bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unravelling the basis of variability in cobalamin levels in the general population
Authors: Andrew Toby , Gill Raj , Gillham-Nasenya Irina , Ahmadi Kourosh R. 
Published: April 2013

Cobalamin (Cbl) is an essential B vitamin involved in the normal functioning of the nervous system, the formation of key components of blood, DNA synthesis and methylation, and energy production. Physiological levels of Cbl vary greatly within populations, although the basis for this variability remains largely unknown. We conducted a twin study to characterise the basis of variation in plasma Cbl levels and to test whether common genetic polymorphisms in genes known to cause defects in inborn errors of Cbl metabolism and transport are also associated with mean plasma Cbl levels in the general population. The present results showed that plasma levels of Cbl were heritable, with genetic and phenotypic variance increasing with age, and levels significantly correlated with age, BMI, exercise, alcohol consumption, smoking status, social class and folate levels, which collectively accounted for up to 15 % of Cbl variation. Of eight genes responsible for the defects of the Cbl metabolic pathway (cblA–G and mut), MMAA, MMACHC, MTRR and MUT harboured polymorphisms that showed evidence of association with Cbl levels. Characterisation of the heritable component of variation in Cbl levels can facilitate the early diagnosis and prognosis of Cbl insufficiency/deficiency in individuals at a higher risk of associated diseases.
KGVDB: a population-based genomic map of CNVs tagged by SNPs in Koreans
Authors: Moon Sanghoon , Jung Kwang Su , Kim Young Jin , Hwang Mi Yeong , Han Kyungsook , Lee Jong-Young , Park Kiejung , Kim Bong-Jo 
Published: April 2013

Abstract
Summary: Despite a growing interest in a correlation between copy number variations (CNVs) and flanking single nucleotide polymorphisms, few databases provide such information. In particular, most information on CNV available so far was obtained in Caucasian and Yoruba populations, and little is known about CNV in Asian populations. This article presents a database that provides CNV regions tagged by single nucleotide polymorphisms in about 4700 Koreans, which were detected under strict quality control, manually curated and experimentally validated.
Availability: KGVDB is freely available for non-commercial use at http://biomi.cdc.go.kr/KGVDB.
Contact: kbj6181@cdc.go.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
OCSANA: optimal combinations of interventions from network analysis
Authors: Vera-Licona Paola , Bonnet Eric , Barillot Emmanuel , Zinovyev Andrei 
Published: April 2013

Abstract
Targeted therapies interfering with specifically one protein activity are promising strategies in the treatment of diseases like cancer. However, accumulated empirical experience has shown that targeting multiple proteins in signaling networks involved in the disease is often necessary. Thus, one important problem in biomedical research is the design and prioritization of optimal combinations of interventions to repress a pathological behavior, while minimizing side-effects. OCSANA (optimal combinations of interventions from network analysis) is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes. When specified by the user, OCSANA seeks to additionally minimize the side effects that a combination of interventions can cause on specified off-target nodes. With the crucial ability to cope with very large networks, OCSANA includes an exact solution and a novel selective enumeration approach for the combinatorial interventions’ problem.
Availability: The latest version of OCSANA, implemented as a plugin for Cytoscape and distributed under LGPL license, is available together with source code at http://bioinfo.curie.fr/projects/ocsana.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: paola.vera-licona@curie.fr
Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites
Authors: Chen Xiang , Qiu Jian-Ding , Shi Shao-Ping , Suo Sheng-Bao , Huang Shu-Yun , Liang Ru-Ping 
Published: April 2013

Abstract
Motivation: Systematic dissection of the ubiquitylation proteome is emerging as an appealing but challenging research topic because of the significant roles ubiquitylation play not only in protein degradation but also in many other cellular functions. High-throughput experimental studies using mass spectrometry have identified many ubiquitylation sites, primarily from eukaryotes. However, the vast majority of ubiquitylation sites remain undiscovered, even in well-studied systems. Because mass spectrometry–based experimental approaches for identifying ubiquitylation events are costly, time-consuming and biased toward abundant proteins and proteotypic peptides, in silico prediction of ubiquitylation sites is a potentially useful alternative strategy for whole proteome annotation. Because of various limitations, current ubiquitylation site prediction tools were not well designed to comprehensively assess proteomes.
Results: We present a novel tool known as UbiProber, specifically designed for large-scale predictions of both general and species-specific ubiquitylation sites. We collected proteomics data for ubiquitylation from multiple species from several reliable sources and used them to train prediction models by a comprehensive machine-learning approach that integrates the information from key positions and key amino acid residues. Cross-validation tests reveal that UbiProber achieves some improvement over existing tools in predicting species-specific ubiquitylation sites. Moreover, independent tests show that UbiProber improves the areas under receiver operating characteristic curves by ∼15% by using the Combined model.
Availability: The UbiProber server is freely available on the web at http://bioinfo.ncu.edu.cn/UbiProber.aspx. The software system of UbiProber can be downloaded at the same site.
Contact: jdqiu@ncu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
NetworkTrail—a web service for identifying and visualizing deregulated subnetworks
Authors: Stöckel Daniel , Müller Oliver , Kehl Tim , Gerasch Andreas , Backes Christina , Rurainski Alexander , Keller Andreas , Kaufmann Michael , Lenhof Hans-Peter 
Published: April 2013

Abstract
Summary: The deregulation of biochemical pathways plays a central role in many diseases like cancer or Parkinsons’s disease. In silico tools for calculating these deregulated pathways may help to gain new insights into pathogenic mechanisms and may open novel avenues for therapy stratification in the sense of personalized medicine. Here, we present NetworkTrail, a web service for the detection of deregulated pathways and subgraphs in biological networks. NetworkTrail uses a state-of-the-art integer linear programming-based approach for this task and offers interfaces to the Biological Network Analyzer (BiNA) and Cytoscape Web for visualizing the resulting subnetworks. By providing an accessible interface to otherwise hard-to-use command line tools, the new web service enables non-experts to quickly and reliably carry out this type of network analyses.
Availability and implementation: NetworkTrail is a JavaServer Pages-based web service. The algorithm for finding deregulated subnetworks has been implemented in C++. NetworkTrail is available at http://networktrail.bioinf.uni-sb.de/.
Contact: dstoeckel@bioinf.uni-sb.de
A Basic Helix-Loop-Helix Transcription Factor, PtrbHLH, of Poncirus trifoliata Confers Cold Tolerance and Modulates Peroxidase-Mediated Scavenging of Hydrogen Peroxide
Authors: Huang Xiao-San , Wang Wei , Zhang Qian , Liu Ji-Hong 
Published: April 2013

Abstract
The basic helix-loop-helix (bHLH) transcription factors are involved in a variety of physiological processes. However, plant bHLHs functioning in cold tolerance and the underlying mechanisms remain poorly understood. Here, we report the identification and functional characterization of PtrbHLH isolated from trifoliate orange (Poncirus trifoliata). The transcript levels of PtrbHLH were up-regulated under various abiotic stresses, particularly cold. PtrbHLH was localized in the nucleus with transactivation activity. Overexpression of PtrbHLH in tobacco (Nicotiana tabacum) or lemon (Citrus limon) conferred enhanced tolerance to cold under chilling or freezing temperatures, whereas down-regulation of PtrbHLH in trifoliate orange by RNA interference (RNAi) resulted in elevated cold sensitivity. A range of stress-responsive genes was up-regulated or down-regulated in the transgenic lemon. Of special note, several peroxidase (POD) genes were induced after cold treatment. Compared with the wild type, POD activity was increased in the overexpression plants but decreased in the RNAi plants, which was inversely correlated with the hydrogen peroxide (H2O2) levels in the tested lines. Treatment of the transgenic tobacco plants with POD inhibitors elevated the H2O2 levels and greatly compromised their cold tolerance, while exogenous replenishment of POD enhanced cold tolerance of the RNAi line. In addition, transgenic tobacco and lemon plants were more tolerant to oxidative stresses. Yeast one-hybrid assay and transient expression analysis demonstrated that PtrbHLH could bind to the E-box elements in the promoter region of a POD gene. Taken together, these results demonstrate that PtrbHLH plays an important role in cold tolerance, at least in part, by positively regulating POD-mediated reactive oxygen species removal.
Involvement of the Sieve Element Cytoskeleton in Electrical Responses to Cold Shocks
Authors: Hafke Jens B. , Ehlers Katrin , Föller Jens , Höll Sabina-Roxana , Becker Stefanie , van Bel Aart J.E. 
Published: April 2013

AbstractThis study dealt with the visualization of the sieve element (SE) cytoskeleton and its involvement in electrical responses to local cold shocks, exemplifying the role of the cytoskeleton in Ca2+-triggered signal cascades in SEs. High-affinity fluorescent phalloidin as well as immunocytochemistry using anti-actin antibodies demonstrated a fully developed parietal actin meshwork in SEs. The involvement of the cytoskeleton in electrical responses and forisome conformation changes as indicators of Ca2+ influx was investigated by the application of cold shocks in the presence of diverse actin disruptors (latrunculin A and cytochalasin D). Under control conditions, cold shocks elicited a graded initial voltage transient, ƊV1, reduced by external La3+ in keeping with the involvement of Ca2+ channels, and a second voltage transient, ƊV2. Cytochalasin D had no effect on ƊV1, while ƊV1 was significantly reduced with 500 nm latrunculin A. Forisome dispersion was triggered by cold shocks of 4°C or greater, which was indicative of an all-or-none behavior. Forisome dispersion was suppressed by incubation with latrunculin A. In conclusion, the cytoskeleton controls cold shock-induced Ca2+ influx into SEs, leading to forisome dispersion and sieve plate occlusion in fava bean (Vicia faba).
Reduced Tonoplast Fast-Activating and Slow-Activating Channel Activity Is Essential for Conferring Salinity Tolerance in a Facultative Halophyte, Quinoa
Authors: Bonales-Alatorre Edgar , Shabala Sergey , Chen Zhong-Hua , Pottosin Igor 
Published: April 2013

Abstract
Halophyte species implement a “salt-including” strategy, sequestering significant amounts of Na+ to cell vacuoles. This requires a reduction of passive Na+ leak from the vacuole. In this work, we used quinoa (Chenopodium quinoa) to investigate the ability of halophytes to regulate Na+-permeable slow-activating (SV) and fast-activating (FV) tonoplast channels, linking it with Na+ accumulation in mesophyll cells and salt bladders as well as leaf photosynthetic efficiency under salt stress. Our data indicate that young leaves rely on Na+ exclusion to salt bladders, whereas old ones, possessing far fewer salt bladders, depend almost exclusively on Na+ sequestration to mesophyll vacuoles. Moreover, although old leaves accumulate more Na+, this does not compromise their leaf photochemistry. FV and SV channels are slightly more permeable for K+ than for Na+, and vacuoles in young leaves express less FV current and with a density unchanged in plants subjected to high (400 mm NaCl) salinity. In old leaves, with an intrinsically lower density of the FV current, FV channel density decreases about 2-fold in plants grown under high salinity. In contrast, intrinsic activity of SV channels in vacuoles from young leaves is unchanged under salt stress. In vacuoles of old leaves, however, it is 2- and 7-fold lower in older compared with young leaves in control- and salt-grown plants, respectively. We conclude that the negative control of SV and FV tonoplast channel activity in old leaves reduces Na+ leak, thus enabling efficient sequestration of Na+ to their vacuoles. This enables optimal photosynthetic performance, conferring salinity tolerance in quinoa species.
Elucidation of the Structure and Reaction Mechanism of Sorghum Hydroxycinnamoyltransferase and Its Structural Relationship to Other Coenzyme A-Dependent Transferases and Synthases
Authors: Walker Alexander M. , Hayes Robert P. , Youn Buhyun , Vermerris Wilfred , Sattler Scott E. , Kang ChulHee 
Published: April 2013

Abstract
Hydroxycinnamoyltransferase (HCT) from sorghum (Sorghum bicolor) participates in an early step of the phenylpropanoid pathway, exchanging coenzyme A (CoA) esterified to p-coumaric acid with shikimic or quinic acid as intermediates in the biosynthesis of the monolignols coniferyl alcohol and sinapyl alcohol. In order to elucidate the mode of action of this enzyme, we have determined the crystal structures of SbHCT in its apo-form and ternary complex with shikimate and p-coumaroyl-CoA, which was converted to its product during crystal soaking. The structure revealed the roles of threonine-36, serine-38, tyrosine-40, histidine-162, arginine-371, and threonine-384 in catalysis and specificity. Based on the exact chemistry of p-coumaroyl-CoA and shikimic acid in the active site and an analysis of kinetic and thermodynamic data of the wild type and mutants, we propose a role for histidine-162 and threonine-36 in the catalytic mechanism of HCT. Considering the calorimetric data, substrate binding of SbHCT should occur sequentially, with p-coumaroyl-CoA binding prior to the acyl acceptor molecule. While some HCTs can use both shikimate and quinate as an acyl acceptor, SbHCT displays low activity toward quinate. Comparison of the structure of sorghum HCT with the HCT involved in chlorogenic acid synthesis in coffee (Coffea canephora) revealed many shared features. Taken together, these observations explain how CoA-dependent transferases with similar structural features can participate in different biochemical pathways across species.
Characterization of the Complex Regulation of AtALMT1 Expression in Response to Phytohormones and Other Inducers
Authors: Kobayashi Yasufumi , Kobayashi Yuriko , Sugimoto Miki , Lakshmanan Venkatachalam , Iuchi Satoshi , Kobayashi Masatomo , Bais Harsh P. , Koyama Hiroyuki 
Published: April 2013

Abstract
In Arabidopsis (Arabidopsis thaliana), malate released into the rhizosphere has various roles, such as detoxifying rhizotoxic aluminum (Al) and recruiting beneficial rhizobacteria that induce plant immunity. ALUMINUM-ACTIVATED MALATE TRANSPORTER1 (AtALMT1) is a critical gene in these responses, but its regulatory mechanisms remain unclear. To explore the mechanism of the multiple responses of AtALMT1, we profiled its expression patterns in wild-type plants, in transgenic plants harboring various deleted promoter constructs, and in mutant plants with defects in signal transduction in response to various inducers. AtALMT1 transcription was clearly induced by indole-3-acetic acid (IAA), abscisic acid (ABA), low pH, and hydrogen peroxide, indicating that it was able to respond to multiple signals, while it was not induced by methyl jasmonate and salicylic acid. The IAA-signaling double mutant nonphototropic hypocotyls4-1; auxin-responsive factor19-1 and the ABA-signaling mutant aba insensitive1-1 did not respond to auxin and ABA, respectively, but both showed an Al response comparable to that of the wild type. A synthetic microbe-associated molecular pattern peptide, flagellin22 (flg22), induced AtALMT1 transcription but did not induce the transcription of IAA- and ABA-responsive biomarker genes, indicating that both Al and flg22 responses of AtALMT1 were independent of IAA and ABA signaling. An in planta β-glucuronidase reporter assay identified that the ABA response was regulated by a region upstream (−317 bp) from the first ATG codon, but other stress responses may share critical regulatory element(s) located between −292 and −317 bp. These results illustrate the complex regulation of AtALMT1 expression during the adaptation to abiotic and biotic stresses.
The Arabidopsis B-BOX Protein BBX25 Interacts with HY5, Negatively Regulating BBX22 Expression to Suppress Seedling Photomorphogenesis
Authors: Gangappa Sreeramaiah N. , Crocco Carlos D. , Johansson Henrik , Datta Sourav , Hettiarachchi Chamari , Holm Magnus , Botto Javier F. 
Published: April 2013

Abstract
ELONGATED HYPOCOTYL5 (HY5) is a basic domain/leucine zipper (bZIP) transcription factor, central for the regulation of seedling photomorphogenesis. Here, we identified a B-BOX (BBX)–containing protein, BBX25/SALT TOLERANCE HOMOLOG, as an interacting partner of HY5, which has been previously found to physically interact with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1). BBX25 physically interacts with HY5 both in vitro and in vivo. By physiological and genetic approaches, we showed that BBX25 is a negative regulator of seedling photomorphogenesis. BBX25 and its homolog BBX24 regulate deetiolation processes and hypocotyl shade avoidance response in an additive manner. Moreover, genetic relationships of bbx25 and bbx24 with hy5 and cop1 revealed that BBX25 and BBX24 additively enhance COP1 and suppress HY5 functions. BBX25 accumulates in a light-dependent manner and undergoes COP1-mediated degradation in dark and light conditions. Furthermore, a protoplast cotransfection assay showed that BBX24 and BBX25 repress BBX22 expression by interfering with HY5 transcriptional activity. As HY5 binds to the BBX22 promoter and promotes its expression, our results identify a direct mechanism through which the expression of BBX22 is regulated. We suggest that BBX25 and BBX24 function as transcriptional corepressors, probably by forming inactive heterodimers with HY5, downregulating BBX22 expression for the fine-tuning of light-mediated seedling development.
BINDING PROTEIN Is a Master Regulator of the Endoplasmic Reticulum Stress Sensor/Transducer bZIP28 in Arabidopsis
Authors: Srivastava Renu , Deng Yan , Shah Shweta , Rao Aragula Gururaj , Howell Stephen H. 
Published: April 2013

Abstract
BINDING PROTEIN (BiP) is a major chaperone in the endoplasmic reticulum (ER) lumen, and this study shows that BiP binds to the C-terminal tail of the stress sensor/transducer bZIP28, a membrane-associated transcription factor, retaining it in the ER under unstressed conditions. In response to ER stress, BiP dissociates from bZIP28, allowing it to be mobilized from the ER to the Golgi where it is proteolytically processed and released to enter the nucleus. Under unstressed conditions, BiP binds to bZIP28 as it binds to other client proteins, through its substrate binding domain. BiP dissociates from bZIP28 even when bZIP28's exit from the ER or its release from the Golgi is blocked. Both BiP1 and BiP3 bind bZIP28, and overexpression of either BiP detains bZIP28 in the ER under stress conditions. A C-terminally truncated mutant of bZIP28 eliminating most of the lumenal domain does not bind BiP and is not retained in the ER under unstressed conditions. BiP binding sites in the C-terminal tail of bZIP28 were identified in a phage display system. BiP was found to bind to intrinsically disordered regions on bZIP28's lumen-facing tail. Thus, the dissociation of BiP from the C-terminal tail of bZIP28 is a major switch that activates one arm of the unfolded protein response signaling pathway in plants.
Four major disaster occurrences and the Spanish language media: a lack of risk communication
Authors: David Benavides Abraham 
Published: April 2013

Purpose– The Hispanic community is the fastest growing ethnic group in the USA and is currently the largest minority group with tremendous buying power. This trend has seen a significant growth with respect to the Spanish-language media in recent years. Along with the media ' s ability to entertain, comes the responsibility to educate and warn its audiences of eminent threats and disasters. The aim of this paper is to look at the Spanish-language media ' s efforts to warn and prepare its listeners for local and national emergencies.Design/methodology/approach– Using descriptive and explanatory methods the author looks at the failures of the Spanish language media to communicate emergency warnings in both the Saragosa, Texas tornado and in the case of hurricane Katrina.Findings– Research indicated that pressure from constituents, however, forced a change on the Spanish language industry.Research limitations/implications– The research was limited by not having first hand contact with the Spanish language media.Practical implications– The practical implication of this research which has social overtones is that providing disaster warnings to the non-English speaking population in the USA is achievable. Emergency managers and first responders need to be aware of issues regarding non-English speakers.Social implications– The implications for this research is that all individuals will be notified of emergencies even non-English speakers.Originality/value– The issues on non-English speakers in emergency situations have come up before. Nevertheless, this work identifies a practical solution by involving the Spanish language media in emergency alerts. It is essential that this tremendous resource be involved in emergency alerts.
A comparative study on the national counterpart aid model for post-disaster recovery and reconstruction
Authors: Xu Jiuping , Lu Yi 
Published: April 2013

Purpose
– External assistance is often urgently required when an area is struck by a catastrophe. Central government-oriented aid (CGA), national non-governmental organizations aid (NNA), and international humanitarian aid (IHA) are three typical aid models, and national counterpart aid (NCA) is an innovative model for post-Wenchuan earthquake recovery and reconstruction (PWERR). The purpose of this paper is to make a comparative study of the aid models in order to develop recommendations on external assistance for better post-disaster recovery and reconstruction (PDRR).

Design/methodology/approach
– This study was performed in three steps: a case study on the NCA model during the PWERR; a documentary research on the CGA, NNA and IHA models; and a comparative analysis of the four models.

Findings
– The results of the comparative study show that the NCA model is more efficient and effective than the other three typical aid models. However it must be based on the premise of a centralized government.

Practical implications
– The NCA model contributes to disaster management in a developing country context. It develops a viable model for developing countries in coping with the catastrophe, can enhance their ability for domestic self-assistance, and has reference to the construction of national integrated disaster management systems.

Originality/value
– This paper empirically researches the innovative NCA model, and compares it with commonly used aid models for the PDRR. Although it is a Chinese experience, the systematic inter-governmental collaboration of the NCA model has reference to other countries in disaster management.