bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indoor-Biofilter Growth and Exposure to Airborne Chemicals Drive Similar Changes in Plant Root Bacterial Communities
Authors: Russell Jacob A. , Hu Yi , Chau Linh , Pauliushchyk Margarita , Anastopoulos Ioannis , Anandan Shivanthi , Waring Michael S. 
Published: May 2014

ABSTRACT

Due to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean indoor air of harmful volatile organic compounds (VOCs), which are typically found at concentrations higher indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide, but little is known about the root microbial communities of such artificially grown plants, how or whether they differ from those of plants grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigated how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through 16S rRNA amplicon sequencing, we compared root bacterial communities from soil-grown plants with those from two biowalls, while also comparing communities from roots exposed to clean versus VOC-laden air in a laboratory biofiltration system. The results showed differences in bacterial communities between soil-grown and biowall-grown plants and between bacterial communities from plant roots exposed to clean air and those from VOC-exposed plant roots. Both biowall-grown and VOC-exposed roots harbored enriched levels of bacteria from the genus
Hyphomicrobium
. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize that these bacteria are important VOC degraders. While different strains of
Hyphomicrobium
proliferated in the two studied biowalls and our lab experiment, strains were shared across plant species, suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters.
Biomineralization of Uranium by PhoY Phosphatase Activity Aids Cell Survival in Caulobacter crescentus
Authors: Yung Mimi C. , Jiao Yongqin 
Published: May 2014

ABSTRACT

Caulobacter crescentus
is known to tolerate high levels of uranium [U(VI)], but its detoxification mechanism is poorly understood. Here we show that
C. crescentus
is able to facilitate U(VI) biomineralization through the formation of U-P
i
precipitates via its native alkaline phosphatase activity. The U-P
i
precipitates, deposited on the cell surface in the form of meta-autunite structures, have a lower U/P
i
ratio than do chemically produced precipitates. The enzyme that is responsible for the phosphatase activity and thus the biomineralization process is identified as PhoY, a periplasmic alkaline phosphatase with broad substrate specificity. Furthermore, PhoY is shown to confer a survival advantage on
C. crescentus
toward U(VI) under both growth and nongrowth conditions. Results obtained in this study thus highlight U(VI) biomineralization as a resistance mechanism in microbes, which not only improves our understanding of bacterium-mineral interactions but also aids in defining potential ecological niches for metal-resistant bacteria.
Tagging Frogs with Passive Integrated Transponders Causes Disruption of the Cutaneous Bacterial Community and Proliferation of Opportunistic Fungi
Authors: Antwis Rachael E. , Garcia Gerardo , Fidgett Andrea L. , Preziosi Richard F. 
Published: May 2014

ABSTRACT

Symbiotic bacterial communities play a key role in protecting amphibians from infectious diseases including chytridiomycosis, caused by the pathogenic fungus
Batrachochytrium dendrobatidis
. Events that lead to the disruption of the bacterial community may have implications for the susceptibility of amphibians to such diseases. Amphibians are often marked both in the wild and in captivity for a variety of reasons, and although existing literature indicates that marking techniques have few negative effects, the response of cutaneous microbial communities has not yet been investigated. Here we determine the effects of passive integrated transponder (PIT) tagging on culturable cutaneous microbial communities of captive Morelet's tree frogs (
Agalychnis moreletii
) and assess the isolated bacterial strains for anti-
B. dendrobatidis
activity
in vitro
. We find that PIT tagging causes a major disruption to the bacterial community associated with the skin of frogs (∼12-fold increase in abundance), as well as a concurrent proliferation in resident fungi (up to ∼200-fold increase). Handling also caused a disruption the bacterial community, although to a lesser extent than PIT tagging. However, the effects of both tagging and handling were temporary, and after 2 weeks, the bacterial communities were similar to their original compositions. We also identify two bacterial strains that inhibit
B. dendrobatidis
, one of which increased in abundance on PIT-tagged frogs at 1 day postmarking, while the other was unaffected. These results show that PIT tagging has previously unobserved consequences for cutaneous microbial communities of frogs and may be particularly relevant for studies that intend to use PIT tagging to identify individuals involved in trials to develop probiotic treatments.
Insect Stage-Specific Receptor Adenylate Cyclases Are Localized to Distinct Subdomains of the Trypanosoma brucei Flagellar Membrane
Authors: Saada Edwin A. , Kabututu Z. Pius , Lopez Miguel , Shimogawa Michelle M. , Langousis Gerasimos , Oberholzer Michael , Riestra Angelica , Jonsson Zophonias O. , Wohlschlegel James A. , Hill Kent L. 
Published: May 2014

ABSTRACT

Increasing evidence indicates that the
Trypanosoma brucei
flagellum (synonymous with cilium) plays important roles in host-parasite interactions. Several studies have identified virulence factors and signaling proteins in the flagellar membrane of bloodstream-stage
T. brucei
, but less is known about flagellar membrane proteins in procyclic, insect-stage parasites. Here we report on the identification of several receptor-type flagellar adenylate cyclases (ACs) that are specifically upregulated in procyclic
T. brucei
parasites. Identification of insect stage-specific ACs is novel, as previously studied ACs were constitutively expressed or confined to bloodstream-stage parasites. We show that procyclic stage-specific ACs are glycosylated, surface-exposed proteins that dimerize and possess catalytic activity. We used gene-specific tags to examine the distribution of individual AC isoforms. All ACs examined localized to the flagellum. Notably, however, while some ACs were distributed along the length of the flagellum, others specifically localized to the flagellum tip. These are the first transmembrane domain proteins to be localized specifically at the flagellum tip in
T. brucei
, emphasizing that the flagellum membrane is organized into specific subdomains. Deletion analysis reveals that C-terminal sequences are critical for targeting ACs to the flagellum, and sequence comparisons suggest that differential subflagellar localization might be specified by isoform-specific C termini. Our combined results suggest insect stage-specific roles for a subset of flagellar adenylate cyclases and support a microdomain model for flagellar cyclic AMP (cAMP) signaling in
T. brucei
. In this model, cAMP production is compartmentalized through differential localization of individual ACs, thereby allowing diverse cellular responses to be controlled by a common signaling molecule.
Distinct Innate Immune Phagocyte Responses to Aspergillus fumigatus Conidia and Hyphae in Zebrafish Larvae
Authors: Knox Benjamin P. , Deng Qing , Rood Mary , Eickhoff Jens C. , Keller Nancy P. , Huttenlocher Anna 
Published: May 2014

ABSTRACT

Aspergillus fumigatus
is the most common filamentous fungal pathogen of immunocompromised hosts, resulting in invasive aspergillosis (IA) and high mortality rates. Innate immunity is known to be the predominant host defense against
A. fumigatus
; however, innate phagocyte responses to
A. fumigatus
in an intact host and their contributions to host survival remain unclear. Here, we describe a larval zebrafish
A. fumigatus
infection model amenable to real-time imaging of host-fungal interactions in live animals. Following infection with
A. fumigatus
, innate phagocyte populations exhibit clear preferences for different fungal morphologies: macrophages rapidly phagocytose conidia and form aggregates around hyphae, while the neutrophil response is dependent upon the presence of hyphae. Depletion of macrophages rendered host larvae susceptible to invasive disease. Moreover, a zebrafish model of human leukocyte adhesion deficiency with impaired neutrophil function also resulted in invasive disease and impaired host survival. In contrast, macrophage-deficient but not neutrophil-deficient larvae exhibited attenuated disease following challenge with a less virulent (Δ
laeA
) strain of
A. fumigatus
, which has defects in secondary metabolite production. Taking these results together, we have established a new vertebrate model for studying innate immune responses to
A. fumigatus
that reveals distinct roles for neutrophils and macrophages in mediating host defense against IA.
Intracellular β-Glucosidases CEL1a and CEL1b Are Essential for Cellulase Induction on Lactose in Trichoderma reesei
Authors: Xu Jintao , Zhao Guolei , Kou Yanbo , Zhang Weixin , Zhou Qingxin , Chen Guanjun , Liu Weifeng 
Published: May 2014

ABSTRACT

Lactose (1,4-
O
-β-
d
-galacto-pyranosyl-
d
-glucose) induces cellulolytic enzymes in
Trichoderma reesei
and is in fact one of the most important soluble carbon sources used to produce cellulases on an industrial level. The mechanism underlying the induction is, however, not fully understood. In this study, we investigated the cellular functions of the intracellular β-glucosidases CEL1a and CEL1b in the induction of cellulase genes by lactose in
T. reesei
. We demonstrated that while CEL1a and CEL1b were functionally equivalent in mediating the induction, the simultaneous absence of these intracellular β-glucosidases abolished
cbh1
gene expression on lactose.
d
-Galactose restored the efficient cellulase gene induction in the Δ
cel1a
strain independently of its reductive metabolism, but not in the Δ
cel1a
Δ
cel1b
strain. A further comparison of the transcriptional responses of the Δ
cel1a
Δ
cel1b
strain complemented with wild-type CEL1a or a catalytically inactive CEL1a version and the Δ
cel1a
strain constitutively expressing CEL1a or the
Kluyveromyces lactis
β-galactosidase LAC4 showed that both the CEL1a protein and its glycoside hydrolytic activity were indispensable for cellulase induction by lactose. We also present evidence that intracellular β-glucosidase-mediated lactose induction is further conveyed to XYR1 to ensure the efficiently induced expression of cellulase genes.
Heterochromatin Controls γH2A Localization in Neurospora crassa
Authors: Sasaki Takahiko , Lynch Kelsey L. , Mueller Caitlin V. , Friedman Steven , Freitag Michael , Lewis Zachary A. 
Published: May 2014

ABSTRACTIn response to genotoxic stress, ATR and ATM kinases phosphorylate H2A in fungi and H2AX in animals on a C-terminal serine. The resulting modified histone, called γH2A, recruits chromatin-binding proteins that stabilize stalled replication forks or promote DNA double-strand-break repair. To identify genomic loci that might be prone to replication fork stalling or DNA breakage inNeurospora crassa, we performed chromatin immunoprecipitation (ChIP) of γH2A followed by next-generation sequencing (ChIP-seq). γH2A-containing nucleosomes are enriched inNeurosporaheterochromatin domains. These domains are comprised of A·T-rich repetitive DNA sequences associated with histone H3 methylated at lysine-9 (H3K9me), the H3K9me-binding protein heterochromatin protein 1 (HP1), and DNA cytosine methylation. H3K9 methylation, catalyzed by DIM-5, is required for normal γH2A localization. In contrast, γH2A is not required for H3K9 methylation or DNA methylation. Normal γH2A localization also depends on HP1 and a histone deacetylase, HDA-1, but is independent of the DNA methyltransferase DIM-2. γH2A is globally induced indim-5mutants under normal growth conditions, suggesting that the DNA damage response is activated in these mutants in the absence of exogenous DNA damage. Together, these data suggest that heterochromatin formation is essential for normal DNA replication or repair.
TbKAP6, a Mitochondrial HMG Box-Containing Protein in Trypanosoma brucei, Is the First Trypanosomatid Kinetoplast-Associated Protein Essential for Kinetoplast DNA Replication and Maintenance
Authors: Wang Jianyang , Pappas-Brown Valeria , Englund Paul T. , Jensen Robert E. 
Published: May 2014

ABSTRACT

Kinetoplast DNA (kDNA), the mitochondrial genome of trypanosomatids, is a giant planar network of catenated minicircles and maxicircles.
In vivo
kDNA is organized as a highly condensed nucleoprotein disk. So far, in
Trypanosoma brucei
, proteins involved in the maintenance of the kDNA condensed structure remain poorly characterized. In
Crithidia fasciculata
, some small basic histone H1-like
k
inetoplast-
a
ssociated
p
roteins (CfKAP) have been shown to condense isolated kDNA networks
in vitro
. High-mobility group (HMG) box-containing proteins, such as mitochondrial transcription factor A (TFAM) in mammalian cells and Abf2 in the budding yeast, have been shown essential for the packaging of mitochondrial DNA (mtDNA) into mitochondrial nucleoids, remodeling of mitochondrial nucleoids, gene expression, and maintenance of mtDNA. Here, we report that TbKAP6, a mitochondrial HMG box-containing protein, is essential for parasite cell viability and involved in kDNA replication and maintenance. The RNA interference (RNAi) depletion of TbKAP6 stopped cell growth. Replication of both minicircles and maxicircles was inhibited. RNAi or overexpression of TbKAP6 resulted in the disorganization, shrinkage, and loss of kDNA. Minicircle release, the first step in kDNA replication, was inhibited immediately after induction of RNAi, but it quickly increased 3-fold upon overexpression of TbKAP6. Since the release of covalently closed minicircles is mediated by a type II topoisomerase (topo II), we examined the potential interactions between TbKAP6 and topo II. Recombinant TbKAP6 (rTbKAP6) promotes the topo II-mediated decatenation of kDNA. rTbKAP6 can condense isolated kDNA networks
in vitro
. These results indicate that TbKAP6 is involved in the replication and maintenance of kDNA.
An overview and methodological assessment of systematic reviews and meta-analyses of enhanced recovery programmes in colorectal surgery
Authors: Chambers Duncan , Paton Fiona , Wilson Paul , Eastwood Alison , Craig Dawn , Fox Dave , Jayne David , McGinnes Erika 
Published: May 2014

ObjectivesTo identify and critically assess the extent to which systematic reviews of enhanced recovery programmes for patients undergoing colorectal surgery differ in their methodology and reported estimates of effect.DesignReview of published systematic reviews. We searched the Cochrane Database of Systematic Reviews, the Database of Abstracts of Reviews of Effects (DARE) and Health Technology Assessment (HTA) Database from 1990 to March 2013. Systematic reviews of enhanced recovery programmes for patients undergoing colorectal surgery were eligible for inclusion.Primary and secondary outcome measuresThe primary outcome was length of hospital stay. We assessed changes in pooled estimates of treatment effect over time and how these might have been influenced by decisions taken by researchers as well as by the availability of new trials. The quality of systematic reviews was assessed using the Centre for Reviews and Dissemination (CRD) DARE critical appraisal process.Results10 systematic reviews were included. Systematic reviews of randomised controlled trials have consistently shown a reduction in length of hospital stay with enhanced recovery compared with traditional care. The estimated effect tended to increase from 2006 to 2010 as more trials were published but has not altered significantly in the most recent review, despite the inclusion of several unique trials. The best estimate appears to be an average reduction of around 2.5 days in primary postoperative length of stay. Differences between reviews reflected differences in interpretation of inclusion criteria, searching and analytical methods or software.ConclusionsSystematic reviews of enhanced recovery programmes show a high level of research waste, with multiple reviews covering identical or very similar groups of trials. Where multiple reviews exist on a topic, interpretation may require careful attention to apparently minor differences between reviews. Researchers can help readers by acknowledging existing reviews and through clear reporting of key decisions, especially on inclusion/exclusion and on statistical pooling.
Identifying hopelessness in population research: a validation study of two brief measures of hopelessness
Authors: Fraser Lindsay , Burnell Matthew , Salter Laura Currin , Fourkala Evangelia-Ourania , Kalsi Jatinderpal , Ryan Andy , Gessler Sue , Gidron Yori , Steptoe Andrew , Menon Usha 
Published: May 2014

ObjectiveHopelessness is an important construct in psychosocial epidemiology, but there is great pressure on the length of questionnaire measures in large-scale population and clinical studies. We examined the validity and test–retest reliability of two brief measures of hopelessness, an existing negatively worded two-item measure of hopelessness (Brief-H-Neg) and a positively worded version of the same instrument (Brief-H-Pos).DesignCohort study.SettingControl arm of the UK Collaborative Trial of Ovarian Cancer Screening.ParticipantsA non-clinical research-based sample of 5000 postmenopausal women selected from 56 512 participants.Primary and secondary outcome measuresSpearman's rank correlation of brief measures of hopelessness with the Beck Hopelessness Scale (BHS). Spearman's rank correlation with the Centre for Epidemiological Studies Depression Scale (CES-D) and change in mean score on repeat testing.MethodsTwo short hopelessness measures, a negatively worded brief measure of hopelessness (Brief-H-Neg) and a positively worded brief measure of hopelessness (Brief-H-Pos), were administered by postal questionnaire to 5000 women together with the 20-item BHS and 20-item CES-D. The Brief-H-Neg and Brief-H-Pos were readministered to 500 women after a 2-week interval.Results2413 postmenopausal women (mean age 68.9 years) completed the questionnaire. The Brief-H-Neg and Brief-H-Pos correlated 0.93 and 0.87 with the BHS after correction for attenuation and their association with the CES-D mirrored that seen with the BHS (Spearman's rank correlation 0.88 and 0.68, respectively). There was no change in mean scores on the two measures with repeat testing in the 433 women who completed them and test–retest reliability was good (intraclass correlations Brief-H-Neg 0.67 and Brief-H-Pos 0.72).ConclusionsThese findings provide support for the validity of the Brief-H-Neg and Brief-H-Pos. These brief measures are likely to be useful in large population studies assessing hopelessness.Trial registration numberNCT00058032.
Improving skills and care standards in the support workforce for older people: a realist review
Authors: Rycroft-Malone Jo , Burton Christopher , Hall Beth , McCormack Brendan , Nutley Sandra , Seddon Diane , Williams Lynne 
Published: May 2014

IntroductionIn the context of a population that is growing older, and a number of high-profile scandals about care standards in hospital and community settings, having a skilled and knowledgeable workforce caring for older people is an ethical and policy imperative. Support workers make up the majority of the workforce in health and social care services for older people (aged 65 years and over), and yet little is known about the best way to facilitate their development. Given this gap, this review will draw on evidence to address the question: how can workforce development interventions improve the skills and the care standards of support workers within older people's health and social care services?Methods and analysisAs we are interested in how and why workforce development interventions might work, in what circumstances and with whom, we will conduct a realist review, sourcing evidence from health, social care, policing and education. The review will be conducted in four steps over 18 months to (1) construct a theoretical framework, that is, the review’s programme theories; (2) retrieve, review and synthesise evidence relating to interventions designed to develop the support workforce guided by the programme theories; (3) ‘test out’ our synthesis findings and refine the programme theories, establish their practical relevance/potential for implementation and (4) formulate recommendations about improvements to current workforce development interventions to contribute to the improvement of care standards in older people's health and social care services, potentially transferrable to other services.Ethics and disseminationEthical approval is not required to undertake this review. Knowledge exchange activities through stakeholder engagement and online postings are embedded throughout the lifetime of the project. The main output from this review will be a new theory driven framework for skill development for the support workforce in health and social care for older people.Trial registration numberCRD42013006283.
Cyclostratigraphy: data filtering as a source of spurious spectral peaks
Authors: Vaughan Simon , Bailey Robin J. , Smith David G. 
Published: May 2014

Abstract

Searches for periodic signals (candidate Milankovitch cycles) in stratigraphic data often make use of methods of spectral analysis, some of which have come to be regarded as standard and therefore reliable. In this paper we highlight a problem with the application of filtering, or smoothing, to the data
prior
to spectral analysis. Such preprocessing is frequently used to amplify the signal-to-noise ratio at the expected wavelength. Using synthetic random data, we demonstrate how filtering generates artificial spectral peaks close to the characteristic wavelength of the filter. When applying the same preprocessing methods to actual stratigraphic data, we find that it is possible to replicate some recently published results claiming to show cyclicity. We recommend that filtering and other preprocessing techniques be used with great care: spectral peaks occurring close to the characteristic scale of the applied filter are likely to be artefacts of preprocessing.