bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of the sulfate deficiency response in the marine microalga Emiliania huxleyi
Authors: Bochenek Michal , Etherington Graham J. , Koprivova Anna , Mugford Sam T. , Bell Thomas G. , Malin Gill , Kopriva Stanislav 
Published: May 2013

Summary

The response to sulfate deficiency of plants and freshwater green algae has been extensively analysed by system biology approaches. By contrast, seawater sulfate concentration is high and very little is known about the sulfur metabolism of marine organisms.
Here, we used a combination of metabolite analysis and transcriptomics to analyse the response of the marine microalga Emiliania huxleyi as it acclimated to sulfate limitation.
Lowering sulfate availability in artificial seawater from 25 to 5 mM resulted in significant reduction in growth and intracellular concentrations of dimethylsulfoniopropionate and glutathione. Sulfate‐limited E. huxleyi cells showed increased sulfate uptake but sulfate reduction to sulfite did not seem to be regulated. Sulfate limitation in E. huxleyi affected expression of 1718 genes. The vast majority of these genes were upregulated, including genes involved in carbohydrate and lipid metabolism, and genes involved in the general stress response.
The acclimation response of E. huxleyi to sulfate deficiency shows several similarities to the well‐described responses of Arabidopsis and Chlamydomonas, but also has many unique features. This dataset shows that even though E. huxleyi is adapted to constitutively high sulfate concentration, it retains the ability to re‐program its gene expression in response to reduced sulfate availability.
Vegetation limits the impact of a warm climate on boreal wildfires
Authors: Girardin Martin P. , Ali Adam A. , Carcaillet Christopher , Blarquez Olivier , Hély Christelle , Terrier Aurélie , Genries Aurélie , Bergeron Yves 
Published: May 2013

Summary

Strategic introduction of less flammable broadleaf vegetation into landscapes was suggested as a management strategy for decreasing the risk of boreal wildfires projected under climatic change. However, the realization and strength of this offsetting effect in an actual environment remain to be demonstrated.
Here we combined paleoecological data, global climate models and wildfire modelling to assess regional fire frequency (RegFF, i.e. the number of fires through time) in boreal forests as it relates to tree species composition and climate over millennial time‐scales.
Lacustrine charcoals from northern landscapes of eastern boreal Canada indicate that RegFF during the mid‐Holocene (6000–3000 yr ago) was significantly higher than pre‐industrial RegFF (ad c. 1750). In southern landscapes, RegFF was not significantly higher than the pre‐industrial RegFF in spite of the declining drought severity. The modelling experiment indicates that the high fire risk brought about by a warmer and drier climate in the south during the mid‐Holocene was offset by a higher broadleaf component.
Our data highlight an important function for broadleaf vegetation in determining boreal RegFF in a warmer climate. We estimate that its feedback may be large enough to offset the projected climate change impacts on drought conditions.
Spatiotemporal changes in the role of cytokinin during root development
Authors: Del Bianco Marta , Giustini Leonardo , Sabatini Sabrina 
Published: May 2013

SummaryThe root is a dynamic system whose structure is regulated by a complex network of interactions between hormones. The primary root meristem is specified in the embryo. After germination, the primary root meristem grows and then reaches a final size that will be maintained during the life of the plant. Subsequently, secondary structures such as lateral roots and root nodules form via the re‐specification of differentiated cells. Cytokinin plays key roles in the regulation of root development. Down‐regulation of the cytokinin response is required for the specification of a new stem cell niche, during both embryo and lateral root development. In the root meristem, cytokinin signalling regulates the longitudinal zonation of the meristem by controlling cell differentiation. Moreover, cytokinin regulates radial patterning of root vasculature by promoting protophloem cell identity and by spatially inhibiting protoxylem formation. In this review, an effort is made to describe the known details of the role of cytokinin during root development, taking into account also the interactions between cytokinin and other hormones. Attention is given on the dynamicity of cytokinin signalling output during different developmental events. Indeed, there is much evidence that the effects of cytokinin change as organs grow, underlining the importance of the spatiotemporal specificity of cytokinin signalling.

Contents

Summary
324

I.
Introduction
324

II.
Cytokinin cellular pathway
325

III.
Cytokinin signalling in root development
327

IV.
Spatiotemporal variations of cytokinin signalling
332

V.
Concluding remarks
334

Acknowledgements
335

References
335
Ultrasound‐guided parasacral approach to the sciatic nerve block in children
Authors: Dillow Jennifer M. , Rosett Randy L. , Petersen Timothy R. , Vagh Firoz S. , Hruschka James A. , Lam Nicholas C. K. 
Published: May 2013

SummaryBackgroundThe parasacral (PS) approach to sciatic nerve blockade has the potential for safe and effective use in children, but has never been studied in this population. Its potential advantages include increased posterior cutaneous nerve block reliability, potential for hip joint analgesia, and decreased nerve depth, making ultrasound guidance easier.ObjectiveTo assess the efficacy of an ultrasound‐guided PS sciatic nerve block in children.MethodsNineteen patients, 1–16 years old, scheduled for lower limb surgery with peripheral nerve blockade (PNB) were prospectively enrolled. A PS sciatic block was performed using both ultrasound guidance and nerve stimulation, and 0.5 ml·kg−1 ropivacaine 0.2% (maximum 20 ml) was administered. Patient demographics, the time to perform the block, the lowest intensity of nerve stimulation, evoked response, identification of gluteal arteries, and amount of narcotic given were recorded. Postoperatively, pain scores, block success or failure, block duration, and complications were recorded.ResultsThe block was performed using the PS approach in 95% of the cases. The success rate was 100% in the PS sciatic blocks performed. The pain scores for all patients in the first postsurgical hour were zero, except one patient that had a pain score of 3 of 10 at 30 min; his pain improved to 0 of 10 after administration of one dose of fentanyl and distraction techniques. The blocks lasted 17.3 ± 5.4 h. No complications were identified.ConclusionThe PS approach is an effective option for sciatic nerve blockade to provide postoperative pain relief in children having lower extremity surgery.
Positive blood culture is not associated with increased mortality in patients with sepsis‐induced acute respiratory distress syndrome
Authors: Yang Szu‐Chun , Liao Kuang‐Ming , Chen Chang‐Wen , Lin Wei‐Chieh 
Published: May 2013

AbstractBackground and objectivePrevious studies have demonstrated that positive blood culture could contribute to poorer outcomes in patients with pneumonia. However, the impact of positive blood culture on the outcomes of patients with sepsis‐induced acute respiratory distress syndrome (ARDS) has not been evaluated.MethodsAn observational study that prospectively screened 4861 patients admitted to medical or surgical intensive care units (ICUs) of a tertiary referral centre was performed.ResultsAmong 4861 admitted patients, 146 diagnosed with sepsis‐induced ARDS were enrolled (mean age: 66.1 years). Lower PaO2/FiO2, decreased respiratory system compliance, and higher lung injury scores (LIS) on the day of ARDS diagnosis were associated with positive blood cultures (n = 68) rather than negative blood cultures (n = 78). There was no relationship between positive blood culture and in‐hospital mortality. Kaplan–Meier estimates also revealed that positive blood culture was not associated with 60‐day mortality but with an increased length of stay in the hospital and in the ICU (P = 0.007 and P = 0.016, respectively). Using multivariate logistic regression, higher LIS was independently associated with positive blood culture. In addition, chronic pulmonary disease, lower platelet count, higher LIS, and the development of shock on the diagnosis of ARDS, were independent risk factors for in‐hospital mortality.ConclusionsThis study suggests that the presence of positive blood culture is not associated with increased mortality; however, the mean durations of hospital and ICU stays in patients with sepsis‐induced ARDS are increased.
Effects of whole body vibration training in patients with severe chronic obstructive pulmonary disease
Authors: Pleguezuelos Eulogio , Pérez Maria Engracia , Guirao Lluis , Samitier Beatriz , Costea Maria , Ortega Pilar , González Maria Victoria , Del Carmen Virgilio Amin. , Ovejero Laura , Moreno Eva , Miravitlles Marc 
Published: May 2013

AbstractBackground and objectiveTo determine if whole body vibration training (WBVT) improves muscular force and modifies functional capacity parameters in patients with severe chronic obstructive pulmonary disease (COPD).MethodsWe performed a randomized controlled trial in the outpatient Physical Medicine and Rehabilitation Department of a general hospital. Sixty stable male patients with COPD and mean forced expiratory volume in 1 s (FEV1) 34.3% (predicted) were enrolled with 51 patients completing the study. Participants were randomized into two groups: Whole Body Vibration Training Group (WBVTG), (n = 26) undergoing three sessions per week for a total of 6 weeks and a Control Group (CG) (n = 25) without intervention. The main outcome measures were isokinetic knee flexor and extensor testing in a concentric–concentric regime and exercise capacity measured by the 6‐min walking test (6MWT). Secondary outcomes were pulmonary muscular assessment with maximum inspiratory pressure (MIP) and maximum expiratory pressure (MEP).ResultsNo significant differences were observed between groups in maximum moment of isokinetic knee flexor/extensor testing force in a concentric‐concentric regime. In contrast, WBVTG patients showed a significant increase in the 6MWT (81.2 ± 9.2) meters; mean ± SD; P < 0.001). There was also a significant decrease in maximum oxygen desaturation in the 6MWT after 6 weeks of training (3.1 ± 1.1; P = 0.01). There were significant differences between groups in MIP and MEP at the end of the study in favour of the WBVTG.ConclusionsWBVT provided significant improvements in functional capacity in severe COPD patients without changes in muscular force.
An ambulance referral network improves access to emergency obstetric and neonatal care in a district of rural Burundi with high maternal mortality
Authors: Tayler‐Smith K. , Zachariah R. , Manzi M. , Van den Boogaard W. , Nyandwi G. , Reid T. , De Plecker E. , Lambert V. , Nicolai M. , Goetghebuer S. , Christiaens B. , Ndelema B. , Kabangu A. , Manirampa J. , Harries A. D. 
Published: May 2013

AbstractObjectivesIn 2006, Médecins sans Frontières (MSF) established an emergency obstetric and neonatal care (EmONC) referral facility linked to an ambulance referral system for the transfer of women with obstetric complications from peripheral maternity units in Kabezi district, rural Burundi. This study aimed to (i) describe the communication and ambulance service together with the cost; (ii) examine the association between referral times and maternal and early neonatal deaths; and (iii) assess the impact of the referral service on coverage of complicated obstetric cases and caesarean sections.MethodsData were collected for the period January to December 2011, using ambulance log books, patient registers and logistics records.ResultsIn 2011, there were 1478 ambulance call‐outs. The median referral time (time from maternity calling for an ambulance to the time the patient arrived at the MSF referral facility) was 78 min (interquartile range, 52–130 min). The total annual cost of the referral system (comprising 1.6 ambulances linked with nine maternity units) was € 85 586 (€ 61/obstetric case transferred or € 0.43/capita/year). Referral times exceeding 3 h were associated with a significantly higher risk of early neonatal deaths (OR, 1.9; 95% CI, 1.1–3.2). MSF coverage of complicated obstetric cases and caesarean sections was estimated to be 80% and 92%, respectively.ConclusionThis study demonstrates that it is possible to implement an effective communication and transport system to ensure access to EmONC and also highlights some of the important operational factors to consider, particularly in relation to minimising referral delays.
Cost‐effectiveness of prospective red blood cell antigen matching to prevent alloimmunization among sickle cell patients
Authors: Kacker Seema , Ness Paul M. , Savage William J. , Frick Kevin D. , Shirey R. Sue , King Karen E. , Tobian Aaron A.R. 
Published: May 2013

BackgroundSickle cell disease is associated with extensive health care utilization; estimated lifetime costs exceed $460,000 per patient. Approximately 30% of chronically transfused sickle cell patients become alloimmunized to red blood cell antigens, but these patients cannot be identified a priori. Prospective antigen matching can prevent alloimmunization, but is costly and may not benefit most patients.Study Design and MethodsA Markov‐based model was constructed to compare the health and financial implications of four alternative antigen‐matching strategies for chronically transfused sickle cell patients. The strategies varied by the group of patients receiving matched blood (all patients prophylactically or only patients with a history of alloimmunization [history‐based]), and by the extent of antigen matching (limited to C, E, and K, or extended to 11 antigens). Direct medical costs and alloimmunization events were assessed over 10‐ and 20‐year periods, for a hypothetical cohort of initially transfusion‐naive patients and for a dynamic population.ResultsWithin a hypothetical cohort of initially transfusion‐naive patients, implementing prophylactic limited matching for all chronically transfused patients instead of history‐based limited matching is expected to cost an additional $765.56 million over 10 years, but result in 2072 fewer alloimmunization events. Within the same cohort, implementing prospective extensive matching is expected to cost $1.86 billion more than history‐based extensive matching, but result in 2424 fewer alloimmunization events. Averting a single alloimmunization event using prospective matching would cost $369,482 to $769,284. Among a dynamic population over 10 years, prospective limited matching is expected to cost $358.34 million more than history‐based limited matching.ConclusionsWhile prospective matching for all transfused patients would reduce alloimmunization, this strategy requires considerable expenditure.
Cationic Antimicrobial Peptides and Biogenic Silver Nanoparticles Kill Mycobacteria without Eliciting DNA Damage and Cytotoxicity in Mouse Macrophages
Authors: Mohanty Soumitra , Jena Prajna , Mehta Ranjit , Pati Rashmirekha , Banerjee Birendranath , Patil Satish , Sonawane Avinash 
Published: May 2013

ABSTRACT

With the emergence of multidrug-resistant mycobacterial strains, better therapeutic strategies are required for the successful treatment of the infection. Although antimicrobial peptides (AMPs) and silver nanoparticles (AgNPs) are becoming one of the popular antibacterial agents, their antimycobacterial potential is not fully evaluated. In this study, we synthesized biogenic-silver nanoparticles using bacterial, fungal, and plant biomasses and analyzed their antibacterial activities in combination with AMPs against mycobacteria.
Mycobacterium smegmatis
was found to be more susceptible to AgNPs compared to
M. marinum
. We found that NK-2 showed enhanced killing effect with NP-1 and NP-2 biogenic nanoparticles at a 0.5-ppm concentration, whereas LLKKK-18 showed antibacterial activity only with NP-2 at 0.5-ppm dose against
M. smegmatis
. In case of
M. marinum
NK-2 did not show any additive activity with NP-1 and NP-2 and LLKKK-18 alone completely inhibited the bacterial growth. Both NP-1 and NP-2 also showed increased killing of
M. smegmatis
in combination with the antituberculosis drug rifampin. The sizes and shapes of the AgNPs were determined by transmission electron microscopy and dynamic light scattering. AgNPs showed no cytotoxic or DNA damage effects on macrophages at the mycobactericidal dose, whereas treatment with higher doses of AgNPs caused toxicity and micronuclei formation in cytokinesis blocked cells. Macrophages actively endocytosed fluorescein isothiocyanate-labeled AgNPs resulting in nitric oxide independent intracellular killing of
M. smegmatis
. Apoptosis and cell cycle studies showed that treatment with higher dose of AgNPs arrested macrophages at the G
1
-phase. In summary, our data suggest the combined effect of biogenic-AgNPs and antimicrobial peptides as a promising antimycobacterial template.
Comparative Persistence of Subgroups of F-Specific RNA Phages in River Water
Authors: Yang Yongheng , Griffiths Mansel W. 
Published: May 2013

ABSTRACT
F-specific (F+) RNA phages are widely used as indicators for the presence of fecal contamination and/or enteric viruses in water, and identifying subgroups of F+ RNA phages provides an approach for microbial source tracking. Different survival characteristics of the F+ RNA phage subgroups result in a misinterpretation of their original proportion in water, thus giving misleading information when they are used for microbial source tracking. This study investigated the comparative persistence of subgroups of F+ RNA phages in river water under different conditions. Results suggested that temperature and pH are the major factors affecting the persistence of F+ RNA phages in river water, and organic substances promote phage survival. The comparative persistence patterns of subgroups of F+ RNA phages varied and may bias extrapolation of their initial proportions in surface water. Thus, the characteristics of water should be taken into consideration and the results should be carefully interpreted when F+ RNA phages are used for microbial source tracking.
Differential Role of Manduca sexta Aminopeptidase-N and Alkaline Phosphatase in the Mode of Action of Cry1Aa, Cry1Ab, and Cry1Ac Toxins from Bacillus thuringiensis
Authors: Flores-Escobar Biviana , Rodríguez-Magadan Hector , Bravo Alejandra , Soberón Mario , Gómez Isabel 
Published: May 2013

ABSTRACT

Aminopeptidase-N (APN1) and alkaline phosphatase (ALP) proteins located in the midgut epithelium of
Manduca sexta
have been implicated as receptors for Cry1Aa, Cry1Ab, and Cry1Ac insecticidal proteins produced by
Bacillus thuringiensis
subsp.
kurstaki
. In this study, we analyzed the roles of ALP and APN1 in the toxicity of these three Cry1A proteins. Ligand blot analysis using brush border membrane vesicles of
M. sexta
showed that Cry1Aa and Cry1Ab bind preferentially to ALP during early instars while binding to APN was observed after the third instar of larval development. Cry1Ac binds to APN throughout all larval development, with no apparent binding to ALP. ALP was cloned from
M. sexta
midgut RNA and expressed in
Escherichia coli
. Surface plasmon resonance binding analysis showed that recombinant ALP binds to Cry1Ac with 16-fold lower affinity than to Cry1Aa or Cry1Ab. Downregulation of APN1 and ALP expression by RNA interference (RNAi) using specific double-stranded RNA correlated with a reduction of transcript and protein levels. Toxicity analysis of the three Cry1A proteins in ALP- or APN1-silenced larvae showed that Cry1Aa relies similarly on both receptor molecules for toxicity. In contrast, RNAi experiments showed that ALP is more important than APN for Cry1Ab toxicity, while Cry1Ac relied principally on APN1. These results indicated that ALP and APN1 have a differential role in the mode of action of Cry1A toxins, suggesting that
B. thuringiensis
subsp.
kurstaki
produces different Cry1A toxins that in conjunction target diverse midgut proteins to exert their insecticidal effect.
Functional Screening of Metagenome and Genome Libraries for Detection of Novel Flavonoid-Modifying Enzymes
Authors: Rabausch U. , Juergensen J. , Ilmberger N. , Böhnke S. , Fischer S. , Schubach B. , Schulte M. , Streit W. R. 
Published: May 2013

ABSTRACT

The functional detection of novel enzymes other than hydrolases from metagenomes is limited since only a very few reliable screening procedures are available that allow the rapid screening of large clone libraries. For the discovery of flavonoid-modifying enzymes in genome and metagenome clone libraries, we have developed a new screening system based on high-performance thin-layer chromatography (HPTLC). This
m
etagenome
e
xtract
t
hin-layer chromatography
a
nalysis (META) allows the rapid detection of glycosyltransferase (GT) and also other flavonoid-modifying activities. The developed screening method is highly sensitive, and an amount of 4 ng of modified flavonoid molecules can be detected. This novel technology was validated against a control library of 1,920 fosmid clones generated from a single
Bacillus cereus
isolate and then used to analyze more than 38,000 clones derived from two different metagenomic preparations. Thereby we identified two novel UDP glycosyltransferase (UGT) genes. The metagenome-derived
gtfC
gene encoded a 52-kDa protein, and the deduced amino acid sequence was weakly similar to sequences of putative UGTs from
Fibrisoma
and
Dyadobacter
. GtfC mediated the transfer of different hexose moieties and exhibited high activities on flavones, flavonols, flavanones, and stilbenes and also accepted isoflavones and chalcones. From the control library we identified a novel macroside glycosyltransferase (MGT) with a calculated molecular mass of 46 kDa. The deduced amino acid sequence was highly similar to sequences of MGTs from
Bacillus thuringiensis
. Recombinant MgtB transferred the sugar residue from UDP-glucose effectively to flavones, flavonols, isoflavones, and flavanones. Moreover, MgtB exhibited high activity on larger flavonoid molecules such as tiliroside.
Manganese and Zinc Regulate Virulence Determinants in Borrelia burgdorferi
Authors: Troxell Bryan , Ye Meiping , Yang Youyun , Carrasco Sebastian E. , Lou Yongliang , Yang X. Frank 
Published: May 2013

ABSTRACT

Borrelia burgdorferi
, the causative agent of Lyme disease, must adapt to two diverse niches, an arthropod vector and a mammalian host. RpoS, an alternative sigma factor, plays a central role in spirochetal adaptation to the mammalian host by governing expression of many genes important for mammalian infection.
B. burgdorferi
is known to be unique in metal utilization, and little is known of the role of biologically available metals in
B. burgdorferi
. Here, we identified two transition metal ions, manganese (Mn
2+
) and zinc (Zn
2+
), that influenced regulation of RpoS. The intracellular Mn
2+
level fluctuated approximately 20-fold under different conditions and inversely correlated with levels of RpoS and the major virulence factor OspC. Furthermore, an increase in intracellular Mn
2+
repressed temperature-dependent induction of RpoS and OspC; this repression was overcome by an excess of Zn
2+
. Conversely, a decrease of intracellular Mn
2+
by deletion of the Mn
2+
transporter gene,
bmtA
, resulted in elevated levels of RpoS and OspC. Mn
2+
affected RpoS through BosR, a Fur family homolog that is required for
rpoS
expression: elevated intracellular Mn
2+
levels greatly reduced the level of BosR protein but not the level of
bosR
mRNA. Thus, Mn
2+
and Zn
2+
appeared to be important in modulation of the RpoS pathway that is essential to the life cycle of the Lyme disease spirochete. This finding supports the emerging notion that transition metals such as Mn
2+
and Zn
2+
play a critical role in regulation of virulence in bacteria.