bluuebunny/crossref_metadata_2025 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

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

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

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

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

Umbilicaria 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

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

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

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

Background

Although 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.

Methods

Nine 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.

Results

Similar 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.

Conclusions

This 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.
Acute myocardial infarction due to coronary thrombosis caused by blunt chest trauma
Authors: Treuth Gregory M , Baibars Motaz , Alraiyes Abdul Hamid , Alraies M Chadi
Published: April 2014

A 65-year-old man presented to the emergency department following an anterior chest trauma. He had significant chest pain and chest X-ray was significant for revealed multiple rib fractures and negative. CT scan of the chest ruled out pulmonary embolism or aortic dissection. However, few hours later he developed hypotension requiring admission to medical intensive care unit and intravenous vasopressors. Further workup showed ST elevation myocardial infarction involving the anterior ECG leads. Emergent coronary angiography was performed with intervention to the mid-left anterior descending occlusion. Cardiogenic shock resolved and patient was discharged few days later. One-year follow-up with echocardiogram showed stable ischaemic cardiomyopathy with improved left ventricular ejection fraction to 50%.
Graves’ disease as an uncommon cause of acute pericarditis
Authors: Kortekaas Kirsten , van der Lienden Bas , Jong Simone , Riezebos Robert
Published: April 2014

Acute pericarditis is either dry, fibrinous or effusive, independent of its aetiology. A case is presented involving a 44-year-old man with acute pericarditis. The cause was established to be an aggravation of Graves’ disease due to non-compliance with treatment. Pericarditis is an uncommon cardiac complication of Graves’ disease and is associated with more recurrent episodes when not detected. Pharmacological treatment should include anti-inflammatory drugs in combination with treatment for hyperthyroidism. The specific pathophysiological link between the two conditions is still to be elucidated.
Cystic schwannoma of the recurrent laryngeal nerve: a rare finding posing diagnostic difficulties
Authors: Knulst Rowan , Bosman Willem-Maarten , Ritchie Ewan D , da Costa Andy
Published: April 2014

A 49-year-old woman with a painless mass in the neck was examined by the surgeon. Imaging and cytology prior to surgery suggested the mass to be either a thyroid cyst or a branchial cleft cyst. After surgery, the patient reported a hoarse voice and the pathologist confirmed the removed lesion to be a cystic schwannoma of the left recurrent laryngeal nerve. The inconclusive imaging results, combined with colloid-like material in the punctate should prompt the investigator to include cystic schwannoma in the differential diagnosis. With the probability of a neurogenic origin of the mass in mind, nerve-sparing surgery can be performed. As a future prospect, positron emission tomography scans are mentioned as a modality with possibilities to discriminate a cystic schwannoma from other common cystic lesions.
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

Objective

This qualitative interview study explored perceptions of the phrases ‘population health’, ‘public health’ and ‘community health’.

Setting

Accountable care organisations (ACOs), and public health or similar agencies in different parts of the USA.

Participants

Purposive sample of 29 interviewees at four ACOs, and 10 interviewees at six public health or similar agencies.

Results

Interviewees 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.

Conclusions

Conflating 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.
Safety measurement and monitoring in healthcare: a framework to guide clinical teams and healthcare organisations in maintaining safety
Authors: Vincent Charles , Burnett Susan , Carthey Jane
Published: April 2014

Patients, clinicians and managers all want to be reassured that their healthcare organisation is safe. But there is no consensus about what we mean when we ask whether a healthcare organisation is safe or how this is achieved. In the UK, the measurement of harm, so important in the evolution of patient safety, has been neglected in favour of incident reporting. The use of softer intelligence for monitoring and anticipation of problems receives little mention in official policy. The Francis Inquiry report into patient treatment at the Mid Staffordshire NHS Foundation Trust set out 29 recommendations on measurement, more than on any other topic, and set the measurement of safety an absolute priority for healthcare organisations. The Berwick review found that most healthcare organisations at present have very little capacity to analyse, monitor or learn from safety and quality information. This paper summarises the findings of a more extensive report and proposes a framework which can guide clinical teams and healthcare organisations in the measurement and monitoring of safety and in reviewing progress against safety objectives. The framework has been used so far to promote self-reflection at both board and clinical team level, to stimulate an organisational check or analysis in the gaps of information and to promote discussion of ‘what could we do differently’.
Improving the safety and efficiency of nurse medication rounds through the introduction of an automated dispensing cabinet
Authors: Cottney Alan
Published: April 2014

Information 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.
Rare presentation of intracranial vascular blowout after tumor resection and radiation therapy
Authors: Alaraj Ali , Behbahani Mandana , Valyi-Nagy Tibor , Aardsma Nathan , Aletich Victor A
Published: April 2014

A middle-aged patient presented with a rapidly growing right dural-based extra-axial posterior clinoid mass extending to the right cavernous sinus that was surgically resected. Histological examination showed solid growth of primitive neuroectodermal tumor arising from the third nerve. Following surgical resection, the patient was further managed by radiation and chemotherapy. Two years later the patient developed new intracranial hemorrhage in the area adjacent to the previous surgical cavity. A cerebral angiogram showed contrast extravasation at the junction of the posterior communicating artery (Pcom) and the right posterior cerebral artery (PCA), with an expanding pseudoaneurysm. This was managed with N-butyl cyanoacrylate embolization. Autopsy showed microscopic recurrence of tumor into the PCA/PCom region with invasion of the wall of the Pcom. This case report illustrates the concept of vascular blowout in intracranial cerebral vasculature. It appears that, in the presence of risk factors that contribute to weakening of vessel walls (surgery, radiation, tumor recurrence), a blowout can occur intracranially.
Genetic risks of supplementing trout populations with native stocks: a simulation case study from current Pyrenean populations
Authors: Fernández-Cebrián Raquel , Araguas Rosa Maria , Sanz Nuria , García-Marín Jose Luis
Published: April 2014

The risks of supplementation must be examined to assess the genetic effects to native wild populations before full implementation or exclusion of programs that involve captive breeding and release. Real genetic data can be applied to simulations of genetic changes in populations of interest and subsequently used in risk assessment. Ancestral Mediterranean brown trout (Salmo trutta) lineages exhibit complex population structure among native populations. Genetically divergent Atlantic stocks were maintained and released in the Mediterranean rivers as recreational fish, which resulted in hybridization and introgression with local populations. Therefore, we designed a new supplementation program based on native stocks and evaluated the genetic risks associated with releasing native fish in recreational fisheries. Our simulation was delimited by the observed population genetic structure and available hatchery facilities in the study region. Supplementation with native stocks maintained estimates of gene diversity indexes (total diversity (HT), local diversity (HS), and population differentiation (GST)). However, simulations indicated that long-term supplementation significantly reduced genetic diversity among locations because of a homogenizing effect of populations along each management unit. Therefore, such reinforcements compromised the conservation of local genetic variation. Nevertheless, replacement of current foreign stocks with native stocks can be an important step towards promoting the value of preserving local diversity among anglers.
First documented case of human infection with ovine Shiga-toxin-producingEscherichia coliserotype O52:H45
Authors: Bekal Sadjia , Ramsay Danielle , Rallu Fabien , Pilon Pierre , Gilmour Matthew , Johnson Roger , Tremblay Cécile
Published: April 2014

We report a concurrent case of infection with non-O157 Shiga-toxin-producing Escherichia coli (STEC) strain in an 8-month-old child. Laboratory and epidemiological investigations indicated child exposure to contaminated sheep meat following the Muslim feast of sacrifice (Eid al-Adha). Microbiological and molecular typing confirmed that the ovine strain O52:H45 (stx1+, eae–, hlyA–) was the causal agent. This is the first documented case of human infection to this STEC serotype.
Heart rate at 4 s after the onset of exercise in endurance-trained men
Authors: Zaniqueli Divanei , Morra Elis Aguiar , Dantas Eduardo Miranda , Baldo Marcelo Perim , Carletti Luciana , Perez Anselmo José , Rodrigues Sérgio Lamêgo , Mill José Geraldo
Published: April 2014

It has been suggested that the increase in heart rate (HR) at the onset of exercise is caused by vagal withdrawal. In fact, endurance runners show a lower HR in maximum aerobic tests. However, it is still unknown whether endurance runners have a lower HR at 4 s after the onset of exercise (4th-sec-HR). We sought to measure the HR at the onset of the 4 s exercise test (4-sET), clarifying its relationship to heart rate variability (HRV), spectral indices, and cardiac vagal index (CVI) in endurance runners (ER) and healthy untrained controls (CON). HR at 4th-sec-HR, CVI, and percent HR increase during exercise were analyzed in the 4-sET. High frequency spectrum (HF-nu), low frequency spectrum (LF-nu), and low frequency/high frequency band ratio (LF/HF) were analyzed from the HRV. ER showed a significantly higher HF, and both a lower LF and LF/HF ratio compared with the CON. ER presented a significantly lower 4th-sec-HR, although neither CVI nor HR increases during exercise were statistically different from the CON. In conclusion, ER presented a lower 4th-sec-HR secondary to increased vagal influence over the sinus node. CVI seems to be too weak to use for discriminating individuals with respect to the magnitude of HR vagal control.
Present status on experimental search for pentaquarks
Authors: Liu Tianbo , Mao Yajun , Ma Bo-Qiang
Published: April 2014

It has been ten years since the first report for a positive strangeness pentaquark-like baryon state. However, the existence of the pentaquark state is still controversial. Some contradictions between the experiments are unsolved. In this paper, we review the experimental search for the pentaquark candidates Θ+, Θ++, Ξ- -, [Formula: see text] and N* in detail. We review the experiments with positive results and compare the experiments with similar conditions but opposite results.
Holographic charge transport in 2+1 dimensions at finite N
Authors: Bai Shan , Pang Da-Wei
Published: April 2014

We study holographic charge transport in (2+1) dimensions at finite N, whose dual gravity background is given by perturbative black hole solution in Einstein theory plus cubic terms of Weyl tensor. We consider the higher derivative corrections to the standard Maxwell action, given by the interacting terms between the Weyl tensor and the field strength. We calculate the DC conductivity by using both the membrane paradigm and the Kubo's formula and find precise agreement. We compute the AC conductivity and find an analog of the crossover from "metal" to "bad metal" in the low frequency limit. Moreover, the conductivity becomes a constant in the large frequency limit. We derive two universal relations for the Green's functions and observe that they are exactly the same as the infinite N counterparts.
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

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
.
Air toxics and epigenetic effects: ozone altered microRNAs in the sputum of human subjects
Authors: Fry Rebecca C. , Rager Julia E. , Bauer Rebecca , Sebastian Elizabeth , Peden David B. , Jaspers Ilona , Alexis Neil E.
Published: April 2014

Ozone (O3) is a criteria air pollutant that is associated with numerous adverse health effects, including altered respiratory immune responses. Despite its deleterious health effects, possible epigenetic mechanisms underlying O3-induced health effects remain understudied. MicroRNAs (miRNAs) are epigenetic regulators of genomic response to environmental insults and unstudied in relationship to O3 inhalation exposure. Our objective was to test whether O3 inhalation exposure significantly alters miRNA expression profiles within the human bronchial airways. Twenty healthy adult human volunteers were exposed to 0.4 ppm O3 for 2 h. Induced sputum samples were collected from each subject 48 h preexposure and 6 h postexposure for evaluation of miRNA expression and markers of inflammation in the airways. Genomewide miRNA expression profiles were evaluated by microarray analysis, and in silico predicted mRNA targets of the O3-responsive miRNAs were identified and validated against previously measured O3-induced changes in mRNA targets. Biological network analysis was performed on the O3-associated miRNAs and mRNA targets to reveal potential associated response signaling and functional enrichment. Expression analysis of the sputum samples revealed that O3 exposure significantly increased the expression levels of 10 miRNAs, namely miR-132, miR-143, miR-145, miR-199a*, miR-199b-5p, miR-222, miR-223, miR-25, miR-424, and miR-582-5p. The miRNAs and their predicted targets were associated with a diverse range of biological functions and disease signatures, noted among them inflammation and immune-related disease. The present study shows that O3 inhalation exposure disrupts select miRNA expression profiles that are associated with inflammatory and immune response signaling. These findings provide novel insight into epigenetic regulation of responses to O3 exposure.
Total body skeletal muscle mass: estimation by creatine (methyl-d3) dilution in humans
Authors: Clark Richard V. , Walker Ann C. , O'Connor-Semmes Robin L. , Leonard Michael S. , Miller Ram R. , Stimpson Stephen A. , Turner Scott M. , Ravussin Eric , Cefalu William T. , Hellerstein Marc K. , Evans William J.
Published: April 2014

Current methods for clinical estimation of total body skeletal muscle mass have significant limitations. We tested the hypothesis that creatine ( methyl-d3) dilution (D3-creatine) measured by enrichment of urine D3-creatinine reveals total body creatine pool size, providing an accurate estimate of total body skeletal muscle mass. Healthy subjects with different muscle masses [ n = 35: 20 men (19–30 yr, 70–84 yr), 15 postmenopausal women (51–62 yr, 70–84 yr)] were housed for 5 days. Optimal tracer dose was explored with single oral doses of 30, 60, or 100 mg D3-creatine given on day 1. Serial plasma samples were collected for D3-creatine pharmacokinetics. All urine was collected through day 5. Creatine and creatinine (deuterated and unlabeled) were measured by liquid chromatography mass spectrometry. Total body creatine pool size and muscle mass were calculated from D3-creatinine enrichment in urine. Muscle mass was also measured by magnetic resonance imaging (MRI), dual-energy x-ray absorptiometry (DXA), and traditional 24-h urine creatinine. D3-creatine was rapidly absorbed and cleared with variable urinary excretion. Isotopic steady-state of D3-creatinine enrichment in the urine was achieved by 30.7 ± 11.2 h. Mean steady-state enrichment in urine provided muscle mass estimates that correlated well with MRI estimates for all subjects ( r = 0.868, P < 0.0001), with less bias compared with lean body mass assessment by DXA, which overestimated muscle mass compared with MRI. The dilution of an oral D3-creatine dose determined by urine D3-creatinine enrichment provides an estimate of total body muscle mass strongly correlated with estimates from serial MRI with less bias than total lean body mass assessment by DXA.
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

Therapeutic 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

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 >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

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.
Genome-Wide Study of Hypomethylated and Induced Genes in Patients with Liver Cancer Unravels Novel Anticancer Targets
Authors: Stefanska Barbara , Cheishvili David , Suderman Matthew , Arakelian Ani , Huang Jian , Hallett Michael , Han Ze-Guang , Al-Mahtab Mamun , Akbar Sheikh Mohammad Fazle , Khan Wasif Ali , Raqib Rubhana , Tanvir Imrana , Khan Haseeb Ahmed , Rabbani Shafaat A. , Szyf Moshe
Published: April 2014

Purpose: We utilized whole-genome mapping of promoters that are activated by DNA hypomethylation in hepatocellular carcinoma (HCC) clinical samples to shortlist novel targets for anticancer therapeutics. We provide a proof of principle of this approach by testing six genes short-listed in our screen for their essential role in cancer growth and invasiveness.

Experimental Design: We used siRNA- or shRNA-mediated depletion to determine whether inhibition of these genes would reduce human tumor xenograft growth in mice as well as cell viability, anchorage-independent growth, invasive capacities, and state of activity of nodal signaling pathways in liver, breast, and bladder cancer cell lines.

Results: Depletion of EXOSC4, RNMT, SENP6, WBSCR22, RASAL2, and NENF effectively and specifically inhibits cancer cell growth and cell invasive capacities in different types of cancer, but, remarkably, there is no effect on normal cell growth, suggesting a ubiquitous causal role for these genes in driving cancer growth and metastasis. Depletion of RASAL2 and NENF in vitro reduces their growth as explants in vivo in mice. RASAL2 and NENF depletion interferes with AKT, WNT, and MAPK signaling pathways as well as regulation of epigenetic proteins that were previously demonstrated to drive cancer growth and metastasis.

Conclusion: Our results prove that genes that are hypomethylated and induced in tumors are candidate targets for anticancer therapeutics in multiple cancer cell types. Because these genes are particularly activated in cancer, they constitute a group of targets for specific pharmacologic inhibitors of cancer and cancer metastasis. Clin Cancer Res; 20(12); 3118–32. ©2014 AACR.
Overexpression of Sirt7 Exhibits Oncogenic Property and Serves as a Prognostic Factor in Colorectal Cancer
Authors: Yu Hongyan , Ye Wen , Wu Jiangxue , Meng Xiangqi , Liu Ran-yi , Ying Xiaofang , Zhou Yi , Wang Hui , Pan Changchuan , Huang Wenlin
Published: April 2014

Purpose: Sirtuins play an important role in cancer development. Sirt7, as a member of this family, is frequently overexpressed in certain carcinomas, but the oncogenic mechanism is seldom reported. In this study, Sirt7 was characterized for its role in colorectal cancer aggressiveness and underlying molecular mechanisms.

Experimental Design: Quantitative PCR, Western blotting, and immunohistochemistry were performed to study Sirt7 expression in a cohort of colorectal cancer tissues and non-tumor tissues and cells. A series of in vitro and in vivo assays was performed to elucidate the function of Sirt7 in colorectal cancer and its underlying mechanisms. Association between the Sirt7 signature and survival was examined using Kaplan–Meier analysis and log-rank tests.

Results: The Sirt7 protein level significantly correlated with tumor stage (P = 0.029), lymph node metastasis (P = 0.046), and poor patient survival (P < 0.05). Sirt7 knockdown significantly inhibited colorectal cancer cell proliferation, colony formation, and motility. Ectopic Sirt7 expression promoted colony formation, induced a more invasive phenotype, and accelerated cell growth both in vitro and in vivo. Moreover, Sirt7 enhanced MAPK pathway activity concomitantly with p-ERK and p-MEK upregulation. In Sirt7-overexpressing cells, the mesenchymal markers vimentin and fibronectin were upregulated, and the epithelial markers E-cadherin and β-catenin were downregulated, which was linked to enhanced invasion by colorectal cancer cells.

Conclusion: Our findings suggest that Sirt7 plays an important role in the development and progression of human colorectal cancer and functions as a valuable marker of colorectal cancer prognosis. Clin Cancer Res; 20(13); 3434–45. ©2014 AACR.
FGFR1 mRNA and Protein Expression, not Gene Copy Number, Predict FGFR TKI Sensitivity across All Lung Cancer Histologies
Authors: Wynes Murry W. , Hinz Trista K. , Gao Dexiang , Martini Michael , Marek Lindsay A. , Ware Kathryn E. , Edwards Michael G. , Böhm Diana , Perner Sven , Helfrich Barbara A. , Dziadziuszko Rafal , Jassem Jacek , Wojtylak Szymon , Sejda Aleksandra , Gozgit Joseph M. , Bunn Paul A. , Camidge D. Ross , Tan Aik-Choon , Hirsch Fred R. , Heasley Lynn E.
Published: April 2014

Purpose: FGFR1 gene copy number (GCN) is being evaluated as a biomarker for FGFR tyrosine kinase inhibitor (TKI) response in squamous cell lung cancers (SCC). The exclusive use of FGFR1 GCN for predicting FGFR TKI sensitivity assumes increased GCN is the only mechanism for biologically relevant increases in FGFR1 signaling. Herein, we tested whether FGFR1 mRNA and protein expression may serve as better biomarkers of FGFR TKI sensitivity in lung cancer.

Experimental Design: Histologically diverse lung cancer cell lines were submitted to assays for ponatinib sensitivity, a potent FGFR TKI. A tissue microarray composed of resected lung tumors was submitted to FGFR1 GCN, and mRNA analyses and the results were validated with The Cancer Genome Atlas (TCGA) lung cancer data.

Results: Among 58 cell lines, 14 exhibited ponatinib sensitivity (IC50 values ≤ 50 nmol/L) that correlated with FGFR1 mRNA and protein expression, but not with FGFR1 GCN or histology. Moreover, ponatinib sensitivity associated with mRNA expression of the ligands, FGF2 and FGF9. In resected tumors, 22% of adenocarcinomas and 28% of SCCs expressed high FGFR1 mRNA. Importantly, only 46% of SCCs with increased FGFR1 GCN expressed high mRNA. Lung cancer TCGA data validated these findings and unveiled overlap of FGFR1 mRNA positivity with KRAS and PIK3CA mutations.

Conclusions: FGFR1 dependency is frequent across various lung cancer histologies, and FGFR1 mRNA may serve as a better biomarker of FGFR TKI response in lung cancer than FGFR1 GCN. The study provides important and timely insight into clinical testing of FGFR TKIs in lung cancer and other solid tumor types. Clin Cancer Res; 20(12); 3299–309. ©2014 AACR.
Base Excision Repair Defects Invoke Hypersensitivity to PARP Inhibition
Authors: Horton Julie K. , Stefanick Donna F. , Prasad Rajendra , Gassman Natalie R. , Kedar Padmini S. , Wilson Samuel H.
Published: April 2014

PARP-1 is important for the recognition of both endogenous and exogenous DNA damage, and binds to DNA strand breaks including intermediates of base excision repair (BER). Once DNA-bound, PARP-1 becomes catalytically activated synthesizing PAR polymers onto itself and other repair factors (PARylation). As a result, BER repair proteins such as XRCC1 and DNA polymerase β (pol β) are more efficiently and rapidly recruited to sites of DNA damage. In the presence of an inhibitor of PARP activity (PARPi), PARP-1 binds to sites of DNA damage, but PARylation is prevented. BER enzyme recruitment is hindered, but binding of PARP-1 to DNA is stabilized, impeding DNA repair and leading to double-strand DNA breaks (DSB). Deficiencies in pol β−/− and Xrcc1−/− cells resulted in hypersensitivity to the PARP inhibitor 4-AN and reexpression of pol β or XRCC1, in these contexts, reversed the 4-AN hypersensitivity phenotype. BER deficiencies also showed evidence of replication defects that lead to DSB-induced apoptosis upon PARPi treatment. Finally, the clinically relevant PARP inhibitors olaparib and veliparib also exhibited hypersensitivity in both pol β−/− and Xrcc1−/− BER-deficient cells. These results reveal heightened sensitivity to PARPi as a function of BER deficiency.

Implications: BER deficiency represents a new therapeutic opportunity to enhance PARPi efficacy.

Visual Overview: http://mcr.aacrjournals.org/content/12/8/1128/F1.large.jpg.

Mol Cancer Res; 12(8); 1128–39. ©2014 AACR.
The H2.0-Like Homeobox Transcription Factor Modulates Yolk Sac Vascular Remodeling in Mouse Embryos
Authors: Prahst Claudia , Kasaai Bahar , Moraes Filipa , Jahnsen Espen D. , Larrivee Bruno , Villegas David , Pardanaud Luc , Pibouin-Fragner Laurence , Zhang Feng , Zaun Hans C. , Eichmann Anne , Jones Elizabeth A.V.
Published: April 2014

Objective—

The H2.0-like homeobox transcription factor (HLX) plays an essential role in visceral organogenesis in mice and has been shown to regulate angiogenic sprouting in vitro and in zebrafish embryos. We therefore examined the role of HLX in vascular development in mouse and avian embryos.

Approach and Results—

In situ hybridization showed that
Hlx
is expressed in a subset of sprouting blood vessels in postnatal mouse retinas and embryos.
Hlx
expression was conserved in quail embryos and upregulated in blood vessels at the onset of circulation. In vitro assays showed that
Hlx
is dynamically regulated by growth factors and shear stress alterations. Proangiogenic vascular endothelial growth factor induces
Hlx
expression in cultured endothelial cells, whereas signals that induce stalk cell identity lead to a reduction in
Hlx
expression. HLX was also downregulated in embryos in which flow was ablated, whereas injection of a starch solution, which increases blood viscosity and therefore shear stress, causes an upregulation in HLX. HLX knockdown in vitro resulted in a reduction in tip cell marker expression and in reduced angiogenic sprouting, but
Hlx
−/−
embryos showed no defect in vascular sprouting at E8.5, E9.5, or E11.5 in vivo. Vascular remodeling of the capillary plexus was altered in
Hlx
−/−
embryos, with a modestly enlarged venous plexus and reduction of the arterial plexus.

Conclusions—

Our findings indicate not only that
Hlx
regulates sprouting in vitro, but that its role in sprouting is nonessential in vivo. We find HLX is regulated by shear stress and a subtle defect in vascular remodeling is present in knockout embryos.