bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shifts in Abundance and Diversity of Mobile Genetic Elements after the Introduction of Diverse Pesticides into an On-Farm Biopurification System over the Course of a Year
Authors: Dealtry Simone , Holmsgaard Peter N. , Dunon Vincent , Jechalke Sven , Ding Guo-Chun , Krögerrecklenfort Ellen , Heuer Holger , Hansen Lars H. , Springael Dirk , Zühlke Sebastian , Sørensen Søren J. , Smalla Kornelia 
Published: April 2014

ABSTRACT

Biopurification systems (BPS) are used on farms to control pollution by treating pesticide-contaminated water. It is assumed that mobile genetic elements (MGEs) carrying genes coding for enzymes involved in degradation might contribute to the degradation of pesticides. Therefore, the composition and shifts of MGEs, in particular, of IncP-1 plasmids carried by BPS bacterial communities exposed to various pesticides, were monitored over the course of an agricultural season. PCR amplification of total community DNA using primers targeting genes specific to different plasmid groups combined with Southern blot hybridization indicated a high abundance of plasmids belonging to IncP-1, IncP-7, IncP-9, IncQ, and IncW, while IncU and IncN plasmids were less abundant or not detected. Furthermore, the integrase genes of class 1 and 2 integrons (
intI1
,
intI2
) and genes encoding resistance to sulfonamides (
sul1
,
sul2
) and streptomycin (
aadA
) were detected and seasonality was revealed. Amplicon pyrosequencing of the IncP-1
trfA
gene coding for the replication initiation protein revealed high IncP-1 plasmid diversity and an increase in the abundance of IncP-1β and a decrease in the abundance of IncP-1ε over time. The data of the chemical analysis showed increasing concentrations of various pesticides over the course of the agricultural season. As an increase in the relative abundances of bacteria carrying IncP-1β plasmids also occurred, this might point to a role of these plasmids in the degradation of many different pesticides.
Evaluation of Amphotericin B and Chloramphenicol as Alternative Drugs for Treatment of Chytridiomycosis and Their Impacts on Innate Skin Defenses
Authors: Holden Whitney M. , Ebert Alexander R. , Canning Peter F. , Rollins-Smith Louise A. 
Published: April 2014

ABSTRACT

Chytridiomycosis, an amphibian skin disease caused by the emerging fungal pathogen
Batrachochytrium dendrobatidis
, has been implicated in catastrophic global amphibian declines. The result is an alarming decrease in amphibian diversity that is a great concern for the scientific community. Clinical trials testing potential antifungal drugs are needed to identify alternative treatments for amphibians infected with this pathogen. In this study, we quantified the MICs of chloramphenicol (800 μg/ml), amphotericin B (0.8 to 1.6 μg/ml), and itraconazole (Sporanox) (20 ng/ml) against
B. dendrobatidis
. Both chloramphenicol and amphotericin B significantly reduced
B. dendrobatidis
infection in naturally infected southern leopard frogs (
Rana
[
Lithobates
]
sphenocephala
), although neither drug was capable of complete fungal clearance. Long-term exposure of
R. sphenocephala
to these drugs did not inhibit antimicrobial peptide (AMP) synthesis, indicating that neither drug is detrimental to this important innate skin defense. However, we observed that chloramphenicol, but not amphotericin B or itraconazole, inhibited the growth of multiple
R. sphenocephala
skin bacterial isolates
in vitro
at concentrations below the MIC against
B. dendrobatidis
. These results indicate that treatment with chloramphenicol might dramatically alter the protective natural skin microbiome when used as an antifungal agent. This study represents the first examination of the effects of alternative antifungal drug treatments on amphibian innate skin defenses, a crucial step to validating these treatments for practical applications.
Draft Genome Sequence of Deinococcus phoenicis, a Novel Strain Isolated during the Phoenix Lander Spacecraft Assembly
Authors: Stepanov Victor G. , Vaishampayan Parag , Venkateswaran Kasthuri , Fox George E. 
Published: April 2014

ABSTRACT

Deinococcus phoenicis
strain 1P10ME
T
is a radiation- and desiccation-resistant bacterium isolated from a cleanroom facility where the Phoenix Lander spacecraft was assembled. In order to facilitate investigations of the nature of the extreme resistance of
D. phoenicis
to bactericidal factors, a draft genome sequence of
D. phoenicis
was determined.
Full-Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas protegens CHA0
Authors: Jousset Alexandre , Schuldes Joerg , Keel Christoph , Maurhofer Monika , Daniel Rolf , Scheu Stefan , Thuermer Andrea 
Published: April 2014

ABSTRACT

We report the complete genome sequence of the free-living bacterium
Pseudomonas protegens
(formerly
Pseudomonas fluorescens
) CHA0, a model organism used in plant-microbe interactions, biological control of phytopathogens, and bacterial genetics.
Draft Genome Sequence ofUmbilicaria muehlenbergiiKoLRILF000956, a Lichen-Forming Fungus Amenable to Genetic Manipulation
Authors: Park Sook-Young , Choi Jaeyoung , Lee Gir-Won , Jeong Min-Hye , Kim Jung A , Oh Soon-Ok , Lee Yong-Hwan , Hur Jae-Seoun 
Published: April 2014

ABSTRACTUmbilicaria muehlenbergiistrain KoLRILF000956 is amenable toAgrobacterium tumefaciens-mediated transformation (ATMT), making it the only known genetically tractable lichen-forming fungus to date. We report another advancement in lichen genetics, a draft genome assembly forU. muehlenbergiiwith a size of 34,812,353 bp and a GC content of 47.12%, consisting of seven scaffolds.
Steady-State Hydrogen Peroxide Induces Glycolysis in Staphylococcus aureus and Pseudomonas aeruginosa
Authors: Deng Xin , Liang Haihua , Ulanovskaya Olesya A. , Ji Quanjiang , Zhou Tianhong , Sun Fei , Lu Zhike , Hutchison Alan L. , Lan Lefu , Wu Min , Cravatt Benjamin F. , He Chuan 
Published: April 2014

ABSTRACT

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from human pathogens
Staphylococcus aureus
and
Pseudomonas aeruginosa
can be readily inhibited by reactive oxygen species (ROS)-mediated direct oxidation of their catalytic active cysteines. Because of the rapid degradation of H
2
O
2
by bacterial catalase, only steady-state but not one-dose treatment with H
2
O
2
rapidly induces glycolysis and the pentose phosphate pathway (PPP). We conducted transcriptome sequencing (RNA-seq) analyses to globally profile the bacterial transcriptomes in response to a steady level of H
2
O
2
, which revealed profound transcriptional changes, including the induced expression of glycolytic genes in both bacteria. Our results revealed that the inactivation of GAPDH by H
2
O
2
induces metabolic levels of glycolysis and the PPP; the elevated levels of fructose 1,6-biphosphate (FBP) and 2-keto-3-deoxy-6-phosphogluconate (KDPG) lead to dissociation of their corresponding glycolytic repressors (GapR and HexR, respectively) from their cognate promoters, thus resulting in derepression of the glycolytic genes to overcome H
2
O
2
-stalled glycolysis in
S. aureus
and
P. aeruginosa
, respectively. Both GapR and HexR may directly sense oxidative stresses, such as menadione.
Elucidating the Process of Activation of Methyl-Coenzyme M Reductase
Authors: Prakash Divya , Wu Yonnie , Suh Sang-Jin , Duin Evert C. 
Published: April 2014

ABSTRACT

Methyl-coenzyme M reductase (MCR) catalyzes the reversible reduction of methyl-coenzyme M (CH
3
-S-CoM) and coenzyme B (HS-CoB) to methane and heterodisulfide CoM-S-S-CoB (HDS). MCR contains the hydroporphinoid nickel complex coenzyme F
430
in its active site, and the Ni center has to be in its Ni(I) valence state for the enzyme to be active. Until now, no
in vitro
method that fully converted the inactive MCR
silent
-Ni(II) form to the active MCR
red1
-Ni(I) form has been described. With the potential use of recombinant MCR in the production of biofuels and the need to better understand this enzyme and its activation process, we studied its activation under nonturnover conditions and achieved full MCR activation in the presence of dithiothreitol and protein components A2, an ATP carrier, and A3a. It was found that the presence of HDS promotes the inactivation of MCR
red1
, which makes it essential that the activation process is isolated from the methane formation assay, which tends to result in minimal activation rates. Component A3a is a multienzyme complex that includes the
mcrC
gene product, an Fe-protein homolog, an iron-sulfur flavoprotein, and protein components involved in electron bifurcation. A hypothetical model for the cellular activation process of MCR is presented.
Analysis of Surface-Exposed Outer Membrane Proteins in Helicobacter pylori
Authors: Voss Bradley J. , Gaddy Jennifer A. , McDonald W. Hayes , Cover Timothy L. 
Published: April 2014

ABSTRACT

More than 50
Helicobacter pylori
genes are predicted to encode outer membrane proteins (OMPs), but there has been relatively little experimental investigation of the
H. pylori
cell surface proteome. In this study, we used selective biotinylation to label proteins localized to the surface of
H. pylori
, along with differential detergent extraction procedures to isolate proteins localized to the outer membrane. Proteins that met multiple criteria for surface-exposed outer membrane localization included known adhesins, as well as Cag proteins required for activity of the
cag
type IV secretion system, putative lipoproteins, and other proteins not previously recognized as cell surface components. We identified sites of nontryptic cleavage consistent with signal sequence cleavage, as well as C-terminal motifs that may be important for protein localization. A subset of surface-exposed proteins were highly susceptible to proteolysis when intact bacteria were treated with proteinase K. Most Hop and Hom OMPs were susceptible to proteolysis, whereas Hor and Hof proteins were relatively resistant. Most of the protease-susceptible OMPs contain a large protease-susceptible extracellular domain exported beyond the outer membrane and a protease-resistant domain at the C terminus with a predicted β-barrel structure. These features suggest that, similar to the secretion of the VacA passenger domain, the N-terminal domains of protease-susceptible OMPs are exported through an autotransporter pathway. Collectively, these results provide new insights into the repertoire of surface-exposed
H. pylori
proteins that may mediate bacterium-host interactions, as well as the cell surface topology of these proteins.
Fear of oxygen therapy for children in Malawi
Authors: Stevenson Anna Clare , Edwards Christopher , Langton Josephine , Zamawe Collins , Kennedy Neil 
Published: April 2014

BackgroundAlthough pneumonia is a common cause of death in children in Malawi, healthcare staff frequently encounter patients or carers who refuse oxygen therapy. This qualitative study documents factors that influence acceptance or refusal of oxygen therapy for children in Malawi.MethodsNine group interviews involving 86 participants were held in community and hospital settings in rural and urban Malawi. Eleven in-depth interviews of healthcare staff providing oxygen were held in a central hospital. Thematic analysis of transcripts of the audio recordings was carried out to identify recurring themes.ResultsSimilar ideas were identified in the group interviews and in-depth staff interviews. Past experiences of oxygen use (direct and indirect, positive and negative) had a strong influence on views of oxygen. A recurrent theme was fear of oxygen, often due to a perceived association between death and recent oxygen use. Fears were intensified by a lack of familiarity with equipment used to deliver oxygen, distrust of medical staff and concerns about cost of oxygen.ConclusionsThis study identifies reasons for refusal of oxygen therapy for children in a low-income country. Findings from the study suggest that training of healthcare staff to address fears of parents, and information, education and communication (IEC) approaches that improve public understanding of oxygen and provide positive examples of its use are likely to be helpful in improving uptake of oxygen therapy in Malawi.
Improving population health one person at a time? Accountable care organisations: perceptions of population health—a qualitative interview study
Authors: Noble Douglas J , Greenhalgh Trisha , Casalino Lawrence P 
Published: April 2014

ObjectiveThis qualitative interview study explored perceptions of the phrases ‘population health’, ‘public health’ and ‘community health’.SettingAccountable care organisations (ACOs), and public health or similar agencies in different parts of the USA.ParticipantsPurposive sample of 29 interviewees at four ACOs, and 10 interviewees at six public health or similar agencies.ResultsInterviewees working for ACOs most often viewed ‘population health’ as referring to a defined group of their organisation's patients, though a few applied the phrase to people living in a geographical area. In contrast, interviewees working for public health agencies were more likely to consider ‘population health’ from a geographical perspective.ConclusionsConflating geographical population health with the health of ACOs’ patients may divert attention and resources away from organisations that use non-medical means to improve the health of geographical populations. As ACOs battle to control costs of their population of patients, it would be more accurate to consider using a more specific phrase, such as ‘population of attributed patients’, to refer to ACOs’ efforts to care for the health of their defined group of patients.
Improving the safety and efficiency of nurse medication rounds through the introduction of an automated dispensing cabinet
Authors: Cottney Alan 
Published: April 2014

AbstractInformation technology (IT) systems are being utilised with increasing frequency at the prescribing and dispensing stage of the medicines-use process in UK hospitals. However, much less development has taken place with regard to the implementation of IT systems at the administration stage of medicines-use. A technology that has been implemented widely at the administration stage in North American hospitals is the automated dispensing cabinet (ADC), which has been shown to reduce nurse medication administration errors and reduce the time that nurses spend administering medication. The current project was undertaken to assess whether these benefits would be realised with the introduction of an ADC on an inpatient ward in a UK mental health hospital.Nurses were observed administering medication before and after the implementation of an ADC on a ward at East London NHS Foundation Trust (ELFT). The findings from these observations showed that the use of the ADC led to a reduction in the medication administration error rate from 8.9% to 7.2%; however, this reduction was solely accounted for by a reduction in errors of negligible clinical severity. The types of administration errors noted after implementation of the ADC remained largely unchanged from beforehand. The ADC was found to reduce the amount of time that nurses spent administering medication from 2.94 min per dose to 2.37 min per dose. It is estimated that this reduction could generate around 66 min of additional free nursing time per ward per day.As a standalone device, the ADC was found to improve the efficiency of the medicines-use process, but had little meaningful effect on medication administration error rate at ELFT. However, it could be anticipated that additional benefit with regard to reducing medication administration errors may be demonstrated if the ADC was used in combination with other IT systems, such as electronic prescribing.
Physical modelling of large-scale deformational systems in the South Polar Layered Deposits (Promethei Lingula, Mars): new geological constraints and climatic implications
Authors: Guallini Luca , Pauselli Cristina , Brozzetti Francesco , Marinangeli Lucia 
Published: April 2014

Abstract

Deformation systems (DSs) locally affect the South Polar Layered Deposits (SPLDs) along the margins of the Promethei Lingula ice sheet (part of the southern Martian ice-dome). One example is the ‘S
2
’ deformation system, characterized by a complex pattern of brittle and brittle–ductile structures related to kilometre-scale shear zones that deform the sequence. Moreover, soft-sediment structures affect one layer located at the base of the S
2
. An earlier structural analysis suggested that: (1) two deformation stages (D
1
, in which the shear zones developed, and D
2
, in which the D
1
structures were reactivated by deep-seated gravitational slope deformation) occurred, driven by gravity; and (2) there are variations in the bulk composition of the SPLD (which is inferred to be mainly composed of water ice plus basaltic dust). This work supports these structural results through thermal and mechanical modelling of the S
2
sequence. Our modelling results suggest that several layers within the S
2
system are probably composed of, or are mixed with, CO
2
ice, and that the development of the observed deformation is inconsistent with present-day physical conditions. Soft-sediment structures probably formed under warmer surface temperatures during the past, with those warmer temperatures favouring or even triggering ice flow/basal sliding of the Promethei Lingula.

Supplementary material:

The complete description of the stratigraphy of the analysed S
2
sequence (in table format) is available at
http://www.geolsoc.org.uk/SUP18746
.
LSECtin Expressed on Melanoma Cells Promotes Tumor Progression by Inhibiting Antitumor T-cell Responses
Authors: Xu Feng , Liu Jing , Liu Di , Liu Biao , Wang Min , Hu Zhiyuan , Du Xuemei , Tang Li , He Fuchu 
Published: April 2014

AbstractTherapeutic antibodies that target T-cell co-inhibitory molecules display potent antitumor effects in multiple types of cancer. LSECtin is a cell surface lectin of the DC-SIGN family expressed in dendritic cells that inhibits T-cell responses. LSECtin limits T-cell activity in infectious disease, but it has not been studied in cancer. Here we report the finding that LSECtin is expressed commonly in melanomas where it blunts tumor-specific T-cell responses. When expressed in B16 melanoma cells, LSECtin promoted tumor growth, whereas its blockade slowed tumor growth in either wild-type or LSECtin-deficient mice. The tumor-promoting effects of LSECtin were abrogated in Rag1−/− mice or in response to CD4+ or CD8+ T-cell depletion. Mechanistic investigations determined that LSECtin inhibited the proliferation of tumor-specific effector T cells by downregulating the cell cycle kinases CDK2, CDK4, and CDK6. Accordingly, as expressed in B16, tumor cells LSECtin inhibited tumor-specific T-cell responses relying upon proliferation in vitro and in vivo. Notably, LSECtin interacted with the co-regulatory molecule LAG-3, the blockade of which restored IFNγ secretion that was reduced by melanoma-derived expression of LSECtin. Together, our findings reveal that common expression of LSECtin in melanoma cells engenders a mechanism of immune escape, with implications for novel immunotherapeutic combination strategies. Cancer Res; 74(13); 3418–28. ©2014 AACR.
Transient Induction of ING4 by Myc Drives Prostate Epithelial Cell Differentiation and Its Disruption Drives Prostate Tumorigenesis
Authors: Berger Penny L. , Frank Sander B. , Schulz Veronique V. , Nollet Eric A. , Edick Mathew J. , Holly Brittany , Chang Ting-Tung A. , Hostetter Galen , Kim Suwon , Miranti Cindy K. 
Published: April 2014

Abstract
The mechanisms by which Myc overexpression or Pten loss promotes prostate cancer development are poorly understood. We identified the chromatin remodeling protein, ING4, as a crucial switch downstream of Myc and Pten that is required for human prostate epithelial differentiation. Myc-induced transient expression of ING4 is required for the differentiation of basal epithelial cells into luminal cells, while sustained ING4 expression induces apoptosis. ING4 expression is lost in &gt;60% of human primary prostate tumors. ING4 or Pten loss prevents epithelial cell differentiation, which was necessary for tumorigenesis. Pten loss prevents differentiation by blocking ING4 expression, which is rescued by ING4 re-expression. Pten or ING4 loss generates tumor cells that co-express basal and luminal markers, indicating prostate oncogenesis occurs through disruption of an intermediate step in the prostate epithelial differentiation program. Thus, we identified a new epithelial cell differentiation switch involving Myc, Pten, and ING4, which when disrupted leads to prostate tumorigenesis. Myc overexpression and Pten loss are common genetic abnormalities in prostate cancer, whereas loss of the tumor suppressor ING4 has not been reported. This is the first demonstration that transient ING4 expression is absolutely required for epithelial differentiation, its expression is dependent on Myc and Pten, and it is lost in the majority of human prostate cancers. This is the first demonstration that loss of ING4, either directly or indirectly through loss of Pten, promotes Myc-driven oncogenesis by deregulating differentiation. The clinical implication is that Pten/ING4 negative and ING4-only negative tumors may reflect two distinct subtypes of prostate cancer. Cancer Res; 74(12); 3357–68. ©2014 AACR.
API5 Confers Tumoral Immune Escape through FGF2-Dependent Cell Survival Pathway
Authors: Noh Kyung Hee , Kim Seok-Ho , Kim Jin Hee , Song Kwon-Ho , Lee Young-Ho , Kang Tae Heung , Han Hee Dong , Sood Anil K. , Ng Joanne , Kim Kwanghee , Sonn Chung Hee , Kumar Vinay , Yee Cassian , Lee Kyung-Mi , Kim Tae Woo 
Published: April 2014

Abstract
Identifying immune escape mechanisms used by tumors may define strategies to sensitize them to immunotherapies to which they are otherwise resistant. In this study, we show that the antiapoptotic gene API5 acts as an immune escape gene in tumors by rendering them resistant to apoptosis triggered by tumor antigen-specific T cells. Its RNAi-mediated silencing in tumor cells expressing high levels of API5 restored antigen-specific immune sensitivity. Conversely, introducing API5 into API5low cells conferred immune resistance. Mechanistic investigations revealed that API5 mediated resistance by upregulating FGF2 signaling through a FGFR1/PKCδ/ERK effector pathway that triggered degradation of the proapoptotic molecule BIM. Blockade of FGF2, PKCδ, or ERK phenocopied the effect of API5 silencing in tumor cells expressing high levels of API5 to either murine or human antigen-specific T cells. Our results identify a novel mechanism of immune escape that can be inhibited to potentiate the efficacy of targeted active immunotherapies. Cancer Res; 74(13); 3556–66. ©2014 AACR.