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Sequencing Projects (sequencing + project)
Kinds of Sequencing Projects Selected AbstractsA role for endogenous reverse transcriptase in tumorigenesis and as a target in differentiating cancer therapyGENES, CHROMOSOMES AND CANCER, Issue 1 2006Paola Sinibaldi-Vallebona An unexpected result emerging from completion of the genome sequencing project is that a large portion of mammalian genomes is constituted by retrotransposons. A large body of published data supports the conclusion that retrotransposons are biologically active elements and indicates that retrotransposition is an ongoing process in mammalian genomes. Retroelements can act as insertional mutagens altering the coding integrity of genes and, recently, have been found to also affect the expression of cellular genes at the epigenetic level: in this light, they are a potential threat in that these events can trigger the onset of several pathologies including cancer. Retroelement genes, and particularly the gene coding for reverse transcriptase (RT), are typically expressed at high levels in transformed cells and tumors. In recent work, we have found that drug-mediated inhibition of the endogenous RT activity, or silencing of expression of active retrotransposons of the LINE-1 family by RNA interference, down-regulate cell growth and induce the activation of differentiating functions in several cancer cell lines. Moreover, the inhibition of endogenous RT activity in vivo antagonizes the growth of human tumors in animal models. In this review, we discuss newly emerging concepts on the role of retrotransposons and suggest that an abnormally high level of the RT activity that they encode may contribute to the loss of control in the proliferation and differentiation programs typical of transformed cells. In this light, RT-coding elements may be regarded as promising targets in the development of novel, differentiation-inducing approaches to cancer therapy. © 2005 Wiley-Liss, Inc. [source] The case for sequencing the genome of the electric eel Electrophorus electricusJOURNAL OF FISH BIOLOGY, Issue 2 2008J. S. Albert A substantial international community of biologists have proposed the electric eel Electrophorus electricus (Teleostei: Gymnotiformes) as an important candidate for genome sequencing. In this study, the authors outline the unique advantages that a genome sequencing project of this species would offer society for developing new ways of producing and storing electricity. Over tens of millions of years, electric fish have evolved an exceptional capacity to generate a weak (millivolt) electric field in the water near their body from specialized muscle-derived electric organs, and simultaneously, to sense changes in this field that occur when it interacts with foreign objects. This electric sense is used both to navigate and orient in murky tropical waters and to communicate with other members of the same species. Some species, such as the electric eel, have also evolved a strong voltage organ as a means of stunning prey. This organism, and a handful of others scattered worldwide, convert chemical energy from food directly into workable electric energy and could provide important clues on how this process could be manipulated for human benefit. Electric fishes have been used as models for the study of basic biological and behavioural mechanisms for more than 40 years by a large and growing research community. These fishes represent a rich source of experimental material in the areas of excitable membranes, neurochemistry, cellular differentiation, spinal cord regeneration, animal behaviour and the evolution of novel sensory and motor organs. Studies on electric fishes also have tremendous potential as a model for the study of developmental or disease processes, such as muscular dystrophy and spinal cord regeneration. Access to the genome sequence of E. electricus will provide society with a whole new set of molecular tools for understanding the biophysical control of electromotive molecules, excitable membranes and the cellular production of weak and strong electric fields. Understanding the regulation of ion channel genes will be central for efforts to induce the differentiation of electrogenic cells in other tissues and organisms and to control the intrinsic electric behaviours of these cells. Dense genomic sequence information of E. electricus will also help elucidate the genetic basis for the origin and adaptive diversification of a novel vertebrate tissue. The value of existing resources within the community of electric fish research will be greatly enhanced across a broad range of physiological and environmental sciences by having a draft genome sequence of the electric eel. [source] Double-stranded RNA-mediated gene silencing of cysteine proteases (falcipain-1 and -2) of Plasmodium falciparumMOLECULAR MICROBIOLOGY, Issue 5 2002Pawan Malhotra Summary Malaria remains a public health problem of enormous magnitude, affecting over 500 million people every year. Lack of success in the past in the development of new drug/vaccines has mainly been attributed to poor understanding of the functions of different parasite proteins. Recently, RNA interference (RNAi) has emerged as a simple and incisive technique to study gene functions in a variety of organisms. In this study, we report the results of RNAi by double-stranded RNA of cysteine protease genes (falcipain -1 and -2) in the malaria parasite, Plasmodium falciparum. Using RNAi directed towards falcipain genes, we demonstrate that blocking the expression of these genes results in severe morphological abnormalities in parasites, inhibition of parasite growth in vitro and substantial accumulation of haemoglobin in the parasite. The inhibitory effects produced by falcipain double-stranded (ds)RNAs are reminiscent of the effects observed upon administering E-64, a cysteine protease inhibitor. The parasites treated with falcipain's dsRNAs also show marked reduction in the levels of corresponding endogenous falcipain mRNAs. We also demonstrate that dsRNAs of falcipains are broken into short interference RNAs , 25 nucleotides in size, a characteristic of RNAi, which in turn activates sequence-specific nuclease activity in the malaria parasites. These results thus provide more evidence for the existence of RNAi in P. falciparum and also suggest possibilities for using RNAi as an effective tool to determine the functions of the genes identified from the P. falciparum genome sequencing project. [source] The stem canker (blackleg) fungus, Leptosphaeria maculans, enters the genomic eraMOLECULAR PLANT PATHOLOGY, Issue 3 2005T. ROUXEL SUMMARY Leptosphaeria maculans is the most ubiquitous pathogen of Brassica crops, and mainly oilseed brassicas (oilseed rape, canola), causing the devastating ,stem canker' or ,blackleg'. This review summarizes our current knowledge on the pathogen, from taxonomic issues to specific life traits. It mainly illustrates the importance of formal genetics approaches on the pathogen side to dissect the interaction with the host plants. In addition, this review presents the main current research topics on L. maculans and focuses on the L. maculans genome initiative recently begun, including its main research issues. Taxonomy:,Leptosphaeria maculans (Desm.) Ces. & de Not. (anamorph Phoma lingam Tode ex Fr.). Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes (Loculoascomycetes), Order Pleosporales, Genus Leptosphaeria, Species maculans. Host range:, cultivated Brassicas such as Brassica napus (oilseed rape, canola), B. rapa, B. juncea, B. oleracea, etc., along with numerous wild crucifers species. Arabidopsis thaliana was recently reported to be a potential host for L. maculans. Primary disease symptoms are greyish-green collapse of cotyledon or leaf tissue, without a visible margin, bearing tiny black spots (pycnidia). The fungus then develops an endophytic symptomless growth for many months. Secondary symptoms, at the end of the growing season, are dry necroses of the crown tissues with occasional blackening (stem canker or blackleg) causing lodging of the plants. Pseudothecia differentiate on leftover residues. Seedling damping-off and premature ripening are also reported under certain environmental conditions. Useful websites:,Leptosphaeria maculans sequencing project at Genoscope: http://www.genoscope.cns.fr/externe/English/Projets/Projet_DM/organisme_DM.html; the SECURE site: http://www.secure.rothamsted.ac.uk/ the ,Blackleg' group at the University of Melbourne: http://www.botany.unimelb.edu.au/blackleg/overview.htm [source] Molecular Tools to Study Physcomitrella patensPLANT BIOLOGY, Issue 3 2005W. Frank Abstract: The moss Physcomitrella patens has become a suitable model plant system for the analysis of diverse aspects of modern plant biology. The research strategies have been influenced by the implementation of state-of-the-art cell culture and molecular biology techniques. The forthcoming completion of the Physcomitrella genome sequencing project will generate many open questions, the examination of which will rely on a diverse set of molecular tools. Within this article, we intend to introduce the essential cell culture and molecular biology techniques which have been adopted in recent years to make Physcomitrella amenable to a wide range of genetic analyses. Many research groups have made valuable contributions to improve the methodology for the study of Physcomitrella. We would like to apologise to all colleagues whose important contributions could not be cited within this manuscript. [source] Identifications of expressed sequence tags from Pacific threadfin (Polydactylus sexfilis) skeletal muscle cDNA libraryAQUACULTURE RESEARCH, Issue 4 2010Shizu Watanabe Abstract Pacific threadfin (Polydactylus sexfilis), locally known as Moi, is a desirable fish for aquaculture and recreational fishing. To understand the basic mechanism of muscle formation and its impacts on flesh quality, we established a cDNA library using mRNA of the skeletal muscle tissue from fingerlings. The library size was 1.1 × 108 plaque forming units mg,1 and the percentage of recombinant clones was >81%. A pilot sequencing project from 181 clones identified 129 useful expressed sequence tags (ESTs), of which 90 ESTs exhibited significant homology to known genes and 39 ESTs have low homologies to unknown genes by blast algorithm. The most abundant EST from the pilot sequence data is nikotinamide riboside kinase 2 (59 times), followed by 60S ribosomal protein L24 (12 times) and ribosomal protein L8 (5 times). Fourteen novel genes were retrieved from the sequenced clones and subjected to gene ontology annotation. Four mRNA sequences were identified as significant regulators of transcription, including Not2p, Tsc22 domain family 2, LIM domain binding factor 3 and mesenchyme homeobox 2. These results suggest that the muscle cDNA library is an useful source for identifying EST sequences of Pacific threadfin. [source] Microbial aldo-keto reductasesFEMS MICROBIOLOGY LETTERS, Issue 2 2002Elizabeth M Ellis Abstract The aldo-keto reductases (AKR) are a superfamily of enzymes with diverse functions in the reduction of aldehydes and ketones. AKR enzymes are found in a wide range of microorganisms, and many open reading frames encoding related putative enzymes have been identified through genome sequencing projects. Established microbial members of the superfamily include the xylose reductases, 2,5-diketo- d -gluconic acid reductases and ,-keto ester reductases. The AKR enzymes share a common (,/,)8 structure, and conserved catalytic mechanism, although there is considerable variation in the substrate-binding pocket. The physiological function of many of these enzymes is unknown, but a variety of methods including gene disruptions, heterologous expression systems and expression profiling are being employed to deduce the roles of these enzymes in cell metabolism. Several microbial AKR are already being exploited in biotransformation reactions and there is potential for other novel members of this important superfamily to be identified, studied and utilized in this way. [source] Genomic BLAST: custom-defined virtual databases for complete and unfinished genomesFEMS MICROBIOLOGY LETTERS, Issue 2 2002Leda Cummings Abstract BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes. [source] Microarray-based DNA profiling to study genomic aberrations,IUBMB LIFE, Issue 7 2008Nic Waddell Abstract High throughput microarrays were initially developed to analyse the expression of many RNA transcripts in parallel. The technology has since been adapted to a variety of applications, one of which is the analysis of the genome to study DNA dosage and sequence content. Advances in microarray fabrication and completion of large-scale genome sequencing projects have enabled the rapid development of affordable array-based methods for high-resolution genome-wide assessment of DNA alterations. This review will describe the evolution of microarray assays to study genomic aberrations and will highlight how they have enabled researchers to gain insight into the biology of human diseases and how they will benefit research in the future. © 2008 IUBMB IUBMB Life, 60(7): 437,440, 2008 [source] MicroReview: Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomesMOLECULAR MICROBIOLOGY, Issue 5 2005Elizabeth S. Egan Summary Historically, the prokaryotic genome was assumed to consist of a single circular replicon. However, as more microbial genome sequencing projects are completed, it is becoming clear that multipartite genomes comprised of more than one chromosome are not unusual among prokaryotes. Chromosomes are distinguished from plasmids by the presence of essential genes as well as characteristic cell cycle-linked replication kinetics; unlike plasmids, chromosomes initiate replication once per cell cycle. The existence of multipartite prokaryotic genomes raises several questions regarding how multiple chromosomes are replicated and segregated during the cell cycle. These divided genomes also introduce questions regarding chromosome evolution and genome stability. In this review, we discuss these and other issues, with particular emphasis on the cholera pathogen Vibrio cholerae. [source] Redox Regulation and Flower Development: A Novel Function for GlutaredoxinsPLANT BIOLOGY, Issue 5 2006S. Xing Abstract: Glutaredoxins (GRXs) are small, ubiquitous oxidoreductases that have been intensively studied in E. coli, yeast and humans. They are involved in a large variety of cellular processes and exert a crucial function in the response to oxidative stress. GRXs can reduce disulfides by way of conserved cysteines, located in conserved active site motifs. As in E. coli, yeast, and humans, GRXs with active sites of the CPYC and CGFS type are also found in lower and higher plants, however, little has been known about their function. Surprisingly, 21 GRXs from Arabidopsis thaliana contain a novel, plant-specific CC type motif. Lately, information on the function of CC type GRXs and redox regulation, in general, is accumulating. This review focuses on recent findings indicating that GRXs, glutathione and redox regulation, in general, seem to be involved in different processes of development, so far, namely in the formation of the flower. Recent advances in EST and genome sequencing projects allowed searching for the presence of the three different types of the GRX subclasses in other evolutionary informative plant species. A comparison of the GRX subclass composition from Physcomitrella, Pinus, Oryza, Populus, and Arabidopsis is presented. This analysis revealed that only two CC type GRXs exist in the bryophyte Physcomitrella and that the CC type GRXs group expanded during the evolution of land plants. The existence of a large CC type subclass in angiosperms supports the assumption that their capability to modify target protein activity posttranslationally has been integrated into crucial plant specific processes involved in higher plant development. [source] Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas speciesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 10 2009Ayshwarya Ravichandran Abstract Protein phosphorylation on serine, threonine, and tyrosine is well established as a crucial regulatory posttranslational modification in eukaryotes. With the recent whole-genome sequencing projects reporting the presence of serine/threonine kinases and two-component proteins both in prokaryotes and eukaryotes, the importance of protein phosphorylation in archaea and bacteria is gaining acceptance. While conventional biochemical methods failed to obtain a snapshot of the bacterial phosphoproteomes, advances in MS methods have paved the way for in-depth mapping of phosphorylation sites. Here, we present phosphoproteomes of two ecologically diverse non-enteric Gram-negative bacteria captured by a nanoLC-MS-based approach combined with a novel phosphoenrichment method. While the phosphoproteome data from the two species are not very similar, the results reflect high similarity to the previously published dataset in terms of the pathways the phosphoproteins belong to. This study additionally provides evidence to prior observations that protein phosphorylation is common in bacteria. Notably, phosphoproteins identified in Pseudomonas aeruginosa belong to motility, transport, and pathogenicity pathways that are critical for survival and virulence. We report, for the first time, that motility regulator A, probably acting via the novel secondary messenger cyclic diguanylate monophosphate, significantly affects protein phosphorylation in Pseudomonas putida. [source] Shotgun proteomic analysis of Chlamydia trachomatisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2005Paul Skipp Abstract Chlamydiae are widespread bacterial pathogens responsible for a broad range of diseases, including sexually transmitted infections, pneumonia and trachoma. To validate the existence of hitherto hypothetical proteins predicted from recent chlamydial genome sequencing projects and to examine the patterns of expression of key components at the protein level, we have surveyed the expressed proteome of Chlamydia trachomatis strain,L2. A combination of two-dimensional gel analysis, multi-dimensional protein identification (MudPIT) and nanocapillary liquid chromatography-tandem mass spectrometry allowed a total of 328,chlamydial proteins to be unambiguously assigned. Proteins identified as being expressed in the metabolically inert form, elementary body, of Chlamydia include the entire set of predicted glycolytic enzymes, indicating that metabolite flux rather than de novo synthesis of this pathway is triggered upon infection of host cells. An enzyme central to cell wall biosynthesis was also detected in the intracellular form, reticulate body, of Chlamydia, suggesting that the peptidoglycan is produced during growth within host cells. Other sets of proteins identified include 17 outer membrane-associated proteins of potential significance in vaccine studies and 67,proteins previously annotated as hypothetical or conserved hypothetical. Taken together, ,35% of the predicted proteome for C.,trachomatis has been experimentally verified, representing the most extensive survey of any chlamydial proteome to date. [source] Preparing undergraduates to participate in the post-genome era: A capstone laboratory experience in proteomics,BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 6 2003Eric S. Eberhardt Abstract Proteomics is one of the important new disciplines to emerge from the genome sequencing projects of the last decade. In order to introduce our students to the techniques and promise of this emerging field, a capstone laboratory experience has been developed. The exercise involves multiple aspects of proteomics research including microbial culturing methods, two-dimensional gel electrophoresis techniques, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry, and database mining. Over a 12-week semester, students design their own experiments and apply a proteomic approach to investigate the heat shock response in Escherichia coli. In the trial presented in this article, students successfully identified several major heat shock proteins. The laboratory outlined here can be readily adapted to explore a wide variety of responses in metabolic pathways or responses resulting from other environmental insults or stresses. Additionally, the laboratory can be modified to explore the proteomes of organelles, tissues, and other model organisms. [source] Genome Sequencing and Comparative Genomics of Tropical Disease PathogensCELLULAR MICROBIOLOGY, Issue 12 2003Jane M. Carlton Summary The sequencing of eukaryotic genomes has lagged behind sequencing of organisms in the other domains of life, archae and bacteria, primarily due to their greater size and complexity. With recent advances in ,high-throughput ,technologies ,such ,as ,robotics and improved computational resources, the number of eukaryotic genome sequencing projects has in-creased significantly. Among these are a number of sequencing projects of tropical pathogens of medical and veterinary importance, many of which are responsible for causing widespread morbidity and mortality in peoples of developing countries. Uncovering the complete gene complement of these organisms is proving to be of immense value in the develop-ment of novel methods of parasite control, such as antiparasitic drugs and vaccines, as well as the development of new diagnostic tools. Combining pathogen genome sequences with the host and vector genome sequences is promising to be a robust method for the identification of host,pathogen interactions. Finally, comparative sequencing of related species, especially of organisms used as model systems in the study of the disease, is beginning to realize its potential in the identification of genes, and the evolutionary forces that shape the genes, that are involved in evasion of the host immune response. [source] | ||||||||||||||||||||||