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Search Results: 1 - 10 of 444465 matches for " David M. Soderlund "
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Functional Expression of Rat Nav1.6 Voltage-Gated Sodium Channels in HEK293 Cells: Modulation by the Auxiliary β1 Subunit
Bingjun He, David M. Soderlund
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0085188
Abstract: The Nav1.6 voltage-gated sodium channel α subunit isoform is abundantly expressed in the adult rat brain. To assess the functional modulation of Nav1.6 channels by the auxiliary β1 subunit we expressed the rat Nav1.6 sodium channel α subunit by stable transformation in HEK293 cells either alone or in combination with the rat β1 subunit and assessed the properties of the reconstituted channels by recording sodium currents using the whole-cell patch clamp technique. Coexpression with the β1 subunit accelerated the inactivation of sodium currents and shifted the voltage dependence of channel activation and steady-state fast inactivation by approximately 5–7 mV in the direction of depolarization. By contrast the β1 subunit had no effect on the stability of sodium currents following repeated depolarizations at high frequencies. Our results define modulatory effects of the β1 subunit on the properties of rat Nav1.6-mediated sodium currents reconstituted in HEK293 cells that differ from effects measured previously in the Xenopus oocyte expression system. We also identify differences in the kinetic and gating properties of the rat Nav1.6 channel expressed in the absence of the β1 subunit compared to the properties of the orthologous mouse and human channels expressed in this system.
TCW: Transcriptome Computational Workbench
Carol Soderlund, William Nelson, Mark Willer, David R. Gang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0069401
Abstract: Background The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. Methodology The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. Conclusion It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.
A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni
Adema, Coen M;Luo, Mei-Zhong;Hanelt, Ben;Hertel, Lynn A;Marshall, Jennifer J;Zhang, Si-Ming;DeJong, Randall J;Kim, Hye-Ran;Kudrna, David;Wing, Rod A;Soderlund, Cari;Knight, Matty;Lewis, Fred A;Caldeira, Roberta Lima;Jannotti-Passos, Liana K;Carvalho, Omar dos Santos;Loker, Eric S;
Memórias do Instituto Oswaldo Cruz , 2006, DOI: 10.1590/S0074-02762006000900027
Abstract: to provide a novel resource for analysis of the genome of biomphalaria glabrata, members of the international biomphalaria glabrata genome initiative (biology.unm.edu/biomphalaria-genome.html), working with the arizona genomics institute (agi) and supported by the national human genome research institute (nhgri), produced a high quality bacterial artificial chromosome (bac) library. the bb02 strain b. glabrata, a field isolate (belo horizonte, minas gerais, brasil) that is susceptible to several strains of schistosoma mansoni, was selfed for two generations to reduce haplotype diversity in the offspring. high molecular weight dna was isolated from ovotestes of 40 snails, partially digested with hindiii, and ligated into pagibac1 vector. the resulting b. glabrata bac library (bg_bba) consists of 61824 clones (136.3 kb average insert size) and provides 9.05 ′ coverage of the 931 mb genome. probing with single/low copy number genes from b. glabrata and fingerprinting of selected bac clones indicated that the bac library sufficiently represents the gene complement. bac end sequence data (514 reads, 299860 nt) indicated that the genome of b. glabrata contains ~ 63% at, and disclosed several novel genes, transposable elements, and groups of high frequency sequence elements. this bg_bba bac library, available from agi at cost to the research community, gains in relevance because bb02 strain b. glabrata is targeted whole genome sequencing by nhgri.
Fixed point sets of maps homotopic to a given map
Soderlund Christina L
Fixed Point Theory and Applications , 2006,
Abstract: Let be a self-map of a compact, connected polyhedron and a closed subset. We examine necessary and sufficient conditions for realizing as the fixed point set of a map homotopic to . For the case where is a subpolyhedron, two necessary conditions were presented by Schirmer in 1990 and were proven sufficient under appropriate additional hypotheses. We will show that the same conditions remain sufficient when is only assumed to be a locally contractible subset of . The relative form of the realization problem has also been solved for a subpolyhedron of . We also extend these results to the case where is a locally contractible subset.
Fixed point sets of maps homotopic to a given map
Christina L. Soderlund
Fixed Point Theory and Applications , 2006, DOI: 10.1155/fpta/2006/46052
Abstract: Let f:X ¢ ’X be a self-map of a compact, connected polyhedron and | ¢ X a closed subset. We examine necessary and sufficient conditions for realizing | as the fixed point set of a map homotopic to f. For the case where | is a subpolyhedron, two necessary conditions were presented by Schirmer in 1990 and were proven sufficient under appropriate additional hypotheses. We will show that the same conditions remain sufficient when | is only assumed to be a locally contractible subset of X. The relative form of the realization problem has also been solved for | a subpolyhedron of X. We also extend these results to the case where | is a locally contractible subset.
An elm EST database for identifying leaf beetle egg-induced defense genes
Kerstin Büchel, Eric McDowell, Will Nelson, Anne Descour, Jonathan Gershenzon, Monika Hilker, Carol Soderlund, David R Gang, Trevor Fenning, Torsten Meiners
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-242
Abstract: Here we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i) untreated control elms, and elms treated with (ii) egg laying and feeding by elm leaf beetles, (iii) feeding, (iv) artificial transfer of egg clutches, and (v) methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs) were identified which clustered into 52,823 unique transcripts (Unitrans) and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant) database, particularly to those from Vitis, Ricinus, Populus and Arabidopsis. Comparative in silico analysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction, transport and primary metabolism.Here we present a dataset for a large-scale study of the mechanisms of plant defense against insect eggs in a co-evolved, natural ecological plant–insect system. The EST database analysis provided here is a first step in elucidating the transcriptional responses of elm to elm leaf beetle infestation, and adds further to our knowledge on insect egg-induced transcriptomic changes in plants. The sequences identified in our comparative analysis give many hints about novel defense mechanisms directed towards eggs.
固体润滑透平轴承 第一部分:在316℃下使用的自润滑复合材料和保持器的制备
M.N.Gardos,A.A.Castillo,J.W.Herrick,R.A.Soderlund,聂明德
摩擦学学报 , 1990,
Abstract: 研制了聚丙烯腈基石墨纤维的三维正交平板编织物和圆筒编织物,并且设计了织物增强的自润滑聚酰亚胺复合材料板和管的制造方法。一种带有加热装置的水压机、平面压板和心轴可扩张的模具可用于制备作为ASTM类试验和摩擦学筛选试验用的平板状和管状复合材料毛坯,也可用于制造自润滑球轴承保持器。这些保持器的主要作用是要在316℃(600°F)下进行固体润滑透平轴承试验过程中可给高速系统补充润滑剂。制造技术中的实际制约因素受编织设计中综合处理方法的支配。这些方法必然要改变环状毛坯各部分的最大尺寸和局部强度。合理的设计工艺是要在不明显降低保持器横档牢固性的情况下增加球-球兜孔部位的强度。已经制取了薄截面的、在室温下强度高达238.2×10~6Pa和密度仅约为1.6g/cm~3的聚合物增强的环形保持器。
Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids
Hyun Jo Koo, Eric T McDowell, Xiaoqiang Ma, Kevin A Greer, Jeremy Kapteyn, Zhengzhi Xie, Anne Descour, HyeRan Kim, Yeisoo Yu, David Kudrna, Rod A Wing, Carol A Soderlund, David R Gang
BMC Plant Biology , 2013, DOI: 10.1186/1471-2229-13-27
Abstract: In order to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, we evaluated an assembled collection of expressed sequence tags (ESTs) from eight different ginger and turmeric tissues. Comparisons to publicly available sorghum rhizome ESTs revealed a total of 777 gene transcripts expressed in ginger/turmeric and sorghum rhizomes but apparently absent from other tissues. The list of rhizome-specific transcripts was enriched for genes associated with regulation of tissue growth, development, and transcription. In particular, transcripts for ethylene response factors and AUX/IAA proteins appeared to accumulate in patterns mirroring results from previous studies regarding rhizome growth responses to exogenous applications of auxin and ethylene. Thus, these genes may play important roles in defining rhizome growth and development. Additional associations were made for ginger and turmeric rhizome-enriched MADS box transcription factors, their putative rhizome-enriched homologs in sorghum, and rhizomatous QTLs in rice. Additionally, analysis of both primary and specialized metabolism genes indicates that ginger and turmeric rhizomes are primarily devoted to the utilization of leaf supplied sucrose for the production and/or storage of specialized metabolites associated with the phenylpropanoid pathway and putative type III polyketide synthase gene products. This finding reinforces earlier hypotheses predicting roles of this enzyme class in the production of curcuminoids and gingerols.A significant set of genes were found to be exclusively or preferentially expressed in the rhizome of ginger and turmeric. Specific transcription factors and other regulatory genes were found that were common to the two species and that are excellent candidates for involvement in rhizome growth, differentiation and development. Large classes of enzymes involved in specialized metabolism were also found to have apparent tissue-specific expres
Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
HyeRan Kim, Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip SanMiguel, James C Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Goicoechea, Lincoln Stein, Doreen Ware, Scott A Jackson, Carol Soderlund, Rod A Wing
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-2-r45
Abstract: Comparative genomics is a powerful tool for unraveling the evolutionary history and gene functionality of related species. The availability of high resolution genetic and physical maps and genome assemblies has established comparative genomics platforms in organisms ranging from bacteria and fungi to animals and plants [1-7]. The majority of sequence-based eukaryotic platforms have focused on comparisons between genera [8-11]. Although highly informative, the divergence times between genera are often too distant to be useful for the identification of conserved noncoding sequences such as transcription factor binding sites, enhancers and matrix attachment regions (for example, see [12,13]). Sequence comparisons between species within a single genus have focused primarily on orthologous loci or genomic regions [14,15]. Whole genome comparative platforms within a genus are still in their infancy, with the most notable exception being the generation of whole genome shotgun assemblies of 12 Drosophila species that span an evolutionary time frame of approximately 60 million years [16].In plants, rice (Oryza sativa) and thale cress (Arabidopsis thaliana) are important model systems for functional and evolutionary biology. Both genomes have been completely sequenced [17,18] and serve as the reference sequences for the major monocot and dicot plant lineages. Rice has added significance by virtue of being the world's most important crop, directly feeding half the human population. The population that depends on rice is expected to double in 25-50 years and there is thus an intense effort by breeders to double current rice yields using less land and water and on poorer soils [19]. To achieve this goal, the plant biology community is engaged in a concerted effort to functionally characterize all plant genes in both model plants using approaches including genetics, transgenetics, and comparative genomics. These efforts have significance not only to world food and bio-energy secu
Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains
William Nelson, Meizhong Luo, Jianxin Ma, Matt Estep, James Estill, Ruifeng He, Jayson Talag, Nicholas Sisneros, David Kudrna, HyeRan Kim, Jetty SS Ammiraju, Kristi Collura, Arvind K Bharti, Joachim Messing, Rod A Wing, Phillip SanMiguel, Jeffrey L Bennetzen, Carol Soderlund
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-621
Abstract: A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the SalI MSLL libraries being the most highly enriched (31% align to an EST contig), while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%). These two techniques were compared with other gene-enrichment methods, and shown to be complementary.MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of epigenetic boundaries are barely understood at this time, MSLL technology flags both approximate boundaries and methylated genes that deserve additional investigation. MSLL and HMPR sequences provide a valuable resource for maize genome annotation, and are a uniquely valuable complement to any plant genome sequencing project. In order to make these results fully accessible to the community, a web display was developed that shows the alignment of MSLL, HMPR, and other gene-rich sequences to the BACs; this display is continually updated with the l
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