bluuebunny/crossref_metadata_2025_split huggingface dataset:
Episodic bamboo die‐off, neighbourhood interactions and tree seedling performance in a Patagonian mixed forest
Authors: Caccia Fernando D. , Kitzberger Thomas , Chaneton Enrique J. 
Published: November 2014

Summary

Episodic mass flowering and subsequent die‐off of bamboo understories may generate rare opportunities for tree regeneration by altering consumer–seedling interactions as much as by increasing light availability to seedlings. We hypothesized that bamboo dieback interacts with canopy neighbourhood composition in creating recruitment microsites for tree seedling species with varied shade tolerance and susceptibility to herbivory.

We conducted a 2‐year experiment in a Patagonian mixed forest altered by extensive, but patchy dieback of the bamboo Chusquea culeou. Newly emerged seedlings of Nothofagus alpina (more shade‐tolerant) and Nothofagus dombeyi (less shade‐tolerant) were planted in conspecific and heterospecific canopy neighbourhoods, with either a flowered (dead) or non‐flowered (live) bamboo understorey. Seedlings were placed inside and outside mesh cages to assess mortality from vertebrate or invertebrate consumers.

Vertebrate exclusion increased seedling survival regardless of bamboo condition. Seedling loss to invertebrates decreased with bamboo die‐off, resulting in higher survival of N. alpina in dead than in live patches. In contrast, bamboo die‐off increased N. dombeyi mortality by wilting, which counteracted the benefits of seedling release from consumers. Bamboo die‐off increased light availability and enhanced seedling growth for both species.

Nothofagus alpina seedlings were less damaged or killed by invertebrates under heterospecific canopies than under conspecifics (associational resistance), whereas N. dombeyi performance was unaffected by neighbourhood composition. Bamboo die‐off did not change seedling performance patterns observed across canopy neighbourhoods with live bamboo understories.

Synthesis. Gaps created by bamboo die‐off can exert both positive and negative, species‐specific effects on the likelihood of tree seedling establishment. We conclude that infrequent understorey disturbances coupled with canopy neighbourhood effects mediated by seedling herbivores may drive gap‐phase succession within old‐growth forests.
Physiological characterization of anaerobic ammonium oxidizing bacterium ‘Candidatus Jettenia caeni’
Authors: Ali Muhammad , Oshiki Mamoru , Awata Takanori , Isobe Kazuo , Kimura Zenichiro , Yoshikawa Hiroaki , Hira Daisuke , Kindaichi Tomonori , Satoh Hisashi , Fujii Takao , Okabe Satoshi 
Published: November 2014

SummaryTo date, six candidate genera of anaerobic ammonium‐oxidizing (anammox) bacteria have been identified, and numerous studies have been conducted to understand their ecophysiology. In this study, we examined the physiological characteristics of an anammox bacterium in the genus ‘Candidatus Jettenia’. Planctomycete KSU‐1 was found to be a mesophilic (20–42.5°C) and neutrophilic (pH 6.5–8.5) bacterium with a maximum growth rate of 0.0020 h−1. Planctomycete KSU‐1 cells showed typical physiological and structural features of anammox bacteria; i.e. 29N2 gas production by coupling of 15NH4+ and 14NO2−, accumulation of hydrazine with the consumption of hydroxylamine and the presence of anammoxosome. In addition, the cells were capable of respiratory ammonification with oxidation of acetate. Notably, the cells contained menaquinone‐7 as a dominant respiratory quinone. Proteomic analysis was performed to examine underlying core metabolisms, and high expressions of hydrazine synthase, hydrazine dehydrogenase, hydroxylamine dehydrogenase, nitrite/nitrate oxidoreductase and carbon monoxide dehydrogenase/acetyl‐CoA synthase were detected. These proteins require iron or copper as a metal cofactor, and both were dominant in planctomycete KSU‐1 cells. On the basis of these experimental results, we proposed the name ‘Ca. Jettenia caeni’ sp. nov. for the bacterial clade of the planctomycete KSU‐1.
Physiological and cell morphology adaptation of Bacillus subtilis at near‐zero specific growth rates: a transcriptome analysis
Authors: Overkamp Wout , Ercan Onur , Herber Martijn , van Maris Antonius J. A. , Kleerebezem Michiel , Kuipers Oscar P. 
Published: November 2014

SummaryNutrient scarcity is a common condition in nature, but the resulting extremely low growth rates (below 0.025 h−1) are an unexplored research area in Bacillus subtilis. To understand microbial life in natural environments, studying the adaptation of B. subtilis to near‐zero growth conditions is relevant. To this end, a chemostat modified for culturing an asporogenous B. subtilis sigF mutant strain at extremely low growth rates (also named a retentostat) was set up, and biomass accumulation, culture viability, metabolite production and cell morphology were analysed. During retentostat culturing, the specific growth rate decreased to a minimum of 0.00006 h−1, corresponding to a doubling time of 470 days. The energy distribution between growth and maintenance‐related processes showed that a state of near‐zero growth was reached. Remarkably, a filamentous cell morphology emerged, suggesting that cell separation is impaired under near‐zero growth conditions. To evaluate the corresponding molecular adaptations to extremely low specific growth, transcriptome changes were analysed. These revealed that cellular responses to near‐zero growth conditions share several similarities with those of cells during the stationary phase of batch growth. However, fundamental differences between these two non‐growing states are apparent by their high viability and absence of stationary phase mutagenesis under near‐zero growth conditions.
The FlxABCD‐HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough
Authors: Ramos Ana Raquel , Grein Fabian , Oliveira Gonçalo P. , Venceslau Sofia S. , Keller Kimberly L. , Wall Judy D. , Pereira Inês A. C. 
Published: November 2014

SummaryFlavin‐based electron bifurcation (FBEB) is an important mechanism for the energy metabolism of anaerobes. A new family of NADH dehydrogenases, the flavin oxidoreductase (FlxABCD, previously called FloxABCD), was proposed to perform FBEB in sulphate‐reducing organisms coupled with heterodisulfide reductase (HdrABC). We found that the hdrABC‐flxABCD gene cluster is widespread among anaerobic bacteria, pointing to a general and important role in their bioenergetics. In this work, we studied FlxABCD of Desulfovibrio vulgaris Hildenborough. The hdr‐flx genes are part of the same transcriptional unit and are increased in transcription during growth in ethanol‐sulfate, and to a less extent during pyruvate fermentation. Two mutant strains were generated: one where expression of the hdr‐flx genes was interrupted and another lacking the flxA gene. Both strains were unable to grow with ethanol‐sulfate, whereas growth was restored in a flxA‐complemented strain. The mutant strains also produced very reduced amounts of ethanol compared with the wild type during pyruvate fermentation. Our results show that in D. vulgaris, the FlxABCD‐HdrABC proteins are essential for NADH oxidation during growth on ethanol, probably involving a FBEB mechanism that leads to reduction of ferredoxin and the small protein DsrC, while in fermentation they operate in reverse, reducing NAD+ for ethanol production.
Spatial structuring of bacterial communities within individual Ginkgo biloba trees
Authors: Leff Jonathan W. , Del Tredici Peter , Friedman William E. , Fierer Noah 
Published: November 2014

SummaryPlant‐associated microorganisms affect the health of their hosts in diverse ways, yet the distribution of these organisms within individual plants remains poorly understood. To address this knowledge gap, we assessed the spatial variability in bacterial community diversity and composition found on and in aboveground tissues of individual Ginkgo biloba trees. We sampled bacterial communities from > 100 locations per tree, including leaf, branch and trunk samples and used high‐throughput sequencing of the 16S rRNA gene to determine the diversity and composition of these communities. Bacterial community structure differed strongly between bark and leaf samples, with bark samples harbouring much greater bacterial diversity and a community composition distinct from leaves. Within sample types, we observed clear spatial patterns in bacterial diversity and community composition that corresponded to the samples' proximity to the exterior of the tree. The composition of the bacterial communities found on trees is highly variable, but this variability is predictable and dependent on sampling location. Moreover, this work highlights the importance of carefully considering plant spatial structure when characterizing the microbial communities associated with plants and their impacts on plant hosts.
Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols
Authors: Croes Sarah , Weyens Nele , Colpaert Jan , Vangronsveld Jaco 
Published: November 2014

SummaryPlant‐associated bacteria are intensively investigated concerning their characteristics for plant growth promotion, biocontrol mechanisms and enhanced phytoremediation efficiency. To obtain endophytes, different sampling and isolation protocols are used although their representativeness is not always clearly demonstrated. The objective of this study was to acquire representative pictures of the cultivable bacterial root, stem and leaf communities for all Brassica napus L. individuals growing on the same field.For each plant organ, genotypic identifications of the endophytic communities were performed using three replicates. Root replicates were composed of three total root systems, whereas stem and leaf replicates needed to consist of six independent plant parts in order to be representative. Greater variations between replicates were found when considering phenotypic characteristics. Correspondence analysis revealed reliable phenotypic results for roots and even shoots, but less reliable ones for leaves. Additionally, realistic Shannon–Wiener biodiversity indices were calculated for all three organs and showed similar Evenness factors.Furthermore, it was striking that all replicates and thus the whole plant contained Pseudomonas and Bacillus strains although aboveground and belowground plant tissues differed in most dominant bacterial genera and characteristics.
Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing ‘phyloh’ as a novel phylogenetic diversity analysis tool
Authors: Sandionigi A. , Vicario S. , Prosdocimi E. M. , Galimberti A. , Ferri E. , Bruno A. , Balech B. , Mezzasalma V. , Casiraghi M. 
Published: November 2014

AbstractThe study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.
Occupational allergic contact dermatitis to chromium from cement: Estimating the size of the problem in Australia
Authors: Wong Celestine C , Gamboni Sarah E , Palmer Amanda M , Nixon Rosemary L 
Published: November 2014

AbstractBackgroundAllergic contact dermatitis (ACD) caused by chromium in cement is a significant occupational hazard. However, legislation in Europe over the past two decades to reduce the concentration of chromium in cement to <2 ppm through the addition of ferrous sulphate to cement, has seen a significant decrease in the incidence of chromium allergy. No such legislation exists in Australia.MethodsA retrospective analysis of results from the Patchcams database of patients attending the Occupational Dermatology Clinic at the Skin & Cancer Foundation, Melbourne, who were patch tested for chromium between 1 January 1993 to 31 December 2013, was conducted.ResultsOur review revealed that there has not been any significant change in the number of cases of ACD to chromium attributed to sensitisation through cement. Based on our data, we estimate that a minimum of 24 cases of chromium occupational ACD (OACD) from cement is found in Australia yearly, causing considerable morbidity, often associated with an inability to work, costly workers' compensation claims and sometimes the development of the disabling condition, persistent post‐occupational dermatitis.ConclusionThese findings highlight the need for high‐level discussions about adopting European legislation in Australia in order to reduce the likelihood of developing chromium OACD from cement.
Radiotherapy alone in patients with Merkel cell carcinoma: The Westmead Hospital experience of 41 patients
Authors: Veness Michael , Howle Julie 
Published: November 2014

AbstractObjectivesTo review the role of radiotherapy as treatment (RTx) alone in patients with Merkel cell carcinoma (MCC).MethodsData on 41 patients with MCC treated with RTx alone between 1993 and 2013 at Westmead Hospital, Sydney, were reviewed and analysed.ResultsThe patients' median age was 80 (range 45–96 years) among 18 (44%) women and 23 (56%) men. All but one patient were white and six (15%) were immunosuppressed. Most (59%) were irradiated at initial diagnosis with the remainder treated in the relapse setting. The median duration of follow up was 39 months. Head and neck was the most frequently treated site (63%). The median lesion size was 30 mm (range 5–130 mm). The in‐field control rate was 85%. Most out‐of‐field relapses were to visceral organs. Overall survival at 5 years was 40%.ConclusionsPatients with MCC treated with RTx alone experience a high likelihood of obtaining in‐field disease control. Doses of 50–55 Gy in 20–25 fractions are recommended but lower doses (25 Gy in five fractions) are still effective. A minority will be cured with many patients subsequently dying of systemic relapse.
Early urinary diversion with ileal conduit and vesicovaginostomy in the treatment of radiation cystitis due to carcinoma cervix: a study from a tertiary care hospital in South India
Authors: Banerji John Samuel , Devasia Antony , Kekre Nitin Sudhakar , Chacko Ninan 
Published: November 2014

AbstractBackgroundTo study the magnitude of radiation cystitis following radiation therapy for carcinoma cervix, and propose an algorithm to decide on early diversion, with or without vesicovaginostomy.MethodsWomen who developed radiation cystitis following radiotherapy for carcinoma cervix from January 1998 to December 2011 were included in this retrospective study. Electronic hospital records were analysed to document the presence of radiation cystitis. All women who developed evidence of radiation‐induced cystitis, according to the common toxicity and Radiation Therapy Oncology Group criteria, were included in the study. We looked at transfusion requirements, number of hospital admissions, quality of life and cost involved. Chi‐square tests were done where applicable. SPSS version 16 was used for analysis.ResultsOf the 902 patients who received radiation for carcinoma cervix in the 13‐year period, 62 (6.87%) developed grade 3/4 cystitis. Twenty‐eight of them underwent ileal conduit diversion, with 18 undergoing concomitant vesicovaginostomy. When compared with the patients who did not have diversion, the transfusion requirements, number of hospital admissions and quality of life had a statistically significant difference. Cost analysis of early diversion too showed a marginal benefit with early diversion. The limitation of the study was that it was retrospective in nature.ConclusionIn radiation cystitis, multiple hospital admissions and consequential increase in cost is the norm. In severe disease, early diversion is a prudent, cost‐effective approach with good quality of life and early return to normal activity.
Randomized controlled trial of accelerated rehabilitation versus standard protocol following surgical repair of ruptured Achilles tendon
Authors: Porter Mark D. , Shadbolt Bruce 
Published: November 2014

AbstractBackgroundThere is no consensus regarding the optimal management of the acutely ruptured Achilles tendon (TA). Functional bracing alone achieves outcomes similar to those of surgical repair. Surgical repair combined with immediate mobilization may improve the clinical outcome further. The purpose of our study was to determine if an accelerated rehabilitation programme following surgical repair of the ruptured TA could improve clinical outcome, relative to the standard protocol.MethodsPatients with an acutely ruptured TA were randomly allocated to undergo an accelerated programme (AP) or standard programme (SP), following surgery. Outcome was assessed at 12 months post‐surgery using the Achilles tendon Total Rupture Score (ATRS), the heel‐raise height and the time taken to return to running.ResultsFifty‐one patients completed the study, 25 in the AP group and 26 in the SP group. At 12 months post‐surgery, the ATRS results were similar in the two treatment groups (87.46 in AP with standard error (SE) of 0.735 versus 87.12 in SP with SE of 0.75) while the AP group had less lengthening of the TA (0.385 cm, SE 0.166 versus 1.00 cm, SE 0.169) and a more rapid return to running (17.231 weeks, SE 0.401 versus 21.08 weeks, SE 0.409), than the SP group.ConclusionThe accelerated rehabilitation programme resulted in less tendon lengthening, more rapid return to running, but similar ATRS relative to the standard rehabilitation. Immobilization following TA repair may prolong recovery.
“All of Me”: PsychologizingTurkish‐Dutch Police Officers in theNetherlands
Authors: Mutsaers Paul 
Published: November 2014

AbstractThis article offers a critical take on the excessive use of psychological applications in the work sphere, that is, management techniques that open up the psyche of the individual employee to interceptions, evaluations, and manipulations by superiors. It builds upon existing work on the psychologization of labor under the aegis of human resource apparatuses and contributes to it by centralizing the role that confessions have in this process. The article details the careers ofFehim andHalil, bothTurkish‐Dutch officers working for aDutch police agency. The field data, which have been obtained through an ethnographic fieldwork between 2008 and 2013, offer an insight into how psychological applications (such as personal development plans, “fireplace sessions,” empowerment courses, personality surveys, etc.) affect labor relations. The analysis opens up pathways for a better understanding of ethnic inequality in the workplace.
Evolution of proline biosynthesis: enzymology, bioinformatics, genetics, and transcriptional regulation
Authors: Fichman Yosef , Gerdes Svetlana Y. , Kovács Hajnalka , Szabados László , Zilberstein Aviah , Csonka Laszlo N. 
Published: November 2014

ABSTRACTProline is not only an essential component of proteins but it also has important roles in adaptation to osmotic and dehydration stresses, redox control, and apoptosis. Here, we review pathways of proline biosynthesis in the three domains of life. Pathway reconstruction from genome data for hundreds of eubacterial and dozens of archaeal and eukaryotic organisms revealed evolutionary conservation and variations of this pathway across different taxa. In the most prevalent pathway of proline synthesis, glutamate is phosphorylated to γ‐glutamyl phosphate by γ‐glutamyl kinase, reduced to γ‐glutamyl semialdehyde by γ‐glutamyl phosphate reductase, cyclized spontaneously to Δ1‐pyrroline‐5‐carboxylate and reduced to proline by Δ1‐pyrroline‐5‐carboxylate reductase. In higher plants and animals the first two steps are catalysed by a bi‐functional Δ1‐pyrroline‐5‐carboxylate synthase. Alternative pathways of proline formation use the initial steps of the arginine biosynthetic pathway to ornithine, which can be converted to Δ1‐pyrroline‐5‐carboxylate by ornithine aminotransferase and then reduced to proline or converted directly to proline by ornithine cyclodeaminase. In some organisms, the latter pathways contribute to or could be fully responsible for the synthesis of proline. The conservation of proline biosynthetic enzymes and significance of specific residues for catalytic activity and allosteric regulation are analysed on the basis of protein structural data, multiple sequence alignments, and mutant studies, providing novel insights into proline biosynthesis in organisms. We also discuss the transcriptional control of the proline biosynthetic genes in bacteria and plants.
Enhanced thermic effect of food, postprandial NEFA suppression and raised adiponectin in obese women who eat slowly
Authors: Reddy Narendra L. , Peng Chenjing , Carreira Marcos C. , Halder Louise , Hattersley John , Piya Milan K. , Tripathi Gyanendra , Randeva Harpal S. , Casanueva Felipe F. , McTernan Philip G. , Kumar Sudhesh , Barber Thomas M. 
Published: November 2014

SummaryObjectiveMeal duration may influence cardiometabolic health. The aim of this study was to explore postprandial effects of meal duration on human metabolism and appetite.DesignPostprandial comparisons following a standard meal eaten slowly over 40 min (‘D40’) and the same meal eaten quickly over 10 min (‘D10’) on a different day. Each participant therefore acted as their own control, thereby limiting confounding factors.PatientsObese premenopausal Caucasian women (n = 10) with confirmed normoglycaemia were recruited from an obesity clinic at UHCW, Coventry UK. Subjects underwent whole‐body calorimetry (8‐h) on two separate days.MeasurementsFollowing standard lunch (D40 vs D10), 4‐h postprandial analysis included thermic effect of food (TEF) and bloods taken at predefined times (including baseline fasting). Analytes included lipid profile, adiponectin, insulin, glucose, ghrelin, leptin, endotoxin, gut and pancreatic hormones. Appetite was measured using visual‐analogue scales and ad libitum food intake at subsequent meal. Paired sample t‐tests [including area under the curve (AUC)] were used to compare D40 and D10 trials.ResultsPostprandial TEF (over 240‐min) was significantly greater for D40 than D10 [mean (SEM): 80·9 kcal (3·8) vs 29·9 kcal (3·4); 10·6% vs 3·9%, respectively, P = 0·006; AUC 71·7 kcal.h vs 22·4 kcal.h, respectively, P = 0·02]. Postprandial plasma NEFA was significantly lower, and adiponectin levels were significantly higher for D40 than D10 [AUC (SEM): NEFA 627 μmol.h/l (56) vs 769 μmol.h/l (60), respectively, P = 0·02; adiponectin 33·4 μg.h/ml (3·9) vs 27·3 μg.h/ml (3·8), respectively, P = 0·04]. Other postprandial analytes and appetite measures were equivalent.ConclusionsIn obese women, eating slowly associates with enhanced TEF, elevated serum adiponectin and suppressed NEFA.