bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Fusarium culmorum Tri Gene Transcription on Deoxynivalenol and D3G Levels in Two Different Barley Cultivars
Authors: Faltusová Zuzana , Chrpová Jana , Salačová Linda , Džuman Zbyněk , Pavel Jozef , Zachariášová Milena , Hajšlová Jana , Ovesná Jaroslava
Published: December 2014

Fusarium culmorum is a phytopathogenic fungus causing Fusarium head blight (FHB), which negatively affects cereals by producing mycotoxins, such as deoxynivalenol (DON). In this work, two barley cultivars, Chevron and Pedant, with different degrees of resistance to FHB were inoculated with F. culmorum. The transcription levels of the Fusarium Tri genes and barley UDP‐glycosyltransferase genes were investigated. The amounts of pathogen, DON and the detoxification product deoxynivalenol‐3‐O‐glucoside (D3G) were monitored. The greatest amounts of pathogen were detected at 21 days postinoculation (dpi) and were much lower in cv. Chevron than in cv. Pedant. No differences in the total DON conversion to D3G were observed between the cultivars. Ubiquitin‐conjugating enzyme (UBC) was identified and then used as a reference gene to monitor transcription of the Fusarium Tri genes in infected barley. Transcription of the F. culmorum Tri5, Tri4, Tri6 and Tri10 genes differed between the two cultivars. In the susceptible cultivar (Pedant), transcription of the Tri genes gradually increased from 1 dpi. In the more resistant Chevron, transcription of the Tri genes dramatically increased after 14 dpi and reached a maximum at 21 dpi. This very high but delayed transcription of Tri genes did not, however, result in a large accumulation of the mycotoxin DON. The difference between the cultivars in the transcription of barley defence genes (HvUGT13248 [GT2] and HvUGT5876 [GT1]) for UDP‐glycosyltransferases reflects the barley samples’ levels of infection. The difference in resistance to F. culmorum infection in the two cultivars is most likely not due to differences in DON detoxification, but may be due to activity against the pathogen and delayed transcription of the pathogen's Tri genes.
Associations between meal size, gastric emptying and post‐prandial plasma glucose, insulin and lactate concentrations in meal‐fed cats
Authors: Coradini M. , Rand J. S. , Filippich L. J. , Morton J. M. , O'Leary C. A.
Published: December 2014

Plasma glucose and insulin concentrations are increased for 12–24 h in healthy cats following moderate‐ to high‐carbohydrate meals. This study investigated associations between gastric emptying time and post‐prandial plasma glucose, insulin and lactate concentrations in cats fed an extruded dry, high‐carbohydrate, moderate‐fat, low‐protein diet (51, 28, 21% metabolizable energy, respectively) once daily by varying meal volume. Eleven healthy, non‐obese, neutered adult cats were enrolled in a prospective study and fed to maintain body weight. Ultrasound examinations were performed for up to 26 h, and blood collections over 24 h after eating meals containing approximately 100% and 50% of the cats’ daily caloric intake (209 and 105 kJ/kg BW, respectively). Gastric emptying time was increased after a meal of 209 kJ/kg BW compared with 105 kJ/kg BW (median gastric emptying times 24 and 14 h, respectively; p = 0.03). Time for glucose to return to fasting was longer after the 209 kJ/kg BW meal (median 20 h; 25th and 75th percentiles 15 and 23 h, respectively) than the 105 kJ/kg BW meal (13, 12 and 14 h; p < 0.01); however, peak glucose was not higher after the 209 kJ/kg BW meal compared with the 105 kJ/kg BW meal [(mean ± SD) 6.6 ± 0.6 and 7.8 ± 1.2 mmol/l, respectively, p = 0.07]. Times for insulin to return to fasting were not significantly longer after the 209 kJ/kg BW meal than the 105 kJ/kg BW meal (p = 0.29).d‐ andl‐lactate concentrations were not associated with gastric emptying time or post‐prandial blood glucose and insulin. Based on results obtained, prolonged gastric emptying contributes to prolonged post‐prandial hyperglycemia in cats meal fed a high‐carbohydrate, low‐protein, dry diet and fasting times for cats’ meal‐fed diets of similar composition should be 14–26 h, depending on meal size.
Psychological and behavioural characteristics that distinguish street gang members in custody
Authors: Alleyne Emma , Wood Jane L. , Mozova Katarina , James Mark
Published: December 2014

Purpose

Using social dominance theory, the primary aim of this study was to examine the attitudes and beliefs that reinforce status hierarchies and facilitate aggressive behaviour within and between gangs. The aim was also to determine whether these socio‐cognitive processes distinguished gang‐involved youth from non‐gang offenders in a custodial setting.

Methods

Gang‐involved youth and non‐gang offenders were recruited from a young offender institution located in the United Kingdom. Questionnaires assessing psychological (i.e., moral disengagement strategies, anti‐authority attitudes, hypermasculinity, and social dominance orientation) and behavioural (i.e., group crime) characteristics were administered individually. We hypothesized that gang‐involved youth would be affiliated with groups who engaged in more criminal activity than non‐gang offenders, and that they would report higher levels of endorsements than non‐gang youth across all of the psychological measures.

Results

We found that gang‐involved youth were affiliated with groups who engage in more crimes than non‐gang offenders. We also found that social dominance orientation was an important factor related to gang involvement along with measures assessing group‐based hierarchies such as hypermasculinity, anti‐authority attitudes, and the moral disengagement strategies displacement of responsibility, dehumanization, and euphemistic labeling.

Conclusions

These findings fit within a social dominance theoretical framework as they highlight key psychological factors that feed into perceived status‐driven hierarchies that distinguish gang members from other types of offenders. These factors could be key to developments in treatment provision within custodial settings.
Health‐related quality of life among patients with primary sclerosing cholangitis
Authors: Haapamäki Johanna , Tenca Andrea , Sintonen Harri , Barner‐Rasmussen Nina , Färkkilä Martti A.
Published: December 2014

Background & Aims

To assess health‐related quality of life (HRQoL) of patients with primary sclerosing cholangitis (PSC), and to compare it with that of the general population. Also, to examine changes inHRQoL in newly diagnosedPSCpatients at a follow‐up 1–2 years later, and to compare theirHRQoL withHRQoL of newly diagnosed inflammatory bowel disease (IBD) patients. Furthermore, sources of and need for disease‐related information amongPSCpatients were surveyed.

Methods

Primary sclerosing cholangitis patients filled in the survey questionnaire when attending an endoscopic retrograde cholangiography examination. The 15D served as a generalHRQoL instrument. The follow‐up questionnaire was mailed to the newly diagnosed patients 1–2 years later.

Results

No significant difference was seen in 15D scores betweenPSCpatients and general population, but the dimensions of excretion (P < 0.001), depression (P = 0.003), distress (P = 0.003) and vitality (P = 0.005) were significantly lower inPSC. Age and symptoms affectedHRQoL but severity of biliary changes did not. Those with newly diagnosedIBDhad lower 15D scores than those withPSC. No significant changes were observed in 15D scores of newPSCpatients in the follow‐up. Many patients were dissatisfied with information received.

Conclusion

Newly diagnosedPSCpatients have betterHRQoL than doIBDpatients, and no significantHRQoL changes were observed in the mean follow‐up of 1.58 years afterPSCdiagnosis.ERCfindings did not correlate withHRQoL or symptoms.HRQoL ofPSCpatients was mostly comparable with that of general population, but special attention should be paid to patients' psychological well‐being.
Overexpression of a NAC transcription factor delays leaf senescence and increases grain nitrogen concentration in wheat
Authors: Zhao D. , Derkx A. P. , Liu D.‐C. , Buchner P. , Hawkesford M. J.
Published: December 2014

Increasing the duration of leaf photosynthesis during grain filling using slow‐senescing functional stay‐green phenotypes is a possible route for increasing grain yields in wheat (Triticum aestivumL.). However, delayed senescence may negatively affect nutrient remobilisation and hence reduce grain protein concentrations and grain quality. A novelNAC1‐type transcription factor (hereafter TaNAC‐S) was identified in wheat, with gene expression located primarily in leaf/sheath tissues, which decreased during post‐anthesis leaf senescence. Expression of TaNAC‐S in the second leaf correlated with delayed senescence in two doubled‐haploid lines of an Avalon × Cadenza population (lines 112 and 181), which were distinct for leaf senescence. Transgenic wheat plants overexpressing TaNAC‐S resulted in delayed leaf senescence (stay‐green phenotype). Grain yield, aboveground biomass, harvest index and total grain N content were unaffected, butNACover‐expressing lines had higher grain N concentrations at similar grain yields compared to non‐transgenic controls. These results indicate that TaNAC‐S is a negative regulator of leaf senescence, and that delayed leaf senescence may lead not only to increased grain yields but also to increased grain protein concentrations.
Two Methods of Vitrification Followed by In Vitro Culture of the Ovine Ovary: Evaluation of the Follicular Development and Ovarian Extracellular Matrix
Authors: Bandeira FT , Carvalho AA , Castro SV , Lima LF , Viana DA , Evangelista JSAM , Pereira MJS , Campello CC , Figueiredo JR , Rodrigues APR
Published: December 2014

Contents

The aim of this study was to evaluate the influence of two vitrification techniques on the extra cellular matrix (ECM) and ovarian follicular development. The ovarian cortex was fragmented (9 mm3) and divided into six groups, viz. fresh control, cultured control, vitrified by the Ovarian Tissue Cryosystem (OTC) method, conventional solid surface vitrification (SSV) method, OTC/cultured and SSV/cultured. Follicles from all the fragments were analysed for morphology, development and viability. The ECM was evaluated based on the condition of collagen and reticular fibres and the immunolocalization of type I collagen and fibronectin. After 7 days of culture, the tissue vitrified by OTC revealed a higher percentage (p < 0.05) of morphologically normal (30.66%) and viable (60.00%) follicles when compared with those vitrified using the SSV technique (21.33% and 23.00%). In all the fragments cultured, regardless of the vitrification method, a significantly higher percentage of developing follicles was observed when compared with the non‐cultured tissue. Analysis of the type I collagen showed increased immunostaining after the in vitro culture in the vitrified fragments. In conclusion, the OTC is better for preserving the follicular viability and morphology and maintaining the integrity of the extracellular matrix components of the ovine ovary.
Mineralogy of Early Cambrian Ni‐Mo Polymetallic Black Shale at the Sancha Deposit, South China: Implications for Ore Genesis
Authors: Han Shanchu , Hu Kai , Cao Jian , Pan Jiayong , Liu Yin , Bian Lizeng , Shi Chunhua
Published: December 2014

The mineralogy of the Early Cambrian Ni–Mo polymetallic black shale ores at the Sancha deposit, South China, was investigated to better the understanding of the complex ore genesis by optical microscope, electron microprobe, and scanning electron microscope. Analytical results show that the sulfides in the ore bed mainly comprise C/MoS2 mixed‐layer phase (MoSC), millerite, and pyrite. Of these, MoSC and millerite are the main ore minerals of Mo and Ni, respectively. Pyrite is subdivided into six types based on its morphology, occurrence, relationship to Ni‐ and Mo‐bearing minerals, and chemical composition. Many millerite crystals cut early‐formed MoSC, implying that these two minerals formed at different stages. The concentrations of biogenic elements (e.g., Sb) in the MoSC are high compared with those in millerite, implying a close relationship between MoSC and organic matter. These data provide a new and improved understanding of the complex ore genesis at the Sancha deposit, and can be applied to other black‐shale‐hosted mineral deposits worldwide.
A Study on the Mineralization of the Woxi Au–Sb–W Deposit, Western Hunan, China
Authors: Liang Yi , Wang Guogang , Liu Shengyou , Sun Yuzhen , Huang Yonggang , Hoshino Kenichi
Published: December 2014

The Woxi Au–Sb–W deposit in the western Hunan Province, China, is of hydrothermal vein type characterized by a rare mineral assemblage of stibnite, scheelite and native gold, of which gold fineness ranges from 998.6 to 1000. The mineralization sequence observed in the deposit is, from early to late, coarse‐grained pyrite – scheelite – stibnite – Pb–Sb–S minerals – sphalerite (+ cubanite) – fine‐grained pyrite. Native gold may have precipitated with scheelte. Microthermometric and LA–ICP–MS analyses of fluid inclusions in scheelite, quartz associated with scheelite and stibnite and barren quartz clarified that there may be at least three types of hydrothermal fluids during the vein formation in the Woxi deposit. Scheelite and native gold precipitated from the fluid of high temperature and salinity with high concentrations of metal elements, followed by stibnite precipitation. The later fluid of the highest temperature and salinity with low concentrations of the elements yielded the sphalerite mineralization. The latest fluid of low temperature and salinity with low concentrations of the elements is observed mainly in barren quartz. The remarkably high Au/Ag concentration ratios determined in the fluid inclusions in scheelite might be the reason for the extremely high gold fineness of native gold.
Study of Carbon‐Bearing Particles in Ascending Geogas Flows in theDongshengmiao Polymetallic Pyrite Deposit, InnerMongolia,China
Authors: Hu Guai , Cao Jianjin , Hopke Philip K. , Holub Robert Frantisek
Published: December 2014

Samples of ascending geogas flow particles were collected on toSiNgrids directly in theQuaternary sediments overlying theDongshengmiao polymetallic pyrite deposit, China. Corresponding soil samples were collected in the surface ofDongshengmiao district at the same time. After pretreatment, theseSiNgrid samples were analyzed by transmission electron microscopy. The tests focused on the characteristics of particles including size, shape, chemical composition, structure and association. The results show that there are numerous carbon‐bearing particles in particulate samples of the ascending geogas flow. The particles contain organic matter, carbonate or carbonate mixed with other minerals. These carbon‐bearing particles generally contain metallic elements likeFe/Zn/Au/Cu/Pb. However, all of the soil particles do not contain elementalCand only consist of common elements (O,Na,Mg,Al,Si,Ca,Ti) just like the composition of earth crust. Through a comparison between the particles from different sources, the carbon‐bearing particles were found to come only from the deep earth and carried useful information about concealed deposits as they pass through the deep‐seated orebodies. Given the influences of organic matter on mineralization, the carbon‐bearing particle may provide information on the deposit genesis. Combining the use of geogas particle for prospecting with characteristics of large depth, and the carbon‐bearing materials' close spatial and genetic relationship with orebodies, we propose a new prospecting method based on the characteristics of carbon‐bearing particles, including morphology, size, chemical component and ultra‐microstructure. This approach could be applied to the exploration of deposits deep in the earth and abundant in carbon‐bearing matter. This approach can provide efficient and effective deposit exploration.
A Tilting Approach to Ranking Influence
Authors: Genton Marc G. , Hall Peter
Published: December 2014

We suggest a new approach, which is applicable for general statistics computed from random samples of univariate or vector-valued or functional data, to assessing the influence that individual data have on the value of a statistic, and to ranking the data in terms of that influence. Our method is based on, first, perturbing the value of the statistic by ‘tilting’, or reweighting, each data value, where the total amount of tilt is constrained to be the least possible, subject to achieving a given small perturbation of the statistic, and, then, taking the ranking of the influence of data values to be that which corresponds to ranking the changes in data weights. It is shown, both theoretically and numerically, that this ranking does not depend on the size of the perturbation, provided that the perturbation is sufficiently small. That simple result leads directly to an elegant geometric interpretation of the ranks; they are the ranks of the lengths of projections of the weights onto a ‘line’ determined by the first empirical principal component function in a generalized measure of covariance. To illustrate the generality of the method we introduce and explore it in the case of functional data, where (for example) it leads to generalized boxplots. The method has the advantage of providing an interpretable ranking that depends on the statistic under consideration. For example, the ranking of data, in terms of their influence on the value of a statistic, is different for a measure of location and for a measure of scale. This is as it should be; a ranking of data in terms of their influence should depend on the manner in which the data are used. Additionally, the ranking recognizes, rather than ignores, sign, and in particular can identify left- and right-hand ‘tails’ of the distribution of a random function or vector.
Estimation of Extreme Quantiles for Functions of Dependent Random Variables
Authors: Gong Jinguo , Li Yadong , Peng Liang , Yao Qiwei
Published: December 2014

We propose a new method for estimating the extreme quantiles for a function of several dependent random variables. In contrast with the conventional approach based on extreme value theory, we do not impose the condition that the tail of the underlying distribution admits an approximate parametric form, and, furthermore, our estimation makes use of the full observed data. The method proposed is semiparametric as no parametric forms are assumed on the marginal distributions. But we select appropriate bivariate copulas to model the joint dependence structure by taking advantage of the recent development in constructing large dimensional vine copulas. Consequently a sample quantile resulting from a large bootstrap sample drawn from the fitted joint distribution is taken as the estimator for the extreme quantile. This estimator is proved to be consistent under the regularity conditions on the closeness between a quantile set and its truncated set, and the empirical approximation for the truncated set. The simulation results lend further support to the reliable and robust performance of the method proposed. The method is further illustrated by a real world example in backtesting financial risk models.
Optimal Designs for the Prediction of Individual Parameters in Hierarchical Models
Authors: Prus Maryna , Schwabe Rainer
Published: December 2014

Characterizations of optimal designs are derived for the prediction of individual response curves within the framework of hierarchical linear mixed models. It is shown that the so-obtained optimal designs may differ substantially from those propagated in the literature so far and that the latter may become useless in terms of their performance.
Novel tools for stepping source brachytherapy treatment planning: Enhanced geometrical optimization and interactive inverse planning
Authors: Dinkla Anna M. , van der Laarse Rob , Koedooder Kees , Petra Kok H. , van Wieringen Niek , Pieters Bradley R. , Bel Arjan
Published: December 2014

Purpose:

Dose optimization for stepping source brachytherapy can nowadays be performed using automated inverse algorithms. Although much quicker than graphical optimization, an experienced treatment planner is required for both methods. With automated inverse algorithms, the procedure to achieve the desired dose distribution is often based on trial‐and‐error.

Methods:

A new approach for stepping source prostate brachytherapy treatment planning was developed as a quick and user‐friendly alternative. This approach consists of the combined use of two novel tools: Enhanced geometrical optimization (EGO) and interactive inverse planning (IIP). EGO is an extended version of the common geometrical optimization method and is applied to create a dose distribution as homogeneous as possible. With the second tool, IIP, this dose distribution is tailored to a specific patient anatomy by interactively changing the highest and lowest dose on the contours.

Results:

The combined use of EGO–IIP was evaluated on 24 prostate cancer patients, by having an inexperienced user create treatment plans, compliant to clinical dose objectives. This user was able to create dose plans of 24 patients in an average time of 4.4 min/patient. An experienced treatment planner without extensive training in EGO–IIP also created 24 plans. The resulting dose‐volume histogram parameters were comparable to the clinical plans and showed high conformance to clinical standards.

Conclusions:

Even for an inexperienced user, treatment planning with EGO–IIP for stepping source prostate brachytherapy is feasible as an alternative to current optimization algorithms, offering speed, simplicity for the user, and local control of the dose levels.
The first clinical treatment with kilovoltage intrafraction monitoring (KIM): A real‐time image guidance method
Authors: Keall Paul J. , Aun Ng Jin , O'Brien Ricky , Colvill Emma , Huang Chen‐Yu , Rugaard Poulsen Per , Fledelius Walther , Juneja Prabhjot , Simpson Emma , Bell Linda , Alfieri Florencia , Eade Thomas , Kneebone Andrew , Booth Jeremy T.
Published: December 2014

Purpose:

Kilovoltage intrafraction monitoring (KIM) is a real‐time image guidance method that uses widely available radiotherapy technology, i.e., a gantry‐mounted x‐ray imager. The authors report on the geometric and dosimetric results of the first patient treatment using KIM which occurred on September 16, 2014.

Methods:

KIM uses current and prior 2D x‐ray images to estimate the 3D target position during cancer radiotherapy treatment delivery. KIM software was written to process kilovoltage (kV) images streamed from a standard C‐arm linear accelerator with a gantry‐mounted kV x‐ray imaging system. A 120° pretreatment kV imaging arc was acquired to build the patient‐specific 2D to 3D motion correlation. The kV imager was activated during the megavoltage (MV) treatment, a dual arc VMAT prostate treatment, to estimate the 3D prostate position in real‐time. All necessary ethics, legal, and regulatory requirements were met for this clinical study. The quality assurance processes were completed and peer reviewed.

Results:

During treatment, a prostate position offset of nearly 3 mm in the posterior direction was observed with KIM. This position offset did not trigger a gating event. After the treatment, the prostate motion was independently measured using kV/MV triangulation, resulting in a mean difference of less than 0.6 mm and standard deviation of less than 0.6 mm in each direction. The accuracy of the marker segmentation was visually assessed during and after treatment and found to be performing well. During treatment, there were no interruptions due to performance of the KIM software.

Conclusions:

For the first time, KIM has been used for real‐time image guidance during cancer radiotherapy. The measured accuracy and precision were both submillimeter for the first treatment fraction. This clinical translational research milestone paves the way for the broad implementation of real‐time image guidance to facilitate the detection and correction of geometric and dosimetric errors, and resultant improved clinical outcomes, in cancer radiotherapy.
Immunization with Brucella VirB Proteins Reduces Organ Colonization in Mice through a Th1-Type Immune Response and Elicits a Similar Immune Response in Dogs
Authors: Pollak Cora N. , Wanke María Magdalena , Estein Silvia M. , Delpino M. Victoria , Monachesi Norma E. , Comercio Elida A. , Fossati Carlos A. , Baldi Pablo C.
Published: December 2014

VirB proteins fromBrucellaspp. constitute the type IV secretion system, a key virulence factor mediating the intracellular survival of these bacteria. Here, we assessed whether a Th1-type immune response against VirB proteins may protect mice fromBrucellainfection and whether this response can be induced in the dog, a natural host forBrucella. Splenocytes from mice immunized with VirB7 or VirB9 responded to their respective antigens with significant and specific production of gamma interferon (IFN-γ), whereas interleukin-4 (IL-4) was not detected. Thirty days after an intraperitoneal challenge with liveBrucella abortus, the spleen load of bacteria was almost 1 log lower in mice immunized with VirB proteins than in unvaccinated animals. As colonization reduction seemed to correlate with a Th1-type immune response against VirB proteins, we decided to assess whether such a response could be elicited in the dog. Peripheral blood mononuclear cells (PBMCs) from dogs immunized with VirB proteins (three subcutaneous doses in QuilA adjuvant) produced significantly higher levels of IFN-γ than cells from control animals uponin vitrostimulation with VirB proteins. A skin test to assess specific delayed-type hypersensitivity was positive in 4 out of 5 dogs immunized with either VirB7 or VirB9. As both proteins are predicted to locate in the outer membrane ofBrucellaorganisms, the ability of anti-VirB antibodies to mediate complement-dependent bacteriolysis ofB. caniswas assessedin vitro. Sera from dogs immunized with either VirB7 or VirB9, but not from those receiving phosphate-buffered saline (PBS), produced significant bacteriolysis. These results suggest that VirB-specific responses that reduce organ colonization byBrucellain mice can be also elicited in dogs.
Tuberculosis Vaccine Types and Timings
Authors: Orme Ian M.
Published: December 2014

Traditionally, the design of new vaccines directed againstMycobacterium tuberculosis, the most successful bacterial pathogen on the planet, has focused on prophylactic candidates that would be given to individuals while they are still young. It is becoming more apparent, however, that there are several types of vaccine candidates now under development that could be used under various conditions. Thus, in addition to prophylactic vaccines, such as recombinantMycobacterium bovisBCG or BCG-boosting vaccines, other applications include vaccines that could prevent infection, vaccines that could be given in emergency situations as postexposure vaccines, vaccines that could be used to facilitate chemotherapy, and vaccines that could be used to reduce or prevent relapse and reactivation disease. These approaches are discussed here, including the type of immunity we are trying to specifically target, as well as the limitations of these approaches.
Draft Genome Sequence of the Novel Black-Pigmented
Planococcus
sp. Strain CAU13
Authors: Unverferth Cameron A. , Santisteban Ian C. , Setterdahl Aaron T.
Published: December 2014

Presented here is the whole-genome sequence of a previously uncharacterized species of the genus
Planococcus
. A 16S sequence analysis shows that this bacterium exhibits 98% sequence identity to the closest relative of
Planococcus kocurii
. Whereas most species of
Planococcus
produce yellow to orange pigments, the species described here produces black pigmentation.
A Newly Sequenced Alcaligenes faecalis Strain: Implications for Novel Temporal Symbiotic Relationships
Authors: Hernández-Mendoza Armando , Lozano-Aguirre Beltrán Luis Fernando , Martínez-Ocampo Fernando , Quiroz-Castañeda Rosa Estela , Dantán-González Edgar
Published: December 2014

We report here the draft genome sequence of
Alcaligenes faecalis
strain MOR02, a bacterium that is able to colonize nematodes in a temporary fashion and kill insects for their own benefit. The availability of the genome should enable us to explain these phenotypes.
Complete Genome Sequence of a Common Midwife Toad Virus-Like Ranavirus Associated with Mass Mortalities in Wild Amphibians in the Netherlands
Authors: van Beurden Steven J. , Hughes Joseph , Saucedo Bernardo , Rijks Jolianne , Kik Marja , Haenen Olga L. M. , Engelsma Marc Y. , Gröne Andrea , Verheije M. Helene , Wilkie Gavin
Published: December 2014

A ranavirus associated with mass mortalities in wild water frogs (
Pelophylax
spp.) and other amphibians in the Netherlands since 2010 was isolated, and its complete genome sequence was determined. The virus has a genome of 107,772 bp and shows 96.5% sequence identity with the common midwife toad virus from Spain.
Whole-Genome Sequence of Borrelia garinii Strain 935T Isolated from
Ixodes persulcatus
in South Korea
Authors: Noh Yoontae , Kim Su Yeon , Lee Yeong Seon , Kim Dae-Won , Kwon Taesoo , Hwang Kyu-Jam
Published: December 2014

We report here the genome sequence of
Borrelia garinii
strain 935T isolated from
Ixodes persulcatus
in South Korea. The 1,176,739 bp (G+C content, 27.73%) genome consists of 1,194 coding regions, 4 rRNA genes, and 33 aminoacyl-tRNA synthetase genes. This is the first whole-genome report of a Korean
Borrelia
species isolate.
Complete Genome Sequence of a Klebsiella pneumoniae Isolate with Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci
Authors: Conlan Sean , Deming Clayton , Tsai Yu-Chih , Lau Anna F. , Dekker John P. , Korlach Jonas , Segre Julia A.
Published: December 2014

Klebsiella pneumoniae
is an important nosocomial pathogen, and multidrug-resistant strains have become a worldwide concern. Here, we report the complete genome of a
K. pneumoniae
isolate with chromosomally integrated
bla
KPC
genes and a colibactin synthesis locus.
Draft Genome Sequence of Clostridium butyricum Strain NOR 33234, Isolated from an Elderly Patient with Diarrhea
Authors: Kwok Jamie S. L. , Ip Margaret , Chan Ting-Fung , Lam Wai-Yip , Tsui Stephen K. W.
Published: December 2014

Clostridium butyricum
is one of the species frequently present in patients' stool samples. However, the identification of this species is sometimes difficult. Here, we present the draft genome of
Clostridium butyricum
NOR 33234, which was isolated from a patient with suspected
Clostridium difficile
infection-associated diarrhea and resembles
Clostridium clostridioforme
in biochemical tests.
Whole-Genome Analysis of Aeromonas hydrophila Strain 187, Exhibiting Quorum-Sensing Activity
Authors: Chan Xin-Yue , Chua Kek Heng , Yin Wai-Fong , Puthucheary S. D. , Chan Kok-Gan
Published: December 2014

Aeromonas hydrophila
is a quorum-sensing (QS) bacterium that causes diarrhea in humans upon infection. Here, we report the genome of pathogenic
Aeromonas hydrophila
strain 187, which possesses a QS gene responsible for signaling molecule
N
-acyl homoserine lactone (AHL) synthesis and has been found to be located at contig 36.
Infection with Mycobacterium microti in Animals in France
Authors: Michelet Lorraine , de Cruz Krystel , Zanella Gina , Aaziz Rachid , Bulach Tabatha , Karoui Claudine , Hénault Sylvie , Joncour Guy , Boschiroli Maria Laura
Published: December 2014

We describe here 35 animal cases of tuberculosis due to
Mycobacterium microti
in France (2002–2014). Recently, molecular tools that overcome the difficulty of confirming infection by this potentially zoonotic agent have revealed an increasing number of cases, suggesting that its prevalence may have been underestimated.
Correlation between Sputum and Bronchoalveolar Lavage Fluid Cultures
Authors: Dubourg Grégory , Abat Cédric , Rolain Jean-Marc , Raoult Didier
Published: December 2014

A correlation study of the cultured bacteria from paired sputum and bronchoalveolar lavage fluid samples was performed. The rates of concordant culture-positive paired specimens that were isolated within 1 or 7 days were 93.7% and 96.5%, respectively, suggesting that the culture of readily collectable sputum specimens may result in useful microbiologic diagnosis.
First Report of Sphingomonas koreensis as a Human Pathogen in a Patient with Meningitis
Authors: Marbjerg Lis H. , Gaini Shahin , Justesen Ulrik S.
Published: December 2014

Sphingomonas koreensis
is an aerobic Gram-negative rod originally described in 2001 following isolation from natural mineral water in Korea. Here, we report a case study with
Sphingomonas koreensis
as the causative agent of meningitis. To our knowledge, this is the first documented case of
Sphingomonas koreensis
as a human pathogen.
Comparison of the Next-Generation Xpert MRSA/SA BC Assay and the GeneOhm StaphSR Assay to Routine Culture for Identification of Staphylococcus aureus and Methicillin-Resistant S. aureus in Positive-Blood-Culture Broths
Authors: Buchan Blake W. , Allen Stephen , Burnham Carey-Ann D. , McElvania TeKippe Erin , Davis Thomas , Levi Michael , Mayne Donna , Pancholi Preeti , Relich Ryan F. , Thomson Richard , Ledeboer Nathan A.
Published: December 2014

A bloodstream infection with
Staphylococcus aureus
, including methicillin-resistant
S. aureus
(MRSA), is a serious condition that carries a high mortality rate and is also associated with significant hospital costs. The rapid and accurate identification and differentiation of methicillin-susceptible
S. aureus
(MSSA) and MRSA directly from positive blood cultures has demonstrated benefits in both patient outcome and cost-of-care metrics. We compare the next-generation Xpert MRSA/SA BC (Xpert) assay to the GeneOhm StaphSR (GeneOhm) assay for the identification and detection of
S. aureus
and methicillin resistance in prospectively collected blood culture broths containing Gram-positive cocci. All results were compared to routine bacterial culture as the gold standard. Across 8 collection and test sites, the Xpert assay demonstrated a sensitivity of 99.6% (range, 96.4% to 100%) and a specificity of 99.5% (range, 98.0% to 100%) for identifying
S. aureus
, as well as a sensitivity of 98.1% (range, 87.5% to 100%) and a specificity of 99.6% (range, 98.3% to 100%) for identifying MRSA. In comparison, the GeneOhm assay demonstrated a sensitivity of 99.2% (range, 95.2% to 100%) and a specificity of 96.5% (range, 89.2% to 100%) for identifying
S. aureus
, as well as a sensitivity of 94.3% (range, 87.5% to 100%) and a specificity of 97.8% (range, 96.1% to 100%) for identifying MRSA. Five of six cultures falsely reported as negative for MRSA by the GeneOhm assay were correctly identified as positive by the Xpert assay, while one culture falsely reported as negative for MRSA by the Xpert assay was correctly reported as positive by the GeneOhm assay.
Assessment of Coinfection of Sexually Transmitted Pathogen Microbes by Use of the Anyplex II STI-7 Molecular Kit
Authors: Berçot B. , Amarsy R. , Goubard A. , Aparicio C. , Loeung H. U. , Segouin C. , Gueret D. , Jacquier H. , Meunier F. , Mougari F. , Cambau E.
Published: December 2014

Anyplex STI-7 is a new molecular kit that detects seven sexually transmitted pathogens. Among 202 subjects screened for genital infection, 143 (70.4%) were diagnosed with at least one pathogen, in concordance with reference methods. In addition, the Anyplex STI-7 demonstrated coinfections, such as that with
Ureaplasma parvum
and
Chlamydia trachomatis
, in young women.
The Proteasomal Rpn11 Metalloprotease Suppresses Tombusvirus RNA Recombination and Promotes Viral Replication via Facilitating Assembly of the Viral Replicase Complex
Authors: Prasanth K. Reddisiva , Barajas Daniel , Nagy Peter D.
Published: December 2014

RNA viruses co-opt a large number of cellular proteins that affect virus replication and, in some cases, viral genetic recombination. RNA recombination helps viruses in an evolutionary arms race with the host's antiviral responses and adaptation of viruses to new hosts. Tombusviruses and a yeast model host are used to identify cellular factors affecting RNA virus replication and RNA recombination. In this study, we have examined the role of the conserved Rpn11p metalloprotease subunit of the proteasome, which couples deubiquitination and degradation of proteasome substrates, in tombusvirus replication and recombination in
Saccharomyces cerevisiae
and plants. Depletion or mutations of Rpn11p lead to the rapid formation of viral RNA recombinants in combination with reduced levels of viral RNA replication in yeast or
in vitro
based on cell extracts. Rpn11p interacts with the viral replication proteins and is recruited to the viral replicase complex (VRC). Analysis of the multifunctional Rpn11p has revealed that the primary role of Rpn11p is to act as a “matchmaker” that brings the viral p92
pol
replication protein and the DDX3-like Ded1p/RH20 DEAD box helicases into VRCs. Overexpression of Ded1p can complement the defect observed in
rpn11
mutant yeast by reducing TBSV recombination. This suggests that Rpn11p can suppress tombusvirus recombination via facilitating the recruitment of the cellular Ded1p helicase, which is a strong suppressor of viral recombination, into VRCs. Overall, this work demonstrates that the co-opted Rpn11p, which is involved in the assembly of the functional proteasome, also functions in the proper assembly of the tombusvirus VRCs.

IMPORTANCE
RNA viruses evolve rapidly due to genetic changes based on mutations and RNA recombination. Viral genetic recombination helps viruses in an evolutionary arms race with the host's antiviral responses and facilitates adaptation of viruses to new hosts. Cellular factors affect viral RNA recombination, although the role of the host in virus evolution is still understudied. In this study, we used a plant RNA virus, tombusvirus, to examine the role of a cellular proteasomal protein, called Rpn11, in tombusvirus recombination in a yeast model host, in plants, and
in vitro
. We found that the cellular Rpn11 is subverted for tombusvirus replication and Rpn11 has a proteasome-independent function in facilitating viral replication. When the Rpn11 level is knocked down or a mutated Rpn11 is expressed, then tombusvirus RNA goes through rapid viral recombination and evolution. Taken together, the results show that the co-opted cellular Rpn11 is a critical host factor for tombusviruses by regulating viral replication and genetic recombination.
Reduction of HIV-1 Infectivity through Endoplasmic Reticulum-Associated Degradation-Mediated Env Depletion
Authors: Casini Antonio , Olivieri Michele , Vecchi Lara , Burrone Oscar R. , Cereseto Anna
Published: December 2014

During the HIV-1 replicative cycle, the gp160 envelope is processed in the secretory pathway to mature into the gp41 and gp120 subunits. Misfolded proteins located within the endoplasmic reticulum (ER) are proteasomally degraded through the ER-associated degradation (ERAD) pathway, a quality control system operating in this compartment. Here, we exploited the ERAD pathway to induce the degradation of gp160 during viral production, thus leading to the release of gp120-depleted viral particles.
The Genome of the Nucleopolyhedrosis-Causing Virus from Tipula oleracea Sheds New Light on the Nudiviridae Family
Authors: Bézier Annie , Thézé Julien , Gavory Frederick , Gaillard Julien , Poulain Julie , Drezen Jean-Michel , Herniou Elisabeth A.
Published: December 2014

A large double-stranded DNA (dsDNA) virus that produces occlusion bodies, typical of baculoviruses, has been described to infect crane fly larvae of the genus
Tipula
(Diptera, Tipulidae). Because of a lack of genomic data, this virus has remained unclassified. Electron microscopy of an archival virus isolated from
Tipula oleracea
,
T. oleracea
nudivirus (ToNV), showed irregularly shaped occlusion bodies measuring from 2 to 5 μm in length and 2 μm in middiameter, filled with rod-shape virions containing single nucleocapsids within a bilayer envelope. Whole-genome amplification and Roche 454 sequencing revealed a complete circular genome sequence of 145.7 kb, containing five direct repeat regions. We predicted 131 open reading frames, including a homolog of the polyhedrin gene encoding the major occlusion body protein of
T. paludosa
nucleopolyhedrovirus (NPV). BLAST searches demonstrated that ToNV had 21 of the 37 baculovirus core genes but shared 52 genes with nudiviruses (NVs). Phylogenomic analyses indicated that ToNV clearly belongs to the
Nudiviridae
family but should probably be assigned to a new genus. Among nudiviruses, ToNV was most closely related to the
Penaeus monodon
NV and
Heliothis zea
NV clade but distantly related to
Drosophila innubia
NV, the other nudivirus infecting a Diptera. Lastly, ToNV was found to be most closely related to the nuvidirus ancestor of bracoviruses. This was also reflected in terms of gene content, as ToNV was the only known exogenous virus harboring homologs of the
Cc50C22.6
and
27b
(
Cc50C22.7
) genes found in the nudiviral genomic cluster involved in bracovirus particle production.

IMPORTANCE
The
Nudiviridae
is a family of arthropod dsDNA viruses from which striking cases of endogenization have been reported (i.e., symbiotic bracoviruses deriving from a nudivirus and the endogenous nudivirus of the brown planthopper). Although related to baculoviruses, relatively little is known about the genomic diversity of exogenous nudiviruses. Here, we characterized, morphologically and genetically, an archival sample of the
Tipula oleracea
nudivirus (ToNV), which has the particularity of forming occlusion bodies. Comparative genomic and phylogenomic analyses showed ToNV to be to date the closest known relative of the exogenous ancestor of bracoviruses and that ToNV should be assigned to a new genus. Moreover, we revised the homology relationships of nudiviral genes and identified a new set of 32 core genes for the
Nudiviridae
, of which 21 were also baculovirus core genes. These findings provide important insights into the evolutionary history of large arthropod dsDNA viruses.
Functional Comparison of Herpes Simplex Virus 1 (HSV-1) and HSV-2 ICP27 Homologs Reveals a Role for ICP27 in Virion Release
Authors: Park Donglim , Lalli Joseph , Sedlackova-Slavikova Lenka , Rice Stephen A.
Published: December 2014

Numerous studies have focused on the regulatory functions of ICP27, an immediate-early (IE) protein of herpes simplex virus 1 (HSV-1). However, its homolog in HSV-2, termed ICP27t2, has been little studied. Here, we used two different approaches to functionally compare ICP27t2 and ICP27. In transfection-based assays, ICP27t2 closely resembled ICP27 in its capacity to enhance HSV-1 late gene expression, suppress the splicing of a viral intron, and complement the growth of an HSV-1 ICP27 null mutant. To study ICP27t2 in the context of viral infection, we engineered K2F1, an HSV-1 mutant that encodes ICP27t2 in place of ICP27. In Vero cells, K2F1 replicated with wild-type (WT) kinetics and yields, expressed delayed-early and late proteins normally, and was fully capable of activating several cellular signal transduction pathways that are ICP27 dependent. Thus, we conclude that ICP27t2 and ICP27 are functionally very similar and that ICP27t2 can mediate all ICP27 activities that are required for HSV-1 replication in cell culture. Surprisingly, however, we found that K2F1 forms plaques that are morphologically different from those of WT HSV-1. Investigation of this trait demonstrated that it results from the decreased release of progeny virions into the culture medium. This appears to be due to a reduction in the detachment of K2F1 progeny from the extracellular surface of the infected cell. We identified two HSV-1 ICP27 amino-terminal deletion mutants with a similar release defect. Together, these results demonstrate that ICP27 plays a heretofore-unappreciated role in modulating the efficiency of progeny virion release.

IMPORTANCE
ICP27 is an essential, multifunctional regulatory protein that has a number of critical roles in the HSV-1 life cycle. Although ICP27 homologs are encoded by all known members of the
Herpesviridae
, previous work with several of these homologs has shown that they cannot substitute for ICP27 in the context of HSV-1-infected cells. Here, we identify ICP27t2 as the first homolog that can efficiently replace ICP27 in HSV-1 infection. Unexpectedly, our results also reveal that the sequence of the ICP27 gene can affect the release of HSV-1 progeny virions from the infected cell. Thus, our comparative study has revealed a novel function for ICP27 in the regulation of virus release.
Postentry Restriction of Mason-Pfizer Monkey Virus in Mouse Cells
Authors: Wang Gary Z. , Goff Stephen P.
Published: December 2014

Mason-Pfizer monkey virus (M-PMV) is a prototypical betaretrovirus responsible for simian AIDS (SAIDS) in rhesus macaques. It has been shown previously that mouse cells are resistant to infection by HIV-1 and other primate lentiviruses. However, the susceptibility of mouse cells to primate retroviruses such as M-PMV remains unexplored. In the present study, using single-round green fluorescent protein (GFP) reporter viruses, we showed that various mouse cell lines are unable to support the early stages of M-PMV replication. The block to infection occurs postentry and is independent of the viral envelope. Using quantitative real-time PCR, we showed that the block to infection occurs after reverse transcription but before formation of circular DNA or proviral DNA. Finally, we showed that the M-PMV block in mouse cells is not attributable to the previously characterized mouse restriction factor
Fv1
. Overall, these findings suggest that mouse cells exhibit a previously uncharacterized block to M-PMV infection.

IMPORTANCE
Here we document a novel postentry restriction to M-PMV infection in mouse cells. The block occurs after reverse transcription but before the formation of circular or proviral DNA and is independent of the previous characterized mouse restriction factor
Fv1
.
Influenza Virus Reservoirs and Intermediate Hosts: Dogs, Horses, and New Possibilities for Influenza Virus Exposure of Humans
Authors: Parrish Colin R. , Murcia Pablo R. , Holmes Edward C.
Published: December 2014

Influenza A virus (IAV) infections in hosts outside the main aquatic bird reservoirs occur periodically. Although most such cross-species transmission events result in limited onward transmission in the new host, sustained influenza outbreaks have occurred in poultry and in a number of mammalian species, including humans, pigs, horses, seals, and mink. Recently, two distinct strains of IAV have emerged in domestic dogs, with each circulating widely for several years. Here, we briefly outline what is known about the role of intermediate hosts in influenza emergence, summarize our knowledge of the new canine influenza viruses (CIVs) and how they provide key new information on the process of host adaptation, and assess the risk these viruses pose to human populations.