bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relative importance of autotrophic and heterotrophic microbial communities in the planktonic food web of the Bay of Quinte, Lake Ontario 2000–2007
Authors: Munawar M. , Fitzpatrick M. , Niblock H. , Lorimer J. 
Published: March 2011

The structure and function of the microbial and planktonic communities of the Bay of Quinte, Lake Ontario were studied for 8 years from 2000 to 2007. The bay has a long history of eutrophication and has undergone remediation efforts which included reductions in phosphorus loadings and the implementation of a long term research and monitoring program (1972–present) conducted by Fisheries and Oceans Canada along with other federal and provincial agencies. Microbial loop research was added in 2000 to the ongoing monitoring program which included nutrients, phytoplankton, zooplankton, benthos and fish so that a comprehensive picture of food web linkages would emerge. The structure of the microbial-planktonic food web was determined based on microscopic analysis of bacteria, autotrophic picoplankton (APP), heterotrophic nanoflagellates (HNF), ciliates, phytoplankton and zooplankton and was compared to a traditional grazing food chain consisting of phytoplankton and zooplankton. On a seasonal weighted mean basis, HNF biomass (fresh weight) of 1.7–8.4 g m−3 at Belleville and 1.1–6.3 C m−3 at Conway exceeded that of zooplankton in virtually all observations and was often greater than the combination of phytoplankton and zooplankton. Furthermore, the results showed that HNF contributed upwards to 85% of the organic carbon pool on a seasonal weighted mean basis. Various parameters in the upper bay relating trophic status to autotrophic communities were measured including: point source phosphorus loadings (&gt;10 kg d−1); primary production (&gt;300 g C m−2 y−1); chlorophyll a (&gt;12 μg l−1) and phytoplankton biomass (&gt;3 g m−3) which indicated that the upper bay remained eutrophic. This was also confirmed by the “battery of tests” strategy of ecological indicators developed in our laboratory to assess trophic status, health, and potential Beneficial Use Impairments. Based on our observations spanning 8 years, it was concluded that the microbial food web was dominated by heterotrophic communities which are still widely ignored in Great Lakes research and monitoring efforts. Our data clearly demonstrates that future studies and management strategies should include the “microbial loop” to obtain a holistic picture of the structure, function and dynamics of the lower food web.
Study of melt flow dynamics and influence on quality for CO2 laser fusion cutting
Authors: Riveiro A , Quintero F , Lusquiños F , Comesaña R , Pou J 
Published: March 2011

The understanding of melt flow dynamics during fusion laser cutting is still a topic of great importance because this determines the quality characteristics of the processed workpiece. Despite the complexity of the experimental study of the physical processes involved in this technique, fusion laser cutting can be visualized during the processing of glass because this material absorbs the laser radiation provided by a CO2 laser but shows transparency to visible radiation. Then, we present in this work the results of the study of the melt flow dynamics during laser cutting of glass. Under different experimental conditions, the dynamics of the cutting front and its complete geometry (front wall inclination), and the evolution of the melt along the cut edge were analysed using a high-speed video camera to study the process. A phenomenon concerning the plasma plume formed during the process was observed, which has not been previously reported in the literature. This can displace the normal shock wave (MSD) commonly formed in the inlet kerf and can affect the assist gas flow into the kerf.
On the other hand, the analysis of the recorded images allowed the determination of not only the amount of molten material along the cut edge but also the direction and velocity of the melt. Relevant processing parameters affecting the flow of molten material were assessed. These results were used as a basis to explain the different processes involved in the generation of dross, a typical imperfection appearing in laser cutting.
Silencing of Soybean Seed Storage Proteins Results in a Rebalanced Protein Composition Preserving Seed Protein Content without Major Collateral Changes in the Metabolome and Transcriptome
Authors: Schmidt Monica A. , Barbazuk W. Brad , Sandford Michael , May Greg , Song Zhihong , Zhou Wenxu , Nikolau Basil J. , Herman Eliot M. 
Published: March 2011

AbstractThe ontogeny of seed structure and the accumulation of seed storage substances is the result of a determinant genetic program. Using RNA interference, the synthesis of soybean (Glycine max) glycinin and conglycinin storage proteins has been suppressed. The storage protein knockdown (SP−) seeds are overtly identical to the wild type, maturing to similar size and weight, and in developmental ontogeny. The SP− seeds rebalance the proteome, maintaining wild-type levels of protein and storage triglycerides. The SP− soybeans were evaluated with systems biology techniques of proteomics, metabolomics, and transcriptomics using both microarray and next-generation sequencing transcript sequencing (RNA-Seq). Proteomic analysis shows that rebalancing of protein content largely results from the selective increase in the accumulation of only a few proteins. The rebalancing of protein composition occurs with small alterations to the seed’s transcriptome and metabolome. The selectivity of the rebalancing was further tested by introgressing into the SP− line a green fluorescent protein (GFP) glycinin allele mimic and quantifying the resulting accumulation of GFP. The GFP accumulation was similar to the parental GFP-expressing line, showing that the GFP glycinin gene mimic does not participate in proteome rebalancing. The results show that soybeans make large adjustments to the proteome during seed filling and compensate for the shortage of major proteins with the increased selective accumulation of other proteins that maintains a normal protein content.
HISTONE DEACETYLASE6 Interacts with FLOWERING LOCUS D and Regulates Flowering in Arabidopsis
Authors: Yu Chun-Wei , Liu Xuncheng , Luo Ming , Chen Chiayang , Lin Xiaodong , Tian Gang , Lu Qing , Cui Yuhai , Wu Keqiang 
Published: March 2011

Abstract
Histone acetylation and deacetylation play an important role in epigenetic controls of gene expression. HISTONE DEACETYLASE6 (HDA6) is a REDUCED POTASSIUM DEPENDENCY3-type histone deacetylase, and the Arabidopsis (Arabidopsis thaliana) hda6 mutant axe1-5 displayed a late-flowering phenotype. axe1-5/flc-3 double mutants flowered earlier than axe1-5 plants, indicating that the late-flowering phenotype of axe1-5 was FLOWERING LOCUS C (FLC) dependent. Bimolecular fluorescence complementation, in vitro pull-down, and coimmunoprecipitation assays revealed the protein-protein interaction between HDA6 and the histone demethylase FLD. It was found that the SWIRM domain in the amino-terminal region of FLD and the carboxyl-terminal region of HDA6 are responsible for the interaction between these two proteins. Increased levels of histone H3 acetylation and H3K4 trimethylation at FLC, MAF4, and MAF5 were found in both axe1-5 and fld-6 plants, suggesting functional interplay between histone deacetylase and demethylase in flowering control. These results support a scenario in which histone deacetylation and demethylation cross talk are mediated by physical association between HDA6 and FLD. Chromatin immunoprecipitation analysis indicated that HDA6 bound to the chromatin of several potential target genes, including FLC and MAF4. Genome-wide gene expression analysis revealed that, in addition to genes related to flowering, genes involved in gene silencing and stress response were also affected in hda6 mutants, revealing multiple functions of HDA6. Furthermore, a subset of transposons was up-regulated and displayed increased histone hyperacetylation, suggesting that HDA6 can also regulate transposons through deacetylating histone.
The pharmacodynamic and pharmacokinetic profile of intranasal crushed buprenorphine and buprenorphine/naloxone tablets in opioid abusers
Authors: Middleton Lisa S. , Nuzzo Paul A. , Lofwall Michelle R. , Moody David E. , Walsh Sharon L. 
Published: March 2011

ABSTRACTAims  Sublingual buprenorphine and buprenorphine/naloxone are efficacious opioid dependence pharmacotherapies, but there are reports of their diversion and misuse by the intranasal route. The study objectives were to characterize and compare their intranasal pharmacodynamic and pharmacokinetic profiles.Design  A randomized, double‐blind, placebo‐controlled, cross‐over study.Setting  An in‐patient research unit at the University of Kentucky.Participants  Healthy adults (n = 10) abusing, but not physically dependent on, intranasal opioids.Measurements  Six sessions (72 hours apart) tested five intranasal doses [0/0, crushed buprenorphine (2, 8 mg), crushed buprenorphine/naloxone (2/0.5, 8/2 mg)] and one intravenous dose (0.8 mg buprenorphine/0.2 mg naloxone for bioavailability assessment). Plasma samples, physiological, subject‐ and observer‐rated measures were collected before and for up to 72 hours after drug administration.Findings  Both formulations produced time‐ and dose‐dependent increases on subjective and physiological mu‐opioid agonist effects (e.g. ‘liking’, miosis). Subjects reported higher subjective ratings and street values for 8 mg compared to 8/2 mg, but these differences were not statistically significant. No significant formulation differences in peak plasma buprenorphine concentration or time–course were observed. Buprenorphine bioavailability was 38–44% and Tmax was 35–40 minutes after all intranasal doses. Naloxone bioavailability was 24% and 30% following 2/0.5 and 8/2 mg, respectively.Conclusions  It is difficult to determine if observed differences in abuse potential between intranasal buprenorphine and buprenorphine/naloxone are clinically relevant at the doses tested. Greater bioavailability and faster onset of pharmacodynamic effects compared to sublingual administration suggests a motivation for intranasal misuse in non‐dependent opioid abusers. However, significant naloxone absorption from intranasal buprenorphine/naloxone administration may deter the likelihood of intranasal misuse of buprenorphine/naloxone, but not buprenorphine, in opioid‐dependent individuals.
Population pharmacokinetic analysis of sorafenib in patients with solid tumours
Authors: Jain Lokesh , Woo Sukyung , Gardner Erin R. , Dahut William L. , Kohn Elise C. , Kummar Shivaani , Mould Diane R. , Giaccone Giuseppe , Yarchoan Robert , Venitz Jürgen , Figg William D. 
Published: March 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• Sorafenib is a multikinase inhibitor with activity against B‐raf, C‐raf, VEGFR2, PDGFRβ and FGFR1.• Sorafenib is clinically approved for the treatment of renal cell carcinoma (RCC) and hepatocellular carcinoma (HCC).• The pharmacokinetics (PK) of sorafenib are highly variable between subjects.• Sorafenib exposure increases less than dose proportionally (likely due to limited solubility).• Sorafenib undergoes enterohepatic recycling (EHC).WHAT THIS STUDY ADDS• This is the first study to characterize the PK of sorafenib using a model based on sorafenib's known disposition characteristics such as delayed/solubility‐limited GI absorption and EHC. The parameterization of the EHC model used a square wave function to describe the gall bladder emptying.• This study evaluated the effect of baseline bodyweight, BSA, age, gender, liver function parameters, kidney function parameters and genotype with respect to CYP3A4*1B, CYP3A5*3C, UGT1A9*3 and UGT1A9*5 on sorafenib PK. No clinically important covariates were identified.• This model can be used to simulate and explore alternative dosing regimens and to develop exposure–response relationships for sorafenib.AIMS To characterize the pharmacokinetics (PK) of sorafenib in patients with solid tumours and to evaluate the possible effects of demographic, clinical and pharmacogenetic (CYP3A4*1B, CYP3A5*3C, UGT1A9*3 and UGT1A9*5) covariates on the disposition of sorafenib.METHODS PK were assessed in 111 patients enrolled in five phase I and II clinical trials, where sorafenib 200 or 400 mg was administered twice daily as a single agent or in combination therapy. All patients were genotyped for polymorphisms in metabolic enzymes for sorafenib. Population PK analysis was performed by using nonlinear mixed effects modelling (NONMEM). The final model was validated using visual predictive checks and nonparametric bootstrap analysis.RESULTS A one compartment model with four transit absorption compartments and enterohepatic circulation (EHC) adequately described sorafenib disposition. Baseline bodyweight was a statistically significant covariate for distributional volume, accounting for 4% of inter‐individual variability (IIV). PK model parameter estimates (range) for an 80 kg patient were clearance 8.13 l h−1 (3.6–22.3 l h−1), volume 213 l (50–1000 l), mean absorption transit time 1.98 h (0.5–13 h), fraction undergoing EHC 50% and average time to gall bladder emptying 6.13 h.CONCLUSIONS Overall, population PK analysis was consistent with known biopharmaceutical/PK characteristics of oral sorafenib. No clinically important PK covariates were identified.
Oleanolic acid inhibits hypertrophic scarring in the rabbit ear model
Authors: Wei Y.-J. , Yan X.-Q. , Ma L. , Wu J.-G. , Zhang H. , Qin L.-P. 
Published: March 2011

Summary
Background. Hypertrophic scarring, a common proliferative disorder of dermal fibroblasts, results from an overproduction of collagen and excessive deposition of extracellular matrix. Although treatment with surgical excision or steroid hormones can modify the symptoms, numerous treatment-related complications have been described.
Aim. To investigate the effects of oleanolic acid (OA), a naturally occurring triterpenoid, on hypertrophic scarring in a rabbit ear model.
Methods. A rabbit ear model of hypertrophic scarring was used, with wounds produced with a biopsy punch. Oleanolic acid (2.5%, 5% and 10%) was applied once daily to the scars for 22 days. On postoperative day 28, the scars were excised, and the tissue used for histological examination and assays of the levels of collagens I and III, matrix metalloproteinase (MMP)-1 and transforming growth factor (TGF)-β1. The scar elevation index (SEI) was also determined.
Results. Treatment with different concentrations of oleanolic acid (OA) for 22 days significantly inhibited hypertrophic scarring in rabbit ear tissue. Levels of TGF-β1, collagen I and collagen III were significantly decreased and levels of MMP-1 significantly increased in the scar tissue. SEI was also significantly reduced. Histological findings showed significant amelioration of the scar tissue.
Conclusions. OA suppresses hypertrophic scarring in the rabbit ear model and may be an effective cure for human hypertrophic scarring.
Generalized granuloma annulare with open comedones in photoexposed areas
Authors: Bhushan P. , Aggarwal A. , Yadav R. , Baliyan V. 
Published: March 2011

Summary
Granuloma annulare (GA) is a noninfectious necrobiotic granuloma, which can present as localized or generalized patterns. We present a case of generalized GA with multiple large open comedones over the lesions in a woman with hypothyroidism and diabetes mellitus. GA is associated with collagen and elastic-fibre damage, which may lead to loss of follicular support and resultant open comedone formation, analogous to solar elastosis or senile comedones. The rapid recovery of our patient after treatment with of oral hypoglycaemics supports the role of insulin resistance as a predisposing factor for GA.
Study of enrofloxacin and flumequine residues depletion in eggs of laying hens after oral administration
Authors: CORNEJO J. , LAPIERRE L. , IRAGÜEN D. , CORNEJO S. , CASSUS G. , RICHTER P. , SAN MARTÍN B. 
Published: March 2011

Cornejo, J., Lapierre, L., Iragüen, D., Cornejo, S., Cassus, G., Richter, P., San Martín, B. Study of enrofloxacin and flumequine residues depletion in eggs of laying hens after oral administration. J. vet. Pharmacol. Therap. 35, 67–72.Two groups of laying hens (each n = 12) were administered 10 mg/kg enrofloxacin (ENRO) (group A) or 26.6 mg/kg flumequine (FLU) (group B) by gastric catheter daily for five consecutive days. A third group (n = 6) was untreated controls. Eggs were collected from day one of treatment and up to 30 days after withdrawal of the drug. Egg white and yolk from each egg were separated, and ENRO, its metabolite ciprofloxacin (CIP) and FLU residues were analysed by a high‐performance liquid chromatography method with fluorescence detection. The sum of ENRO and CIP was detectable in egg white on the first day of treatment in high‐level concentrations (2007.7 μg/kg) and remained steady during administration. In egg yolk, residues were detectable at day one in lower concentrations (324.4 μg/kg), increasing to the end of treatment. After treatment, these residues decreased and were detectable up to day 8 in egg white, and day 10 in yolk. FLU residues during drug administration in white were detectable in high concentrations from day one to five (6788.4–6525.9 μg/kg), and in yolk, concentrations were lower during administration (629.6–853.9 μg/kg). After drug withdrawal, FLU residues remained longer in egg white (30 days) than in yolk (26 days). For both drugs, differences of concentrations between matrices were significant.
Reprogramming the infection mechanism of a filamentous phage
Authors: Lorenz Stefan H. , Schmid Franz X. 
Published: March 2011

SummaryWhen they infect Escherichia coli cells, the filamentous phages IF1 and fd first interact with a pilus and then target TolA as their common receptor. They use the domains N2 and N1 of their gene‐3‐proteins (G3P) for these interactions but differ in the mechanism of infection. In G3P of phage IF1, N1 and N2 are independent modules that are permanently binding‐active. G3P of phage fd is usually in a closed state in which N1 and N2 are tightly associated. The TolA binding site is thus inaccessible and the phage incompetent for infection. Partial unfolding and prolyl isomerization must occur to abolish the domain interactions and expose the TolA binding site. This complex mechanism of phage fd could be changed to the simple infection mechanism of phage IF1 by reprogramming its G3P following physicochemical rules of protein stability. The redesigned phage fd was robust and as infectious as wild‐type phage fd.
Alanyl‐phosphatidylglycerol synthase: mechanism of substrate recognition during tRNA‐dependent lipid modification in Pseudomonas aeruginosa
Authors: Hebecker Stefanie , Arendt Wiebke , Heinemann Ilka U. , Tiefenau Jana H. J. , Nimtz Manfred , Rohde Manfred , Söll Dieter , Moser Jürgen 
Published: March 2011

SummaryBacterial lipid homeostasis plays an important role for the adaptation to changing environments and under conditions of antimicrobial treatment. The tRNA‐dependent aminoacylation of the phospholipid phosphatidylglycerol catalysed by aminoacyl‐phosphatidylglycerol synthases was shown to render various organisms less susceptible to antibacterial agents. Therefore, this type of enzyme might provide a new target to potentiate the efficacy of existing antimicrobials. This study makes use of the Pseudomonas aeruginosa alanyl‐phosphatidylglycerol synthase to identify the minimal core domain of this transmembrane protein, which is capable of alanyl‐phosphatidylglycerol biosynthesis. Using this catalytic fragment we established a reliable activity assay that was used to study the enzymatic mechanism by analysing an overall of 33 mutant proteins in vitro. Substrate recognition was analysed by using aminoacylated microhelices as analogues of the natural tRNA substrate. The enzyme even tolerated mutated versions of this minimal substrate, which indicates that neither the intact tRNA, nor the individual sequence of the acceptor stem is a determinant for substrate recognition. Furthermore, the analysis of derivatives of phosphatidylglycerol indicated that the polar head group of the phospholipid is specifically recognized by the enzyme, whereas modification of an individual fatty acid or even the deletion of a single fatty acid did not abolish A‐PG synthesis.
Anti‐activator QslA defines the quorum sensing threshold and response in Pseudomonas aeruginosa
Authors: Seet Qihui , Zhang Lian‐Hui 
Published: March 2011

SummaryQuorum sensing (QS) in a bacterial population is activated when extracellular concentration of QS signal reaches a threshold, but how this threshold is determined remains largely unknown. In this study, we report the identification and characterization of a novel anti‐activator encoded by qslA in Pseudomonas aeruginosa. The null mutation of qslA elevated AHL‐dependent QS and PQS signalling, increased the expression of QS‐dependent genes, and enhanced the virulence factor production and pathogenicity. We further present evidence that modulation of QS by QslA is due to protein–protein interaction with LasR, which prevents LasR from binding to its target promoter. QslA also influences the threshold concentration of QS signal needed for QS activation; in the absence of qslA, QS is activated by nine times less N‐3‐oxo‐dodecanoyl‐homoserine lactone (3‐oxo‐C12‐HSL) than that in wild type. The findings from this study depict a new mechanism that governs the QS threshold in P. aeruginosa.
The Aspergillus nidulans CENP‐E kinesin motor KipA interacts with the fungal homologue of the centromere‐associated protein CENP‐H at the kinetochore
Authors: Herrero Saturnino , Takeshita Norio , Fischer Reinhard 
Published: March 2011

SummaryChromosome segregation is an essential process for nuclear and cell division. The microtubule cytoskeleton, molecular motors and protein complexes at the microtubule plus ends and at kinetochores play crucial roles in the segregation process. Here we identified KatA (KipAtarget protein, homologue of CENP‐H) as a kinesin‐7 (KipA, homologue of human CENP‐E) interacting protein in Aspergillus nidulans. KatA located at the kinetochore during the whole cell cycle and colocalized with KipA and partially with the putative microtubule polymerase AlpA (XMAP215) during mitosis. Deletion of katA was lethal at 37°C and caused severe growth and morphology defects at room temperature. KipA was shown before to play an important role in growth directionality determination and our new results suggest a second function of KipA in the interaction between the microtubule plus ends and the kinetochores during mitosis.