bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Histone-Like Nucleoid Structuring Protein (H-NS) Is a Negative Regulator of the Lateral Flagellar System in the Deep-Sea Bacterium Shewanella piezotolerans WP3
Authors: Jian Huahua , Xu Guanpeng , Gai Yingbao , Xu Jun , Xiao Xiang 
Published: February 2016

ABSTRACT

Although the histone-like nucleoid structuring protein (H-NS) is well known for its involvement in the adaptation of mesophilic bacteria, such as
Escherichia coli
, to cold environments and high-pressure stress, an understanding of the role of H-NS in the cold-adapted benthic microorganisms that live in the deep-sea ecosystem, which covers approximately 60% of the earth's surface, is still lacking. In this study, we characterized the function of H-NS in
Shewanella piezotolerans
WP3, which was isolated from West Pacific sediment at a depth of 1,914 m. An
hns
gene deletion mutant (WP3Δ
hns
) was constructed, and comparative whole-genome microarray analysis was performed. H-NS had a significant influence (fold change, >2) on the expression of a variety of WP3 genes (274 and 280 genes were upregulated and downregulated, respectively), particularly genes related to energy production and conversion. Notably, WP3Δ
hns
exhibited higher expression levels of lateral flagellar genes than WP3 and showed enhanced swarming motility and lateral flagellar production compared to those of WP3. The DNA gel mobility shift experiment showed that H-NS bound specifically to the promoter of lateral flagellar genes. Moreover, the high-affinity binding sequences of H-NS were identified by DNase I protection footprinting, and the results support the “binding and spreading” model for H-NS functioning. To our knowledge, this is the first attempt to characterize the function of the universal regulator H-NS in a deep-sea bacterium. Our data revealed that H-NS has a novel function as a repressor of the expression of genes related to the energy-consuming secondary flagellar system and to swarming motility.
Bacterial Succession in the Broiler Gastrointestinal Tract
Authors: Ranjitkar Samir , Lawley Blair , Tannock Gerald , Engberg Ricarda M. 
Published: February 2016

ABSTRACT

A feeding trial was performed with broilers receiving a diet of wheat-based feed (WBF), maize-based feed (MBF), or maize-based concentrates supplemented with 15% or 30% crimped kernel maize silage (CKMS-15 or CKMS-30, respectively). The aim of the study was to investigate the bacterial community compositions of the crop, gizzard, ileum, and cecum contents in relation to the feeding strategy and age (8, 15, 22, 25, 29, or 36 days). Among the four dietary treatments, bacterial diversity was analyzed for MBF and CKMS-30 by 454 pyrosequencing of the 16S rRNA gene. Since the diets had no significant influence on bacterial diversity, data were pooled for downstream analysis. With increasing age, a clear succession of bacterial communities and increased bacterial diversity were observed.
Lactobacillaceae
(belonging mainly to the genus
Lactobacillus
) represented most of the
Firmicutes
at all ages and in all segments of the gut except the cecum. The development of a “mature” microbiota in broilers occurred during the period from days 15 to 22. Striking increases in the relative abundances of
Lactobacillus salivarius
(17 to 36%) and clostridia (11 to 18%), and a concomitant decrease in the relative abundance of
Lactobacillus reuteri
, were found in the ileum after day 15. The concentration of deconjugated bile salts increased in association with the increased populations of
L. salivarius
and clostridia. Both
L. salivarius
and clostridia deconjugate bile acids, and increases in the abundances of these bacteria might be associated with growth reduction and gastrointestinal (GI) disorders occurring in the critical period of broiler life between days 20 and 30.
Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog
Authors: Esson Kaitlin C. , Lin Xueju , Kumaresan Deepak , Chanton Jeffrey P. , Murrell J. Colin , Kostka Joel E. 
Published: February 2016

ABSTRACT

The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (
pmoA
) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH
4
g dry weight soil
−1
day
−1
. Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4%
in situ
to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the
13
C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera
Methylocystis
(type II;
Alphaproteobacteria
),
Methylomonas
, and
Methylovulum
(both, type I;
Gammaproteobacteria
). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for
pmoA
in surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNA
pmoA
amplicons from field samples confirmed that the dominant active methanotrophs were
Methylocystis
and
Methylomonas
. Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera
Methylomonas
and
Methylovulum
(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.
Rapid Detection of Viable Bacillus anthracis Spores in Environmental Samples by Using Engineered Reporter Phages
Authors: Sharp Natasha J. , Molineux Ian J. , Page Martin A. , Schofield David A. 
Published: February 2016

ABSTRACT

Bacillus anthracis
, the causative agent of anthrax, was utilized as a bioterrorism agent in 2001 when spores were distributed via the U.S. postal system. In responding to this event, the Federal Bureau of Investigation used traditional bacterial culture viability assays to ascertain the extent of contamination of the postal facilities within 24 to 48 h of environmental sample acquisition. Here, we describe a low-complexity, second-generation reporter phage assay for the rapid detection of viable
B. anthracis
spores in environmental samples. The assay uses an engineered
B. anthracis
reporter phage (Wβ::
luxAB
-2) which transduces bioluminescence to infected cells. To facilitate low-level environmental detection and maximize the signal response, expression of
luxAB
in an earlier version of the reporter phage (Wβ::
luxAB
-1) was optimized. These alterations prolonged signal kinetics, increased light output, and improved assay sensitivity. Using Wβ::
luxAB
-2, detection of
B. anthracis
spores was 1 CFU in 8 h from pure cultures and as low as 10 CFU/g in sterile soil but increased to 10
5
CFU/g in unprocessed soil due to an unstable signal and the presence of competing bacteria. Inclusion of semiselective medium, mediated by a phage-expressed antibiotic resistance gene, maintained signal stability and enabled the detection of 10
4
CFU/g in 6 h. The assay does not require spore extraction and relies on the phage infecting germinating cells directly in the soil sample. This reporter phage displays promise for the rapid detection of low levels of spores on clean surfaces and also in grossly contaminated environmental samples from complex matrices such as soils.
Killing of Staphylococcus aureus via Magnetic Hyperthermia Mediated by Magnetotactic Bacteria
Authors: Chen Changyou , Chen Linjie , Yi Yong , Chen Chuanfang , Wu Long-Fei , Song Tao 
Published: February 2016

ABSTRACT

Staphylococcus aureus
is a common hospital and household pathogen. Given the emergence of antibiotic-resistant derivatives of this pathogen resulting from the use of antibiotics as general treatment, development of alternative therapeutic strategies is urgently needed. Here, we assess the feasibility of killing
S. aureus
cells
in vitro
and
in vivo
through magnetic hyperthermia mediated by magnetotactic bacteria that possess magnetic nanocrystals and demonstrate magnetically steered swimming. The
S. aureus
suspension was added to magnetotactic MO-1 bacteria either directly or after coating with anti-MO-1 polyclonal antibodies. The suspensions were then subjected to an alternating magnetic field (AMF) for 1 h.
S. aureus
viability was subsequently assessed through conventional plate counting and flow cytometry. We found that approximately 30% of the
S. aureus
cells mixed with uncoated MO-1 cells were killed after AMF treatment. Moreover, attachment between the magnetotactic bacteria and
S. aureus
increased the killing efficiency of hyperthermia to more than 50%. Using mouse models, we demonstrated that magnetic hyperthermia mediated by antibody-coated magnetotactic MO-1 bacteria significantly improved wound healing. These results collectively demonstrated the effective eradication of
S. aureus
both
in vitro
and
in vivo
, indicating the potential of magnetotactic bacterium-mediated magnetic hyperthermia as a treatment for
S. aureus
-induced skin or wound infections.
Endovascular repair or open repair for ruptured abdominal aortic aneurysm: a Cochrane systematic review
Authors: Badger S A , Harkin D W , Blair P H , Ellis P K , Kee F , Forster R 
Published: February 2016

ObjectivesEmergency endovascular aneurysm repair (eEVAR) may improve outcomes for patients with ruptured abdominal aortic aneurysm (RAAA). The study aim was to compare the outcomes for eEVAR with conventional open surgical repair for the treatment of RAAA.SettingA systematic review of relevant publications was performed. Randomised controlled trials (RCTs) comparing eEVAR with open surgical repair for RAAA were included.Participants3 RCTs were included, with a total of 761 patients with RAAA.InterventionsMeta-analysis was performed with fixed-effects models with ORs and 95% CIs for dichotomous data and mean differences with 95% CIs for continuous data.Primary and secondary outcome measuresPrimary outcome was short-term mortality. Secondary outcome measures included aneurysm-specific and general complication rates, quality of life and economic analysis.ResultsOverall risk of bias was low. There was no difference between the 2 interventions on 30-day (or in-hospital) mortality, OR 0.91 (95% CI 0.67 to 1.22; p=0.52). 30-day complications included myocardial infarction, stroke, composite cardiac complications, renal complications, severe bowel ischaemia, spinal cord ischaemia, reoperation, amputation and respiratory failure. Reporting was incomplete, and no robust conclusion was drawn. For complication outcomes that did include at least 2 studies in the meta-analysis, there was no clear evidence to support a difference between eEVAR and open repair. Longer term outcomes and cost per patient were evaluated in only a single study, thus precluding definite conclusions.ConclusionsOutcomes between eEVAR and open repair, specifically 30-day mortality, are similar. However, further high-quality trials are required, as the paucity of data currently limits the conclusions.
Which are the most useful scales for predicting repeat self-harm? A systematic review evaluating risk scales using measures of diagnostic accuracy
Authors: Quinlivan L , Cooper J , Davies L , Hawton K , Gunnell D , Kapur N 
Published: February 2016

ObjectivesThe aims of this review were to calculate the diagnostic accuracy statistics of risk scales following self-harm and consider which might be the most useful scales in clinical practice.DesignSystematic review.MethodsWe based our search terms on those used in the systematic reviews carried out for the National Institute for Health and Care Excellence self-harm guidelines (2012) and evidence update (2013), and updated the searches through to February 2015 (CINAHL, EMBASE, MEDLINE, and PsychINFO). Methodological quality was assessed and three reviewers extracted data independently. We limited our analysis to cohort studies in adults using the outcome of repeat self-harm or attempted suicide. We calculated diagnostic accuracy statistics including measures of global accuracy. Statistical pooling was not possible due to heterogeneity.ResultsThe eight papers included in the final analysis varied widely according to methodological quality and the content of scales employed. Overall, sensitivity of scales ranged from 6% (95% CI 5% to 6%) to 97% (CI 95% 94% to 98%). The positive predictive value (PPV) ranged from 5% (95% CI 3% to 9%) to 84% (95% CI 80% to 87%). The diagnostic OR ranged from 1.01 (95% CI 0.434 to 2.5) to 16.3 (95%CI 12.5 to 21.4). Scales with high sensitivity tended to have low PPVs.ConclusionsIt is difficult to be certain which, if any, are the most useful scales for self-harm risk assessment. No scales perform sufficiently well so as to be recommended for routine clinical use. Further robust prospective studies are warranted to evaluate risk scales following an episode of self-harm. Diagnostic accuracy statistics should be considered in relation to the specific service needs, and scales should only be used as an adjunct to assessment.
Comparison of a lateral flow milk progesterone test with enzyme immunoassay as an aid for reproductive status determination in cows
Authors: Waldmann A. , Raud A. 
Published: February 2016

The lateral flow test (LFT) is an immunochromatographic method that utilises an immunostrip for non‐laboratory diagnostic purposes. The present study evaluated a milk progesterone LFT against the enzyme immunoassay (EIA) to confirm oestrus and a non‐pregnancy diagnosis. In total, 277 milk samples from 70 cows were analysed, collected on the day of artificial insemination and at 19 days, 21 days and 24 days post insemination. The level of accuracy of the LFT compared with the EIA was 95.0 per cent for milk samples containing <2 ng/ml progesterone and 97.0 per cent for milk samples containing >10 ng/ml progesterone. The validation of oestrus by the LFT was 98.6 per cent accurate using 2 ng/ml progesterone as the EIA estimate for oestrus. The test performance for a non‐pregnancy diagnosis was subject to the day of milk sampling, showing the highest accuracy on day 24 post insemination for both tests. When optimised for maximum specificity, and compared with rectal palpation, the LFT had a sensitivity and specificity for non‐pregnancy diagnosis on day 24 post insemination of 75.0 per cent and 100.0 per cent, respectively, with an overall accuracy of 84.4 per cent. The corresponding characteristics for the quantitative EIA were 85.0 per cent, 100.0 per cent and 90.6 per cent, respectively. The LFT results compared favourably with the quantitative milk progesterone EIA.
Post-rift subsidence of the French Guiana hyper-oblique margin: from rift-inherited subsidence to Amazon deposition effect
Authors: Sapin Francois , Davaux Mélanie , Dall'asta Massimo , Lahmi Marjolaine , Baudot Gautier , Ringenbach Jean-Claude 
Published: February 2016

Abstract
The recent surge of exploration activities over distal margins, with the acquisition of more and more high-quality and deep seismic data, has led to enhance concepts of the deformation and subsidence history of passive margins in general and sheared margins in particular. The French Guiana sheared margin is very narrow. The thinning of the upper crust is accommodated by few major faults relayed by well-expressed transfer zones, giving a general oblique trend to the margin. Another possible effect of the shear component during the rifting is the presence in the distal domain of a Moho high. Its exhumation is coeval with the emplacement of a deltaic system coming from the Demerara Plateau, evidencing a probably important early subsidence of the margin. This early subsidence in the late-rifting stage is increased during the early drifting, when the thinned crust reached its isostatic/thermal equilibrium in the Cenomano-Turonian before suffering an important Late Cretaceous sedimentation load. In the Palaeogene, starving of the margin and significant uplifts in the Guiana Craton are observed, possibly resulting from the rise of the Purus Arch (Andes fore-bulge?). Finally, the Amazon deposition by the Late Miocene–Pliocene provoked a large subsidence in the distal domain.
A Genome-Wide Association Study of Cutaneous Squamous Cell Carcinoma among European Descendants
Authors: Siiskonen Satu J. , Zhang Mingfeng , Li Wen-Qing , Liang Liming , Kraft Peter , Nijsten Tamar , Han Jiali , Qureshi Abrar A. 
Published: February 2016

Abstract
Background: No GWAS on the risk of cutaneous squamous cell carcinoma (SCC) has been published. We conducted a multistage genome-wide association study (GWAS) to identify novel genetic loci for SCC.
Methods: The study included 745 SCC cases and 12,805 controls of European descent in the discovery stage and 531 SCC cases and 551 controls of European ancestry in the replication stage. We selected 64 independent loci that showed the most significant associations with SCC in the discovery stage (linkage disequilibrium r2 &lt; 0.4) for replication.
Results: Rs8063761 in the DEF8 gene on chromosome 16 showed the strongest association with SCC (P = 1.7 × 10−9 in the combined set; P = 1.0 × 10−6 in the discovery set and P = 4.1 × 10−4 in the replication set). The variant allele of rs8063761 (T allele) was associated with a decreased expression of DEF8 (P = 1.2 × 10−6). Besides, we validated four other SNPs associated with SCC in the replication set, including rs9689649 in PARK2 gene (P = 2.7 × 10−6 in combined set; P = 3.2 × 10−5 in the discovery; and P = 0.02 in the replication), rs754626 in the SRC gene (P = 1.1 × 10−6 in combined set; P = 1.4 × 10−5 in the discovery and P = 0.02 in the replication), rs9643297 in ST3GAL1 gene (P = 8.2 × 10−6 in combined set; P = 3.3 × 10−5 in the discovery; and P = 0.04 in the replication), and rs17247181 in ERBB2IP gene (P = 4.2 × 10−6 in combined set; P = 3.1 × 10−5 in the discovery; and P = 0.048 in the replication).
Conclusion: Several genetic variants were associated with risk of SCC in a multistage GWAS of subjects of European ancestry.
Impact: Further studies are warranted to validate our finding and elucidate the genetic function of these variants. Cancer Epidemiol Biomarkers Prev; 25(4); 714–20. ©2016 AACR.
Identification of Niclosamide as a Novel Anticancer Agent for Adrenocortical Carcinoma
Authors: Satoh Kei , Zhang Lisa , Zhang Yaqin , Chelluri Raju , Boufraqech Myriem , Nilubol Naris , Patel Dhaval , Shen Min , Kebebew Electron 
Published: February 2016

Abstract
Purpose: Adrenocortical carcinoma (ACC) is a rare and aggressive cancer, and no current effective therapy is available for locally advanced and metastatic ACC. Drug repurposing is an emerging approach for identifying new indications for existing drugs, especially for rare cancers such as ACC. The objective of this study was to use quantitative high-throughput screening to identify agents with antineoplastic activity against ACC.
Experimental Design: A screening of 4,292 compounds was performed on three ACC cell lines: BD140A, SW-13, and NCI-H295R.
Results: Twenty-one active compounds were identified, with an efficacy of &gt;80% in all three cell lines. Of these, niclosamide showed higher efficacy and lower IC50 than established anti-ACC drugs. We then validated niclosamide-inhibited cellular proliferation in all three ACC cell lines. Next, we investigated the mechanism by which niclosamide inhibited ACC cell proliferation, and found that it induced caspase-dependent apoptosis and G1 cell-cycle arrest. Niclosamide also decreased cellular migration and reduced the level of mediators of epithelial-to-mesenchymal transition, such as N-cadherin and vimentin. Furthermore, niclosamide treatment resulted in decreased expression of β-catenin. We also evaluated the effect of niclosamide on energy metabolism in ACC cell lines and found it resulted in mitochondrial uncoupling. Niclosamide treatment inhibited ACC tumor growth with no observed toxicity in mice in vivo.
Conclusions: Our findings suggest that niclosamide has anti-ACC activity through its inhibition of multiple altered cellular pathways and cellular metabolism in ACC. Our results provide a preclinical rationale for evaluating niclosamide therapy in a clinical trial for ACC. Clin Cancer Res; 22(14); 3458–66. ©2016 AACR.
Applying Small Molecule Signal Transducer and Activator of Transcription-3 (STAT3) Protein Inhibitors as Pancreatic Cancer Therapeutics
Authors: Arpin Carolyn C. , Mac Stephen , Jiang Yanlin , Cheng Huiwen , Grimard Michelle , Page Brent D.G. , Kamocka Malgorzata M. , Haftchenary Sina , Su Han , Ball Daniel P. , Rosa David A. , Lai Ping-Shan , Gómez-Biagi Rodolfo F. , Ali Ahmed M. , Rana Rahul , Hanenberg Helmut , Kerman Kagan , McElyea Kyle C. , Sandusky George E. , Gunning Patrick T. , Fishel Melissa L. 
Published: February 2016

AbstractConstitutively activated STAT3 protein has been found to be a key regulator of pancreatic cancer and a target for molecular therapeutic intervention. In this study, PG-S3-001, a small molecule derived from the SH-4-54 class of STAT3 inhibitors, was found to inhibit patient-derived pancreatic cancer cell proliferation in vitro and in vivo in the low micromolar range. PG-S3-001 binds the STAT3 protein potently, Kd = 324 nmol/L by surface plasmon resonance, and showed no effect in a kinome screen (&gt;100 cancer-relevant kinases). In vitro studies demonstrated potent cell killing as well as inhibition of STAT3 activation in pancreatic cancer cells. To better model the tumor and its microenvironment, we utilized three-dimensional (3D) cultures of patient-derived pancreatic cancer cells in the absence and presence of cancer-associated fibroblasts (CAF). In this coculture model, inhibition of tumor growth is maintained following STAT3 inhibition in the presence of CAFs. Confocal microscopy was used to verify tumor cell death following treatment of 3D cocultures with PG-S3-001. The 3D model was predictive of in vivo efficacy as significant tumor growth inhibition was observed upon administration of PG-S3-001. These studies showed that the inhibition of STAT3 was able to impact the survival of tumor cells in a relevant 3D model, as well as in a xenograft model using patient-derived cells. Mol Cancer Ther; 15(5); 794–805. ©2016 AACR.