Journal Club

Liangjiao (Sep 24): Export of Salicylic Acid from the Chloroplast Requires the Multidrug and Toxin Extrusion-Like Transporter EDS5.Plant Physiol.
Liangjiao (Mar 12): Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thalianaroots. PNAS
Scott (Feb 19): MetabolieProfiling
Moh'd (Jan 29): Aspen SUCROSE TRANSPORTER3 allocates carbon into wood fibers.  Plant Physiol.
Hao (Jan 15): An atypical tubulin kinase mediates stress-induced microtubule depolymerization in Arabidopsis. Current Biology
CJ (Dec 4): (1) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (2) RNA-guided human genome editing via Cas9. Science
Yingying (Nov 20): CLASP interacts with Sorting Nexin 1 to link microtubules and auxin transport via PIN2 recycling in Arabidopsis thaliana. Developmental Cell
Ed (Nov 6): iReckon: Simultaneous isoform discovery and abundance estimation from RNA-Seq data. Genome Research
Cicy (Oct 30): A bioinformatic tool for the identification of transcriptomic impronts related to reactive oxygen species type and origin provides new insights into stress responses.  Plant Physiology.
Patrick (Oct 9): Nitrogen deprivation promotes Populus root growth through global transcriptome reprogramming and activation of hierarchical genetic networks.  New Phytologist
Scott (Sep 25): The dual effect of abscisic acid on stomata.  New Phytologist
Vanessa (Sep 11): Site-directed mutagenesis of StSUT1 reveals target amino acids of regulation and stability. Biochimie
Baggi (Aug 28): Coexistence but independent biosynthesis of catechyl and guaiacyl/syringyl lignin polymers in seed coats.  Plant Cell
Rhodesia (Aug 14): Salicylic acid regulates plasmodesmata closure during innate immune response in Arabidopsis. Plant Cell
Liangjiao (Jul 24): Photosynthetic sucrose acts as cotyledon-derived long-distance signal to control root growth during early seedling development in Arabidopsis. PNAS
Mohd (July 10): Arabidopsis sucrose transporter SUT4 interacts with cytochrome b5-2 to regulate seed germination in response to sucrose and glucose. Molecular Plant
Hao (June 26): Dynamic regulation of cortical microtubule organization through prefoldin-DELLA interaction. Current Biology
Yingying (Jun 12): Impaired Cellulose Synthase Guidance Leads to Stem Torsion and Twists Phyllotactic Patterns in Arabidopsis. Current Biology
Ed (May 23): Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing.  BMC Genomics
CJ (Apr 25): Widespread dynamic DNA methylation in response to biotic stress.  PNAS
Cicy (Mar 28): Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants.  PNAS
Baggi (Mar 7): An Arabidopsis cell wall proteoglycan consists of pectin and arabinoxylan covalently linked to an arabinogalactan protein.  Plant Cell
Liangjiao (Feb 21): The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose. PNAS
Vanessa (Feb 7): ABA regulates apoplastic sugar transport and is a potential signal for cold-induced pollen sterility in rice. Plant Cell Physiol
Henrique (Jan 24): 13C NMR-based metabolomics for the classification of green coffee beans according to variety and origin. Journal of Agricultural and Food Chemistry
Scott (Jan 7, 2013): Tie-dyed2 Encodes a Callose Synthase That Functions in Vein Development and Affects Symplastic Trafficking within the Phloem of Maize Leaves Molecular Plant
Hao (Nov 21): Localization of Cell Wall Polysaccharides in Normal and Compression Wood of Radiata Pine: Relationships with Lignification and Microfibril Orientation Plant Physiology
Sunil (Nov 7): Analysis of Xylem Sap from Functional (Nonembolized) and Nonfunctional (Embolized) Vessels of Populus nigra: Chemistry of Refilling. Plant Physiology
Prashant (Oct 17): Microtubules are essential for guard-cell function in Vicia and Arabidopsis. Molecular Plant
Henrique (Oct 3): Use of the growing environment as a source of variation to identify the quantitative trait transcripts and modules of co-expressed genes that determine chlorogenic acid accumulation.  Plant Cell Environ
Ed (Sep 19): SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biology
Cicy (Aug 29): Comparative Evolution of Photosynthetic Genes in Response to Polyploid and Nonpolyploid Duplication. Plant Physiology
Liangjiao (Aug 10): Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1.PNAS
Han-Yi (Jul 27): Contribution of CoA ligases to benzenoid biosynthesis in petunia flowers.  Plant Cell
Vanessa (Jul 13): Clone history shapes Populus drought responses.  PNAS
CJ (June 15): Trans chromosomal methylation in Arabidopsis hybrids. PNAS
Baggi (June 1): Over-expression of a putative poplar glycosyltransferase gene, PtGT1, in tobacco increases lignin content and causes early flowering. J Exp Bot
Scott (May 18): Transcriptome response to embolism formation in stems of Populus trichocarpa provides insight into signaling and the biology of refilling. Plant Physiology
Duo (April 27): The monosaccharide transporter gene family in Arabidopsis and rice: a history of duplications, adaptive evolution, and functional divergence. Mol Biol Evol
Ed (Mar 30): Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Research
Prashant (Mar 16): Cobtorin target analysis reveals that pectin functions in the deposition of cellulose microfibrils in parallel with cortical microtubules. Plant Journal
Cicy (Mar 2): Contrasting patterns of evolution following whole genome versus tandem suplication events in Populus. Genome Research
Liangjiao (Feb 17): Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions.PNAS
Chris (Feb 3): Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. Science
Han-Yi (Jan 20, 2012): Independent Recruitment of an O-Methyltransferase for Syringyl Lignin Biosynthesis in Selaginella moellendorffii. Plant Cell
Baggi (Nov 11): Cellulose and lignin biosynthesis is altered by ozone in wood of hybrid poplar (Populus tremula3alba). Journal of Exp Botany
Scott (Oct 21): Neonicotinoid insecticides induce salicylate-associated plant defense responses PNAS
Vanessa (Oct 7): Flowering Locus T duplication coordinates reproductive and vegetative growth in perennial poplar. PNAS
Ed (Sept 23): Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Research.
Mark (Sept 9): MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics.
Duo (Aug 26): Sugar transporters for intercellular exchange and nutrition of pathogens. Nature.
Liangjiao (Aug 12): Amino Acid Homeostasis Modulates Salicylic Acid–Associated Redox Status and Defense Responses in Arabidopsis. Plant Cell.
Eric (July 29): A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation. BMC Plant Biology
Feng (July 15): Leaf senescence is accompanied by an early disruption of the microtubule network in Arabidopsis. Plant Physiol
Chris (July 1): Activation of sucrose transport in defoliated Lolium perenne L.: An example of apoplastic phloem loading plasticity. Plant Cell Physiol
Han-Yi (June 17): Novel hydroxycinnamoyl-coenzyme A quinate transferase genes from artichoke are involved in the synthesis of chlorogenicacid. Plant Physiol. 2010 153: 1224-1238.
CJ (June 3): Small RNA duplexes function as mobile silencing signals between plant cells. Science 328: 912-916.
Prashant (May 20): Microtubule-Associated Proteins MAP65-1 and MAP65-2 Positively Regulate Axial Cell Growth in Etiolated Arabidopsis Hypocotyls.Plant Cell
Wenbing (May 6): Evidence for a Role of Gibberellins in Salicylic Acid-Modulated Early Plant Responses to Abiotic Stress in Arabidopsis Seeds. Plant Physiol 150:1335-1344 (2009)
Ed (April 22): Isoform-level microRNA-155 target prediction using RNA-seq. Nucleic Acid Research.
Baggi (April 8): Qualitative variation in proanthocyanidin composition of Populus species and hybrids: Genetics is the Key . Journal of Chemical Ecology
Mark (March 25): A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiology
Liangjiao (March 11):Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. PNAS
Scott (Feb 25): Transcriptome profiles of hybrid poplar (Populus trichocarpa x deltoides) reveal rapid changes in undamaged, systemic sink leaves after simulated feeding by forest tent caterpillar (Malacosoma disstria). New Phytologist
Eric (Feb 11): Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics
Feng (Jan 28): Arabidopsis homologs of nucleus- and phragmoplast-localized kinase 2 and 3 and mitogen-activated protein kinase 4 are essential for microtubule organization. Plant Cell
Kate (Jan 14, 2011): Nuclear localization of NPR1 is required for regulation of salicylate tolerance, isochorismate synthase1 expression and salicylate accumulation in Arabidopsis. Journal of Plant Physiology
Duo (Dec 17): Altered Xylem-Phloem Transfer of Amino Acids Affects Metabolism and leads to increased seed yield and oil content in Arabidopsis. Plant Cell
Lindsey (Nov 12): A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions. Plant Physiol
Chris (Oct 22): Analysis of secondary growth in Arabidopsis shoot reveals a positive role of jasmonate signaling in cambium formation. Sehr et al. Plant Journal
Han-Yi (Oct 8): Arabidopsis plants acclimate to water deficit at low cost through changes of carbon usage: An integrated perspective using growth, metabolite, enzyme, and gene expression analysis, Plant Physiology 154: 357-372
WenBing (Sept 17): Arabidopsis HEMERA/pTAC12 Initiates Photomorphogenesis by Phytochromes. Cell 141, 1230–1240.
Mark (Sept 3): MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites, Plant Journal
Ed (Aug 6): Transcript assembly and quantification by RNA-Seq revels unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology
Horace (Jul 9): Supervised Normalization of Microarrays. Mecham et al., Bioinformatics 26(10) 2010
Prashant (June 25): Tobacco mutants with reduced microtubule dynamics are less susceptible to TMV. Ouko et al., Plant Journal, 2010
CJ (June 11): Convergent evolution of syringyl lignin biosynthesis via distinct pathways in the lycophyte Selaginella and flowering plants. Weng et al., Plant Cell, 2010
Baggi (May 21): A metabolic signature of the beneficial interaction of the endophyte Paenibacillus sp. isolate and in vitro-grown poplar plants revealed by metabolomics. Scherling et al., MPMI, 2009.
Lindsey (May 7): Root exudates mediate kin recognition in plants. Biedrzycki et al., Communicative & Integrative Biology, 2010.
Kate (April 16): A comprehensive picture of phloem loading strategies. Rennie and Turgeon, PNAS, 2009
Han-Yi (Apr 2): Engineering monolignol 4-O-methyltransferases to modulate lignin biosynthesis. Bhulya and Liu, JBC, 2009
Scott (Mar 11): A membrane-associated thioredoxin required for plant growth moves from cell to cell, suggestive of a role in intercellular communication. Meng et al. PNAS, 2010
Ed (Feb 26): Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Filichkin et al. Genome Research, 2010
Wenbing (Feb 12): Evolution of a novel phenolic pathway for pollen development. Matsuno et al. Science, 2009
Plagiarism and Scientific Misconduct (Feb 5): slides
CJ: (1) PNAS takes action regarding breach of NIH embargo policy on a PNAS paper (text). (2) Why data-sharing policies matter (text).
Lindsey: "Journal flinches as article on voice analyzer sparks lawsuit threat" (story)
Chuanfu: Data point removal: "Flowering Signal" (paper) (retraction) (commentary)
Kate: "A scientist’s nightmare: Software problem leads to five retractions" (main story) (retraction) (response)
Wenbing: Intentional falsification of data (retraction) (paper)
Scott: Junk science - the Schön scandal (story)
Han-Yi: Falsified experiments and data (at the University of Alabama at Birmingham) (retraction) (paper) (story)
Horace: A dark tale behind two retractions (story) (retraction) (paper)
Ben: Ohio University plagiarism cases: 44 engineering theses in a row (story)
Ed: Is language imitation okay? (story)
Prashant: Two borrowed paragraphs (story)
Baggi: Even retracted papers endure (story)
Mark: It's more than you think (story) (paper)
Metabolite Profiling II (Jan 22):
Lindsey: Identification of defense compounds in Barbarea vulgaris against the herbivore Phyllotreta nemorum by an ecometabolomic approach. Kuzina et al. (Bak group)
Scott: Metabolic profiling of the sink-to-source transition in developing leaves of quaking aspen. Jeong et al. (Tsai lab)
Mark: A molecular timetable for apical bud formation and dormancy induction in poplar. Ruttink et al. (Boerjan group)
Metabolite Profiling I (Jan 15)
Ben: Metabolomic and genetic analyses of flavonol synthesis in Arabidopsis thaliana support the in vivo involvement of leucoanthocyanidin dioxygenase. Stracke et al. (De Vos and Stracke collaboration)
Han-Yi: Decreased mitochondrial activities of malate dehydrogenase and fumarase in tomato lead to altered root growth and architecture via diverse mechanisms. van der Merwe et al. (Moritz and Fernie collaboration)
Wenbing: Upgrading root physiology for stress tolerance by ectomycorrhizas: Insights from metabolite and transcriptional profiling into reprogramming for stress anticipation. Luo et al. (Polle group)
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