Abstract Vacuoles play central roles in plant growth, development, and stress responses. To better understand vacuole function biogenesis we have characterized the vegetative vacuolar proteome from Arabidopsis thaliana. were isolated protoplasts derived rosette leaf tissue. Total purified proteins then subjected either to multidimensional liquid chromatography/tandem mass spectrometry or one-dimensional SDS-PAGE coupled with nano-liquid (nano-LC MS/MS). ensure maximum coverage of proteome, a...

Multicellular organs are composed of distinct cell types with unique assemblages translated mRNAs. Here, ribosome-associated mRNAs were immunopurified from specific populations intact seedlings using Arabidopsis thaliana lines expressing a FLAG-epitope tagged ribosomal protein L18 (FLAG-RPL18) via developmentally regulated promoters. The profiling in ribosome complexes, referred to as the translatome, identified differentially expressed 21 defined by cell-specific expression FLAG-RPL18....

WUSCHEL (WUS) is a homeodomain transcription factor produced in cells of the niche/organizing center (OC) shoot apical meristems. WUS specifies stem cell fate and also restricts its own levels by activating negative regulator, CLAVATA3 ( CLV3 ), adjacent central zone (CZ). Here we show that protein, after being synthesized OC, migrates into CZ, where it activates binding to promoter elements. Using computational model, maintenance gradient essential regulate number. Migration cell-inducing...

Abstract We have used cDNA microarrays to examine changes in gene expression during Arabidopsis seed development and compare wild-type mutant wrinkled1 (wri1) seeds that an 80% reduction oil. Between 5 13 days after flowering, a period preceding including the major accumulation of storage oils proteins, ∼35% genes represented on array changed at least twofold, but larger fraction (65%) showed little or no change expression. Genes whose most tended be expressed more than other tissues....

MicroRNAs (miRNAs) are a growing family of small noncoding RNAs that downregulate gene expression in sequence-specific manner. The identification the entire set miRNAs from model organism is critical step toward understanding miRNA-guided regulation. Rice (Oryza sativa) and Arabidopsis thaliana, two plant species with fully sequenced genomes, representatives monocotyledonous dicotyledonous flowering plants, respectively. Thus far, experimental plants has been confined to Arabidopsis....

ChemMine Tools is an online service for small molecule data analysis. It provides a web interface to set of cheminformatics and mining tools that are useful various analysis routines performed in chemical genomics drug discovery. The also offers programmable access options via the R library ChemmineR. primary functionalities fall into five major application areas: visualization, structure comparisons, similarity searching, compound clustering prediction properties. First, users can upload...

Translational regulation contributes to plasticity in metabolism and growth that enables plants survive a dynamic environment. Here, we used the precise mapping of ribosome footprints (RFs) on mRNAs investigate translational under control sublethal hypoxia stress conditions seedlings Arabidopsis thaliana. Ribosomes were obtained by differential centrifugation or immunopurification digested with RNase I generate footprint fragments deep-sequenced. Comparison RF number position genic regions...

Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery chemical genomics. Here, we present the first open-source compound mining framework popular statistical programming environment R. The integration with a powerful maximizes flexibility, expandability programmability provided analysis functions.We discuss algorithms utilities by R package ChemmineR. It contains functions searching, libraries wide spectrum...

Despite the central importance of stem cells in plant growth and development, molecular signatures associated with them have not been revealed. Shoot apical meristems (SAMs) harbor a small set located at tip each they are surrounded by several million differentiating cells. This imposes major limitation isolating pure populations for genomic analyses. We developed system to isolate distinct cell types SAMs, including used this profile gene expression from 4 different samples SAMs. The...

Abstract Background Next-generation sequencing (NGS) has revolutionized how research is carried out in many areas of biology and medicine. However, the analysis NGS data remains a major obstacle to efficient utilization technology, as it requires complex multi-step processing big demanding considerable computational expertise from users. While substantial effort been invested on development software dedicated individual steps experiments, insufficient resources are currently available for...

Abstract To provide a broad analysis of gene expression in developing Arabidopsis seeds, microarrays have been produced that display approximately 2,600 seed-expressed genes. DNA for genes spotted on the arrays were selected from >10,000 clones partially sequenced cDNA library seeds. Based series controls, sensitivity was estimated at one to two copies mRNA per cell and cross hybridization occur if closely related >70% 80% sequence identity. These hybridized experiments with...

Summary Translational regulation was evaluated for over 2000 genes by measurement of the proportion individual mRNA species in polysomal (PS) complexes leaves non‐stressed and moderately dehydration‐stressed Arabidopsis . The amount each polysomes ranged from 23 to 97% significantly reduced a large portion (71%) response dehydration. effect dehydration on translational status varied extensively between species. Sixty per cent dehydration‐inducible mRNAs with twofold or greater increase...

Abstract Large-scale single-pass sequencing of cDNAs from different plants has provided an extensive reservoir for the cloning genes, evaluation tissue-specific gene expression, markers map-based cloning, and annotation genomic sequences. Although as January 2000 GenBank contained over 220,000 entries expressed sequence tags (ESTs) plants, most publicly available plant ESTs are derived vegetative tissues relatively few specifically developing seeds. However, important morphogenetic processes...

Summary The moss Physcomitrella patens contains high levels of arachidonic acid. For its synthesis from linoleic acid by desaturation and elongation, novel D5‐ D6‐ desaturases are required. To isolate one these, PCR‐based cloning was used, resulted in the isolation a full‐length cDNA coding for putatively new desaturase. deduced amino sequence has three domains: N‐terminal segment about 100 acids, with no similarity to any data banks, followed cytochrome b 5 ‐related region C‐terminal low...

The prediction of biologically active compounds is great importance for high-throughput screening (HTS) approaches in drug discovery and chemical genomics. Many computational methods this area focus on measuring the structural similarities between structures. However, traditional similarity measures are often too rigid or consider only global maximum common substructure (MCS) approach provides a more promising flexible alternative predicting bioactive compounds.In article, new backtracking...

Responses of resistant (Mi-1/Mi-1) and susceptible (mi-1/ mi-1) tomato (Solanum lycopersicum) to root-knot nematodes (RKNs; Meloidogyne spp.) infection were monitored using cDNA microarrays, the roles salicylic acid (SA) jasmonic (JA) defense signaling evaluated in these interactions. Array analysis was used compare transcript profiles incompatible compatible interactions roots 24 h after RKN infestation. The jai1 def1 mutant, altered JA signaling, transgenic line NahG, SA presence or...

Leaves and flowers begin life as outgrowths from the edges of shoot apical meristems. Stem cell divisions in meristem center replenish cells that are incorporated into organ primordia at periphery leave meristem. Organ boundaries, regions limited growth separate forming organs meristem, serve to isolate these two domains critical for coordination organogenesis maintenance. Boundary formation maintenance poorly understood processes, despite identification a number boundary-specific...

About 40% of the proteins encoded in eukaryotic genomes are unknown function (PUFs). Their functional characterization remains one main challenges modern biology. In this study we identified PUF encoding genes from Arabidopsis (Arabidopsis thaliana) using a combination sequence similarity, domain-based, and empirical approaches. Large-scale gene expression analyses 1,310 publicly available Affymetrix chips were performed to associate with regulatory networks biological processes known...

The interactions between aphids and their host plants seem to be analogous those of plant-microbial pathogens. Unlike microbial pathogen effectors, little is known about aphid effectors ability interfere with immunity. To date, only three functional have been reported. identify potato (Macrosiphum euphorbiae) we developed a salivary gland transcriptome using Illumina technology. We generated 85 million reads from glands assembled them into 646 contigs. Ab initio sequence analysis predicted...

In animal systems, master regulatory transcription factors (TFs) mediate stem cell maintenance through a direct transcriptional repression of differentiation promoting TFs. Whether similar mechanisms operate in plants is not known. plants, shoot apical meristems serve as reservoirs cells that provide for all above ground organs. WUSCHEL, homeodomain TF produced the niche, migrates into adjacent where it specifies cells. Through high‐resolution genomic analysis, we show WUSCHEL represses...

Significance Mosquitoes transmit some of the most dangerous human diseases. Microarray analysis developmental gene dynamics in female Aedes aegypti fat body has demonstrated that 6,146 genes are differentially expressed during juvenile hormone-dependent posteclosion development. These show striking temporal and functional separation. A RNAi microarray screen revealed a differential action Met down- up-regulation early late PE, respectively. Thus, this study provides substantial evidence...

Endomembrane trafficking relies on the coordination of a highly complex, dynamic network intracellular vesicles. Understanding will require dissection cargo and vesicle dynamics at cellular level in vivo. This is also key to establishing link between vesicular networks their functional roles development. We used high-content screen discover small molecules targeting endomembrane vivo complex eukaryote, Arabidopsis thaliana. Tens thousands were prescreened selected subset was interrogated...