bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinematics of the Dadeldhura klippe shear zones (W Nepal): implications for the foreland evolution of the Himalayan metamorphic core
Authors: Antolín Borja , Godin Laurent , Wemmer Klaus , Nagy Carl 
Published: February 2013

AbstractMapping combined with structural analyses in the foreland edge of the metamorphic core of the Himalayas in SW Nepal highlights the existence of two north‐dipping shear zones with opposite sense of shear. Here, the metamorphic core is mainly affected by non‐coaxial top‐to‐the‐south sense of shear at temperatures between 450 °C and 550 °C that switch to a top‐to‐the‐north sense of shear at the top of the metamorphic core. We regionally correlate this upper shear zone with the South Tibetan detachment system. Ar‐dating on white mica indicates that both shear zones operated between 23 Ma and 17 Ma. Restoration of the folded South Tibetan detachment in far western Nepal yields a minimum dip‐slip distance of 190 km, compatible with predictions made by models of extrusion of a weak mid‐crustal channel. Our results support an orogenic model in which channel flow in the hinterland coexisted with thrust wedge mechanics in the foreland.
Toxocara seropositivity, atopy and asthma: a study in Cuban schoolchildren
Authors: Kanobana K. , Vereecken K. , Junco Diaz R. , Sariego I. , Rojas L. , Bonet Gorbea M. , Polman K. 
Published: February 2013

AbstractIntroductionEvidence suggests that human toxocariasis (HT) could stimulate the onset of allergic diseases such as asthma. More specifically, in subjects having a hypothetical ‘atopic genotype’, HT could boost preexistent allergy symptoms. We tested the latter hypothesis in Cuba, a country where both asthma and HT are prevalent.Material and methodsIn a group of Cuban school‐aged children (n = 958), we investigated the association of Toxocara seropositivity and atopic status with asthma. Toxocara seropositivity was diagnosed with ELISA and atopy by allergen skin prick test. Both physician‐diagnosed asthma and current wheeze, as determined by International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire, were considered. Associations were assessed using multivariable logistic regression analyses, with either ‘physician‐diagnosed asthma’ or ‘current wheeze’ as outcome variable.Results40.1% of the children were Toxocara seropositive. Prevalences were 21.7% for current wheeze and 32.7% for physician‐diagnosed asthma. The odds of having asthma were almost two times higher in atopic children, but only reached borderline significance (OR=1.90, CI 95%: 0.95–3.80 for physician‐diagnosed asthma and OR=1.94, CI 95%: 0.98–3.85 for current wheeze). Toxocara seropositivity and physician‐diagnosed asthma were associated (OR=1.51, CI 95%: 1.01–2.26). Moreover, in children without antibodies to Toxocara, being atopic was significantly associated with having physician‐diagnosed asthma (OR=2.53, CI 95%: 1.63–3.90), while this association was not present in Toxocara positives (OR=1.38, CI 95%: 0.82–2.37).ConclusionOur data confirm previous observations of higher Toxocara seropositivity rates in asthmatic children. Toxocara seropositivity appeared to abrogate the apparent association between atopy and asthma in Cuban children. Although this observation was limited to physician‐diagnosed asthma, it challenges the hypothesis that HT stimulates the onset of allergic diseases such as asthma in atopic individuals.
The risk of transfusion‐transmitted HIV from blood donations of men who have sex with men, 12 months after last sex with a man: 2005–2007 estimates from England and Wales
Authors: Davison K. L. , Conti S. , Brailsford S. R. 
Published: February 2013

The risk of transfusion‐transmitted HIV infection under (i) permanent exclusion and (ii) 12‐month deferral of MSM in England and Wales during 2005–2007 was estimated. Assuming equal compliance with both scenarios, estimated risk under a 12‐month deferral (0.228/million donations [range 0·168–0·306/million donations]) was only marginally greater (0·5%) than that under lifetime exclusion (0·227/million donations [range 0·157–0.318/million donations]), with one extra‐HIV infectious donation every 455 years. Poorer compliance of MSM with a 12‐month deferral would be expected to increase the estimated risk, whereas improved compliance could decrease risk by up to 29·1%.
Bacterial growth in red blood cell units exposed to uncontrolled temperatures: challenging the 30‐minute rule
Authors: Ramirez‐Arcos S. , Perkins H. , Kou Y. , Mastronardi C. , Kumaran D. , Taha M. , Yi Q.‐L. , McLaughlin N. , Kahwash E. , Lin Y. , Acker J. 
Published: February 2013

Background and ObjectivesThe ‘30‐min rule’ requires discarding red blood cells (RBCs) exposed to uncontrolled temperatures for >30 min to ensure safe RBC transfusion. This study was aimed at determining whether multiple room temperature (RT) exposures promote bacterial growth.Materials and MethodsPooled and split RBC units were inoculated with ~1 CFU/ml of Serratia marcescens, Yersinia enterocolitica, Escherichia coli or Staphylococcus epidermidis. Control units remained in storage, while test units were exposed to RT for six 30‐min or three 60‐min intervals. Bacterial concentrations and endotoxin levels were determined after each exposure and at 42 days of storage. RBC core temperature and RT were monitored in mock units with Escort iLog temperature loggers. A mixed model was used for statistical analyses.ResultsRed blood cell core temperature reached 10·7 ± 0·4°C and 14·2 ± 0·2°C during 30‐ and 60‐min exposures, respectively. Staphylococcus epidermidis and E. coli did not grow in either control or exposed RBCs. Yersinia enterocolitica concentration and endotoxin levels were similar in both control and test units. Serratia marcescens concentration and endotoxin levels were higher in exposed units; however, differences between units exposed for 30 min or 60 min were not observed.ConclusionThere is no added risk to RBC safety by increasing RT exposures to 60 min with each removal from storage for up to a total of 3 h during RBC shelf life. Therefore, extending the 30‐min limitation in RBCs exposed to uncontrolled temperatures to 60 min should be considered by regulatory agencies.
Surveillance of Parapoxvirus Among Ruminants in Virginia and Connecticut
Authors: Roess A. A. , McCollum A. M. , Gruszynski K. , Zhao H. , Davidson W. , Lafon N. , Engelmeyer T. , Moyer B. , Godfrey C. , Kilpatrick H. , Labonte A. , Murphy J. , Carroll D. S. , Li Y. , Damon I. K. 
Published: February 2013

SummaryIn 2008, two deer hunters in Virginia and Connecticut were infected with a unique strain of pseudocowpox virus, a parapoxvirus. To estimate the prevalence of this virus, and in an attempt to define the reservoir, Parapoxvirus surveillance was undertaken between November 2009 and January 2010. 125 samples from four ruminant species (cows, goat, sheep and white‐tailed deer) were collected in Virginia, and nine samples from white‐tailed deer were collected in Connecticut. We found no evidence that the parapoxvirus species that infected the deer hunters is circulating among domesticated ruminants or white‐tailed deer. However, parapoxvirus DNA of a different parapoxvirus species, bovine papular stomatitis virus (BPSV), was detected in 31 samples obtained from asymptomatic cattle in Virginia. Parapoxvirus DNA–positive cattle originated from the same counties indicating probable transmission among animals. Molecular analysis identified BPSV as the parapoxvirus affecting animals. Asymptomatic parapoxvirus infections in livestock, particularly young animals, may be common, and further investigation will inform our knowledge of virus transmission.
Putative Antiparasite Defensive System Involving Ribosomal and Nonribosomal Oligopeptides in Cyanobacteria of the Genus Planktothrix
Authors: Rohrlack Thomas , Christiansen Guntram , Kurmayer Rainer 
Published: February 2013

ABSTRACT

Parasitic chytrid fungi can inflict significant mortality on cyanobacteria but frequently fail to keep cyanobacterial dominance and bloom formation in check. Our study tested whether oligopeptide production, a common feature in many cyanobacteria, can be a defensive mechanism against chytrid parasitism. The study employed the cyanobacterial strain
Planktothrix
NIVA-CYA126/8 and its mutants with knockout mutations for microcystins, anabaenopeptins, and microviridins, major oligopeptide classes to be found in NIVA-CYA126/8. Four chytrid strains were used as parasite models. They are obligate parasites of
Planktothrix
and are unable to exploit alternative food sources. All chytrid strains were less virulent to the NIVA-CYA126/8 wild type than to at least one of its oligopeptide knockout mutants. One chytrid strain even failed to infect the wild type, while exhibiting considerable virulence to all mutants. It is therefore evident that producing microcystins, microviridins, and/or anabaenopeptins can reduce the virulence of chytrids to
Planktothrix
, thereby increasing the host's chance of survival. Microcystins and anabaenopeptins are nonribosomal oligopeptides, while microviridins are produced ribosomally, suggesting that
Planktothrix
resists chytrids by relying on metabolites that are produced via distinct biosynthetic pathways. Chytrids, on the other hand, can adapt to the oligopeptides produced by
Planktothrix
in different ways. This setting most likely results in an evolutionary arms race, which would probably lead to
Planktothrix
and chytrid population structures that closely resemble those actually found in nature. In summary, the findings of the present study suggest oligopeptide production in
Planktothrix
to be part of a defensive mechanism against chytrid parasitism.
Norovirus Genotypes Present in Oysters and in Effluent from a Wastewater Treatment Plant during the Seasonal Peak of Infections in Ireland in 2010
Authors: Rajko-Nenow Paulina , Waters Allison , Keaveney Sinéad , Flannery John , Tuite Gráinne , Coughlan Suzie , O'Flaherty Vincent , Doré William 
Published: February 2013

ABSTRACT

We determined norovirus (NoV) concentrations in effluent from a wastewater treatment plant and in oysters during the peak period of laboratory-confirmed cases of NoV infection in Ireland in 2010 (January to March). Weekly samples of influent, secondary treated effluent, and oysters were analyzed using real-time quantitative reverse transcription-PCR for NoV genogroup I (GI) and genogroup II (GII). The mean concentration of NoV GII (5.87 × 10
4
genome copies 100 ml
−1
) in influent wastewater was significantly higher than the mean concentration of NoV GI (1.40 × 10
4
genome copies 100 ml
−1
). The highest concentration of NoV GII (2.20 × 10
5
genome copies 100 ml
−1
) was detected in influent wastewater during week 6. Over the study period, a total of 931 laboratory-confirmed cases of NoV GII infection were recorded, with the peak (
n
= 171) occurring in week 7. In comparison, 16 cases of NoV GI-associated illness were reported during the study period. In addition, the NoV capsid N/S domain was molecularly characterized for selected samples. Multiple genotypes of NoV GI (GI.1, GI.4, GI.5, GI.6, and GI.7) and GII (GII.3, GII.4, GII.6, GII.7, GII.12, GII.13, and GII.17), as well as 4 putative recombinant strains, were detected in the environmental samples. The NoV GII.4 variant 2010 was detected in wastewater and oyster samples and was the dominant strain detected in NoV outbreaks at that time. This study demonstrates the diversity of NoV genotypes present in wastewater during a period of high rates of NoV infection in the community and highlights the potential for the environmental spread of multiple NoV genotypes.
Contact Killing of Bacteria on Copper Is Suppressed if Bacterial-Metal Contact Is Prevented and Is Induced on Iron by Copper Ions
Authors: Mathews Salima , Hans Michael , Mücklich Frank , Solioz Marc 
Published: February 2013

ABSTRACT

Bacteria are rapidly killed on copper surfaces, and copper ions released from the surface have been proposed to play a major role in the killing process. However, it has remained unclear whether contact of the bacteria with the copper surface is also an important factor. Using laser interference lithography, we engineered copper surfaces which were covered with a grid of an inert polymer which prevented contact of the bacteria with the surface. Using
Enterococcus hirae
as a model organism, we showed that the release of ionic copper from these modified surfaces was not significantly reduced. In contrast, killing of bacteria was strongly attenuated. When
E. hirae
cells were exposed to a solid iron surface, the loss of cell viability was the same as on glass. However, exposing cells to iron in the presence of 4 mM CuSO
4
led to complete killing in 100 min. These experiments suggest that contact killing proceeds by a mechanism whereby the metal-bacterial contact damages the cell envelope, which, in turn, makes the cells susceptible to further damage by copper ions.
Use of Loop-Mediated Isothermal Amplification for Detection of Ophiostoma clavatum, the Primary Blue Stain Fungus Associated with Ips acuminatus
Authors: Villari Caterina , Tomlinson Jennifer A. , Battisti Andrea , Boonham Neil , Capretti Paolo , Faccoli Massimo 
Published: February 2013

ABSTRACTLoop-mediated isothermal amplification (LAMP) is an alternative amplification technology which is highly sensitive and less time-consuming than conventional PCR-based methods. Three LAMP assays were developed, two for detection of species of symbiotic blue stain fungi associated withIps acuminatus, a bark beetle infesting Scots pine (Pinus sylvestris), and an additional assay specific toI. acuminatusitself for use as a control. In common with most bark beetles,I. acuminatusis associated with phytopathogenic blue stain fungi involved in the process of exhausting tree defenses, which is a necessary step for the colonization of the plant by the insect. However, the identity of the main blue stain fungus vectored byI. acuminatuswas still uncertain, as well as its frequency of association withI. acuminatusunder outbreak and non-outbreak conditions. In this study, we employed LAMP technology to survey six populations ofI. acuminatussampled from the Southern Alps.Ophiostoma clavatumwas detected at all sampling sites, whileOphiostoma brunneo-ciliatum, reported in part of the literature as the main blue stain fungus associated withI. acuminatus, was not detected on any of the samples. These results are consistent with the hypothesis thatO. clavatumis the main blue stain fungus associated withI. acuminatusin the Southern Alps. The method developed in the course of this work provides a molecular tool by which it will be easy to screen populations and derive important data regarding the ecology of the species involved.
Panmictic Structure of the Cryptosporidium parvum Population in Irish Calves: Influence of Prevalence and Host Movement
Authors: De Waele Valérie , Van den Broeck Frederik , Huyse Tine , McGrath Guy , Higgins Isabella , Speybroeck Niko , Berzano Marco , Raleigh Pat , Mulcahy Grace M. , Murphy Thomas M. 
Published: February 2013

ABSTRACT

In total, 245
Cryptosporidium parvum
specimens obtained from calves in 205 Irish herds between 2003 and 2005 were subtyped by sequencing the glycoprotein gene
gp60
and performing multilocus analysis of seven markers. The transmission dynamics of
C. parvum
and the influence of temporal, spatial, parasitic, and host-related factors on the parasite (sub)populations were studied. The relationship of those factors to the risk of cryptosporidiosis was also investigated using results from 1,368 fecal specimens submitted to the veterinary laboratories for routine diagnosis during 2005. The prevalence was greatest in the northwest and midwest of the country and on farms that bought in calves. The panmixia (random mating) detected in the
C. parvum
population may relate to its high prevalence, the cattle density, and the frequent movement of cattle. However, local variations in these factors were reflected in the
C. parvum
subpopulations. This study demonstrated the importance of biosecurity in the control of bovine cryptosporidiosis (e.g., isolation and testing of calves before introduction into a herd). Furthermore, the zoonotic risk of
C. parvum
was confirmed, as most specimens possessed GP60 and MS1 subtypes previously described in humans.
Degradation of Sulfadiazine by Microbacterium lacus Strain SDZm4, Isolated from Lysimeters Previously Manured with Slurry from Sulfadiazine-Medicated Pigs
Authors: Tappe Wolfgang , Herbst Michael , Hofmann Diana , Koeppchen Stephan , Kummer Sirgit , Thiele Björn , Groeneweg Joost 
Published: February 2013

ABSTRACT

Sulfadiazine (SDZ)-degrading bacterial cultures were enriched from the topsoil layer of lysimeters that were formerly treated with manure from pigs medicated with
14
C-labeled SDZ. The loss of about 35% of the applied radioactivity after an incubation period of 3 years was attributed to CO
2
release due to mineralization processes in the lysimeters. Microcosm experiments with moist soil and soil slurries originating from these lysimeters confirmed the presumed mineralization potential, and an SDZ-degrading bacterium was isolated. It was identified as
Microbacterium lacus
, denoted strain SDZm4. During degradation studies with
M. lacus
strain SDZm4 using pyrimidine-ring labeled SDZ, SDZ disappeared completely but no
14
CO
2
was released during 10 days of incubation. The entire applied radioactivity (AR) remained in solution and could be assigned to 2-aminopyrimidine. In contrast, for parallel incubations but with phenyl ring-labeled SDZ, 56% of the AR was released as
14
CO
2
, 16% was linked to biomass, and 21% remained as dissolved, not yet identified
14
C. Thus, it was shown that
M. lacus
extensively mineralized and partly assimilated the phenyl moiety of the SDZ molecule while forming equimolar amounts of 2-aminopyrimidine. This partial degradation might be an important step in the complete mineralization of SDZ by soil microorganisms.
Denitrifying Alphaproteobacteria from the Arabian Sea That Express
nosZ
, the Gene Encoding Nitrous Oxide Reductase, in Oxic and Suboxic Waters
Authors: Wyman Michael , Hodgson Sylvia , Bird Clare 
Published: February 2013

ABSTRACT

Marine ecosystems are significant sources of the powerful greenhouse gas nitrous oxide (N
2
O). A by-product of nitrification and an intermediate in the denitrification pathway, N
2
O is formed primarily in oxygen-deficient waters and sediments. We describe the isolation of a group of alphaproteobacteria from the suboxic waters of the Arabian Sea that are phylogenetically affiliated with
Labrenzia
spp. and other denitrifiers. Quantitative PCR assays revealed that these organisms were very broadly distributed in this semienclosed ocean basin. Their biogeographical range extended from the productive, upwelling region off the Omani shelf to the clear, oligotrophic waters that are found much further south and also included the mesotrophic waters overlying the oxygen minimum zone (OMZ) in the northeastern sector of the Arabian Sea. These organisms actively expressed NosZ (N
2
O reductase, the terminal step in the denitrification pathway) within the OMZ, an established region of pelagic denitrification. They were found in greatest numbers outside the OMZ, however, and
nosZ
mRNAs were also readily detected near the base of the upper mixed layer in nutrient-poor, oxic regions. Our findings provide firm molecular evidence of a potential sink for N
2
O within well-ventilated, oceanic surface waters in this biogeochemically important region. We show that the
Labrenzia
-like denitrifiers and their close relatives are habitual colonizers of the pseudobenthic environment provided by
Trichodesmium
spp. We develop the conjecture that the O
2
-depleted microzones that occur within the colonies of these filamentous, diazotrophic cyanobacteria might provide unexpected niches for the reduction of nitrogen oxides in tropical and subtropical surface waters.
Use of Degradation Tags To Control Protein Levels in the Cyanobacterium Synechocystis sp. Strain PCC 6803
Authors: Landry Brian P. , Stöckel Jana , Pakrasi Himadri B. 
Published: February 2013

ABSTRACT

We generated a collection of
ssrA
-based C-terminal protein degradation tags with different degradation strengths. The steady-state fluorescence levels of different enhanced yellow fluorescent protein (eYFP) tag variants in a
Synechocystis
sp. indicated a tunable range from 1% to 50% of untagged eYFP.
Defining the RNA-Protein Interactions in the Trypanosome Preribosomal Complex
Authors: Wang Lei , Ciganda Martin , Williams Noreen 
Published: February 2013

ABSTRACT

In eukaryotes, 5S rRNA is transcribed in the nucleoplasm and requires the ribosomal protein L5 to deliver it to the nucleolus for ribosomal assembly. The trypanosome-specific proteins P34 and P37 form a novel preribosomal complex with the eukaryotic conserved L5-5S rRNA complex in the nucleoplasm. Previous results suggested that P34 acts together with L5 to bridge the interaction with 5S rRNA and thus to stabilize 5S rRNA, an important role in the early steps of ribosomal biogenesis. Here, we have delineated the domains of the two protein components, L5 and P34, and regions of the RNA partner, 5S rRNA, that are critical for protein-RNA interactions within the complex. We found that the L18 domain of L5 and the N terminus and RNA recognition motif of P34 bind 5S rRNA. We showed that
Trypanosoma brucei
L5 binds the β arm of 5S rRNA, while P34 binds loop A/stem V of 5S rRNA. We demonstrated that 5S rRNA is able to enhance the association between the protein components of the complex, L5 and P34. Both loop A/stem V and the β arm of 5S rRNA can separately enhance the protein-protein association, but their effects are neither additive nor synergistic. Domains in the two proteins for protein-protein and protein-RNA interactions overlap or are close to each other. This suggests that 5S rRNA binding might cause conformational changes in L5 and P34 and might also bridge the interactions, thus enhancing binding between the protein partners of this novel complex.
The [URE3] Prion in Candida
Authors: Edskes Herman K. , Wickner Reed B. 
Published: February 2013

ABSTRACT

Ure2p, normally a regulator of nitrogen catabolism in
Saccharomyces cerevisiae
, can be a prion (infectious protein) by forming a folded in-register parallel amyloid called [URE3]. Using
S. cerevisiae
as a test bed, we previously showed that Ure2p of
Candida albicans
(CaUre2p) can also form a prion, but that Ure2p of
C. glabrata
(CgUre2p) cannot. Here, we constructed
C. glabrata
strains to test whether CgUre2p can form a prion in its native environment. We find that while CaUre2p can form a [URE3] in
C. glabrata
, CgUre2p cannot, although the latter has a prion domain sequence more similar to that of ScUre2p than that of CaUre2p. This supports the notion that prion formation is not a conserved property of Ure2p but is a pathology arising sporadically. We find that some [URE3
albicans
] variants are restricted in their transmissibility to certain recipient strains. In addition, we show that the
C. glabrata
HO can induce switching of the
C. glabrata
mating type locus.