bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of an Arabidopsis heat‐sensitive mutant reveals that chlorophyll synthase is involved in reutilization of chlorophyllide during chlorophyll turnover
Authors: Lin Yao‐Pin , Lee Tsung‐yuan , Tanaka Ayumi , Charng Yee‐yung 
Published: July 2014

SummaryChlorophylls, the most abundant pigments in the photosynthetic apparatus, are constantly turned over as a result of the degradation and replacement of the damage‐prone reaction center D1 protein of photosystem II. Results from isotope labeling experiments suggest that chlorophylls are recycled by reutilization of chlorophyllide and phytol, but the underlying mechanism is unclear. In this study, by characterization of a heat‐sensitive Arabidopsis mutant we provide evidence of a salvage pathway for chlorophyllide a. A missense mutation in CHLOROPHYLL SYNTHASE (CHLG) was identified and confirmed to be responsible for a light‐dependent, heat‐induced cotyledon bleaching phenotype. Following heat treatment, mutant (chlg‐1) but not wild‐type seedlings accumulated a substantial level of chlorophyllide a, which resulted in a surge of phototoxic singlet oxygen. Immunoblot analysis suggested that the mutation destabilized the chlorophyll synthase proteins and caused a conditional blockage of esterification of chlorophyllide a after heat stress. Accumulation of chlorophyllide a after heat treatment occurred during recovery in the dark in the light‐grown but not the etiolated seedlings, suggesting that the accumulated chlorophyllides were not derived from de novo biosynthesis but from de‐esterification of the existing chlorophylls. Further analysis of the triple mutant harboring the CHLG mutant allele and null mutations of CHLOROPHYLLASE1 (CLH1) and CLH2 indicated that the known chlorophyllases are not responsible for the accumulation of chlorophyllide a in chlg‐1. Taken together, our results show that chlorophyll synthase acts in a salvage pathway for chlorophyll biosynthesis by re‐esterifying the chlorophyllide a produced during chlorophyll turnover.
Arabidopsis CPL4 is an essential C‐terminal domain phosphatase that suppresses xenobiotic stress responses
Authors: Fukudome Akihito , Aksoy Emre , Wu Xiaoqiang , Kumar Krishna , Jeong In Sil , May Kimberly , Russell William K. , Koiwa Hisashi 
Published: July 2014

SummaryEukaryotic gene expression is both promoted and inhibited by the reversible phosphorylation of the C‐terminal domain of RNA polymerase II (pol II CTD). More than 20 Arabidopsis genes encode CTD phosphatase homologs, including four CTD phosphatase‐like (CPL) family members. Although in vitro CTD phosphatase activity has been established for some CPLs, none have been shown to be involved in the phosphoregulation of pol II in vivo. Here we report that CPL4 is a CTD phosphatase essential for the viability of Arabidopsis thaliana. Mass spectrometry analysis identified the pol II subunits RPB1, RPB2 and RPB3 in the affinity‐purified CPL4 complex. CPL4 dephosphorylates both Ser2‐ and Ser5‐PO4 of the CTD in vitro, with a preference for Ser2‐PO4. Arabidopsis plants overexpressing CPL4 accumulated hypophosphorylated pol II, whereas RNA interference‐mediated silencing of CPL4 promoted hyperphosphorylation of pol II. A D128A mutation in the conserved DXDXT motif of the CPL4 catalytic domain resulted in a dominant negative form of CPL4, the overexpression of which inhibited transgene expression in transient assays. Inhibition was abolished by truncation of the phosphoprotein‐binding Breast Cancer 1 C‐terminal domain of CPL4, suggesting that both catalytic function and protein–protein interaction are essential for CPL4‐mediated regulation of gene expression. We were unable to recover a homozygous cpl4 mutant, probably due to the zygotic lethality of this mutation. The reduction in CPL4 levels in CPL4RNAi plants increased transcript levels of a suite of herbicide/xenobiotic‐responsive genes and improved herbicide tolerance, thus suggesting an additional role for CPL4 as a negative regulator of the xenobiotic detoxification pathway.
Serum 25‐hydroxyvitamin D concentrations in dogs – correlation with health and cancer risk
Authors: Selting K. A. , Sharp C. R. , Ringold R. , Thamm D. H. , Backus R. 
Published: July 2014

Abstract25‐hydroxyvitamin D (25(OH)D) is important in bone health as well as many diseases including cancer. Supplementation may increase responsiveness of cancer cells to chemotherapy. Serum 25(OH)D, intact parathyroid hormone (iPTH) and canine C‐reactive protein (c‐CRP) were measured in healthy dogs and dogs with haemoabdomen. Regression analysis determined optimal 25(OH)D concentrations. In healthy dogs (n = 282), mean iPTH concentrations correlated inversely (r2 = 0.88, P < 0.001) to 25(OH)D concentrations. Variation in both iPTH and c‐CRP plateaued at 25(OH)D concentrations of 100–120 ng mL−1. Haemoabdomen dogs (n = 63, 43 malignant and 20 benign) had 25(OH)D concentrations ranging from 19.4 to >150 ng mL−1. Relative risk of cancer increased with decreasing 25(OH)D concentrations [RR = 3.9 for 25(OH)D below 40 ng mL−1 (P = 0.0001)]. Serum 25(OH)D concentrations in dogs vary widely, and are influenced by dietary VitD content. Serum vitD measurement can identify dogs for which supplementation may improve health and response to cancer therapy.
Shedding and Seroprevalence of PathogenicLeptospiraspp. in Sheep and Cattle at a New Zealand Abattoir
Authors: Fang F. , Collins‐Emerson J. M. , Cullum A. , Heuer C. , Wilson P. R. , Benschop J. 
Published: July 2014

SummaryA cross‐sectional study was carried out on sheep and cattle slaughtered at a New Zealand abattoir from September to November 2010 to investigate the supplier‐specific shedding rate, renal carriage rate and seroprevalence of leptospires. In the 2008/2009 season, this abattoir experienced three human leptospirosis cases from 20 staff, of which two were hospitalized. Urine, kidney and blood samples were collected from carcasses of 399 sheep (six suppliers, 17 slaughter lines) and 146 cattle (three suppliers, 22 slaughter lines). The urine and kidney samples were tested by quantitative real‐time PCR (qPCR), while serum samples (from coagulated blood samples) were tested by microscopic agglutination test (MAT). In total, 27% (73/274; 95% CI: 18–37) of urine samples tested positive by qPCR. Species‐specific shedding rates (prevalence of positive urine qPCR) were 31% (95% CI: 17–48) for sheep and 21% (95% CI: 14–30) for cattle. For 545 kidney samples tested, 145 were qPCRpositive (27%; 95% CI: 17–39). The average prevalence of kidney qPCRpositivity was 29% (95% CI: 17–45) for sheep and 21% (95% CI: 15–28) for cattle. Three hundred and thirty of 542 sampled sheep and cattle had antibodies againstLeptospira borgpeterseniiserovar Hardjobovis (Hardjobovis) and/orLeptospira interrogansserovar Pomona (Pomona), based on reciprocalMATtitre ≥1 : 48 (overall seroprevalence of 61%; 95% CI: 48–73). Seroprevalence was 57% (95% CI: 40–72) for sheep and 73% (95% CI: 59–83) for cattle. Among the seropositive animals, 41% (70/170; 95% CI: 30–54) were shedding (tested positive by urine qPCR) and 42% (137/330; 95% CI: 30–54) had renal carriage (tested positive by kidney qPCR). Some risk management options for abattoirs or farms to prevent human leptospirosis infections include vaccination of maintenance hosts, the use of personal protective equipment, and the application of urine qPCRto detect shedding status of stock as surveillance and as an alert.
Experimental Study on the Production of CO-NO-HC Emissions in the Radial Swirling Flow Combustion System
Authors: Ashrul Ishak Mohamad Shaiful , Mohd Jaafar Mohammad Nazri 
Published: July 2014

The main purpose of this paper is to evaluate the production of CO-NO-HC emissions while varying the swirl angle of curve vane radial swirler. Air swirler adds sufficient swirling to the inlet flow to generate central recirculation region (CRZ) which is necessary for flame stability and fuel air mixing enhancement. Therefore designing an appropriate air swirler is a challenge to produce stable, efficient and low emission combustion inside a burner system. Four radial curve vane swirlers with 30o, 40o, 50o and 60o vane angle corresponding to swirl number of 0.366, 0.630, 0.978 and 1.427 respectively were used in this analysis to show the effect of vane angle on emission production at end of combustion chamber. Pollutant NO reduction of more than 10 percent was obtained for the swirl number of 1.427 compared to 0.366. CO emissions were reduced by 20 percent, 25 percent and 38 percent reduction in carbon monoxide (CO) emission for swirl number of 0.630, 0.978 and 1.427 compared to swirl number of 0.366 respectively. Meanwhile, there was a small decrease in unburned HC emissions when increasing the swirl number for the whole range of equivalence ratios. Results show that the swirling action is augmented with the increase in the vane angle, which leads to better performance of CO-NO-HC emission production inside liquid fuel burner system.
A note on modeling of tumor regression for estimation of radiobiological parameters
Authors: Zhong Hualiang , Chetty Indrin 
Published: July 2014

Purpose:Accurate calculation of radiobiological parameters is crucial to predicting radiation treatment response. Modeling differences may have a significant impact on derived parameters. In this study, the authors have integrated two existing models with kinetic differential equations to formulate a new tumor regression model for estimation of radiobiological parameters for individual patients.Methods:A system of differential equations that characterizes the birth‐and‐death process of tumor cells in radiation treatment was analytically solved. The solution of this system was used to construct an iterative model (Z‐model). The model consists of three parameters: tumor doubling time Td, half‐life of dead cells Tr, and cell survival fraction SFD under dose D. The Jacobian determinant of this model was proposed as a constraint to optimize the three parameters for six head and neck cancer patients. The derived parameters were compared with those generated from the two existing models: Chvetsov's model (C‐model) and Lim's model (L‐model). The C‐model and L‐model were optimized with the parameter Td fixed.Results:With the Jacobian‐constrained Z‐model, the mean of the optimized cell survival fractions is 0.43 ± 0.08, and the half‐life of dead cells averaged over the six patients is 17.5 ± 3.2 days. The parameters Tr and SFD optimized with the Z‐model differ by 1.2% and 20.3% from those optimized with the Td‐fixed C‐model, and by 32.1% and 112.3% from those optimized with the Td‐fixed L‐model, respectively.Conclusions:The Z‐model was analytically constructed from the differential equations of cell populations that describe changes in the number of different tumor cells during the course of radiation treatment. The Jacobian constraints were proposed to optimize the three radiobiological parameters. The generated model and its optimization method may help develop high‐quality treatment regimens for individual patients.
Are Rest Intervals Between Stretching Repetitions Effective to Acutely Increase Range of Motion?
Authors: Freitas Sandro R. , Vaz João R. , Bruno Paula M. , Valamatos Maria João , Andrade Ricardo J. , Mil-Homens Pedro 
Published: July 2014

Static stretching with rest between repetitions is often performed to acutely increase joint flexibility.Purpose:To test the effects of the lack of resting between stretching repetitions and the minimal number of stretching repetitions required to change the maximal range of motion (ROM), maximal tolerated joint passive torque (MPT), and submaximal passive torque at a given angle (PT).Methods:Five static stretching repetitions with a 30-s rest-interval (RI) and a no-rest-interval (NRI) stretching protocol were compared. Participants (N = 47) were encouraged to perform the maximal ROM without pain in all the repetitions. Each repetition lasted 90 s. Maximal ROM, MPT, PT, and muscle activity were compared between protocols for the same number of stretching repetitions.Results:The NRI produced a higher increase in maximal ROM and MPT during and after stretching (P < .05). PT decreased in both protocols, although the NRI tended to have a lower decrement across different submaximal angles (.05 < P < .08) in the initial range of the torque-angle curve. Significant changes in maximal ROM (P < .01) and PT (P < .01) were obtained at the 3rd and 2nd repetitions of RI, respectively. The RI did not significantly increase the MPT (P = .12) after stretching; only the NRI did (P < .01).Conclusions:Lack of rest between repetitions more efficiently increased the maximal ROM and capacity to tolerate PT during and after stretching. The use of 30 s rest between repetitions potentiates the decrease in PT. Rest intervals should not be used if the aim is to acutely increase maximal ROM and peak passive torque.
Randomized Comparison of the Efficacies and Tolerabilities of Three Artemisinin-Based Combination Treatments for Children with Acute Plasmodium falciparum Malaria in the Democratic Republic of the Congo
Authors: Onyamboko M. A. , Fanello C. I. , Wongsaen K. , Tarning J. , Cheah P. Y. , Tshefu K. A. , Dondorp A. M. , Nosten F. , White N. J. , Day N. P. J. 
Published: July 2014

ABSTRACT

An open-label, randomized controlled trial was carried out in 2011–2012 in the Democratic Republic of the Congo to test the efficacy, safety, and tolerability of the artemisinin-based combination treatments dihydroartemisinin-piperaquine, amodiaquine-artesunate, and artemether-lumefantrine. Six hundred eighty-four children aged 3 to 59 months with uncomplicated
Plasmodium falciparum
malaria were randomly allocated to each study arm. Children were hospitalized for 3 days, given supervised treatment, and followed up weekly for 42 days. All regimens were well tolerated and rapidly effective. The median parasitemia clearance half-life was 2.2 h, and half-lives were similar between arms (
P
= 0.19). The PCR-uncorrected cure rates by day 42 were 73.0% for amodiaquine-artesunate, 70.2% for artemether-lumefantrine, and 86.3% for dihydroartemisinin-piperaquine (
P
= 0.001). Early treatment failure occurred in three patients (0.5%), one in each arm. The PCR-corrected cure rates were 93.4% for amodiaquine-artesunate, 92.7% for artemether-lumefantrine, and 94.3% for dihydroartemisinin-piperaquine (
P
= 0.78). The last provided a longer posttreatment prophylactic effect than did the other two treatments. The day 7 plasma concentration of piperaquine was below 30 ng/ml in 47% of the children treated with dihydroartemisinin-piperaquine, and the day 7 lumefantrine concentration was below 280 ng/ml in 37.0% of children who received artemether-lumefantrine. Thus, although cure rates were all satisfactory, they could be improved by increasing the dose. (This study has been registered with the International Standard Randomized Controlled Trial Number Register [
www.isrctn.org
] under registration no. ISRCTN20984426.)
In Vitro
Activities of Eight Antifungal Drugs against 104 Environmental and Clinical Isolates of Aureobasidium pullulans
Authors: Najafzadeh M. Javad , Sutton Deanna A. , Keisari M. Saradeghi , Zarrinfar H. , de Hoog G. Sybren , Chowdhary Anuradha , Meis Jacques F. 
Published: July 2014

ABSTRACT

Aureobasidium pullulans
is an unusual agent of phaeohyphomycosis. The
in vitro
activities of antifungals against 104 isolates of
Aureobasidium pullulans
var.
pullulans
and
A. pullulans
var.
melanigenum
revealed low MIC
90
s of amphotericin B, posaconazole, and itraconazole. However, they were resistant to fluconazole (≥64 μg/ml) and had high MICs of voriconazole, isavuconazole, caspofungin, and micafungin.
Agreement between
amoA
Gene-Specific Quantitative PCR and Fluorescence
In Situ
Hybridization in the Measurement of Ammonia-Oxidizing Bacteria in Activated Sludge
Authors: Baptista J. D. C. , Lunn M. , Davenport R. J. , Swan D. L. , Read L. F. , Brown M. R. , Morais C. , Curtis T. P. 
Published: July 2014

ABSTRACT

Microbial abundance is central to most investigations in microbial ecology, and its accurate measurement is a challenging task that has been significantly facilitated by the advent of molecular techniques over the last 20 years. Fluorescence
in situ
hybridization (FISH) is considered the gold standard of quantification techniques; however, it is expensive and offers low sample throughput, both of which limit its wider application. Quantitative PCR (qPCR) is an alternative that offers significantly higher throughput, and it is used extensively in molecular biology. The accuracy of qPCR can be compromised by biases in the DNA extraction and amplification steps. In this study, we compared the accuracy of these two established quantification techniques to measure the abundance of a key functional group in biological wastewater treatment systems, the ammonia-oxidizing bacteria (AOB), in samples from a time-series experiment monitoring a set of laboratory-scale reactors and a full-scale plant. For the qPCR analysis, we tested two different sets of AOB-specific primers, one targeting the 16SrRNA gene and one targeting the ammonia monooxygenase (
amoA
) gene. We found that there was a positive linear logarithmic relationship between FISH and the
amoA
gene-specific qPCR, where the data obtained from both techniques was equivalent at the order of magnitude level. The 16S rRNA gene-specific qPCR assay consistently underestimated AOB numbers.
Nitrogen-Fixing Rhizobial Strains Isolated from Common Bean Seeds: Phylogeny, Physiology, and Genome Analysis
Authors: Mora Yolanda , Díaz Rafael , Vargas-Lagunas Carmen , Peralta Humberto , Guerrero Gabriela , Aguilar Alejandro , Encarnación Sergio , Girard Lourdes , Mora Jaime 
Published: July 2014

ABSTRACT

Rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. Endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. We isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. Nine isolates were obtained, covering most known bean symbiont species, which belong to the
Rhizobium
and
Sinorhizobium
groups. The strains showed several large plasmids, except for a
Sinorhizobium
americanum
isolate. Two strains, one
Rhizobium phaseoli
and one
S. americanum
strain, were thoroughly characterized. Optimal symbiotic performance was observed for both of these strains. The
S. americanum
strain showed biotin prototrophy when subcultured, as well as high pyruvate dehydrogenase (PDH) activity, both of which are key factors in maintaining optimal growth. The
R. phaseoli
strain was a biotin auxotroph, did not grow when subcultured, accumulated a large amount of poly-β-hydroxybutyrate, and exhibited low PDH activity. The physiology and genomes of these strains showed features that may have resulted from their lifestyle inside the seeds: stress sensitivity, a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, a homocitrate synthase (usually present only in free-living diazotrophs), a hydrogenase uptake cluster, and the presence of prophages. We propose that colonization by rhizobia and their presence in
Phaseolus
seeds may be part of a persistence mechanism that helps to retain and disperse rhizobial strains.
Identification of Two Nickel Ion-Induced Genes,
NCI16
and Pc
GST1
, in Paramecium caudatum
Authors: Takenaka Yasuhiro , Haga Nobuyuki , Inoue Ikuo , Nakano Takanari , Ikeda Masaaki , Katayama Shigehiro , Awata Takuya 
Published: July 2014

ABSTRACT

Here, we describe the isolation of two nickel-induced genes in
Paramecium caudatum
,
NCI16
and Pc
GST1
, by subtractive hybridization.
NCI16
encoded a predicted four-transmembrane domain protein (∼16 kDa) of unknown function, and Pc
GST1
encoded glutathione
S
-transferase (GST; ∼25 kDa) with GST and glutathione peroxidase (GPx) activities. Exposing cells to cobalt chloride also caused the moderate upregulation of
NCI16
and Pc
GST1
mRNAs. Both nickel sulfate and cobalt chloride dose dependently induced
NCI16
and Pc
GST1
mRNAs, but with different profiles. Nickel treatment caused a continuous increase in Pc
GST1
and
NCI16
mRNA levels for up to 3 and 6 days, respectively, and a notable increase in H
2
O
2
concentrations in
P. caudatum
.
NCI16
expression was significantly enhanced by incubating cells with H
2
O
2
, implying that
NCI16
induction in the presence of nickel ions is caused by reactive oxygen species (ROS). On the other hand, Pc
GST1
was highly induced by the antioxidant
tert
-butylhydroquinone (tBHQ) but not by H
2
O
2
, suggesting that different mechanisms mediate the induction of
NCI16
and Pc
GST1
. We introduced a luciferase reporter vector with an ∼0.42-kb putative Pc
GST1
promoter into cells and then exposed the transformants to nickel sulfate. This resulted in significant luciferase upregulation, indicating that the putative Pc
GST1
promoter contains a nickel-responsive element. Our nickel-inducible system also may be applicable to the efficient expression of proteins that are toxic to host cells or require temporal control.
Efg1 Directly RegulatesACE2Expression To Mediate Cross Talk between the cAMP/PKA and RAM Pathways during Candida albicans Morphogenesis
Authors: Saputo Sarah , Kumar Anuj , Krysan Damian J. 
Published: July 2014

ABSTRACTThe cyclic AMP/protein kinase A (cAMP/PKA) andregulation ofAce2 andmorphogenesis (RAM) pathways are important regulators of the yeast-to-hypha transition inCandida albicansthat interact genetically during this process. To further understand this interaction, we have characterized the expression ofACE2during morphogenesis. In normoxic, planktonic conditions,ACE2expression is very low in stationary-phase cells at both the mRNA and protein levels. Upon shifting to Spider medium,ACE2/Ace2p levels increase. Although Ace2 is not absolutely required for hypha formation,ace2Δ/Δ mutants show delayed hypha formation in Spider medium (but not others) and morphological changes to the hyphal tip and lateral yeast. We also show that Efg1 directly binds the promoter of Ace2 in stationary phase, andACE2levels are increased in strains lacking Efg1 and the protein kinase A proteins Tpk1 and Tpk2, indicating that the PKA pathway directly regulatesACE2expression.ACE2expression is positively regulated by Tec1 and Brg1, which bind the promoters ofACE2in hyphal cells but not in the yeast phase. Under embedded conditions, Efg1 is dispensable for filamentation and Ace2 is required. We have found thatACE2expression is much higher in embedded cells than in planktonic cells, providing a potential rationale for this observation. Taken together, our observations indicate that the PKA pathway directly regulates the RAM pathway under specific conditions and are consistent with a model where the two pathways carry out similar functions that depend on the specific environmental context.