bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events
Authors: Patrick Ralph , Lê Cao Kim-Anh , Kobe Bostjan , Bodén Mikael 
Published: October 2014

Abstract
Motivation: The determinants of kinase-substrate phosphorylation can be found both in the substrate sequence and the surrounding cellular context. Cell cycle progression, interactions with mediating proteins and even prior phosphorylation events are necessary for kinases to maintain substrate specificity. While much work has focussed on the use of sequence-based methods to predict phosphorylation sites, there has been very little work invested into the application of systems biology to understand phosphorylation. Lack of specificity in many kinase substrate binding motifs means that sequence methods for predicting kinase binding sites are susceptible to high false-positive rates.
Results: We present here a model that takes into account protein–protein interaction information, and protein abundance data across the cell cycle to predict kinase substrates for 59 human kinases that are representative of important biological pathways. The model shows high accuracy for substrate prediction (with an average AUC of 0.86) across the 59 kinases tested. When using the model to complement sequence-based kinase-specific phosphorylation site prediction, we found that the additional information increased prediction performance for most comparisons made, particularly on kinases from the CMGC family. We then used our model to identify functional overlaps between predicted CDK2 substrates and targets from the E2F family of transcription factors. Our results demonstrate that a model harnessing context data can account for the short-falls in sequence information and provide a robust description of the cellular events that regulate protein phosphorylation.
Availability and implementation: The method is freely available online as a web server at the website http://bioinf.scmb.uq.edu.au/phosphopick .
Contact: m.boden@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
A stochastic automaton model for simulating kinesin processivity
Authors: Khataee Hamidreza , Liew Alan Wee-Chung 
Published: October 2014

Abstract
Motivation: Cellular interactions of kinesin-1, an adenosine triphosphate (ATP)-driven motor protein capable of undergoing multiple steps on a microtubule (MT), affect its mechanical processivity, the number of steps taken per encounter with MT. Even though the processivity of kinesin has been widely studied, a detailed study of the factors that affect the stepping of the motor along MT is still lacking.
Results: We model the cellular interactions of kinesin as a probabilistic timed automaton and use the model to simulate the mechanical processivity of the motor. Theoretical analysis suggests: (i) backward stepping tends to be powered by ATP hydrolysis, rather than ATP synthesis, (ii) backward stepping powered by ATP synthesis is more likely to happen with limiting ATP concentration ([ATP]) at high loads and (iii) with increasing load the frequency of backward stepping powered by ATP hydrolysis at high [ATP] is greater than that powered by ATP synthesis at limiting [ATP]. Together, the higher frequency of backward stepping powered by ATP hydrolysis than by ATP synthesis is found to be a reason for the more dramatic falling of kinesin processivity with rising load at high [ATP] compared with that at low [ATP]. Simulation results further show that the processivity of kinesin can be determined by the number of ATP hydrolysis and synthesis kinetic cycles taken by the motor before becoming inactive. It is also found that the duration of a backward stepping cycle at high loads is more likely to be less than that of a forward stepping cycle.
Contact: h.r.khataee@griffithuni.edu.au or a.liew@griffith.edu.au .
Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs
Authors: Zielezinski Andrzej , Karlowski Wojciech M. 
Published: October 2014

Abstract
Motivation: Argonaute-interacting WG/GW proteins are characterized by the presence of repeated sequence motifs containing glycine (G) and tryptophan (W). The motifs seem to be remarkably adaptive to amino acid substitutions and their sequences show non-contiguity. Our previous approach to the detection of GW domains, based on scoring their gross amino acid composition, allowed annotation of several novel proteins involved in gene silencing. The accumulation of new experimental data and more advanced applications revealed some deficiency of the algorithm in prediction selectivity. Additionally, W-motifs, though critical in gene regulation, have not yet been annotated in any available online resources.
Results: We present an improved set of computational tools allowing efficient management and annotation of W-based motifs involved in gene silencing. The new prediction algorithms provide novel functionalities by annotation of the W-containing domains at the local sequence motif level rather than by overall compositional properties. This approach represents a significant improvement over the previous method in terms of prediction sensitivity and selectivity. Application of the algorithm allowed annotation of a comprehensive list of putative Argonaute-interacting proteins across eukaryotes. An in-depth characterization of the domains’ properties indicates its intrinsic disordered character. In addition, we created a knowledge-based portal (whub) that provides access to tools and information on RNAi-related tryptophan-containing motifs.
Availability and implementation: The web portal and tools are freely available at http://www.comgen.pl/whub .
Contact: wmk@amu.edu.pl
Supplementary information: Supplementary data are available at Bioinformatics online.
Tabhu: tools for antibody humanization
Authors: Olimpieri Pier Paolo , Marcatili Paolo , Tramontano Anna 
Published: October 2014

Abstract
Summary: Antibodies are rapidly becoming essential tools in the clinical practice, given their ability to recognize their cognate antigens with high specificity and affinity, and a high yield at reasonable costs in model animals. Unfortunately, when administered to human patients, xenogeneic antibodies can elicit unwanted and dangerous immunogenic responses. Antibody humanization methods are designed to produce molecules with a better safety profile still maintaining their ability to bind the antigen. This can be accomplished by grafting the non-human regions determining the antigen specificity into a suitable human template. Unfortunately, this procedure may results in a partial or complete loss of affinity of the grafted molecule that can be restored by back-mutating some of the residues of human origin to the corresponding murine ones. This trial-and-error procedure is hard and involves expensive and time-consuming experiments. Here we present tools for antibody humanization (Tabhu) a web server for antibody humanization. Tabhu includes tools for human template selection, grafting, back-mutation evaluation, antibody modelling and structural analysis, helping the user in all the critical steps of the humanization experiment protocol.
Availability: http://www.biocomputing.it/tabhu
Contact: anna.tramontano@uniroma1.it , pierpaolo.olimpieri@uniroma1.it
Supplementary information : Supplementary data are available at Bioinformatics online.
Deciphering the origin of flowering plants
Authors: Wang By Ling 
Published: October 2014

Abstract
Colorful flowers decorate our planet with their appealing forms, yet their enigmatic evolutionary origin and rapid early diversification have been regarded as the ‘Goldbach conjecture’ of paleobotany. Else Marie Friis is a prominent professor who in 1981 was the first to identify the small angiosperm flowers that changed our perception of ancestral flowers and opened up a new direction in the study of angiosperm evolution. As a foreign member of Chinese Academy of Sciences (CAS), Professor Friis helps strengthen the scholarly communication and cooperation between China and Europe, especially in paleobotany. NSR got the chance to talk to Professor Friis about her research and developments in this field during her last visit to China. Professor Zhonghe Zhou, a paleontologist at the Institute of Vertebrate Paleontology and Paleoanthropology, CAS, joined the interview.
Factors Associated with Improved Survival after Resection of Pancreatic Adenocarcinoma
Authors: Call Tyler R. , Pace Nathan L. , Thorup Datus B. , Maxfield Derric , Chortkoff Ben , Christensen Joslin , Mulvihill Sean J. 
Published: October 2014

AbstractAbstract
A model based on retrospective analysis of the records of 144 patients who underwent resection of pancreatic adenocarcinoma between 2001 and 2011 predicted median survival of patients to whom dexamethasone is administered and who have epidural analgesia would be increased from 370 days to 651 days compared to similar patients receiving neither dexamethasone nor epidural analgesia.

Background:
Several retrospective studies suggest that perioperative care and anesthetic management for cancer resection may influence cancer recurrence or patient survival. Various intraoperative techniques such as paravertebral blocks, decreased opioid use, immunomodulation, and perioperative antiinflammatory administration, have previously been assessed for improved patient survival. The aim of this study was to assess associations between perioperative management and survival in patients undergoing resection of pancreatic adenocarcinoma.

Methods:
Survival data and anesthetic records for 144 patients who had surgical resection of pancreatic adenocarcinoma from 2001 to 2012 were obtained and associations were sought between survival and 19 predefined variables. The authors performed a propensity weighted multivariable statistical analysis using Cox proportional hazards.

Results:
Median length of survival was 562 days with 95% confidence interval (471, 680). In a multivariable Cox proportional hazard model of survival, the authors found increased survival in patients who received perioperative epidural analgesia and/or intraoperative dexamethasone. There was a 44% hazard ratio reduction, hazard ratio = 0.56, 95% confidence interval (0.38, 0.87), with dexamethasone. Adjuvant postoperative chemotherapy was associated with longer survival. A decrease in survival was noted in patients who received intraoperative blood transfusions, had poorer histologic grade, and advanced tumor stage.

Conclusions:
The authors report an association between perioperative dexamethasone administration and improved survival in human pancreatic adenocarcinoma patients. An association between use of epidural anesthesia during primary pancreatic cancer surgery and prolonged survival was also observed. Previously identified associations between perioperative blood transfusions and poor tumor histologic grade and decreased survival were confirmed. Further investigations regarding the use of perioperative dexamethasone and neuraxial anesthesia in this patient population are warranted.
Massive bursts of transposable element activity in Drosophila
Authors: Kofler Robert , Nolte Viola , Schlötterer Christian 
Published: October 2014

AbstractThe evolutionary dynamics of transposable element (TE) insertions have been of continued interest since TE activity has important implications for genome evolution and adaptation. Here, we infer the transposition dynamics of TEs by comparing their abundance in naturalD. melanogasterandD. simulanspopulations. Sequencing pools of more than 550 South African flies to at least 320-fold coverage, we determined the genome wide TE insertion frequencies in both species. We show that 46 (49%) TE families inD. melanogasterand 44 (47%) inD. simulansexperienced a recent burst of activity. The bursts of activity affected different TE families in the two species. While inD. melanogasterretrotransposons predominated, DNA transposons showed higher activity levels inD. simulans. We propose that the observed TE dynamics are the outcome of the demographic history of the two species, with habitat expansion triggering a period of rapid evolution.
A simple method for constructing magneticEscherichia coli
Authors: Sun Mengyi , Lu Yong-jun 
Published: October 2014

AbstractMagnetic force can serve as an ideal way to control the spatial behavior of microorganisms, because of its flexibility and penetrability. By incubation with the biocompatible compound, ammonium ferric citrate, as an iron source, we magnetizedEscherichia coli, the most programmable chassis in synthetic biology. To enhance the magnetization efficiency, the ferritin protein, FtnA, fromE. coliwas cloned and overexpressed in strain BL21(DE3). The magnetization effect was observed within 30 min after harvest of bacteria, and the concentration of ammonium ferric acid used could be as low as 0.5 mM. Using different shapes of magnetic fields, different patterns could be generated easily. Our method may set up the foundation for a rational design of spatial structure of cell communities, which is important for their actual application.
ArabidopsisTTG2 RegulatesTRYExpression through Enhancement of Activator Complex-Triggered Activation
Authors: Pesch Martina , Dartan Burcu , Birkenbihl Rainer , Somssich Imre E. , Hülskamp Martin 
Published: October 2014

AbstractTrichome patterning in Arabidopsis thaliana is regulated by a regulatory feedback loop of the trichome promoting factors TRANSPARENT TESTA GLABRA1 (TTG1), GLABRA3 (GL3)/ENHANCER OF GL3 (EGL3), and GL1 and a group of homologous R3MYB proteins that act as their inhibitors. Together, they regulate the temporal and spatial expression of GL2 and TTG2, which are considered to control trichome cell differentiation. In this work, we show that TTG2 is a specific activator of TRY (but not CPC or GL2). The WRKY protein TTG2 binds to W-boxes in a minimal promoter fragment of TRY, and these W-boxes are essential for rescue of the try mutant phenotype. We further show that TTG2 alone is not able to activate TRY expression, but rather drastically enhances the activation by TTG1 and GL3. As TTG2 physically interacts with TTG1 and because TTG2 can associate with GL3 through its interaction with TTG1, we propose that TTG2 enhances the activity of TTG1 and GL3 by forming a protein complex.
Myrosin Idioblast Cell Fate and Development Are Regulated by theArabidopsisTranscription Factor FAMA, the Auxin Pathway, and Vesicular Trafficking
Authors: Li Meng , Sack Fred D. 
Published: October 2014

AbstractCrucifer shoots harbor a glucosinolate-myrosinase system that defends against insect predation. Arabidopsis thaliana myrosinase (thioglucoside glucohydrolase [TGG]) accumulates in stomata and in myrosin idioblasts (MIs). This work reports that the basic helix-loop-helix transcription factor FAMA that is key to stomatal development is also expressed in MIs. The loss of FAMA function abolishes MI fate as well as the expression of the myrosinase genes TGG1 and TGG2. MI cells have previously been reported to be located in the phloem. Instead, we found that MIs arise from the ground meristem rather than provascular tissues and thus are not homologous with phloem. Moreover, MI patterning and morphogenesis are abnormal when the function of the ARF-GEF gene GNOM is lost as well as when auxin efflux and vesicular trafficking are chemically disrupted. Stomata and MI cells constitute part of a wider system that reduces plant predation, the so-called “mustard oil bomb,” in which vacuole breakage in cells harboring myrosinase and glucosinolate yields a brew toxic to many animals, especially insects. This identification of the gene that confers the fate of MIs, as well as stomata, might facilitate the development of strategies for engineering crops to mitigate predation.
Habitat evaluation for outbreak of Yangtze voles (Microtus fortis) and management implications
Authors: XU Zhenggang , ZHAO Yunlin , LI Bo , ZHANG Meiwen , SHEN Guo , WANG Yong 
Published: October 2014

AbstractRodent pests severely damage agricultural crops. Outbreak risk models of rodent pests often do not include sufficient information regarding geographic variation. Habitat plays an important role in rodent–pest outbreak risk, and more information about the relationship between habitat and crop protection is urgently needed. The goal of the present study was to provide an outbreak risk map for the Dongting Lake region and to understand the relationship between rodent–pest outbreak variation and habitat distribution. The main rodent pests in the Dongting Lake region are Yangtze voles (Microtus fortis). These pests cause massive damage in outbreak years, most notably in 2007. Habitat evaluation and ecological details were obtained by analyzing the correlation between habitat suitability and outbreak risk, as indicated by population density and historical events. For the source‐sink population, 96.18% of Yangtze vole disaster regions were covered by a 10‐km buffer zone of suitable habitat in 2007. Historical outbreak frequency and peak population density were significantly correlated with the proportion of land covered by suitable habitat (r = 0.68, P = 0.04 and r = 0.76, P = 0.03, respectively). The Yangtze vole population tends to migrate approximately 10 km in outbreak years. Here, we propose a practical method for habitat evaluation that can be used to create integrated pest management plans for rodent pests when combined with basic information on the biology, ecology and behavior of the target species.
Screening of Tea Extract and Theaflavins for Inhibitory Effects on the Biological Activity and Production of Staphylococcal Enterotoxin A
Authors: Shimamura Yuko , Aoki Natsumi , Sugiyama Yuka , Nakayama Tsutomu , Masuda Shuichi 
Published: October 2014

AbstractThis study aimed to develop a novel method with tea extracts and its components, to reduce the risk of foodborne illnesses caused by the bacterial toxin staphylococcal enterotoxin A (SEA). The potential effect of tea extracts, theaflavins, and epitheaflagallin on staphylococcal growth was studied. A broth microdilution method was used to determine the minimum inhibitory concentration of these samples against an SEA‐producing strain, Staphylococcus aureus C‐29. The following assays were performed to evaluate various effects on concentrations of no effect on staphylococcal growth. The interactions of theaflavin‐rich green tea extracts (TGE), theaflavins, and epitheaflagallin to cultured S. aureus C‐29 were determined using Western blot analysis. As a result, all samples suppressed the binding affinity of the anti‐SEA antibody to SEA. Since these samples could react directly with SEA, we examined whether they could bind to SEA. Our results demonstrated that binding of the anti‐SEA antibody to 4 theaflavins‐treated SEA was inhibited in a dose‐dependent manner. On the other hand, the production of SEA was significantly decreased by treatment with TGE and epitheaflagallin. Based on the finding that TGE and epitheaflagallin inhibit the production of SEA, we further examined the relative expression levels of sea toxin‐encoding genes after treatment with TGE and epitheaflagallin with real‐time RT‐PCR. TGE and epitheaflagallin significantly supressed the gene transcription of SEA in S. aureus C‐29. We then tested whether the samples block the biological activity of SEA in murine spleen cells. TGE, theaflavins, and epitheaflagallin became inactivated the biological activity of SEA. These results suggest that edible and safe compounds in tea can be used to inactivate both pathogens and toxins.
Phenolic Profile and Antioxidant Activity of Extracts Prepared from Fermented Heat‐Stabilized Defatted Rice Bran
Authors: Webber Daniel M. , Hettiarachchy Navam S. , Li Ruiqi , Horax Ronny , Theivendran Sivarooban 
Published: October 2014

AbstractHeat‐stabilized, defatted rice bran (HDRB) serves as a potential source of phenolic compounds which have numerous purported health benefits. An estimated 70% of phenolics present in rice bran are esterified to the arabinoxylan residues of the cell walls. Release of such compounds could provide a value‐added application for HDRB. The objective of this study was to extract and quantify phenolics from HDRB using fermentation technology. Out of 8 organisms selected for rice bran fermentation, Bacillus subtilis subspecies subtilis had the maximum phenolic release of 26.8 mg ferulic acid equivalents (FAE) per gram HDRB. Response surface methodology was used to further optimize the release of rice bran phenolics. An optimum of 28.6 mg FAE/g rice bran was predicted at 168 h, 0.01% inoculation level, and 100 mg HDRB/mL. Fermentation of HDRB for 96 h with B. subtilis subspecies subtilis resulted in a significant increase in phenolic yield, phenolic concentration, and radical scavenging capacity. Fermented rice bran had 4.86 mg gentistic acid, 1.38 mg caffeic acid, 6.03 mg syringic acid, 19.02 mg (‐)‐epicatechin, 4.08 mg p‐courmaric acid, 4.64 mg ferulic acid, 10.04 mg sinapic acid, and 17.59 mg benzoic acid per 100 g fermented extract compared to 0.65 mg p‐courmaric acid and 0.36 mg ferulic acid per 100 g nonfermented extract. The high phenolic content and antioxidant activity of fermented HDRB extract indicates that rice bran fermentation under optimized condition is a potential means of meeting the demand for an effective and affordable antioxidant.
Characterization of Physicochemical Properties and IgE‐Binding of Soybean Proteins Derived from the HHP‐Treated Seeds
Authors: Yang Hui , Yang Anshu , Gao Jinyan , Chen Hongbing 
Published: October 2014

AbstractThe aim of this work was to evaluate the characterization of physicochemical properties and IgE‐binding of soybean proteins derived from the high hydrostatic pressure (HHP) treated seeds. Soybean seeds were treated by HHP at different pressures, and changes in the physicochemical properties of soybean proteins were characterized by proteins solubility, free sulfhydryl (SH) content, surface hydrophobicity, and secondary structures. Sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE) and enzyme‐linked immunoabsorbent assay (ELISA) were used to define the proteins patterns and IgE‐binding ability. The results showed that HHP treatment in the ranges of 0 to 500 MPa led to a slight but gradual decline in free SH content. The solubility and hydrophobicity of soybean proteins increased sharply from 100 to 200 MPa, and gradually decreased upon the further increase of pressure. The α‐helix and β‐sheets contents of soybean proteins decreased, while the random coil content increased. The SDS‐PAGE showed that HHP treatment of 100 to 200 MPa could dissociate the proteins, breaking the aggregates into smaller units, while the treatment ranging from 300 to 500 MPa could induce the proteins aggregation into larger units. Moreover, the ELISA revealed that the IgE‐binding of soybean proteins after HHP treatment at 200 MPa decreased 61.7% compared to the untreated group. Our findings suggested that HHP processing could not only modify the physicochemical properties of soybean proteins, but also significantly reduce its IgE‐binding at an appropriate pressure level.