bluuebunny/crossref_metadata_2025_split huggingface dataset:
TOND1confers tolerance to nitrogen deficiency in rice
Authors: Zhang Yangjun , Tan Lubin , Zhu Zuofeng , Yuan Lixing , Xie Daoxin , Sun Chuanqing 
Published: December 2014

SummaryNitrogen (N), the most important mineral nutrient for plants, is critical to agricultural production systems. N deficiency severely affects rice growth and decreases rice yields. However, excessive use of N fertilizer has caused severe pollution to agricultural and ecological environments. The necessity of breeding of crops that require lower input of N fertilizer has been recognized. Here we identified a major quantitative trait locus on chromosome 12,Tolerance Of Nitrogen Deficiency 1(TOND1), that confers tolerance to N deficiency in theindicacultivar Teqing. Sequence verification of 75indicaand 75japonicacultivars from 18 countries and regions demonstrated that only 27.3% of cultivars (41indicacultivars) containTOND1, whereas 72.7% of cultivars, including the remaining 34indicacultivars and all 75japonicacultivars, do not harbor theTOND1allele. Over‐expression ofTOND1increased the tolerance to N deficiency in theTOND1‐deficient rice cultivars. The identification ofTOND1provides a molecular basis for breeding rice varieties with improved grain yield despite decreased input of N fertilizers.
Reactive oxygen species‐provoked mitochondria‐dependent cell death during ageing of elm (Ulmus pumila L.) seeds
Authors: Wang Yu , Li Ying , Xue Hua , Pritchard Hugh W. , Wang Xiaofeng 
Published: December 2014

SummaryPrevious studies have shown that controlled deterioration treatment (CDT) induces programmed cell death in elm (Ulmus pumila L.) seeds, which undergo certain fundamental processes that are comparable to apoptosis in animals. In this study, the essential characteristics of mitochondrial physiology in elm seeds during CDT were identified by cellular ultrastructural analysis, whole‐body optical imaging, Western blotting and semi‐quantitative RT–PCR. The alteration in mitochondrial morphology was an early event during CDT, as indicated by progressive dynamic mitochondrial changes and rupture of the mitochondrial outer membrane; loss of mitochondrial transmembrane potential (Δψm) ensued, and mitochondrial ATP levels decreased. The mitochondrial permeability transition pore inhibitor cyclosporine A effectively suppressed these changes during ageing. The in situ localization of production of reactive oxygen species (ROS), and evaluation of the expression of voltage‐dependent anion‐selective channel and cyclophilin D indicated that the levels of mitochondrial permeability transition pore components were positively correlated with ROS production, leading to an imbalance of the cellular redox potential and ultimately to programmed cell death. Pre‐incubation with ascorbic acid slowed loss of mitochondrial Δψm, and decreased the effect of CDT on seed viability. However, there were no significant changes in multiple antioxidant elements or chaperones in the mitochondria during early stages of ageing. Our results indicate that CDT induces dynamic changes in mitochondrial physiology via increased ROS production, ultimately resulting in an irreversible loss of seed viability.
Liquid chromatography high‐resolution mass spectrometry for fatty acid profiling
Authors: Bromke Mariusz A. , Hochmuth Anton , Tohge Takayuki , Fernie Alisdair R. , Giavalisco Patrick , Burgos Asdrubal , Willmitzer Lothar , Brotman Yariv 
Published: December 2014

SummaryQuantification of fatty acids has been crucial to elucidate lipid biosynthesis pathways in plants. To date, fatty acid identification and quantification has relied mainly on gas chromatography (GC) coupled to flame ionization detection (FID) or mass spectrometry (MS), which requires the derivatization of samples and the use of chemical standards for annotation. Here we present an alternative method based on a simple procedure for the hydrolysis of lipids, so that fatty acids can be quantified by liquid chromatography mass spectrometry (LC‐MS) analysis. Proper peak annotation of the fatty acids in the LC‐MS‐based methods has been achieved by LC‐MS measurements of authentic standard compounds and elemental formula annotation supported by 13C isotope‐labeled Arabidopsis. As a proof of concept, we have compared the analysis by LC‐MS and GC‐FID of two previously characterized Arabidopsis thaliana knock‐out mutants for FAD6 and FAD7 desaturase genes. These results are discussed in light of lipidomic profiles obtained from the same samples. In addition, we performed untargeted LC‐MS analysis to determine the fatty acid content of two diatom species. Our results indicate that both LC‐MS and GC‐FID analyses are comparable, but that because of higher sensitivity and selectivity the LC‐MS‐based method allows for a broader coverage and determination of novel fatty acids.
Identification of Capsular Types in Carbapenem-Resistant Klebsiella pneumoniae Strains by
wzc
Sequencing and Implications for Capsule Depolymerase Treatment
Authors: Pan Yi-Jiun , Lin Tzu-Lung , Lin Yi-Tsung , Su Po-An , Chen Chun-Tang , Hsieh Pei-Fang , Hsu Chun-Ru , Chen Ching-Ching , Hsieh Yu-Chia , Wang Jin-Town 
Published: December 2014

ABSTRACT

Klebsiella pneumoniae
is an important human pathogen associated with a variety of diseases, and the prevalence of multidrug-resistant
K. pneumoniae
(MDRKP) is rapidly increasing. Here we determined the capsular types of 85 carbapenem-resistant
K. pneumoniae
(CRKP) strains by
wzc
sequencing and investigated the presence of carbapenemases and integrons among CRKP strains. Ten CRKP strains (12%) were positive for carbapenemase (imipenemase, 6/85 strains;
K. pneumoniae
carbapenemase, 3/85 strains; Verona integron-encoded metallo-β-lactamase, 1/85 strains). Capsular type K64 accounted for 32 CRKP strains (38%), followed by K62 (13%), K24 (8%), KN2 (7%), and K28 (6%). Sequence types (STs) were determined by multilocus sequence typing (MLST), and the results indicated that ST11, which accounted for 47% of these CRKP strains (40/85 strains), was the major ST. We further isolated a K64-specific capsule depolymerase (K64dep), which could enhance serum and neutrophil killing
in vitro
and increase survival rates for K64
K. pneumoniae
-inoculated mice. The toxicity study demonstrated that mice treated with K64dep showed normal biochemical parameters and no significant histopathological changes of liver, kidney, and spleen, indicating that enzyme treatment did not cause toxicity in mice. Therefore, the findings of capsular type clustering among CRKP strains and effective treatment with capsule depolymerase for MDRKP infections are important for capsule-based vaccine development and therapy.
In Vitro
and
In Vivo
Antiviral Activity and Resistance Profile of Ombitasvir, an Inhibitor of Hepatitis C Virus NS5A
Authors: Krishnan Preethi , Beyer Jill , Mistry Neeta , Koev Gennadiy , Reisch Thomas , DeGoey David , Kati Warren , Campbell Andrew , Williams Laura , Xie Wangang , Setze Carolyn , Molla Akhteruzzaman , Collins Christine , Pilot-Matias Tami 
Published: December 2014

ABSTRACT

Ombitasvir (ABT-267) is a hepatitis C virus (HCV) NS5A inhibitor with picomolar potency, pan-genotypic activity, and 50% effective concentrations (EC
50
s) of 0.82 to 19.3 pM against HCV genotypes 1 to 5 and 366 pM against genotype 6a. Ombitasvir retained these levels of potency against a panel of 69 genotype 1 to 6 chimeric replicons containing the NS5A gene derived from HCV-infected patients, despite the existence of natural sequence diversity within NS5A.
In vitro
resistance selection identified variants that conferred resistance to ombitasvir in the HCV NS5A gene at amino acid positions 28, 30, 31, 58, and 93 in genotypes 1 to 6. Ombitasvir was evaluated
in vivo
in a 3-day monotherapy study in 12 HCV genotype 1-infected patients at 5, 25, 50, or 200 mg dosed once daily. All patients in the study were HCV genotype 1a infected and were without preexisting resistant variants at baseline as determined by clonal sequencing. Decreases in HCV RNA up to 3.1 log
10
IU/ml were observed. Resistance-associated variants at position 28, 30, or 93 in NS5A were detected in patient samples 48 hours after the first dose. Clonal sequencing analysis indicated that wild-type virus was largely suppressed by ombitasvir during 3-day monotherapy, and at doses higher than 5 mg, resistant variant M28V was also suppressed. Ombitasvir was well tolerated at all doses, and there were no serious or severe adverse events. These data support clinical development of ombitasvir in combination with inhibitors targeting HCV NS3/4A protease (ABT-450 with ritonavir) and HCV NS5B polymerase (ABT-333, dasabuvir) for the treatment of chronic HCV genotype 1 infection. (Study M12-116 is registered at ClinicalTrials.gov under registration no. NCT01181427.)
Macrolide-Resistant Mycoplasma pneumoniae in Adults in Zhejiang, China
Authors: Zhou Zibo , Li Xiangzhi , Chen Xiaojian , Luo Fangjun , Pan Changwang , Zheng Xiaoping , Tan Feng 
Published: December 2014

ABSTRACT

Mycoplasma pneumoniae
is a major pathogen causing community-acquired pneumoniae (CAP), which is generally treated with macrolides. In recent years, however, although macrolide-resistant
M. pneumoniae
has been reported frequently, particularly in China, very little is known about the prevalence of macrolide-resistant
M. pneumoniae
infection in adults. In this study, we survey the macrolide-resistant
M. pneumoniae
in adults in Zhejiang province and characterize the mechanisms of resistance to macrolide. Six hundred fifty throat swab samples were collected from adult patients with CAP from January 2012 to August 2014. These samples were assayed by nested PCR and then cultivated for
M. pneumoniae
. All isolates were sequenced to determine the mutation in domain V of the 23S rRNA gene. The activities of 10 antibiotics against macrolide-resistant
M. pneumoniae
isolates were also investigated
in vitro
. Moreover, restriction fragment length polymorphism (RFLP) analysis of the amplified P1 gene was used to type 50 resistant strains. One hundred percent (71/71) of
M. pneumoniae
strains isolated from adults with CAP were resistant to erythromycin (MIC = 128 to >256 μg/ml), clarithromycin (MIC = 128 to >256 μg/ml), and azithromycin (MIC = 32 to >64 μg/ml). Furthermore, all macrolide-resistant
M. pneumoniae
strains identified had an A2063G mutation in domain V of the 23S rRNA gene. Forty-six resistant strains (92.0%) were classified into type I strain on the basis of P1 gene PCR-RFLP analysis. According to these findings, it is suggested that macrolide-resistant
M. pneumoniae
infection is very prevalence among adults in Zhejiang province. Thus, there is necessary to perform the epidemiological monitoring of macrolide-resistant
M. pneumoniae
in the future.
Broad Coverage of Genetically Diverse Strains of Clostridium difficile by Actoxumab and Bezlotoxumab Predicted by
In Vitro
Neutralization and Epitope Modeling
Authors: Hernandez Lorraine D. , Racine Fred , Xiao Li , DiNunzio Edward , Hairston Nichelle , Sheth Payal R. , Murgolo Nicholas J. , Therien Alex G. 
Published: December 2014

ABSTRACT

Clostridium difficile
infections (CDIs) are the leading cause of hospital-acquired infectious diarrhea and primarily involve two exotoxins, TcdA and TcdB. Actoxumab and bezlotoxumab are human monoclonal antibodies that neutralize the cytotoxic/cytopathic effects of TcdA and TcdB, respectively. In a phase II clinical study, the actoxumab-bezlotoxumab combination reduced the rate of CDI recurrence in patients who were also treated with standard-of-care antibiotics. However, it is not known whether the antibody combination will be effective against a broad range of
C. difficile
strains. As a first step toward addressing this, we tested the ability of actoxumab and bezlotoxumab to neutralize the activities of toxins from a number of clinically relevant and geographically diverse strains of
C. difficile
. Neutralization potencies, as measured in a cell growth/survival assay with purified toxins from various
C. difficile
strains, correlated well with antibody/toxin binding affinities. Actoxumab and bezlotoxumab neutralized toxins from culture supernatants of all clinical isolates tested, including multiple isolates of the BI/NAP1/027 and BK/NAP7/078 strains, at antibody concentrations well below plasma levels observed in humans. We compared the bezlotoxumab epitopes in the TcdB receptor binding domain across known TcdB sequences and found that key substitutions within the bezlotoxumab epitopes correlated with the relative differences in potencies of bezlotoxumab against TcdB of some strains, including ribotypes 027 and 078. Combined with
in vitro
neutralization data, epitope modeling will enhance our ability to predict the coverage of new and emerging strains by actoxumab-bezlotoxumab in the clinic.
Inactivation of Murine Norovirus on a Range of Copper Alloy Surfaces Is Accompanied by Loss of Capsid Integrity
Authors: Warnes Sarah L. , Summersgill Emma N. , Keevil C. William 
Published: December 2014

ABSTRACT
Norovirus is one of the most common causes of acute viral gastroenteritis. The virus is spread via the fecal-oral route, most commonly from infected food and water, but several outbreaks have originated from contamination of surfaces with infectious virus. In this study, a close surrogate of human norovirus causing gastrointestinal disease in mice, murine norovirus type 1 (MNV-1), retained infectivity for more than 2 weeks following contact with a range of surface materials, including Teflon (polytetrafluoroethylene [PTFE]), polyvinyl chloride (PVC), ceramic tiles, glass, silicone rubber, and stainless steel. Persistence was slightly prolonged on ceramic surfaces. A previous study in our laboratory observed that dry copper and copper alloy surfaces rapidly inactivated MNV-1 and destroyed the viral genome. In this new study, we have observed that a relatively small change in the percentage of copper, between 70 and 80% in copper nickels and 60 and 70% in brasses, had a significant influence on the ability of the alloy to inactivate norovirus. Nickel alone did not affect virus, but zinc did have some antiviral effect, which was synergistic with copper and resulted in an increased efficacy of brasses with lower percentages of copper. Electron microscopy of purified MNV-1 that had been exposed to copper and stainless steel surfaces suggested that a massive breakdown of the viral capsid had occurred on copper. In addition, MNV-1 that had been exposed to copper and treated with RNase demonstrated a reduction in viral gene copy number. This suggests that capsid integrity is compromised upon contact with copper, allowing copper ion access to the viral genome.
Granzyme-Mediated Regulation of Host Defense in the Liver in Experimental Leishmania donovani Infection
Authors: Murray Henry W. , Mitchell-Flack Marisa , Zheng Hua , Ma Xiaojing 
Published: December 2014

ABSTRACTIn the livers of susceptible C57BL/6 (B6) mice infected withLeishmania donovani, CD8+T cell mechanisms are required for granuloma assembly, macrophage activation, intracellular parasite killing, and self-cure. Since gene expression of perforin and granzymes A and B (GzmA and GzmB), cytolytic proteins linked to CD8+cell effector function, was enhanced in infected liver tissue, B6 mice deficient in these granular proteins were used to gauge host defense roles. Neither perforin nor GzmA was required; however, mice deficient in GzmB (GzmB−/−, GzmB cluster−/−, and GzmA×B cluster double knockout [DKO] mice) showed both delayed granuloma assembly and initially impaired control of parasite replication. Since these two defects in B6 mice were limited to early-stage infection, innately resistant 129/Sv mice were also tested. In this genetic setting, expression of both innate and subsequent T (Th1) cell-dependent acquired resistance, including the self-cure phenotype, was entirely derailed in GzmA×B cluster DKO mice. These results, in susceptible B6 mice for GzmB and in resistant 129/Sv mice for GzmA and/or the GzmB cluster, point to granzyme-mediated host defense regulation in the liver in experimental visceral leishmaniasis.
The Staphylococcus aureus NuoL-Like Protein MpsA Contributes to the Generation of Membrane Potential
Authors: Mayer Sonja , Steffen Wojtek , Steuber Julia , Götz Friedrich 
Published: December 2014

ABSTRACT

In aerobic microorganisms, the entry point of respiratory electron transfer is represented by the NADH:quinone oxidoreductase. The enzyme couples the oxidation of NADH with the reduction of quinone. In the type 1 NADH:quinone oxidoreductase (Ndh1), this reaction is accompanied by the translocation of cations, such as H
+
or Na
+
. In
Escherichia coli
, cation translocation is accomplished by the subunit NuoL, thus generating membrane potential (Δψ). Some microorganisms achieve NADH oxidation by the alternative, nonelectrogenic type 2 NADH:quinone oxidoreductase (Ndh2), which is not cation translocating. Since these enzymes had not been described in
Staphylococcus aureus
, the goal of this study was to identify proteins operating in the NADH:quinone segment of its respiratory chain. We demonstrated that Ndh2 represents a NADH:quinone oxidoreductase in
S. aureus
. Additionally, we identified a hypothetical protein in
S. aureus
showing sequence similarity to the proton-translocating subunit NuoL of complex I in
E. coli
: the NuoL-like protein MpsA. Mutants with deletion of the
nuoL
-like gene
mpsA
and its corresponding operon,
mpsABC
(
mps
for membrane potential-generating system), exhibited a small-colony-variant-like phenotype and were severely affected in Δψ and oxygen consumption rates. The MpsABC proteins did not confer NADH oxidation activity. Using an Na
+
/H
+
antiporter-deficient
E. coli
strain, we could show that MpsABC constitute a cation-translocating system capable of Na
+
transport. Our study demonstrates that MpsABC represent an important functional system of the respiratory chain of
S. aureus
that acts as an electrogenic unit responsible for the generation of Δψ.
Evolution of Aromatic β-Glucoside Utilization by Successive Mutational Steps in Escherichia coli
Authors: Zangoui Parisa , Vashishtha Kartika , Mahadevan Subramony 
Published: December 2014

ABSTRACT

The
bglA
gene of
Escherichia coli
encodes phospho-β-glucosidase A capable of hydrolyzing the plant-derived aromatic β-glucoside arbutin. We report that the sequential accumulation of mutations in
bglA
can confer the ability to hydrolyze the related aromatic β-glucosides esculin and salicin in two steps. In the first step, esculin hydrolysis is achieved through the acquisition of a four-nucleotide insertion within the promoter of the
bglA
gene, resulting in enhanced steady-state levels of the
bglA
transcript. In the second step, hydrolysis of salicin is achieved through the acquisition of a point mutation within the
bglA
structural gene close to the active site without the loss of the original catabolic activity against arbutin. These studies underscore the ability of microorganisms to evolve additional metabolic capabilities by mutational modification of preexisting genetic systems under selection pressure, thereby expanding their repertoire of utilizable substrates.
Specific exercise effects of preventive neuromuscular training intervention on anterior cruciate ligament injury risk reduction in young females: meta-analysis and subgroup analysis
Authors: Sugimoto Dai , Myer Gregory D , Barber Foss Kim D , Hewett Timothy E 
Published: December 2014

ContextClinical trials have demonstrated that preventive neuromuscular training (PNMT) can be effective to reduce ACL injuries in young females. However, the magnitude of the overall effect of PNMT for ACL injury reduction has not reached consensus. In addition, the effects of individual exercises in PNMT that optimise ACL injury reduction are unknown.ObjectiveThe purpose of this project was to systematically review previously published clinical trials and evaluate types of exercises that best support ACL injury reduction in young females.Data sourcesThe key words ‘knee’, ‘anterior cruciate ligament’, ‘ACL’, ‘prospective’, ‘neuromuscular’, ‘training’, ‘female’, and ‘prevention’ were used for studies published from 1995 to May 2012 in PubMed and EBSCO host.Study selectionInclusion criteria for the current analysis were: (1) documented number of ACL injuries, (2) employed a PNMT intervention that aimed to reduce ACL injuries, (3) had a comparison group, (4) used a prospective controlled study design, (5) recruited female athletes and (6) recorded exercises implemented in the PNMT.Data extractionThe number of ACL injuries and female athletes in each group (control and intervention) were extracted. In addition, exercises were categorised into four types and analysed for each investigation.Data synthesisA total of 14 clinical trials met the inclusion criteria. The subgroup analyses identified fewer ACL injuries in PNMT that focused on strengthening (OR 0.32, 95% CI 0.23 to 0.46, p=0.001), proximal control exercises (OR 0.33, 95% CI 0.23 to 0.47, p=0.001) and multiple exercise interventions (OR 0.32, CI 0.22 to 0.46, p=0.001).ConclusionsThe current subgroup analyses indicate strengthening, proximal control exercises and multi exercise genres increased efficacy in PNMT intervention designed to reduce ACL injury in young female athletes.
Cerebrovascular reactivity assessed by transcranial Doppler ultrasound in sport-related concussion: a systematic review
Authors: Gardner Andrew J , Tan Can Ozan , Ainslie Philip N , van Donkelaar Paul , Stanwell Peter , Levi Christopher R , Iverson Grant L 
Published: December 2014

BackgroundTraumatic brain injury influences regulation of cerebral blood flow in animal models and in human studies. We reviewed the use of transcranial Doppler ultrasound (US) to monitor cerebrovascular reactivity following sport-related concussion.Review methodA narrative and systematic review of articles published in the English language, from December 1982 to October 2013.Data sourcesArticles were retrieved via numerous databases using relevant key terms. Observational, cohort, correlational, cross-sectional and longitudinal studies were included.ResultsThree publications met the criteria for inclusion; these provided data from 42 athletes and 33 controls. All three studies reported reductions in cerebrovascular reactivity via transcranial Doppler US.ConclusionsThese initial results support the use of cerebrovascular reactivity as a research tool for identifying altered neurophysiology and monitoring recovery in adult athletes. Larger cross-sectional, prospective and longitudinal studies are required to understand the sensitivity and prognostic value of cerebrovascular reactivity in sport-related concussion.