bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversification of endosymbiosis: replacements, co-speciation and promiscuity of bacteriocyte symbionts in weevils
Authors: Toju Hirokazu , Tanabe Akifumi S , Notsu Yutaka , Sota Teiji , Fukatsu Takema 
Published: February 2013

Abstract
The processes and mechanisms underlying the diversification of host–microbe endosymbiotic associations are of evolutionary interest. Here we investigated the bacteriocyte-associated primary symbionts of weevils wherein the ancient symbiont Nardonella has experienced two independent replacement events: once by Curculioniphilus symbiont in the lineage of Curculio and allied weevils of the tribe Curculionini, and once by Sodalis-allied symbiont in the lineage of grain weevils of the genus Sitophilus. The Curculioniphilus symbiont was detected from 27 of 36 Curculionini species examined, the symbiont phylogeny was congruent with the host weevil phylogeny, and the symbiont gene sequences exhibited AT-biased nucleotide compositions and accelerated molecular evolution. These results suggest that the Curculioniphilus symbiont was acquired by an ancestor of the tribe Curculionini, replaced the original symbiont Nardonella, and has co-speciated with the host weevils over evolutionary time, but has been occasionally lost in several host lineages. By contrast, the Sodalis-allied symbiont of Sitophilus weevils exhibited no host–symbiont co-speciation, no AT-biased nucleotide compositions and only moderately accelerated molecular evolution. These results suggest that the Sodalis-allied symbiont was certainly acquired by an ancestor of the Sitophilus weevils and replaced the original Nardonella symbiont, but the symbiotic association must have experienced occasional re-associations such as new acquisitions, horizontal transfers, replacements and/or losses. We detected Sodalis-allied facultative symbionts in populations of the Curculionini weevils, which might represent potential evolutionary sources of the Sodalis-allied primary symbionts. Comparison of these newcomer bacteriocyte-associated symbiont lineages highlights potential evolutionary trajectories and consequences of novel symbionts after independent replacements of the same ancient symbiont.
The biogeography of fungal communities in wetland sediments along the Changjiang River and other sites in China
Authors: Wu Bing , Tian Jianqing , Bai Chunming , Xiang Meichun , Sun Jingzu , Liu Xingzhong 
Published: February 2013

Abstract
Whether fungal community structure depends more on historical factors or on contemporary factors is controversial. This study used culture-dependent and -independent (polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)) methods to assess the influence of historical and contemporary factors on the distributions of fungi in the wetland sediments at 10 locations along the Changjiang River and at 10 other locations in China. The culture-dependent approach detected greater species diversity (177 operational taxonomic units (OTUs)) than PCR-DGGE analysis (145 OTUs), and the species in the genera of Penicillium (relative frequency=16.8%), Fusarium (15.4%), Aspergillus (7.6%), Trichoderma (5.8%) and Talaromyces (4.2%) were dominant. On the basis of DGGE data, fungal diversity along the Changjiang River increased from upstream to downstream; altitude explained 44.8% of this variation in diversity. And based on the data from all 20 locations, the fungal communities were geographically clustered into three groups: Southern China, Northern China and the Qinghai-Tibetan Plateau. Multivariate regression tree analysis for data from the 20 locations indicated that the fungal community was influenced primarily by location (which explained 61.8% of the variation at a large scale), followed by total potassium (9.4%) and total nitrogen (3.5%) at a local scale. These results are consistent with the concept that geographic distance is the dominant factor driving variation in fungal diversity at a regional scale (1000–4000 km), whereas environmental factors (total potassium and total nitrogen) explain variation in fungal diversity at a local scale (&lt;1000 km).
Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes
Authors: Wang Jianjun , Shen Ji , Wu Yucheng , Tu Chen , Soininen Janne , Stegen James C , He Jizheng , Liu Xingqi , Zhang Lu , Zhang Enlou 
Published: February 2013

Abstract
Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.
RegulatING chromatin regulators: post-translational modification of the ING family of epigenetic regulators
Authors: Satpathy Shankha , Nabbi Arash , Riabowol Karl 
Published: February 2013

The five human ING genes encode at least 15 splicing isoforms, most of which affect cell growth, differentiation and apoptosis through their ability to alter gene expression by epigenetic mechanisms. Since their discovery in 1996, ING proteins have been classified as type II tumour suppressors on the basis of reports describing their down-regulation and mislocalization in a variety of cancer types. In addition to their regulation by transcriptional mechanisms, understanding the range of PTMs (post-translational modifications) of INGs is important in understanding how ING functions are fine-tuned in the physiological setting and how they add to the repertoire of activities affected by the INGs. In the present paper we review the different PTMs that have been reported to occur on INGs. We discuss the PTMs that modulate ING function under normal conditions and in response to a variety of stresses. We also describe the ING PTMs that have been identified by several unbiased MS-based PTM enrichment techniques and subsequent proteomic analysis. Among the ING PTMs identified to date, a subset has been characterized for their biological significance and have been shown to affect processes including subcellular localization, interaction with enzymatic complexes and ING protein half-life. The present review aims to highlight the emerging role of PTMs in regulating ING function and to suggest additional pathways and functions where PTMs may effect ING function.
Effectively addressing complex proteomic search spaces with peptide spectrum matching
Authors: Borges Diogo , Perez-Riverol Yasset , Nogueira Fabio C. S. , Domont Gilberto B. , Noda Jesus , da Veiga Leprevost Felipe , Besada Vladimir , França Felipe M. G. , Barbosa Valmir C. , Sánchez Aniel , Carvalho Paulo C. 
Published: February 2013

Abstract
Summary: Protein identification by mass spectrometry is commonly accomplished using a peptide sequence matching search algorithm, whose sensitivity varies inversely with the size of the sequence database and the number of post-translational modifications considered. We present the Spectrum Identification Machine, a peptide sequence matching tool that capitalizes on the high-intensity b1-fragment ion of tandem mass spectra of peptides coupled in solution with phenylisotiocyanate to confidently sequence the first amino acid and ultimately reduce the search space. We demonstrate that in complex search spaces, a gain of some 120% in sensitivity can be achieved.
Availability: All data generated and the software are freely available for academic use at http://proteomics.fiocruz.br/software/sim.
Contact: paulo@pcarvalho.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Hypoxia-inducible Factor and Target Gene Expression Are Decreased in Patients with Sepsis
Authors: Schäfer Simon T. , Frede Stilla , Winning Sandra , Bick Alexandra , Roshangar Paktis , Fandrey Joachim , Peters Jürgen , Adamzik Michael 
Published: February 2013

Abstract

Background:
Hypoxia-inducible factor-1 (HIF-1) is a molecular key player in response to hypoxemic/inflammatory conditions prevailing in sepsis. In a prospective observational study, we tested the hypotheses that sepsis affects HIF-1α messenger ribonucleic acid (mRNA) expression (primary hypothesis) and also (secondary hypotheses) the expression of the HIF-1α target genes adrenomedullin and β2-integrins. Furthermore, we tested that lipopolysaccharide administration increases HIF-1α mRNA and protein in naive and endotoxin-tolerant monocytes.

Methods:
In 99 patients with sepsis and 48 healthy volunteers, leukocyte HIF-1α mRNA expression (real-time polymerase chain reaction), cytokine concentrations (enzymelinked immunosorbent assay), and intracellular distribution of HIF-1α protein (immunofluorescence staining) were assessed. In vitro, HIF-1α mRNA expression and protein were measured in naive or endotoxin-tolerant (48h; 0.05ng/ml lipopolysaccharide) monocytes, with/without additional lipopolysaccharide (6h; 1 μg/ml).

Results:
In comparison to healthy volunteers, HIF-1α mRNA expression (−67%; P = 0.0001) and HIF-1α protein positive cells (−66.7%; P = 0.01) were decreased in sepsis. mRNA expression of adrenomedullin (−75%), CD11a (−85%), and CD11b (−86%; all P = 0.0001) was also decreased. In contrast, interleukin 6 (P = 0.0001), interleukin 10 (P = 0.0001), and tumor necrosis factor-α (P = 0.0002) concentrations were increased. Of note, HIF-1α mRNA expression was inversely associated with illness severity (Simplified Acute Physiology Score II; r = −0.29; P = 0.0001). In vitro, acute lipopolysaccharide administration of naive monocytic cells increased HIF-1α mRNA expression, whereas HIF-1α mRNA and protein (−60%; P = 0.001) were decreased in endotoxin-tolerant cells, which still up regulated cytokines.

Conclusions:
In sepsis, HIF-1α mRNA expression was suppressed and inversely associated with illness severity. While acute lipopolysaccharide administration increased HIF-1α mRNA expression, prolonged stimulation suppressed HIF-1α expression. The clinical implications of decreased HIF-1α may include maladaption to tissue hypoxia or depressed immune function.
Effect of roller burnishing on pure aluminum alloyed by copper
Authors: Al‐Qawabeha Ubeidulla F. , Al‐Qawabah Safwan M. 
Published: February 2013

PurposeThe purpose of this paper is to review, analyze and present the effects of the roller burnishing process on pure aluminum alloyed by pure copper at 3%, 6% and 9% percentages. Roller burnishing is one of the effective finishing treatment methods in terms of stabilization of surface layers properties along the depth, Roller burnishing is one of the effective methods used to improve the surface layer properties such as microhardness and average surface roughness.Design/methodology/approachThree different Al‐Cu alloys of 3%, 6% and 9% copper additions were prepared and microstructure, micro hardness and mechanical properties investigated. Then the roller burnishing mechanism was applied on Al‐Cu alloys on cylindrical work pieces, different conditions were used, and the results were obtained and discussed.FindingsThe best enhancement in hardness was 46.4% which was achieved at 9% Cu addition, whereas the best enhancement in the flow stress was 101.8% which was achieved at 9% Cu addition. Applying burnishing force 100 and 150 N resulted in an enhancement in the micro hardness of 80% and 102.8%, respectively, in the Al‐Cu% alloy, where the maximum enhancement on the surface roughness was 61% that resulted in pure Al when applying 150 N burnishing forces. Finally it was found that pure aluminum has the highest wear resistance.Originality/valueThis is new work on Al‐Cu alloys, thus the results after implementation of roller burnishing process are of great value and add an extra enhancement in the surface quality.
Careers of skilled migrants
Authors: Al Ariss Akram , Koall Iris , Özbilgin Mustafa , Suutari Vesa 
Published: February 2013

PurposeThe purpose of this editorial is to present an overview of the papers in this special issue.Design/methodology/approachThe paper draws on papers in this special issue.FindingsThere is a multi‐disciplinarily approach of the papers in this issue in connecting fields of management, sociology, migration, and psychology, among others, in the area of international mobility.Originality/valueThe guest editors continue their commitment, in this special issue, to expanding the field of study of migration and the careers of migrants from theoretical and methodological perspectives.
The effect of environmental concern and scepticism on green purchase behaviour
Authors: Albayrak Tahir , Aksoy Şafak , Caber Meltem 
Published: February 2013

PurposeThe aims of the study are: to compare the environmental concern and scepticism levels of the participants and whether or not they display green purchase behaviour; to investigate the influence of environmental concern and scepticism on green purchase behaviour by utilizing the Theory of Planned Behaviour.Design/methodology/approachThe data were collected from participant and non‐participant customers of the e‐invoicing program of Turk Telecom. Customers were clustered into four groups according to their environmental concerns and scepticism levels.FindingsResearch results show that those customers who have a high level of environmental concern and less sceptical reflect a positive attitude, have a high positive subjective norm and perceived behavioural control that motivates them to have stronger intentions to become e‐invoice subscribers in the near future.Originality/valueThe results found in the paper provide clear evidence supporting the Theory of Planned Behaviour in Turkey. Moreover, while most previous studies have employed undergraduate samples which are not representative of common customers, the present study employed a large and real customer sample which strongly represents customers in general.
Radiation Therapy Resources and Guideline‐Concordant Radiotherapy for Early‐Stage Breast Cancer Patients in an Underserved Region
Authors: Yao Nengliang , Matthews Stephen A. , Hillemeier Marianne M. , Anderson Roger T. 
Published: February 2013

ObjectiveTo examine the relationship between radiation therapy resources and guideline‐concordant radiotherapy after breast‐conserving surgery (BCS) in Kentucky.Data SourcesThe SEER registry and Area Resource File provided county‐level data describing cancer care resources and socioeconomic conditions of Kentucky residents.Study DesignThe outcome variable was rate of BCS without radiotherapy in each county for 2000–2007. Eight‐year weighted average rates of radiation therapy providers and hospitals per 100,000 residents were explanatory variables of interest. Exploratory spatial data analyses and spatial econometric models were estimated.Principal FindingsAppalachian counties in Kentucky had significantly fewer radiation oncologists, hospitals with radiation therapy facilities, and surgeons per 100,000 residents than non‐Appalachian counties. The likelihood of BCS without radiation was significantly higher among Appalachian compared to non‐Appalachian women (42.5 percent vs. 29.0 percent, p < .001). Higher proportions of women not receiving recommended radiotherapy after BCS were clustered in Eastern Kentucky around Lexington. This geographic disparity was partially explained by significantly fewer radiation therapy facilities in Appalachian Kentucky in adjusted analyses.ConclusionsScarce radiation therapy resources in Appalachian Kentucky are associated with disparities in receipt of guideline‐concordant radiotherapy, suggesting that policy action is needed to improve the cancer treatment infrastructure in disadvantaged mountainous areas.
Tight coupling of polymerization and depolymerization of polyhydroxyalkanoates ensures efficient management of carbon resources in Pseudomonas putida
Authors: Arias Sagrario , Bassas‐Galia Monica , Molinari Gabriella , Timmis Kenneth N. 
Published: February 2013

SummaryEnvironmental microbes oscillate between feast and famine and need to carefully manage utilization, storage and conversion of reserve products to exploitable sources of carbon and energy. Polyhydroxyalkanoates (PHAs) are storage polymers that serve bacteria as sources of food materials under physiological conditions of carbon demand. In order to obtain insights into the role of PHA depolymerase (PhaZ) and its relationship to a PHA polymerase (PhaC2) in the carbon management activity of Pseudomonas putida strain U, we created a polymerase hyperexpression strain and a depolymerase knockout mutant of this strain, and examined their synthesis of PHA and expression of their PHA genes. This study revealed that hyperexpression of PhaC2 led to the accumulation of higher amounts of PHA (44%wt) than in the wild‐type strain (24%wt) after 24 h of cultivation, which then returned to wild‐type levels by 48 h, as a result of elevated depolymerization. The phaZ mutant, however, accumulated higher levels of PHA than the parental strain (62%wt), which were maintained for at least 96 h. Transcriptional analysis of the pha cluster by RT‐PCR revealed that PHA operon proteins, including depolymerase, are expressed from the beginning of the growth phase. Hyperexpression of the PhaC2 polymerase was accompanied by an increase in the expression of the PhaZ depolymerase and a decrease in expression of another PHA polymerase, PhaC1. This suggests tight regulatory coupling of PHA polymerase and depolymerase activities that act in synergy, and in concert with other PHA proteins, to provide dynamic PHA granule synthesis and remodelling that rapidly and sensitively respond to changes in availability of carbon and the physiological‐metabolic needs of the cell, to ensure optimal carbon resource management.
Thorn‐dwelling ants provide antiherbivore defence for camelthorn trees, Vachellia erioloba, in Namibia
Authors: Campbell Heather , Townsend Ian R. , Fellowes Mark D. E. , Cook James M. 
Published: February 2013

AbstractAnts are widely employed by plants as an antiherbivore defence. A single host plant can associate with multiple, symbiotic ant species, although usually only a single ant species at a time. Different plant‐ant species may vary in the degree to which they defend their host plant. In Kenya, ant–acacia interactions are well studied, but less is known about systems elsewhere in Africa. A southern African species, Vachellia erioloba, is occupied by thorn‐dwelling ants from three different genera. Unusually, multiple colonies of all these ants simultaneously and stably inhabit trees. We investigated if the ants on V. erioloba (i) deter insect herbivores; (ii) differ in their effectiveness depending on the identity of the herbivore; and (iii) protect the tree against an important herbivore, the larvae of the lepidopteran Gonometa postica. We show that experimental exclusion of ants leads to greater levels of herbivory on trees. The ants inhabiting V. erioloba are an effective deterrent against hemipteran and coleopteran, but not lepidopteran herbivores. Defensive services do not vary among ant species, but only Crematogaster ants exhibit aggression towards G. postica. This highlights the potential of the V. erioloba–ant mutualism for studying ant–plant interactions that involve multiple, simultaneously resident thorn‐dwelling ant species.
Relationship between diabetic retinopathy, diabetic macular oedema and erectile dysfunction in type 2 diabetics
Authors: Chew Sky KH , Taouk Yamna , Xie Jing , Nicolaou Theona E , Wang Jie Jin , Wong Tien Y , Lamoureux Ecosse L 
Published: February 2013

AbstractBackgroundTo investigate the relationship of diabetic retinopathy and diabetic macular oedema with erectile dysfunction in patients with type 2 diabetes.DesignHospital‐based, cross‐sectional study.ParticipantsThree hundred twenty‐four men with diabetes from the Diabetic Management Project were recruited.MethodsParticipants underwent a comprehensive interview, a complete eye examination, fasting blood tests, and had retinal and macula assessments using fundus images and optical coherence tomography, respectively. Diabetic retinopathy was categorized as none, mild, moderate, severe non‐proliferative and proliferative, and diabetic macular oedema as none, mild, moderate and severe. Erectile dysfunction was defined as problems achieving or maintaining an erection and was assessed using a self‐reported questionnaire.Main Outcome MeasuresErectile dysfunction.ResultsThe mean ± standard deviation age of 324 men with type 2 diabetes was 65.2 ± 11.1 years. Compared with patients without diabetic retinopathy, those with any retinopathy (odds ratio 2.06, 95% confidence interval 1.22–3.48, P = 0.007) had a twofold increased odds of having erectile dysfunction. Patients with severe non‐proliferative diabetic retinopathy (odds ratio 4.39, 95% confidence interval 1.48–13.0, P = 0.008) and proliferative diabetic retinopathy (odds ratio 2.74, 95% confidence interval 1.44–5.19, P = 0.002) had fourfold and threefold increased odds of having erectile dysfunction, respectively, compared with those without diabetic retinopathy. Diabetic macular oedema, irrespective of presence or severity, was not independently associated with erectile dysfunction.ConclusionThe presence and severity of diabetic retinopathy but not diabetic macular oedema are independently associated with self‐reported erectile dysfunction.