strain ACN001 (= CCTCC 2015182(T) = DSMZ 29979(T)), which was isolated from the liver of a diseased chicken in China in 2010. Strain ACN001 belongs to extraintestinal pathogenic E. coli phylogenetic group B1, and was highly virulent in chicken and mouse models. Whole genome analysis showed that it consists of six different plasmids along with a circular chromosome of 4,936,576 bp, comprising 4,794 protein-coding genes, 108 RNA genes, and 51 pseudogenes, with an average G + C content of 50.56 %. As well as 237 coding sequences, we identified 39 insertion sequences, 12 predicated genomic islands, 8 prophage-related sequences, and 2 clustered regularly interspaced short palindromic repeats regions on the chromosome, suggesting the possible occurrence of horizontal gene transfer in this strain. In addition, most of the virulence and antibiotic resistance genes were located on the plasmids, which would assist in the distribution of pathogenicity and multidrug resistance elements among E. coli populations. Together, the information provided here on APEC isolate ACN001 will assist in future study of APEC strains, and aid in the development of control measures. PMID:26823959

  11. 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…

  12. Partial sequencing of recent Portuguese myxoma virus field isolates exhibits a high degree of genetic stability.

    PubMed

    Muller, A; Silva, E; Abrantes, J; Esteves, P J; Ferreira, P G; Carvalheira, J C; Nowotny, N; Thompson, G

    2010-01-01

    To study genetic changes underlying myxoma virus evolution in its new host, the European rabbit (Oryctolagus cuniculus), we sequenced selected genomic regions of nine recent virulent field strains and a live attenuated vaccine strain ("MAV", Germany). DNA was extracted from cell culture passaged myxoma virus. A total of 4863 bp (approximately 3% of the genome) of 10 regions spanning 12 genes of the myxoma viruses was sequenced and compared to the original virulent strain "Lausanne" and its attenuated field derivative strain "6918". The field strains displayed a maximum of three (strains C43, C95) and a minimum of one (strains CD01, CD05) nucleotide substitutions. These were distributed through all analysed coding regions, except gene M022L (major envelope protein), where all strains were identical to "Lausanne" and "6918". Two new single nucleotide insertions were observed in some of the field strains: within the intergenic region M014L/M015L and within gene M009L, where it leads to a frameshift. These insertions were located after homopolymeric regions. The vaccine strain displayed 37 nucleotide substitutions, predominantly (95%) located in genes M022L and M036L. Interestingly, regions M009L and M014L/M015L of the vaccine were not amplified successfully, suggesting major genomic changes that could account for its attenuated phenotype. Our results support a high degree of genetic stability of myxoma virus over the past five decades. None of the analysed genome regions by its own seems sufficient for the genetic characterisation of field strains. PMID:19709821

  13. 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

  14. 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. PMID:15570957

  15. WIPP (Waste Isolation Pilot Plant) horizon free field fluid transport characteristics

    SciTech Connect

    Peterson, E.W.; Lagus, P.L.; Lie, K.

    1987-12-01

    This report describes the first attempt to measure the free field brine transport characteristics of the host rock. The data, which have been used to estimate the brine permeability, also suggest free field pore pressure values. One borehole was located in a competent predominantly halite bed with the test region positioned approximately nine meters from the rib. A second borehole intersected Marker Bed 139, which is a one meter thick fractured predominantly anhydrite layer. For this second borehole, the test region was positioned approximately 12 meters from the invert/rib intersection. A description of the tests provided in Section 2. Data obtained during these tests are described in Section 3. Analysis of these data and the associated uncertainties inherent in the data interpretation are presented in Section 4. Test results are given in Section 5. Conclusions are provided in Section 6. 13 refs., 65 figs.

  16. The vital activity of organisms in infralow frequency magnetic fields. 5. Isolated blood cells

    SciTech Connect

    Khizhenkov, P.K.; Zinkovich, I.I.; Bilobrov, V.M.

    1995-07-01

    Results are presented of experimental investigations of the effect of alternating magnetic fields H of various amplitudes, shapes, and frequencies on the osmotic resistance of erythrocytes (ORE), the phagocytic activity of leukocytes (PAL), the malonic dialdehyde accumulation (MDA), and the albumen escape to the incubative medium. The specificity and intraspecific variability of the ORE and PAL characteristics are also shown. Under the effect of H the albumen escape was noted to decrease while the MDA concentration became larger.

  17. Hypnocyclicus thermotrophus gen. nov., sp. nov. isolated from a microbial mat in a hydrothermal vent field.

    PubMed

    Roalkvam, Irene; Bredy, Florian; Baumberger, Tamara; Pedersen, Rolf-B; Steen, Ida Helene

    2015-12-01

    The bacterial strain, IR-2T, was isolated from a microbial mat sampled near a hydrothermal vent in the Greenland Sea. Phylogenetic analysis, based on the 16S rRNA gene, showed that the closest relatives of IR-2T were Ilyobacter tartaricus, Ilyobacter insuetus, Propionigenium modestum and Fusobacterium varium (91 % 16S rRNA gene sequence similarity). The cells of the novel strain were Gram-stain-negative and pleomorphic; changing from long motile rods to non-motile ring structures during the growth cycle. Growth occurred at 20-55 °C (optimally at 48 °C), with 1-6 % (w/v) NaCl (optimally with 2 %), and at pH 5.3-8.0 (optimally at pH 6.0-8.0). The strain had obligate fermentative growth on various sugars and yeast extract. The DNA G+C content of strain IR-2T was 25.7 mol%. The cell sugars comprised mainly ribose, mannose and glucose, while the main polar lipids were glycolipids, phospholipids, phosphatidylglycerol and diphosphatidylglycerol. The fatty acid content of strain IR-2 was dominated by saturated and unsaturated iso-branched or anteiso-branched forms. Strain IR-2 represents a novel genus and species, for which the name Hypnocyclicus thermotrophus gen. nov., sp. nov. is proposed. The type strain is IR-2T ( = DSM 100055 = JCM 30901). PMID:26373292

  18. Discovery of a candidate old, isolated neutron star in the field of a galactic cirrus cloud

    NASA Technical Reports Server (NTRS)

    Stocke, John T.; Wang, Q. Daniel; Perlman, Eric S.; Donahue, Megan E.; Schachter, Jonathan F.

    1995-01-01

    New x-ray optical, and radio observations of the bright, unidentified x-ray source MS 0317.7-6647 are presented suggesting that this source is a likely compact stellar remnant. As part of the Einstein Extended Medium Sensivity Survey, this source was discovered serendipitously in the Einstein Imaging Proportional Counter pointing towards the nearby (4.5 Mpc) spiral galaxy NGC 1313. The very high x-ray to optical flux ratio, pointlike ROSAT HRI detection, and extremely soft component in the x-ray spectrum of MS 0317.7-6647 eliminate all the usual classes of optical counterparts to faint x-ray sources except for a very massive x-ray binary (and black hole candidate) in NGC 1313, a nearby, companionless pulsar similar to Geminga, or a very nearby ( approximately 100 pc) isolated, old neutron star slowly accreting interstellar matter onto its magnetic poles. The presence of an IR cirrus cloud which shadows the approximately 0.25 keV x-ray background in this direction supports the latter possibilty.

  19. 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.

  20. 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.

  1. Molecular typing of Iranian field isolates Mycoplasma synoviae and their differentiation from the live commercial vaccine strain MS-H using vlhA gene.

    PubMed

    Bayatzadeh, Mohammad Ali; Pourbakhsh, Seyed Ali; Ashtari, Abass; Abtin, Ali Reza; Abdoshah, Mohammad

    2014-01-01

    1. The single-copy domain of the N-terminal region of the vlhA gene of Mycoplasma synoviae was sequenced, analysed and verified and used to type Iranian field isolates of M. synoviae and the MS-H live vaccine strain. In addition, a restriction fragment length polymorphism (RFLP) method was developed to differentiate between field isolates of Iranian and MS-H vaccine strains. 2. All sequences were analysed and aligned; the percentage similarity of the DNA was calculated and dendrograms were constructed. Based on single nucleotide polymorphism (SNP) that existed in all field isolates in Iran, the PCR-RFLP method allowed the differentiation of all M. synoviae field isolates from the vaccine strain. 3. Using phylogenetic analysis, the isolates were assigned to 8 unique genotypes and, within each group, DNA had a high level of similarity. 4. DNA sequence analysis and PCR-RFLP of the amplicon based on percent similarity and evolutionary relationship appeared to be useful tools for strain differentiation whether M. synoviae clinical isolates from infected chickens were derived from the vaccine strain or wild-type strains. 5. This study confirms the potential value of strain typing for epidemiological purposes and suggests that phylogenetic studies are essential to understand the true relationships between strains. PMID:24405029

  2. Fungicide efflux and the MgMFS1 transporter contribute to the multidrug resistance phenotype in Zymoseptoria tritici field isolates.

    PubMed

    Omrane, Selim; Sghyer, Hind; Audéon, Colette; Lanen, Catherine; Duplaix, Clémentine; Walker, Anne-Sophie; Fillinger, Sabine

    2015-08-01

    Septoria leaf blotch is mainly controlled by fungicides. Zymoseptoria tritici, which is responsible for this disease, displays strong adaptive capacity to fungicide challenge. It developed resistance to most fungicides due to target site modifications. Recently, isolated strains showed cross-resistance to fungicides with unrelated modes of action, suggesting a resistance mechanism known as multidrug resistance (MDR). We show enhanced prochloraz efflux, sensitive to the modulators amitryptiline and chlorpromazine, for two Z. tritici strains, displaying an MDR phenotype in addition to the genotypes CYP51(I381V Y461H) or CYP51(I381V ΔY459/) (G460) , respectively, hereafter named MDR6 and MDR7. Efflux was also inhibited by verapamil in the MDR7 strain. RNA sequencing lead to the identification of several transporter genes overexpressed in both MDR strains. The expression of the MgMFS1 gene was the strongest and constitutively high in MDR field strains. Its inactivation in the MDR6 strain abolished resistance to fungicides with different modes of action supporting its involvement in MDR in Z. tritici. A 519 bp insert in the MgMFS1 promoter was detected in half of the tested MDR field strains, but absent from sensitive field strains, suggesting that the insert is correlated with the observed MDR phenotype. Besides MgMfs1, other transporters and mutations may be involved in MDR in Z. tritici. PMID:25627815

  3. Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field.

    PubMed

    Wu, Yue-Hong; Xu, Lin; Zhou, Peng; Wang, Chun-Sheng; Oren, Aharon; Xu, Xue-Wei

    2015-10-01

    A Gram-stain-negative, motile, aerobic bacterial strain, designated 22DY15T, was isolated from a deep-sea sediment sample collected from a hydrothermal vent field located in the East Pacific Rise. The isolate was a short rod with a single flagellum and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory quinone. The major polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphoglycolipid, one aminolipid and three unidentified phospholipids. The principal fatty acid (>70 %) was C18 : 1ω7c. The genomic DNA G+C content was 64.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22DY15T represents a distinct lineage within the family Rhodobacteraceae. The closest relatives were species of the genera Aliiroseovarius (93.3–96.0 % 16S rRNA gene sequence similarity), Sulfitobacter (94.0–96.0 %) and Loktanella (92.0–95.9 %). Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain 22DY15T could be differentiated from its most closely related genera. Therefore, it is proposed that strain 22DY15T represents a novel species in a new genus of the family Rhodobacteraceae, for which the name Brevirhabdus pacifica gen. nov., sp. nov. is proposed. The type strain of the type species is 22DY15T ( = JCM 19489T = DSM 27767T = CGMCC 1.12416T = MCCC 1K00276T). PMID:26198580

  4. Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta.

    PubMed

    Sánchez, Marta M; Fritze, Dagmar; Blanco, Ana; Spröer, Cathrin; Tindall, Brian J; Schumann, Peter; Kroppenstedt, Reiner M; Diaz, Pilar; Pastor, F I Javier

    2005-03-01

    A Gram-positive, endospore-forming, xylanase-producing bacterium isolated from a rice field was studied taxonomically. The strain grows at 10-40 degrees C and in the presence of lysozyme or 5 % (w/v) NaCl. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone of the isolated strain, while the major fatty acid was anteiso-C(15 : 0). Comparison of 16S rRNA gene sequences showed that strain BP-23(T) fell within the radiation of the cluster comprising Paenibacillus species. The highest 16S rRNA gene sequence similarities were found with Paenibacillus illinoisensis (97.4 %), Paenibacillus pabuli (97.1 %) and Paenibacillus amylolyticus (96.9 %). The DNA-DNA relatedness of strain BP-23(T) with respect to these three species was very low (32.7, 31.6 and 23.0 %, respectively). On the basis of phenotypic and genotypic data, strain BP-23(T) should be placed in the genus Paenibacillus and designated a novel species, for which the name Paenibacillus barcinonensis sp. nov. is proposed. The type strain is BP-23(T) (=CECT 7022(T)=DSM 15478(T)). PMID:15774688

  5. Correlation between convection electric fields in the nightside magnetosphere and several wave and particle phenomena during two isolated substorms.

    NASA Technical Reports Server (NTRS)

    Carpenter, D. L.; Fraser-Smith, A. C.; Unwin, R. S.; Hones, E. W., Jr.; Heacock, R. R.

    1971-01-01

    Correlation of several magnetoionospheric wave and particle phenomena previously linked observationally to magnetospheric substorms and inferred to involve convection electric fields with whistler measurements of convection activity during two relatively isolated substorms. The events occurred at about 0600 UT on July 15, 1965, and about 0500 UT on Oct. 13, 1965. The correlated phenomena include cross-L inward plasma drifts near midnight within the plasmaphere, diffuse auroral radar echoes observed near the dusk meridian, IPDP micropulsations (intervals of pulsations of diminishing period) in the premidnight sector, apparent contractions and expansions of the plasma sheet at about 20 earth radii in the magnetotail, and Pc 1/Pi 1 micropulsation events near or before midnight. Two new vlf phenomena occurred during the October 13 event - a noise band within the plasmasphere associated with a convecting whistler path, and ?hisslers,' falling-tone auroral-hiss forms repeated at intervals of about 2 sec.

  6. 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. PMID:26017345

  7. Biodegradation of diesel oil by an Arabian Sea sediment culture isolated from the vicinity of an oil field.

    PubMed

    Mukherji, Suparna; Jagadevan, Sheeja; Mohapatra, Gita; Vijay, Avinash

    2004-12-01

    Laboratory scale batch studies were performed to test the diesel oil biodegradation ability of ES1 cultures isolated from Arabian Sea sediments obtained from the vicinity of an oil field. This culture could utilize diesel as the sole source of carbon and energy. Under aerobic conditions, 39% loss of diesel oil was observed over 8 days where 80% of the loss was due to aliphatic constituents. Under anoxic nitrate reducing conditions the rate and extent of degradation was significantly lower, i.e., 18% over 50 days. Salt acclimatized cultures could tolerate salinities up to 3.5% and demonstrated optimal performance at a salinity of 0.5%. The optimum N/P ratio for these cultures was found to be in the range of 2:1-5:1. Addition of two trace elemental substance formulations exhibited a significant inhibitory effect on culture growth. This culture has good potential for decontamination of oil-contaminated marine and subsurface environments. PMID:15288270

  8. 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

  9. 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.

  10. Sabin Vaccine Reversion in the Field: a Comprehensive Analysis of Sabin-Like Poliovirus Isolates in Nigeria

    PubMed Central

    Chang, Stewart; Iber, Jane; Zhao, Kun; Adeniji, Johnson A.; Bukbuk, David; Baba, Marycelin; Behrend, Matthew; Burns, Cara C.; Oberste, M. Steven

    2015-01-01

    ABSTRACT To assess the dynamics of genetic reversion of live poliovirus vaccine in humans, we studied molecular evolution in Sabin-like poliovirus isolates from Nigerian acute flaccid paralysis cases obtained from routine surveillance. We employed a novel modeling approach to infer substitution and recombination rates from whole-genome sequences and information about poliovirus infection dynamics and the individual vaccination history. We confirmed observations from a recent vaccine trial that VP1 substitution rates are increased for Sabin-like isolates relative to the rate for the wild type due to increased nonsynonymous substitution rates. We also inferred substitution rates for attenuating nucleotides and confirmed that reversion can occur in days to weeks after vaccination. We combine our observations for Sabin-like virus evolution with the molecular clock for VP1 of circulating wild-type strains to infer that the mean time from the initiating vaccine dose to the earliest detection of circulating vaccine-derived poliovirus (cVDPV) is 300 days for Sabin-like virus type 1, 210 days for Sabin-like virus type 2, and 390 days for Sabin-like virus type 3. Phylogenetic relationships indicated transient local transmission of Sabin-like virus type 3 and, possibly, Sabin-like virus type 1 during periods of low wild polio incidence. Comparison of Sabin-like virus recombinants with known Nigerian vaccine-derived poliovirus recombinants shows that while recombination with non-Sabin enteroviruses is associated with cVDPV, the recombination rates are similar for Sabin isolate-Sabin isolate and Sabin isolate–non-Sabin enterovirus recombination after accounting for the time from dosing to the time of detection. Our study provides a comprehensive picture of the evolutionary dynamics of the oral polio vaccine in the field. IMPORTANCE The global polio eradication effort has completed its 26th year. Despite success in eliminating wild poliovirus from most of the world, polio

  11. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia.

    PubMed

    Winter, David J; Pacheco, M Andreína; Vallejo, Andres F; Schwartz, Rachel S; Arevalo-Herrera, Myriam; Herrera, Socrates; Cartwright, Reed A; Escalante, Ananias A

    2015-12-01

    Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. PMID:26709695

  12. Formation of electrical field accompanying temperature jump in isolated spinach chloroplasts.

    PubMed

    Shimizu, M; Nishimura, M

    1977-03-11

    Temperature-jump-induced absorbance changes of spinach chloroplasts in the dark were studied. After the temperature rise, a fast absorbance decrease and a succeeding slow absorbance increase were observed at the wavelength of 515 nm. The spectrum of the fast phase had positive maxima (increase in absorbance) at 430, 470 and 673 nm and a negative maxima (decrease in absorbance) at 525 nm. Permeant ions, tetraphenylboron-, tetraphenylarsonium+, and tetraphenylphosphonium+, decreased the extent of the fast absorbance change and increased the rate of slow recovery. Additions of inorganic potassium salts had a similar effect. Valinomycin, added in the presence of potassium ion, also increased the rate of slow recovery. These ions and ionophore had a parallel effect also on the recovery of flash-induced 515-nm absorbance change in chloroplasts. Electroneutral nigerericin did not affect the temperature-jump-induced absorbanc change. These results suggest the formation of electrical field across the thylakoid membrane in the dark accompanying the temperature rise. A possible involvement of the movement of water molecules (thermo-osmosis) in the observed absorbance changes is also discussed. PMID:849433

  13. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia

    PubMed Central

    Winter, David J.; Pacheco, M. Andreína; Vallejo, Andres F.; Schwartz, Rachel S.; Arevalo-Herrera, Myriam; Herrera, Socrates

    2015-01-01

    Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. PMID:26709695

  14. Differential Association of Plasmodium falciparum Na+/H+ Exchanger Polymorphism and Quinine Responses in Field- and Culture-Adapted Isolates of Plasmodium falciparum ▿ †

    PubMed Central

    Pelleau, Stéphane; Bertaux, Lionel; Briolant, Sébastien; Ferdig, Michael T.; Sinou, Véronique; Pradines, Bruno; Parzy, Daniel; Jambou, Ronan

    2011-01-01

    Plasmodium falciparum isolates with decreased susceptibility to quinine are increasingly being found in malaria patients. Mechanisms involved in this resistance are not yet understood. Several studies claim that alongside mutations in the Pfcrt and Pfmdr1 genes, the Pfnhe-1 Na+/H+ exchanger polymorphism plays a role in decreasing susceptibility. However, conflicting results on the link between the Pfnhe-1 gene and quinine resistance arise from field- and culture-adapted isolates. We tested the association between Pfnhe-1, Pfcrt, and Pfmdr1 polymorphisms in field- and culture-adapted isolates from various countries with their in vitro susceptibility to quinine. Field isolates presented a higher diversity of the Pfnhe-1 microsatellite sequence than culture-adapted isolates. In culture-adapted isolates but not in field isolates, mutations in the Pfcrt and Pfmdr1 genes, as well as a higher number of DNNND repeats in the Pfnhe-1 gene, were associated with a higher 50% inhibitory concentration (IC50) of quinine. Furthermore, most of the culture-adapted isolates with more than one DNNND repeat in the Pfnhe-1 gene also harbored mutated Pfcrt and Pfmdr1 genes with an apparent cumulative effect on quinine susceptibility. This study supports the involvement of the Pfnhe-1 gene in the modulation of the in vitro quinine response when associated with mutated Pfcrt and Pfmdr1 genes. Culture adaptation could be responsible for selection of specific haplotypes of these three genes. Methods used for drug testing might thus influence the association between Pfnhe-1 polymorphism and quinine susceptibility. However, we do not exclude the possibility that in particular settings, Pfnhe-1 polymorphism can be used as a molecular marker for surveillance of quinine resistance. PMID:21947391

  15. Complete Genome Sequence of a Field Isolate of Classical Swine Fever Virus Belonging to Subgenotype 2.1b from Hunan Province, China.

    PubMed

    Shao, Weixing; Liu, Shuang; Wu, Faxing; Zhang, Zhi; Dong, Yaqin; Li, Xiaocheng

    2015-01-01

    We report the complete genome sequence of a field isolate of classical swine fever virus (CSFV), Hunan 23/2013, belonging to the predominant subgenotype 2.1b. This strain was originally isolated from diseased pigs in Hunan Province, China. This report will help in understanding the molecular diversity of CSFV stains circulating in China and in selecting and developing a suitable vaccine candidate for CSF control. PMID:26205876

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

    PubMed

    Schill, Kristin M; Wang, Yun; Butler, Robert R; Pombert, Jean-François; Reddy, N Rukma; Skinner, Guy E; Larkin, John W

    2016-01-01

    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

  17. 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

  18. 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

  19. Epidemiological Analysis of Salmonella enteritidis Isolates from Humans and Broiler Chickens in Thailand by Phage Typing and Pulsed-Field Gel Electrophoresis

    PubMed Central

    Boonmar, Sumalee; Bangtrakulnonth, Aroon; Pornrunangwong, Srirat; Terajima, Jun; Watanabe, Haruo; Kaneko, Ken-Ichi; Ogawa, Masuo

    1998-01-01

    To determine the phage types (PT) of Salmonella enteritidis found in Thailand and to clarify the potential for human infection by S. enteritidis in broiler chicken meat, human and poultry isolates taken from Thailand between 1990 and 1997 were phage typed and analyzed by pulsed-field gel electrophoresis (PFGE). Ten different PT were found among the 302 isolates phage typed, with PT 4 being the most frequent in human (73.9%) and poultry (76.2%) isolates, followed by PT 1 (8.0%), 8 (3.6%), and 7a (2.2%) in human isolates and by PT 7a (4.9%), 1 (3.7%), and 12 (2.4%) in poultry isolates. Of the 53 isolates analyzed by PFGE, 45 showed an indistinguishable pattern (pattern A) by BlnI-digested PFGE and the other 8 isolates showed a very similar pattern that differed by only a few bands. These results indicate the spread of a genetically identical clone of S. enteritidis in humans and poultry in Thailand. PMID:9542918

  20. Anticoccidial efficacy of semduramicin. 2. Evaluation against field isolates including comparisons with salinomycin, maduramicin, and monensin in battery tests.

    PubMed

    Logan, N B; McKenzie, M E; Conway, D P; Chappel, L R; Hammet, N C

    1993-11-01

    The efficacy of semduramicin (AVIAX), a novel polyether ionophore, was profiled in a series of 57 battery tests conducted in the United States and the United Kingdom. The studies employed mixed and monospecific infections of Eimeria acervulina, Eimeria mivati/Eimeria mitis, Eimeria brunetti, Eimeria maxima, Eimeria necatrix, and Eimeria tenella derived from North American and European field isolates. Ten-day-old broiler cockerels in pens of 8 to 10 birds were continuously medicated in feed beginning 24 h before challenge in tests of 6 to 8 days' duration. At the use level of 25 ppm, semduramicin effectively controlled mortality, lesions, and weight gain depression that occurred in unmedicated, infected controls for all species. In comparison with 60 ppm salinomycin, semduramicin significantly (P < .05) improved weight gain against E. brunetti and E. tenella, lesion control against E. brunetti and E. maxima, and the control of coccidiosis mortality against E. tenella. Salinomycin was superior (P < .05) to all treatments in maintenance of weight gain and control of lesions for E. acervulina. Maduramicin at 5 ppm was inferior (P < .05) to semduramicin in control of E. acervulina and E. maxima lesions, but was superior (P < .05) to all treatments in maintenance of weight gain and control of lesions in E. tenella infections. The data indicate that semduramicin at 25 ppm is well tolerated in broilers and possesses broad spectrum anticoccidial activity. PMID:8265495

  1. 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

  2. Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice Fields

    PubMed Central

    Brito, Patrícia H.; Serrano, Mónica

    2015-01-01

    Here, we report two genome sequences of endospore-forming bacteria isolated from the rice fields of Comporta, Portugal, identified as Bacillus aryabhattai C765 and Bacillus aerophilus C772. Both species were previously identified in air samples from the upper atmosphere, but our findings suggest their presence in a wider range of environmental niches. PMID:25858824

  3. Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field

    PubMed Central

    Bao, Zhihua; Shinoda, Ryo

    2016-01-01

    N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input. PMID:27587832

  4. Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field.

    PubMed

    Bao, Zhihua; Shinoda, Ryo; Minamisawa, Kiwamu

    2016-01-01

    N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input. PMID:27587832

  5. Draft Genome Sequence of Pseudomonas sp. Strain 2-92, a Biological Control Strain Isolated from a Field Plot Under Long-Term Mineral Fertilization

    PubMed Central

    Adam, Zaky; Chen, Qing; Lewis, Christopher T.; Lévesque, C. André; Xu, Renlin

    2014-01-01

    Pseudomonas sp. strain 2-92, isolated from a Canadian field plot under long-term mineral fertilization, strongly inhibits the growth of Fusarium graminearum, Rhizoctonia solani, and Gaeumannomyces graminis. Here, we report the draft genome sequence of Pseudomonas sp. strain 2-92. PMID:24407636

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

    PubMed Central

    Dawar, Chhavi

    2015-01-01

    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. PMID:26472842

  7. ESR in zero field of the photoinduced triplet state in isolated reaction centers of rhodopseudomonas sphaeroides R-26 detected by the singlet ground-state absorbance

    NASA Astrophysics Data System (ADS)

    Den Blanken, H. J.; Van Der Zwet, G. P.; Hoff, A. J.

    1982-01-01

    We have measured zero-field resonance transitions of the triplet state of the primary donor monitoring the transmittance at 890 nm at 1.2 K in isolated reaction centers of Rhodopseudomonas sphaeroides R-26. The transitions correspond to a decrease in transmittance, confirming the energy transfer model for the transitions detected via the antenna fluorescence in whole cells.

  8. 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%.

  9. 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

  10. 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...