bluuebunny/crossref_metadata_2025_split huggingface dataset:
Giardia spp. Are Commonly Found in Mixed Assemblages in Surface Water, as Revealed by Molecular and Whole-Genome Characterization
Authors: Prystajecky Natalie , Tsui Clement K.-M. , Hsiao William W. L. , Uyaguari-Diaz Miguel I. , Ho Jordan , Tang Patrick , Isaac-Renton Judith 
Published: May 2015

ABSTRACTGiardiais the most common parasitic cause of gastrointestinal infections worldwide, with transmission through surface water playing an important role in various parts of the world.Giardia duodenalis(synonyms:G. intestinalisandG. lamblia), a multispecies complex, has two zoonotic subtypes, assemblages A and B. When British Columbia (BC), a western Canadian province, experienced several waterborne giardiasis outbreaks due to unfiltered surface drinking water in the late 1980s, collection of isolates from surface water, as well as from humans and beavers (Castor canadensis), throughout the province was carried out. To better understandGiardiain surface water, 71 isolates, including 29 from raw surface water samples, 29 from human giardiasis cases, and 13 from beavers in watersheds from this historical library were characterized by PCR. Study isolates also included isolates from waterborne giardiasis outbreaks. Both assemblages A and B were identified in surface water, human, and beavers samples, including a mixture of both assemblages A and B in waterborne outbreaks. PCR results were confirmed by whole-genome sequencing (WGS) for one waterborne outbreak and supported the clustering of human, water, and beaver isolates within both assemblages. We concluded that contamination of surface water byGiardiais complex, that the majority of our surface water isolates were assemblage B, and that both assemblages A and B may cause waterborne outbreaks. The higher-resolution data provided by WGS warrants further study to better understand the spread ofGiardia.
Phytobeneficial Properties of Bacteria Isolated from the Rhizosphere of Maize in Southwestern Nigerian Soils
Authors: Abiala M. A. , Odebode A. C. , Hsu S. F. , Blackwood C. B. 
Published: May 2015

ABSTRACT

Biocontrol agents isolated outside Africa have performed inconsistently under field conditions in Africa. The development of indigenous phytobeneficial microbial strains that suit local environments may help enhance competitiveness with
in situ
microorganisms and effectiveness at suppressing local pathogen strains. We isolated bacteria from the rhizosphere of maize growing in southwestern Nigeria and assessed them for growth-promoting characteristics. The best isolates were characterized using 16S rRNA genes and were further evaluated in the greenhouse on maize seedlings. Four isolates (EBS8, IGBR11, EPR2, and ADS14) were outstanding in
in vitro
assays of antagonistic activity against a local strain of
Fusarium verticillioides
, phosphate solubilization efficiency, chitinase enzyme activity, and indole-3-acetic acid production. Inoculation of maize seeds with these isolates resulted in ≥95% maize seed germination and significantly enhanced radicle and plumule length. In the greenhouse, maize seedling height, stem girth, number of leaves, leaf area, shoot mass (dry matter), and nutrient contents were significantly enhanced. The bioprotectant and phytobeneficial effects were strongest and most consistent for isolate EBS8, which was identified as a
Bacillus
strain by 16S rRNA gene analysis. As a bacterial strain that exhibits multiple growth-promoting characteristics and is adapted to local conditions, EBS8 should be considered for the development of indigenous biological fertilizer treatments.
Semiquantitative Performance and Mechanism Evaluation of Carbon Nanomaterials as Cathode Coatings for Microbial Fouling Reduction
Authors: Zhang Qiaoying , Nghiem Joanne , Silverberg Gregory J. , Vecitis Chad D. 
Published: May 2015

ABSTRACT

In this study, we examine bacterial attachment and survival on a titanium (Ti) cathode coated with various carbon nanomaterials (CNM): pristine carbon nanotubes (CNT), oxidized carbon nanotubes (O-CNT), oxidized-annealed carbon nanotubes (OA-CNT), carbon black (CB), and reduced graphene oxide (rGO). The carbon nanomaterials were dispersed in an isopropyl alcohol-Nafion solution and were then used to dip-coat a Ti substrate.
Pseudomonas fluorescens
was selected as the representative bacterium for environmental biofouling. Experiments in the absence of an electric potential indicate that increased nanoscale surface roughness and decreased hydrophobicity of the CNM coating decreased bacterial adhesion. The loss of bacterial viability on the noncharged CNM coatings ranged from 22% for CB to 67% for OA-CNT and was dependent on the CNM dimensions and surface chemistry. For electrochemical experiments, the total density and percentage of inactivation of the adherent bacteria were analyzed semiquantitatively as functions of electrode potential, current density, and hydrogen peroxide generation. Electrode potential and hydrogen peroxide generation were the dominant factors with regard to short-term (3-h) bacterial attachment and inactivation, respectively. Extended-time electrochemical experiments (12 h) indicated that in all cases, the density of total deposited bacteria increased almost linearly with time and that the rate of bacterial adhesion was decreased 8- to 10-fold when an electric potential was applied. In summary, this study provides a fundamental rationale for the selection of CNM as cathode coatings and electric potential to reduce microbial fouling.
Effects of Abiotic and Biotic Stresses on the Internalization and Dissemination of Human Norovirus Surrogates in Growing Romaine Lettuce
Authors: DiCaprio Erin , Purgianto Anastasia , Li Jianrong 
Published: May 2015

ABSTRACT
Human norovirus (NoV) is the major causative agent of fresh-produce-related outbreaks of gastroenteritis; however, the ecology and persistence of human NoV in produce systems are poorly understood. In this study, the effects of abiotic and biotic stresses on the internalization and dissemination of two human NoV surrogates (murine norovirus 1 [MNV-1] and Tulane virus [TV]) in romaine lettuce were determined. To induce abiotic stress, romaine lettuce was grown under drought and flood conditions that mimic extreme weather events, followed by inoculation of soil with MNV-1 or TV. Independently, lettuce plants were infected with lettuce mosaic virus (LMV) to induce biotic stress, followed by inoculation with TV. Plants were grown for 14 days, and viral titers in harvested tissues were determined by plaque assays. It was found that drought stress significantly decreased the rates of both MNV-1 and TV internalization and dissemination. In contrast, neither flood stress nor biotic stress significantly impacted viral internalization or dissemination. Additionally, the rates of TV internalization and dissemination in soil-grown lettuce were significantly higher than those for MNV-1. Collectively, these results demonstrated that (i) human NoV surrogates can be internalized via roots and disseminated to shoots and leaves of romaine lettuce grown in soil, (ii) abiotic stress (drought) but not biotic stress (LMV infection) affects the rates of viral internalization and dissemination, and (iii) the type of virus affects the efficiency of internalization and dissemination. This study also highlights the need to develop effective measures to eliminate internalized viruses in fresh produce.
Energy Conservation Model Based on Genomic and Experimental Analyses of a Carbon Monoxide-Utilizing, Butyrate-Forming Acetogen, Eubacterium limosum KIST612
Authors: Jeong Jiyeong , Bertsch Johannes , Hess Verena , Choi Sunju , Choi In-Geol , Chang In Seop , Müller Volker 
Published: May 2015

ABSTRACT

Eubacterium limosum
KIST612 is one of the few acetogens that can produce butyrate from carbon monoxide. We have used a genome-guided analysis to delineate the path of butyrate formation, the enzymes involved, and the potential coupling to ATP synthesis. Oxidation of CO is catalyzed by the acetyl-coenzyme A (CoA) synthase/CO dehydrogenase and coupled to the reduction of ferredoxin. Oxidation of reduced ferredoxin is catalyzed by the Rnf complex and Na
+
dependent. Consistent with the finding of a Na
+
-dependent Rnf complex is the presence of a conserved Na
+
-binding motif in the
c
subunit of the ATP synthase. Butyrate formation is from acetyl-CoA via acetoacetyl-CoA, hydroxybutyryl-CoA, crotonyl-CoA, and butyryl-CoA and is consistent with the finding of a gene cluster that encodes the enzymes for this pathway. The activity of the butyryl-CoA dehydrogenase was demonstrated. Reduction of crotonyl-CoA to butyryl-CoA with NADH as the reductant was coupled to reduction of ferredoxin. We postulate that the butyryl-CoA dehydrogenase uses flavin-based electron bifurcation to reduce ferredoxin, which is consistent with the finding of
etfA
and
etfB
genes next to it. The overall ATP yield was calculated and is significantly higher than the one obtained with H
2
+ CO
2
. The energetic benefit may be one reason that butyrate is formed only from CO but not from H
2
+ CO
2
.
Thermal Inactivation Kinetics of Human Norovirus Surrogates and Hepatitis A Virus in Turkey Deli Meat
Authors: Bozkurt Hayriye , D'Souza Doris H. , Davidson P. Michael 
Published: May 2015

ABSTRACT

Human noroviruses (HNoV) and hepatitis A virus (HAV) have been implicated in outbreaks linked to the consumption of presliced ready-to-eat deli meats. The objectives of this research were to determine the thermal inactivation kinetics of HNoV surrogates (murine norovirus 1 [MNV-1] and feline calicivirus strain F9 [FCV-F9]) and HAV in turkey deli meat, compare first-order and Weibull models to describe the data, and calculate Arrhenius activation energy values for each model. The
D
(decimal reduction time) values in the temperature range of 50 to 72°C calculated from the first-order model were 0.1 ± 0.0 to 9.9 ± 3.9 min for FCV-F9, 0.2 ± 0.0 to 21.0 ± 0.8 min for MNV-1, and 1.0 ± 0.1 to 42.0 ± 5.6 min for HAV. Using the Weibull model, the
t
D = 1
(time to destroy 1 log) values for FCV-F9, MNV-1, and HAV at the same temperatures ranged from 0.1 ± 0.0 to 11.9 ± 5.1 min, from 0.3 ± 0.1 to 17.8 ± 1.8 min, and from 0.6 ± 0.3 to 25.9 ± 3.7 min, respectively. The
z
(thermal resistance) values for FCV-F9, MNV-1, and HAV were 11.3 ± 2.1°C, 11.0 ± 1.6°C, and 13.4 ± 2.6°C, respectively, using the Weibull model. The
z
values using the first-order model were 11.9 ± 1.0°C, 10.9 ± 1.3°C, and 12.8 ± 1.7°C for FCV-F9, MNV-1, and HAV, respectively. For the Weibull model, estimated activation energies for FCV-F9, MNV-1, and HAV were 214 ± 28, 242 ± 36, and 154 ± 19 kJ/mole, respectively, while the calculated activation energies for the first-order model were 181 ± 16, 196 ± 5, and 167 ± 9 kJ/mole, respectively. Precise information on the thermal inactivation of HNoV surrogates and HAV in turkey deli meat was generated. This provided calculations of parameters for more-reliable thermal processes to inactivate viruses in contaminated presliced ready-to-eat deli meats and thus to reduce the risk of foodborne illness outbreaks.
Use of Hybridization Chain Reaction-Fluorescent
In Situ
Hybridization To Track Gene Expression by Both Partners during Initiation of Symbiosis
Authors: Nikolakakis K. , Lehnert E. , McFall-Ngai M. J. , Ruby E. G. 
Published: May 2015

ABSTRACT

The establishment of a productive symbiosis between
Euprymna scolopes
, the Hawaiian bobtail squid, and its luminous bacterial symbiont,
Vibrio fischeri
, is mediated by transcriptional changes in both partners. A key challenge to unraveling the steps required to successfully initiate this and many other symbiotic associations is characterization of the timing and location of these changes. We report on the adaptation of hybridization chain reaction-fluorescent
in situ
hybridization (HCR-FISH) to simultaneously probe the spatiotemporal regulation of targeted genes in both
E. scolopes
and
V. fischeri
. This method revealed localized, transcriptionally coregulated epithelial cells within the light organ that responded directly to the presence of bacterial cells while, at the same time, provided a sensitive means to directly show regulated gene expression within the symbiont population. Thus, HCR-FISH provides a new approach for characterizing habitat transition in bacteria and for discovering host tissue responses to colonization.
Enterocin F4-9, a Novel
O
-Linked Glycosylated Bacteriocin
Authors: Maky Mohamed Abdelfattah , Ishibashi Naoki , Zendo Takeshi , Perez Rodney Honrada , Doud Jehan Ragab , Karmi Mohamed , Sonomoto Kenji 
Published: May 2015

ABSTRACT

Enterococcus faecalis
F4-9 isolated from Egyptian salted-fermented fish produces a novel bacteriocin, termed enterocin F4-9. Enterocin F4-9 was purified from the culture supernatant by three steps, and its molecular mass was determined to be 5,516.6 Da by mass spectrometry. Amino acid and DNA sequencing showed that the propeptide consists of 67 amino acid residues, with a leader peptide containing a double glycine cleavage site to produce a 47-amino-acid mature peptide. Enterocin F4-9 is modified by two molecules of
N
-acetylglucosamine β-
O
-linked to Ser37 and Thr46. The
O
-linked
N
-acetylglucosamine moieties are essential for the antimicrobial activity of enterocin F4-9. Further analysis of the enterocin F4-9 gene cluster identified
enfC
, which has high sequence similarity to a glycosyltransferase. The antimicrobial activity of enterocin F4-9 covered a limited range of bacteria, including, interestingly, a Gram-negative strain,
Escherichia coli
JM109. Enterocin F4-9 is sensitive to protease, active at a wide pH range, and moderately resistant to heat.
Intracellular Accumulation of Glycine in Polyphosphate-Accumulating Organisms in Activated Sludge, a Novel Storage Mechanism under Dynamic Anaerobic-Aerobic Conditions
Authors: Nguyen Hien Thi Thu , Kristiansen Rikke , Vestergaard Mette , Wimmer Reinhard , Nielsen Per Halkjær 
Published: May 2015

ABSTRACT

Dynamic anaerobic-aerobic feast-famine conditions are applied to wastewater treatment plants to select polyphosphate-accumulating organisms to carry out enhanced biological phosphorus removal. Acetate is a well-known substrate to stimulate this process, and here we show that different amino acids also are suitable substrates, with glycine as the most promising.
13
C-labeled glycine and nuclear magnetic resonance (NMR) were applied to investigate uptake and potential storage products when activated sludge was fed with glycine under anaerobic conditions. Glycine was consumed by the biomass, and the majority was stored intracellularly as free glycine and fermentation products. Subsequently, in the aerobic phase without addition of external substrate, the stored glycine was consumed. The uptake of glycine and oxidation of intracellular metabolites took place along with a release and uptake of orthophosphate, respectively. Fluorescence
in situ
hybridization combined with microautoradiography using
3
H-labeled glycine revealed uncultured actinobacterial
Tetrasphaera
as a dominant glycine consumer. Experiments with
Tetrasphaera elongata
as representative of uncultured
Tetrasphaera
showed that under anaerobic conditions it was able to take up labeled glycine and accumulate this and other labeled metabolites to an intracellular concentration of approximately 4 mM. All components were consumed under subsequent aerobic conditions. Intracellular accumulation of amino acids seems to be a novel storage strategy for polyphosphate-accumulating bacteria under dynamic anaerobic-aerobic feast-famine conditions.
Biochemical and Kinetic Characterization of the Eukaryotic Phosphotransacetylase Class IIa Enzyme from Phytophthora ramorum
Authors: Taylor Tonya , Ingram-Smith Cheryl , Smith Kerry S. 
Published: May 2015

ABSTRACTPhosphotransacetylase (Pta), a key enzyme in bacterial metabolism, catalyzes the reversible transfer of an acetyl group from acetyl phosphate to coenzyme A (CoA) to produce acetyl-CoA and Pi. Two classes of Pta have been identified based on the absence (PtaI) or presence (PtaII) of an N-terminal regulatory domain. PtaIhas been fairly well studied in bacteria and one genus of archaea; however, only theEscherichia coliandSalmonella entericaPtaIIenzymes have been biochemically characterized, and they are allosterically regulated. Here, we describe the first biochemical and kinetic characterization of a eukaryotic Pta from the oomycetePhytophthora ramorum. The two Ptas fromP. ramorum, designated PrPtaII1 and PrPtaII2, both belong to class II. PrPtaII1 displayed positive cooperativity for both acetyl phosphate and CoA and is allosterically regulated. We compared the effects of different metabolites on PrPtaII1 and theS. entericaPtaIIand found that, although the N-terminal regulatory domains share only 19% identity, both enzymes are inhibited by ATP, NADP, NADH, phosphoenolpyruvate (PEP), and pyruvate in the acetyl-CoA/Pi-forming direction but are differentially regulated by AMP. Phylogenetic analysis of bacterial, archaeal, and eukaryotic sequences identified four subtypes of PtaIIbased on the presence or absence of the P-loop and DRTGG subdomains within the N-terminal regulatory domain. Although theE. coli,S. enterica, andP. ramorumenzymes all belong to the IIa subclass, our kinetic analysis has indicated that enzymes within a subclass can still display differences in their allosteric regulation.
Contribution of Demographic and Behavioral Factors on the Changing Incidence Rates of Oropharyngeal and Oral Cavity Cancers in Northern California
Authors: Katzel Jed A. , Merchant Maqdooda , Chaturvedi Anil K. , Silverberg Michael J. 
Published: May 2015

AbstractBackground: It is unknown to what extent patient demographics, smoking, and alcohol use have contributed to changes in oropharyngeal and oral cavity cancer incidence rates.Methods: We performed a cohort study of Kaiser Permanente healthplan members, ages 20 to 89, for years 1995–2010 (n = 2.2 million annual members). Poisson Regression models estimated calendar trends in cancer rates both adjusted for and stratified by age, sex, smoking, and alcohol abuse history.Results: We identified 1,383 human papillomavirus (HPV)–related and 1,344 HPV-unrelated oral cavity and oropharyngeal cancer cases. With adjustment for age and sex, HPV-related cancer incidence rates increased 3.8% per year (P &lt; 0.001) between 1995 and 2010, whereas rates for HPV-unrelated cancers decreased 2.4% per year (P &lt; 0.001). For years 2007 to 2010, with additional adjustment for smoking and alcohol abuse, results were nonsignificant, but similar in magnitude. The increasing rates for HPV-related cancers were more prominent among nonsmokers (+14.5%) compared with smokers (−2.5%; P-interaction = 0.058). The decreased rates for HPV-unrelated sites were more prominent among those ≥60 years (−11.0%) compared with those &lt;60 years (+16.8%; P-interaction = 0.006), among smokers (−9.7%) compared with nonsmokers (+8.4%; P-interaction = 0.055), and among those with an alcohol abuse history (−20.4%) compared with those without a history (+5.8%; P-interaction = 0.009).Conclusions: The observed increasing HPV-related cancer rates are most evident among nonsmokers, whereas the decreasing HPV-unrelated cancer rates are least evident among younger individuals, nonsmokers, and those without an alcohol abuse history.Impact: Continued vigilance for oropharyngeal and oral cavity cancer is warranted, including among those without traditional risk factors such as smoking and alcohol abuse. Cancer Epidemiol Biomarkers Prev; 24(6); 978–84. ©2015 AACR.
Spinal Myxopapillary Ependymomas Demonstrate a Warburg Phenotype
Authors: Mack Stephen C. , Agnihotri Sameer , Bertrand Kelsey C. , Wang Xin , Shih David J. , Witt Hendrik , Hill Nadia , Zayne Kory , Barszczyk Mark , Ramaswamy Vijay , Remke Marc , Thompson Yuan , Ryzhova Marina , Massimi Luca , Grajkowska Wieslawa , Lach Boleslaw , Gupta Nalin , Weiss William A. , Guha Abhijit , Hawkins Cynthia , Croul Sidney , Rutka James T. , Pfister Stefan M. , Korshunov Andrey , Pekmezci Melike , Tihan Tarik , Philips Joanna J. , Jabado Nada , Zadeh Gelareh , Taylor Michael D. 
Published: May 2015

Abstract
Purpose: Myxopapillary ependymoma (MPE) is a distinct histologic variant of ependymoma arising commonly in the spinal cord. Despite an overall favorable prognosis, distant metastases, subarachnoid dissemination, and late recurrences have been reported. Currently, the only effective treatment for MPE is gross-total resection. We characterized the genomic and transcriptional landscape of spinal ependymomas in an effort to delineate the genetic basis of this disease and identify new leads for therapy.
Experimental Design: Gene expression profiling was performed on 35 spinal ependymomas, and copy number profiling was done on an overlapping cohort of 46 spinal ependymomas. Functional validation experiments were performed on tumor lysates consisting of assays measuring pyruvate kinase M activity (PKM), hexokinase activity (HK), and lactate production.
Results: At a gene expression level, we demonstrate that spinal grade II and MPE are molecularly and biologically distinct. These are supported by specific copy number alterations occurring in each histologic variant. Pathway analysis revealed that MPE are characterized by increased cellular metabolism, associated with upregulation of HIF1α. These findings were validated by Western blot analysis demonstrating increased protein expression of HIF1α, HK2, PDK1, and phosphorylation of PDHE1A. Functional assays were performed on MPE lysates, which demonstrated decreased PKM activity, increased HK activity, and elevated lactate production.
Conclusions: Our findings suggest that MPE may be driven by a Warburg metabolic phenotype. The key enzymes promoting the Warburg phenotype: HK2, PKM2, and PDK are targetable by small-molecule inhibitors/activators, and should be considered for evaluation in future clinical trials for MPE. Clin Cancer Res; 21(16); 3750–8. ©2015 AACR.
A Leukemia-Associated CD34/CD123/CD25/CD99+ Immunophenotype IdentifiesFLT3-Mutated Clones in Acute Myeloid Leukemia
Authors: Angelini Daniela F. , Ottone Tiziana , Guerrera Gisella , Lavorgna Serena , Cittadini Michela , Buccisano Francesco , De Bardi Marco , Gargano Francesca , Maurillo Luca , Divona Mariadomenica , Noguera Nélida I. , Consalvo Maria Irno , Borsellino Giovanna , Bernardi Giorgio , Amadori Sergio , Venditti Adriano , Battistini Luca , Lo-Coco Francesco 
Published: May 2015

AbstractPurpose: We evaluated leukemia-associated immunophenotypes (LAIP) and their correlation with fms-like tyrosine kinase 3 (FLT3) and nucleophosmin (NPM1) gene mutational status in order to contribute a better identification of patients at highest risk of relapse in acute myeloid leukemia (AML).Experimental Design: Bone marrow samples from 132 patients with AML were analyzed by nine-color multiparametric flow cytometry. We confirmed the presence of the mutation in diagnostic samples and in sorted cells by conventional RT-PCR and by patient-specific RQ-PCR.Results: Within the CD34+ cell fraction, we identified a discrete population expressing high levels of the IL3 receptor α-chain (CD123) and MIC-2 (CD99) in combination with the IL2 receptor α-chain (CD25). The presence of this population positively correlated with the internal tandem duplications (ITD) mutation in the FLT3 gene (r = 0.71). Receiver operating characteristics showed that, within the CD34+ cell fraction a percentage of CD123/CD99/CD25+ cells ≥11.7% predicted FLT3–ITD mutations with a specificity and sensitivity of &gt;90%. CD34/CD123/CD99/CD25+ clones were also detectable at presentation in 3 patients with FLT3 wild-type/NPM1+ AML who relapsed with FLT3-ITD/NPM1+ AML. Quantitative real-time PCR designed at relapse for each FLT3-ITD in these three cases confirmed the presence of low copy numbers of the mutation in diagnostic samples.Conclusions: Our results suggest that the CD34/CD25/CD123/CD99+ LAIP is strictly associated with FLT3-ITD–positive cells. Clin Cancer Res; 21(17); 3977–85. ©2015 AACR.