bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Chitinolytic Communities Respond to Chitin and pH Alteration in Soil
Authors: Kielak Anna M. , Cretoiu Mariana Silvia , Semenov Alexander V. , Sørensen Søren J. , van Elsas Jan Dirk 
Published: October 2012

ABSTRACT

Chitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA and
chiA
genes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity of
chiA
gene types in soil is enormous and (i) that different
chiA
gene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one of
Actinobacteria
in the immediate response to the added chitin (based on 16S rRNA gene abundance and
chiA
gene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes.
Fluorometric Quantification of Polyphosphate in Environmental Plankton Samples: Extraction Protocols, Matrix Effects, and Nucleic Acid Interference
Authors: Martin Patrick , Van Mooy Benjamin A. S. 
Published: October 2012

ABSTRACT
Polyphosphate (polyP) is a ubiquitous biochemical with many cellular functions and comprises an important environmental phosphorus pool. However, methodological challenges have hampered routine quantification of polyP in environmental samples. We tested 15 protocols to extract inorganic polyphosphate from natural marine samples and cultured cyanobacteria for fluorometric quantification with 4′,6-diamidino-2-phenylindole (DAPI) without prior purification. A combination of brief boiling and digestion with proteinase K was superior to all other protocols, including other enzymatic digestions and neutral or alkaline leaches. However, three successive extractions were required to extract all polyP. Standard addition revealed matrix effects that differed between sample types, causing polyP to be over- or underestimated by up to 50% in the samples tested here. Although previous studies judged that the presence of DNA would not complicate fluorometric quantification of polyP with DAPI, we show that RNA can cause significant interference at the wavelengths used to measure polyP. Importantly, treating samples with DNase and RNase before proteinase K digestion reduced fluorescence by up to 57%. We measured particulate polyP along a North Pacific coastal-to-open ocean transect and show that particulate polyP concentrations increased toward the open ocean. While our final method is optimized for marine particulate matter, different environmental sample types may need to be assessed for matrix effects, extraction efficiency, and nucleic acid interference.
Carboxyethylarginine Synthase Genes Show Complex Cross-Regulation in Streptomyces clavuligerus
Authors: Kwong Thomas , Tahlan Kapil , Anders Cecilia L. , Jensen Susan E. 
Published: October 2012

ABSTRACT

Carboxyethylarginine synthase is the first dedicated enzyme of clavam biosynthesis in
Streptomyces clavuligerus
and is present in two isoforms encoded by two separate genes. When grown on a liquid soy medium, strains with
ceaS1
deleted showed only a mild reduction of clavam biosynthesis, while disruption of
ceaS2
abolished all clavam biosynthesis. Creation of an in-frame
ceaS2
deletion mutant to avoid polarity did not restore clavam production, nor did creation of a site-directed mutant altered only in a single amino acid residue important for activity. Reverse transcriptase PCR analyses of these mutants indicated that the failure to produce clavam metabolites could be traced to reduced or abolished transcription of
ceaS1
in the
ceaS2
mutants, despite the location of
ceaS1
on a replicon completely separate from that of
ceaS2
. Western analyses further showed that the CeaS1 protein (as well as the CeaS2 protein) was absent from the
ceaS2
mutants. Complementation experiments were able to restore clavam production partially, but only by virtue of restoring CeaS2 production. CeaS1 was still absent from the complemented strains. While this dependence of CeaS1 production on the expression of
ceaS2
from its native chromosomal location was seen in all of the
ceaS2
mutants, the effect was limited to growth in liquid medium. When the same mutants were grown on solid soy medium, clavam production was restored and CeaS1 was produced, albeit at low levels compared to the wild type.
Invertase SUC2 Is the Key Hydrolase for Inulin Degradation in Saccharomyces cerevisiae
Authors: Wang Shi-An , Li Fu-Li 
Published: October 2012

ABSTRACT

Specific
Saccharomyces cerevisiae
strains were recently found to be capable of efficiently utilizing inulin, but genetic mechanisms of inulin hydrolysis in yeast remain unknown. Here we report functional characteristics of invertase SUC2 from strain JZ1C and demonstrate that SUC2 is the key enzyme responsible for inulin metabolism in
S. cerevisiae
.
Trypanosoma brucei FKBP12 Differentially Controls Motility and Cytokinesis in Procyclic and Bloodstream Forms
Authors: Brasseur Anaïs , Rotureau Brice , Vermeersch Marjorie , Blisnick Thierry , Salmon Didier , Bastin Philippe , Pays Etienne , Vanhamme Luc , Pérez-Morga David 
Published: October 2012

ABSTRACTFKBP12 proteins are able to inhibit TOR kinases or calcineurin phosphatases upon binding of rapamycin or FK506 drugs, respectively. TheTrypanosoma bruceiFKBP12 homologue (TbFKBP12) was found to be a cytoskeleton-associated protein with specific localization in the flagellar pocket area of the bloodstream form. In the insect procyclic form, RNA interference-mediated knockdown ofTbFKBP12affected motility. In bloodstream cells, depletion of TbFKBP12 affected cytokinesis and cytoskeleton architecture. These last effects were associated with the presence of internal translucent cavities limited by an inside-out configuration of the normal cell surface, with a luminal variant surface glycoprotein coat lined up by microtubules. These cavities, which recreated the streamlined shape of the normal trypanosome cytoskeleton, might represent unsuccessful attempts for cell abscission. We propose that TbFKBP12 differentially affects stage-specific processes through association with the cytoskeleton.
Evidence that Two Pcl-Like Cyclins Control Cdk9 Activity during Cell Differentiation in Aspergillus nidulans Asexual Development
Authors: Kempf Claudia , Bathe Friederike , Fischer Reinhard 
Published: October 2012

ABSTRACT

Cyclin-dependent protein kinases (CDKs) are usually involved in cell cycle regulation. However, Cdk9 is an exception and promotes RNA synthesis through phosphorylation of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAPII). The CTD is comprised of repeating heptapeptides, in which serine residues at positions 2, 5, and 7 are of crucial importance. Ser5 phosphorylation causes transcription initiation and promoter escape. However, RNAPII pauses 20 to 50 bp downstream from the transcription start site, until Cdk9 phosphorylates Ser2. This event relieves the checkpoint and promotes the processivity of elongation. Here we present evidence that in the filamentous fungus
Aspergillus nidulans
, a Cdk9 homologue, PtkA, serves specific functions in conidiophore development. It was previously shown that PtkA interacts with two cyclins, PclA and the T cyclin PchA. Using yeast two-hybrid screens, we identified a third cyclin, PclB, and a kinase, PipA
Bud32
. Both proteins were expressed in hyphae and in conidiophores, but interaction between each protein and PtkA was restricted to the conidiophores. Deletion of
pchA
caused a severe growth defect, and deletion of
pipA
was lethal, suggesting basic functions in PtkA-dependent gene transcription. In contrast, deletion of
pclB
in combination with deletion of
pclA
essentially caused a block in spore formation. We present evidence that the phosphorylation status of the CTD of RNA polymerase II in the conidiophore changes upon deletion of
pclA
or
pclB
. Our results suggest that tissue-specific modulation of Cdk9 activity by PclA and PclB is required for proper differentiation.
Characterization of a Novel Class I Transcription Factor A (CITFA) Subunit That Is Indispensable for Transcription by the Multifunctional RNA Polymerase I of Trypanosoma brucei
Authors: Nguyen Tu N. , Nguyen Bao N. , Lee Ju Huck , Panigrahi Aswini K. , Günzl Arthur 
Published: October 2012

ABSTRACT

Trypanosoma brucei
is the only organism known to have evolved a multifunctional RNA polymerase I (pol I) system that is used to express the parasite's ribosomal RNAs, as well as its major cell surface antigens, namely, the variant surface glycoprotein (VSG) and procyclin, which are vital for establishing successful infections in the mammalian host and the tsetse vector, respectively. Thus far, biochemical analyses of the
T. brucei
RNA pol I transcription machinery have elucidated the subunit structure of the enzyme and identified the class I transcription factor A (CITFA). CITFA binds to RNA pol I promoters, and its CITFA-2 subunit was shown to be absolutely essential for RNA pol I transcription in the parasite. Tandem affinity purification (TAP) of CITFA revealed the subunits CITFA-1 to -6, which are conserved only among kinetoplastid organisms, plus the dynein light chain DYNLL1. Here, by tagging CITFA-6 instead of CITFA-2, a complex was purified that contained all known CITFA subunits, as well as a novel proline-rich protein. Functional studies carried out
in vivo
and
in vitro
, as well as a colocalization study, unequivocally demonstrated that this protein is a bona fide CITFA subunit, essential for parasite viability and indispensable for RNA pol I transcription of ribosomal gene units and the active
VSG
expression site in the mammalian-infective life cycle stage of the parasite. Interestingly, CITFA-7 function appears to be species specific, because expression of an RNA interference (RNAi)-resistant
CITFA-7
transgene from
Trypanosoma cruzi
could not rescue the lethal phenotype of silencing endogenous
CITFA-7
.
Anaerobic Respiration Using a Complete Oxidative TCA Cycle Drives Multicellular Swarming in Proteus mirabilis
Authors: Alteri Christopher J. , Himpsl Stephanie D. , Engstrom Michael D. , Mobley Harry L. T. 
Published: October 2012

ABSTRACT

Proteus mirabilis
rapidly migrates across surfaces using a periodic developmental process of differentiation alternating between short swimmer cells and elongated hyperflagellated swarmer cells. To undergo this vigorous flagellum-mediated motility, bacteria must generate a substantial proton gradient across their cytoplasmic membranes by using available energy pathways. We sought to identify the link between energy pathways and swarming differentiation by examining the behavior of defined central metabolism mutants. Mutations in the tricarboxylic acid (TCA) cycle (
fumC
and
sdhB
mutants) caused altered patterns of swarming periodicity, suggesting an aerobic pathway. Surprisingly, the wild-type strain swarmed on agar containing sodium azide, which poisons aerobic respiration; the
fumC
TCA cycle mutant, however, was unable to swarm on azide. To identify other contributing energy pathways, we screened transposon mutants for loss of swarming on sodium azide and found insertions in the following genes that involved fumarate metabolism or respiration:
hybB
, encoding hydrogenase;
fumC
, encoding fumarase;
argH
, encoding argininosuccinate lyase (generates fumarate); and a quinone hydroxylase gene. These findings validated the screen and suggested involvement of anaerobic electron transport chain components. Abnormal swarming periodicity of
fumC
and
sdhB
mutants was associated with the excretion of reduced acidic fermentation end products. Bacteria lacking SdhB were rescued to wild-type pH and periodicity by providing fumarate, independent of carbon source but dependent on oxygen, while
fumC
mutants were rescued by glycerol, independent of fumarate only under anaerobic conditions. These findings link multicellular swarming patterns with fumarate metabolism and membrane electron transport using a previously unappreciated configuration of both aerobic and anaerobic respiratory chain components.

IMPORTANCE
Bacterial locomotion and the existence of microbes were the first scientific observations that followed the invention of the microscope. A bacterium can swim through a fluid environment or coordinate motion with a group of bacteria and swarm across a surface. The flagellar motor, which propels the bacterium, is fueled by proton motive force. In contrast to the physiology that governs swimming motility, much less is known about the energy sources required for multicellular swarming on surfaces. In this study, we used
Proteus mirabilis
as a model organism to study vigorous swarming behavior and genetic and biochemical approaches to define energy pathways and central metabolism that contribute to multicellular motility. We found that swarming bacteria use a complete aerobic tricarboxylic acid (TCA) cycle but do not respire oxygen as the terminal electron acceptor, suggesting that multicellular cooperation during swarming reduces the amount of energy required by individual bacteria to achieve rapid motility.
Effects of Nitric Oxide Synthase Inhibition on Cutaneous Vasodilation in Response to Acupuncture Stimulation in Humans
Authors: Kimura Kenichi , Takeuchi Hayato , Yuri Kuniko , Wakayama Ikuro 
Published: October 2012

Objectives The aim of the present study was to elucidate the mechanism of cutaneous vasodilation following acupuncture stimulation by investigating the roles of nitric oxide (NO) and axon reflex vasodilation. Methods The subjects were 17 healthy male volunteers. The role of NO was investigated by administering NG-nitro-L-arginine methyl ester hydrochloride (L-NAME, 20 mM), an NO synthase inhibitor or Ringer's solution (control site), via intradermal microdialysis (protocol 1; n=7). The role of axon reflex vasodilation by local sensory neurones was investigated by comparing vasodilation at sites treated with ‘eutectic mixture of local anaesthetics’ (EMLA) cream (2.5% lidocaine and 2.5% prilocaine) with untreated sites (control site) (protocol 2; n=10). After 5 min of baseline recording, acupuncture was applied to PC4 and a control site in proximity to PC4 for 10 min and scanning was performed for 60 min after acupuncture stimulation. Skin blood flow (SkBF) was evaluated by laser Doppler perfusion imaging. Cutaneous vascular conductance (CVC) was calculated from the ratio of SkBF to mean arterial blood pressure. Results In the first protocol, sites administered L-NAME showed significant reductions in CVC responses following acupuncture stimulation compared to control sites (administered Ringer's solution) (p<0.05). In the second protocol, changes in CVC responses after acupuncture stimulation did not differ significantly between treated sites with EMLA cream and untreated sites (p>0.05). Conclusions These data suggest that cutaneous vasodilation in response to acupuncture stimulation may not occur through an axon reflex as previously reported. Rather, NO mechanisms appear to contribute to the vasodilator response.
Mapping and assessing clinical handover training interventions
Authors: Stoyanov Slavi , Boshuizen Henny , Groene Oliver , van der Klink Marcel , Kicken Wendy , Drachsler Hendrik , Barach Paul 
Published: October 2012

BackgroundThe literature reveals a patchwork of knowledge about the effectiveness of handover and transfer of care-training interventions, their influence on handover practices and on patient outcomes. We identified a range of training interventions, defined their content, and then proposed practical measures for improving the training effectiveness of handover practices.MethodsWe applied the Group Concept Mapping approach to identify objectively the shared understanding of a group of experts about patient handover training interventions. We collected 105 declarative statements about handover training interventions from an exhaustive literature review, and from structured expert interviews. The statements were then given to 21 healthcare and training design specialists to sort the statements on similarity in meaning, and rate them on their importance and feasibility.ResultsWe used multidimensional scaling and hierarchical cluster analysis to depict the following seven clusters related to various handover training issues: standardisation, communication, coordination of activities, clinical microsystem care, transfer and impact, training methods and workplace learning.ConclusionsIdeas on handover training interventions, grouped in thematic clusters, and prioritised on importance and feasibility creates a repository of approaches. This allows healthcare institutions to design and test concrete solutions for improving formal training and workplace learning related to handovers, and addressing informal social learning at the organisational level, with the aim of increasing impact on handover practice and patient outcomes. Measures need to be taken to assure a continuum of handover training interventions from formal training through workplace learning through less formal social learning, and to embed this training in the design of the clinical microsystem.
The key actor: a qualitative study of patient participation in the handover process in Europe
Authors: Flink Maria , Hesselink Gijs , Pijnenborg Loes , Wollersheim Hub , Vernooij-Dassen Myrra , Dudzik-Urbaniak Ewa , Orrego Carola , Toccafondi Giulio , Schoonhoven Lisette , Gademan Petra J , Johnson Julie K , Öhlén Gunnar , Hansagi Helen , Olsson Mariann , Barach Paul ,   on behalf of the HANDOVER Research Collaborative
Published: October 2012

BackgroundPatient safety experts have postulated that increasing patient participation in communications during patient handovers will improve the quality of patient transitions, and that this may reduce hospital readmissions. Choosing strategies that enhance patient safety through improved handovers requires better understanding of patient experiences and preferences for participation.ObjectiveThe aim of this paper is to explore the patients’ experiences and perspectives related to the handovers between their primary care providers and the inpatient hospital.MethodsA qualitative secondary analysis was performed, based on individual and focus group patient interviews with 90 patients in five European countries.ResultsThe analysis revealed three themes:patient positioning in the handover process;prerequisites for patient participationandpatient preferences for the handover process.Patients’ participation ranged from being the key actor, to sharing the responsibility with healthcare professional(s), to being passive participants. For active participation patients required both personal and social resources as well as prerequisites such as information and respect. Some patients preferred to be the key actor in charge; others preferred their healthcare professionals to be the key actors in the handover.ConclusionsPatients’ participation is related to the healthcare system, the activity of healthcare professionals’ and patients’ capacity for participation. Patients prefer a handover process where the responsibility is clear and unambiguous. Healthcare organisations need a clear and well-considered system of responsibility for handover processes, that takes into account the individual patient's need of clarity, and support in relation to his/hers own recourses.
“It's like two worlds apart”: an analysis of vulnerable patient handover practices at discharge from hospital
Authors: Groene Raluca Oana , Orrego Carola , Suñol Rosa , Barach Paul , Groene Oliver 
Published: October 2012

BackgroundHandover practices at hospital discharge are relatively under-researched, particularly as regards the specific risks and additional requirements for handovers involving vulnerable patients with limited language, cognitive and social resources.ObjectiveTo explore handover practices at discharge and to focus on the patients’ role in handovers and on the potential additional risks for vulnerable patients.MethodsWe conducted qualitative interviews with patients, hospital professionals and primary care professionals in two hospitals and their associated primary care centres in Catalonia, Spain.ResultsWe identified handover practices at discharge that potentially put patients at risk. Patients did not feel empowered in the handover but were expected to transfer information between care providers. Professionals identified lack of medication reconciliation at discharge, loss of discharge information, and absence of plans for follow-up care in the community as quality and safety problems for discharge handovers. These occurred for all patients, but appeared to be more frequent and have a greater negative effect in patients with limited language comprehension and/or lack of family and social support systems.ConclusionsDischarge handovers are often haphazard. Healthcare professionals do not consider current handover practices safe, with patients expected to transfer information without being empowered to understand and act on it. This can lead to misinformation, omission or duplication of tests or interventions and, potentially, patient harm. Vulnerable patients may be at greater risk given their limited language, cognitive and social resources. Patient safety at discharge could benefit from strategies to enhance patient education and promote empowerment.
Comparing the utility of a novel neonatal resuscitation cart with a generic code cart using simulation: a randomised, controlled, crossover trial
Authors: Chitkara Ritu , Rajani Anand K , Lee Henry C , Hansen Sara F Snyder , Halamek Louis P 
Published: October 2012

ObjectiveTo compare a novel neonatal resuscitation cart (NRC) to a generic code cart (GCC).Study designA prospective, randomised, controlled, crossover trial was performed to compare the utility of the NRC with the GCC during simulated deliveries of extremely low birthweight infants and infants with gastroschisis. Fifteen subjects participated. Mean times and accuracy of equipment and supply retrieval were compared for each scenario using the Wilcoxon test.ResultsMean acquisition times for the NRC were always faster (by 58% to 74%) regardless of scenario (p<0.01). Accuracy of equipment selection did not differ. Ease of use was judged using a Likert scale (1=easiest to use; 5=most difficult), with mean score for NRC 1.1 and GCC 3.7 (p<0.0001). All subjects rated the NRC as easier to use.ConclusionsThe NRC was superior to the GCC in acquisition speed, supply selection and ease of use.