bluuebunny/crossref_metadata_2025_split huggingface dataset:
VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)
Authors: Wong Darren CJ , Sweetman Crystal , Drew Damian P , Ford Christopher M 
Published: December 2013

AbstractBackgroundGene expression datasets in model plants such asArabidopsishave contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine,Vitis vinifera.DescriptionThe new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the AffymetrixVitis viniferaGeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis) whereby the recovered sub-networks reconfirm established plant gene functions and also identify novel associations.ConclusionsTogether, we present valuable insights into grapevine transcriptional regulation by developing network models applicable to researchers in their prioritisation of gene candidates, for on-going study of biological processes related to grapevine development, metabolism and stress responses.
Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica
Authors: Immanen Juha , Nieminen Kaisa , Duchens Silva Héctor , Rodríguez Rojas Fernanda , Meisel Lee A , Silva Herman , Albert Victor A , Hvidsten Torgeir R , Helariutta Ykä 
Published: December 2013

AbstractBackgroundThrough the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species.ResultsTaking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85Populusand 45Prunusgenes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses.ConclusionsIn general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in bothPopulusandPrunusthan in Arabidopsis.
Escherichia coli challenge and one type of smectite alter intestinal barrier of pigs
Authors: Almeida Juliana Abranches Soares , Liu Yanhong , Song Minho , Lee Jeong Jae , Gaskins H Rex , Maddox Carol Wolfgang , Osuna Orlando , Pettigrew James Eugene 
Published: December 2013

AbstractAn experiment was conducted to determine how anE. colichallenge and dietary clays affect the intestinal barrier of pigs. Two groups of 32 pigs (initial BW: 6.9 ± 1.0 kg) were distributed in a 2 × 4 factorial arrangement of a randomized complete block design (2 challenge treatments: sham orE. coli, and 4 dietary treatments: control, 0.3% smectite A, 0.3% smectite B and 0.3% zeolite), with 8 replicates total. Diarrhea score, growth performance, goblet cell size and number, bacterial translocation from intestinal lumen to lymph nodes, intestinal morphology, and relative amounts of sulfo and sialo mucins were measured. TheE. colichallenge reduced performance, increased goblet cell size and number in the ileum, increased bacterial translocation from the intestinal lumen to the lymph nodes, and increased ileal crypt depth. One of the clays (smectite A) tended to increase goblet cell size in ileum, which may indicate enhanced protection. In conclusion,E. coliinfection degrades intestinal barrier integrity but smectite A may enhance it.
G protein-coupled receptors: computer-aided ligand discovery and computational structural analyses in the 2010s
Authors: Costanzi Stefano 
Published: December 2013

AbstractG protein-coupled receptors, or GPCRs, are a large superfamily of proteins found on the plasma membrane of cells. They are involved in most physiological and pathophysiological functions and constitute the target of the majority of marketed drugs. Although these receptors have been historically elusive to attempts of structural determination, GPCR crystallography is now in full blossom, opening the way to structure-based drug discovery and enabling homology modeling. This thematic issue of the journal In Silico Pharmacology, which illustrates how the expanding body of structural knowledge is fostering complex computational analyses of the structure-function relationships of the receptors and their interactions with their ligands, stems from the 31st Camerino-Cyprus-Noordwijkerhout Symposium held in Italy, in May 2013, at the University of Camerino. Specifically, it originates from a session of the symposium entitled “Structure-Based Discovery of Ligands of G Protein-Coupled Receptors: Finally a Reality”, and features a mix of research articles and reviews on the application of computational modeling to the analysis of the structure of GPCRs and the interactions of the receptors with their ligands.
High end GPCR design: crafted ligand design and druggability analysis using protein structure, lipophilic hotspots and explicit water networks
Authors: Mason Jonathan S , Bortolato Andrea , Weiss Dahlia R , Deflorian Francesca , Tehan Benjamin , Marshall Fiona H 
Published: December 2013

Abstract
Purpose
G Protein-Coupled Receptors (GPCRs) are a large family of therapeutically important proteins and as diverse X-ray structures become available it is increasingly possible to leverage structural information for rational drug design.
We present herein approaches that use explicit water networks combined with energetic surveys of the binding site (GRID), providing an enhanced druggability and ligand design approach, with structural understanding of ligand binding, including a ‘magic’ methyl and binding site mutations, and a fast new approach to generate and score waters.

Methods
The GRID program was used to identify lipophilic and hydrogen bonding hotspots. Explicit full water networks were generated and scored for (pseudo)apo structures and ligand-protein complexes using a new approach, WaterFLAP (Molecular Discovery), together with WaterMap (Schrödinger) for (pseudo)apo structures. A scoring function (MetaScore) was developed using a fast computational protocol based on several short adiabatic biased MD simulations followed by multiple short well-tempered metadynamics runs.

Results
Analysis of diverse ligands binding to the adenosine A2A receptor together with new structures for the δ/κ/μ opioid and CCR5 receptors confirmed the key role of lipophilic hotspots in driving ligand binding and thus design; the displacement of ‘unhappy’ waters generally found in these regions provides a key binding energy component. Complete explicit water networks could be robustly generated for protein-ligand complexes using a WaterFLAP based approach. They provide a structural understanding of structure-activity relationships such as a ‘magic methyl’ effect and with the metadynamics approach a useful estimation of the binding energy changes resulting from active site mutations.

Conclusions
The promise of full structure-based drug design (SBDD) for GPCRs is now possible using a combination of advanced experimental and computational data. The conformational thermostabilisation of StaR® proteins provide the ability to easily generate biophysical screening data (binding including fragments, kinetics) and to get crystal structures with both potent and weak ligands. Explicit water networks for apo and ligand-complex structures are a critical ‘third dimension’ for SBDD and are key for understanding ligand binding energies and kinetics. GRID lipophilic hotspots are found to be key drivers for binding. In this context ‘high end’ GPCR ligand design is now enabled.
Deficient spontaneous in vitro apoptosis and increased tmTNF reverse signaling-induced apoptosis of monocytes predict suboptimal therapeutic response of rheumatoid arthritis to TNF inhibition
Authors: Meusch Undine , Klingner Maria , Baerwald Christoph , Rossol Manuela , Wagner Ulf 
Published: December 2013

Abstract
Introduction
In vitro apoptosis of peripheral monocytes in rheumatoid arthritis (RA) is disturbed and influenced by cytokine production and transmembrane TNF (tmTNF) reverse signaling. The goal of the study was the analysis of the predictive value of the rate of in vitro apoptosis for the therapeutic response to anti-TNF treatment.

Methods
Spontaneous and tmTNF reverse signaling-induced apoptosis were determined in vitro in monocytes from 20 RA patients prior to initiation of therapeutic TNF inhibition with etanercept, and the subsequent clinical response was monitored.

Results
Spontaneous in vitro apoptosis was significantly reduced in RA patients compared to controls. Deficiency in spontaneous apoptosis was associated with an insufficient therapeutic response according to the European League Against Rheumatism (EULAR) response criteria and less reduction of the disease activity determined by disease activity score (DAS) 28. High susceptibility to reverse signaling-induced apoptosis was also associated with less efficient reduction in the DAS28. Of note, a strong negative correlation between the two apoptotic parameters was discernible, possibly indicative of two pathogenetically relevant processes counter-regulating each other.
tmTNF reverse signaling induced in vitro production of soluble IL1-RI and IL-1RII only in monocytes not deficient in spontaneous apoptosis, and the levels of soluble IL1-RII were found to be predictive of a good clinical response to Etanercept.

Conclusion
Although tmTNF reverse signaling is able to induce apoptosis of RA monocytes in vitro, this process appears to occur in vitro preferentially in patients with suboptimal therapeutic response. Resistance to spontaneous in vitro apoptosis, in contrast, is a predictor of insufficient response to treatment.
The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution
Authors: Raats Dina , Frenkel Zeev , Krugman Tamar , Dodek Itay , Sela Hanan , Šimková Hana , Magni Federica , Cattonaro Federica , Vautrin Sonia , Bergès Hélène , Wicker Thomas , Keller Beat , Leroy Philippe , Philippe Romain , Paux Etienne , Doležel Jaroslav , Feuillet Catherine , Korol Abraham , Fahima Tzion 
Published: December 2013

Abstract
Background
The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution.

Results
Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere.

Conclusions
This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.
Obligate mutualism within a host drives the extreme specialization of a fig wasp genome
Authors: Xiao Jin-Hua , Yue Zhen , Jia Ling-Yi , Yang Xin-Hua , Niu Li-Hua , Wang Zhuo , Zhang Peng , Sun Bao-Fa , He Shun-Min , Li Zi , Xiong Tuan-Lin , Xin Wen , Gu Hai-Feng , Wang Bo , Werren John H , Murphy Robert W , Wheeler David , Niu Li-Ming , Ma Guang-Chang , Tang Ting , Bian Sheng-Nan , Wang Ning-Xin , Yang Chun-Yan , Wang Nan , Fu Yue-Guan , Li Wen-Zhu , Yi Soojin V , Yang Xing-Yu , Zhou Qing , Lu Chang-Xin , Xu Chun-Yan , He Li-Juan , Yu Li-Li , Chen Ming , Zheng Yuan , Wang Shao-Wei , Zhao Shuang , Li Yan-Hong , Yu Yang-Yang , Qian Xiao-Ju , Cai Yue , Bian Lian-Le , Zhang Shu , Wang Jun-Yi , Yin Ye , Xiao Hui , Wang Guan-Hong , Yu Hui , Wu Wen-Shan , Cook James M , Wang Jun , Huang Da-Wei 
Published: December 2013

Abstract
Background
Fig pollinating wasps form obligate symbioses with their fig hosts. This mutualism arose approximately 75 million years ago. Unlike many other intimate symbioses, which involve vertical transmission of symbionts to host offspring, female fig wasps fly great distances to transfer horizontally between hosts. In contrast, male wasps are wingless and cannot disperse. Symbionts that keep intimate contact with their hosts often show genome reduction, but it is not clear if the wide dispersal of female fig wasps will counteract this general tendency. We sequenced the genome of the fig wasp Ceratosolen solmsi to address this question.

Results
The genome size of the fig wasp C. solmsi is typical of insects, but has undergone dramatic reductions of gene families involved in environmental sensing and detoxification. The streamlined chemosensory ability reflects the overwhelming importance of females finding trees of their only host species, Ficus hispida, during their fleeting adult lives. Despite long-distance dispersal, little need exists for detoxification or environmental protection because fig wasps spend nearly all of their lives inside a largely benign host. Analyses of transcriptomes in females and males at four key life stages reveal that the extreme anatomical sexual dimorphism of fig wasps may result from a strong bias in sex-differential gene expression.

Conclusions
Our comparison of the C. solmsi genome with other insects provides new insights into the evolution of obligate mutualism. The draft genome of the fig wasp, and transcriptomic comparisons between both sexes at four different life stages, provide insights into the molecular basis for the extreme anatomical sexual dimorphism of this species.
Insulin signaling regulates neurite growth during metamorphic neuronal remodeling
Authors: Gu Tingting , Zhao Tao , Hewes Randall S. 
Published: December 2013

Summary
Although the growth capacity of mature neurons is often limited, some neurons can shift through largely unknown mechanisms from stable maintenance growth to dynamic, organizational growth (e.g. to repair injury, or during development transitions). During insect metamorphosis, many terminally differentiated larval neurons undergo extensive remodeling, involving elimination of larval neurites and outgrowth and elaboration of adult-specific projections. Here, we show in the fruit fly, Drosophila melanogaster (Meigen), that a metamorphosis-specific increase in insulin signaling promotes neuronal growth and axon branching after prolonged stability during the larval stages. FOXO, a negative effector in the insulin signaling pathway, blocked metamorphic growth of peptidergic neurons that secrete the neuropeptides CCAP and bursicon. RNA interference and CCAP/bursicon cell-targeted expression of dominant-negative constructs for other components of the insulin signaling pathway (InR, Pi3K92E, Akt1, S6K) also partially suppressed the growth of the CCAP/bursicon neuron somata and neurite arbor. In contrast, expression of wild-type or constitutively active forms of InR, Pi3K92E, Akt1, Rheb, and TOR, as well as RNA interference for negative regulators of insulin signaling (PTEN, FOXO), stimulated overgrowth. Interestingly, InR displayed little effect on larval CCAP/bursicon neuron growth, in contrast to its strong effects during metamorphosis. Manipulations of insulin signaling in many other peptidergic neurons revealed generalized growth stimulation during metamorphosis, but not during larval development. These findings reveal a fundamental shift in growth control mechanisms when mature, differentiated neurons enter a new phase of organizational growth. Moreover, they highlight strong evolutionarily conservation of insulin signaling in neuronal growth regulation.
Mesomere-derived glutamate decarboxylase-expressing blastocoelar mesenchyme cells of sea urchin larvae
Authors: Katow Hideki , Katow Tomoko , Abe Kouki , Ooka Shioh , Kiyomoto Masato , Hamanaka Gen 
Published: December 2013

Summary
The ontogenetic origin of blastocoelar glutamate decarboxylase (GAD)-expressing cells (GADCs) in larvae of the sea urchin Hemicentrotus pulcherrimus was elucidated. Whole-mount in situ hybridisation (WISH) detected transcription of the gene that encodes GAD in H. pulcherrimus (Hp-gad) in unfertilised eggs and all blastomeres in morulae. However, at and after the swimming blastula stage, the transcript accumulation was particularly prominent in clumps of ectodermal cells throughout the embryonic surface. During the gastrula stage, the transcripts also accumulated in the endomesoderm and certain blastocoelar cells. Consistent with the increasing number of Hp-gad transcribing cells, immunoblot analysis indicated that the relative abundance of Hp-Gad increased considerably from the early gastrula stage until the prism stage. The expression pattern of GADCs determined by immunohistochemistry was identical to the pattern of Hp-gad transcript accumulation determined using WISH. In early gastrulae, GADCs formed blastocoelar cell aggregates around the blastopore with primary mesenchyme cells. The increase in the number of blastocoelar GADCs was inversely proportional to the number of ectodermal GADCs ranging from a few percent of total GADCs in early gastrulae to 80% in late prism larvae; this depended on ingression of ectodermal GADCs into the blastocoel. Some of the blastocoelar GADCs were fluorescein-positive in the larvae that developed from the 16-cell stage chimeric embryos; these comprised fluorescein-labeled mesomeres and unlabelled macromeres and micromeres. Our finding indicates that some of the blastocoelar GADCs are derived from the mesomeres and thus they are the new group of mesenchyme cells, the tertiary mesenchyme cells.
Electroporation of Adherent Cells by Direct Lamination of Hydrogel-based Microelectrode Substrates
Authors: Takahashi Daisuke , Sasaki Masato , Nagamine Kuniaki , Torimitsu Keiichi , Nishizawa Matsuhiko 
Published: December 2013

Abstract
We have developed a technique to fabricate Au microelectrodes on hydrogel substrates such as polyacrylamide. Electropolymerization of poly(3,4-ethylenedioxythiophene) (PEDOT) anchors the Au electrodes to the hydrogels. The resulting soft, molecularly permeable hydrogel-based microelectrodes were effective for the electroporation of adherent cells by direct lamination. The electroporation-assisted uptakes of dye molecules and genes were demonstrated for normal human dermal fibroblast cells and human induced pluripotent stem (iPS) cells.
Segmentation of Ohio's Logging Industry Based on Productivity and Cost Variables
Authors: McConnell T. Eric 
Published: December 2013

Abstract
The objective of this research was to develop baseline information regarding the structure and performance of Ohio's logging industry. Questionnaires were distributed on-site at logger chapter meetings across the state. Multivariate clustering was used to group similar types of firms based on responses to 15 productivity and cost variables. Three clusters were identified: Local Mill Suppliers, Product Merchandisers, and Volume-Dependent Producers. The clusters were largely homogeneous as far as the overall makeup and administration of their companies. Clusters did differ regarding haul distance, pieces of equipment owned, and equipment age. Volume-Dependent Producers, while not significantly larger in size statistically, viewed the productivity, present, and future cost variables more pessimistically than the other clusters. The key variable of concern across clusters was the cost of consumables, primarily fuel, paralleling more recent findings in other states.