Functional Genomics Research Papers - Academia.edu (original) (raw)

Whole-genome nucleotide sequencing has revolutionized the genetic, biochemical and molecular biology research on bacteria and indeed, many higher organisms. The genome sequences of the strains of two subspecies of Lactococcus lactis, L.... more

Whole-genome nucleotide sequencing has revolutionized the genetic, biochemical and molecular biology research on bacteria and indeed, many higher organisms. The genome sequences of the strains of two subspecies of Lactococcus lactis, L. lactis subsp. lactis and L. lactis subsp. cremoris, have been determined. These genomic sequences have permitted two important new approaches to be applied in the research of L. lactis. The analysis of the regulation of expression of all genes under specific circumstances at a given point in time is now possible by DNA microarray technology. The elucidation of the full protein complement of the organism as a function of intrinsic or external factors has been made possible by high-throughput protein identification and analysis techniques combined with the gene-derived know-how of the total protein encoding capacity of the genome. These techniques from the genomics arena, transcriptomics and proteomics, have been recently implemented in the study of various aspects of growth and functioning of L. lactis. In this paper we discuss a number of similarities and differences between the two lactococcal genome sequences and review the current status of genomics research in L. lactis. We also propose future directions with respect to both answering fundamental questions more quickly and more completely, as well as opening new avenues for biotechnological applications.

The antimicrobial peptide human α-defensin 5 (HD5) is expressed in Paneth cells, secretory epithelial cells in the small intestine. Unlike other characterized defensins, HD5 is stored in secretory vesicles as a propeptide. The storage... more

The antimicrobial peptide human α-defensin 5 (HD5) is expressed in Paneth cells, secretory epithelial cells in the small intestine. Unlike other characterized defensins, HD5 is stored in secretory vesicles as a propeptide. The storage quantities of HD5 are ∼90-450 µg per cm 2 of mucosal surface area, which is sufficient to generate microbicidal concentrations in the intestinal lumen. HD5 peptides isolated from the intestinal lumen are proteolytically processed forms-HD5(56-94) and HD5(63-94)-that are cleaved at the Arg 55 -Ala 56 and Arg 62 -Thr 63 sites, respectively.We show here that a specific pattern of trypsin isozymes is expressed in Paneth cells, that trypsin colocalizes with HD5 and that this protease can efficiently cleave HD5 propeptide to forms identical to those isolated in vivo. By acting as a prodefensin convertase in human Paneth cells, trypsin is involved in the regulation of innate immunity in the small intestine.

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If we are to make advances in the design of information systems for the processing of functional genomic data, we must carefully examine the concepts of gene and function. Therefore, we must consider the biological models that are used to... more

If we are to make advances in the design of information systems for the processing of functional genomic data, we must carefully examine the concepts of gene and function. Therefore, we must consider the biological models that are used to acquire these data from an epistemological point of view. This article introduces three elements of this view: (i) we reviewed the major concepts and the axioms of the systemic paradigm; (ii) we considered their relevance for the modelling of the biological functions within the framework of an intracellular signalling process; (iii) we present an operational input founded on this methodological viewpoint to illustrate the coherence of a theoretical framework and the use of its formalism for the description and the representation of biological activities. This formalism will guide the modelling and the interpretation of molecular interactions in terms of organisational operations producing and transforming the genetic information; thus, providing a better understanding of the complex relationship between the generation, the circulation and the computation of information when biological systems are set up. To cite this article: M. Roux-Rouquié, J.-L. Le Moigne, C. R. Biologies 325 (2002) 419-430. © 2002 Académies des sciences / Éditions scientifiques et médicales Elsevier SAS systemic modelling / epistemology / biological function / knowledge organisation / information system Résumé -Le paradigme systémique et sa pertinence pour la modélisation des fonctions biologiques. Une avancée dans le domaine de la conception des systèmes d'information pour l'exploitation des données de génomique fonctionnelle nécessite une discussion attentive des concepts de gène et de fonction, et donc une réflexion épistémologique sur les modèles biologiques à l'aide desquels sont établis ces systèmes d'information. Dans cet article, nous avons introduit les éléments de cette réflexion suivant trois axes : (i) un axe conceptuel considère les concepts majeurs et les axiomes du paradigme systémique ; (ii) leur pertinence pour la modélisation des fonctions biologiques est examinée dans le cadre d'un processus de signalisation intracellulaire ; (iii) une entrée opératoire, fondée sur cette réflexion méthodologique, illustre la cohérence apportée par un cadre théorique argumenté et l'utilisation de son formalisme pour la description et la représentation des activités biologiques. Ce formalisme conduit à interpréter le traitement des processus moléculaires en termes d'opérations organisationnelles produisant et transformant l'information génétique et à approfondir l'intelligibilité de la génération, de la circulation et du calcul de l'information dans la mise en place des organisations biologiques. Pour citer cet article : M. Roux-Rouquié, J.-L. Le Moigne, C. R. Biologies 325 (2002) 419-430. © 2002 Académies des sciences / Éditions scientifiques et médicales Elsevier SAS modélisation systémique / épistémologie / fonction biologique / organisation des connaissances / système d'information *Correspondence and reprints.

Cancer develops secondary to genetic and epigenetic changes of multiple genes. The overall 5 year survival rate of cancer is less than 50%. The main reason of this poor outcome lies in the technical limitations of the methods used for... more

Cancer develops secondary to genetic and epigenetic changes of multiple genes. The overall 5 year survival rate of cancer is less than 50%. The main reason of this poor outcome lies in the technical limitations of the methods used for the early detection of cancer. Cancer is characterized by extreme variation. ie.; each cancer is different in its genetic profile. It is possible to detect cancer cells, free “cancer DNA” or “cancer protein” from body fluid(blood, stool and sputum) of cancer patients even when the tumor mass is too small to be visible by radiologic study or endoscopy. The objective of this lecture is to review existing new genomic technology which aims to detect cancer in its early stages by the testing of body fluids for a combination of multiple, cancer-related key genes and marker proteins. The multiplex molecular test system for the early detection of cancer, recognizes multiple cancer related genes and proteins, with high sensitivity and precision. It can also be applied to the management, treatment and prevention of cancer by offering unique information on the nature of the genetic changes and alterations specifically associated with this particular cancer.

Voxelation allows high-throughput acquisition of multiple volumetric images of brain gene expression, similar to those obtained from biomedical imaging systems. To obtain these images, the method employs analysis of spatially registered... more

Voxelation allows high-throughput acquisition of multiple volumetric images of brain gene expression, similar to those obtained from biomedical imaging systems. To obtain these images, the method employs analysis of spatially registered voxels (cubes). For creation of high-resolution maps using voxelation, relatively small voxel sizes are necessary and instruments will be required for semiautomated harvesting of such voxels. Here, we describe two devices that allow spatially registered harvesting of voxels from the human and rodent brain, giving linear resolutions of 3.3 and 1 mm, respectively. Gene expression patterns obtained using these devices showed good agreement with known expression patterns. The voxelation instruments and their future iterations represent a valuable approach to the genome scale acquisition of gene expression patterns in the human and rodent brain. #

Elucidating the signalling mechanisms by which obesity leads to impaired insulin action is critical in the development of therapeutic strategies for the treatment of diabetes 1 . Recently, mice deficient for S6 Kinase 1 (S6K1), an... more

Elucidating the signalling mechanisms by which obesity leads to impaired insulin action is critical in the development of therapeutic strategies for the treatment of diabetes 1 . Recently, mice deficient for S6 Kinase 1 (S6K1), an effector of the mammalian target of rapamycin (mTOR) that acts to integrate nutrient and insulin signals 2 , were shown to be hypoinsulinaemic, glucose intolerant and have reduced b-cell mass 3 . However, S6K1deficient mice maintain normal glucose levels during fasting, suggesting hypersensitivity to insulin 3 , raising the question of their metabolic fate as a function of age and diet. Here, we report that S6K1-deficient mice are protected against obesity owing to enhanced b-oxidation. However on a high fat diet, levels of glucose and free fatty acids still rise in S6K1-deficient mice, resulting in insulin receptor desensitization. Nevertheless, S6K1-deficient mice remain sensitive to insulin owing to the apparent loss of a negative feedback loop from S6K1 to insulin receptor substrate 1 (IRS1), which blunts S307 and S636/S639 phosphorylation; sites involved in insulin resistance 4,5 . Moreover, wild-type mice on a high fat diet as well as K/K A y and ob/ob (also known as Lep/Lep) mice-two genetic models of obesity-have markedly elevated S6K1 activity and, unlike S6K1-deficient mice, increased phosphorylation of IRS1 S307 and S636/S639. Thus under conditions of nutrient satiation S6K1 negatively regulates insulin signalling.

The CD1 family is a large cluster of non-polymorphic, major histocompatibility complex (MHC) class-I-like molecules that bind distinct lipid-based antigens that are recognized by T cells. The most studied group of T cells that interact... more

The CD1 family is a large cluster of non-polymorphic, major histocompatibility complex (MHC) class-I-like molecules that bind distinct lipid-based antigens that are recognized by T cells. The most studied group of T cells that interact with lipid antigens are natural killer T (NKT) cells, which characteristically express a semi-invariant T-cell receptor (NKT TCR) that specifically recognizes the CD1 family member, CD1d. NKT-cell-mediated recognition of the CD1d-antigen complex has been implicated in microbial immunity, tumour immunity, autoimmunity and allergy. Here we describe the structure of a human NKT TCR in complex with CD1d bound to the potent NKT-cell agonist a-galactosylceramide, the archetypal CD1d-restricted glycolipid. In contrast to T-cell receptor-peptide-antigen-MHC complexes, the NKT TCR docked parallel to, and at the extreme end of the CD1d-binding cleft, which enables a lock-and-key type interaction with the lipid antigen. The structure provides a basis for the interaction between the highly conserved NKT TCR a-chain and the CD1d-antigen complex that is typified in innate immunity, and also indicates how variability of the NKT TCR b-chain can impact on recognition of other CD1d-antigen complexes. These findings provide direct insight into how a T-cell receptor recognizes a lipid-antigen-presenting molecule of the immune system.

It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers.... more

It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs.

Engulfment and subsequent degradation of apoptotic cells is an essential step that occurs throughout life in all multicellular organisms 1-3 . ELMO/Dock180/Rac proteins are a conserved signalling module for promoting the internalization... more

Engulfment and subsequent degradation of apoptotic cells is an essential step that occurs throughout life in all multicellular organisms 1-3 . ELMO/Dock180/Rac proteins are a conserved signalling module for promoting the internalization of apoptotic cell corpses 4,5 ; ELMO and Dock180 function together as a guanine nucleotide exchange factor (GEF) for the small GTPase Rac, and thereby regulate the phagocyte actin cytoskeleton during engulfment 4-6 . However, the receptor(s) upstream of the ELMO/ Dock180/Rac module are still unknown. Here we identify brainspecific angiogenesis inhibitor 1 (BAI1) as a receptor upstream of ELMO and as a receptor that can bind phosphatidylserine on apoptotic cells. BAI1 is a seven-transmembrane protein belonging to the adhesion-type G-protein-coupled receptor family, with an extended extracellular region 7-9 and no known ligands. We show that BAI1 functions as an engulfment receptor in both the recognition and subsequent internalization of apoptotic cells. Through multiple lines of investigation, we identify phosphatidylserine, a key 'eat-me' signal exposed on apoptotic cells 10-13 , as a ligand for BAI1. The thrombospondin type 1 repeats within the extracellular region of BAI1 mediate direct binding to phosphatidylserine. As with intracellular signalling, BAI1 forms a trimeric complex with ELMO and Dock180, and functional studies suggest that BAI1 cooperates with ELMO/Dock180/Rac to promote maximal engulfment of apoptotic cells. Last, decreased BAI1 expression or interference with BAI1 function inhibits the engulfment of apoptotic targets ex vivo and in vivo. Thus, BAI1 is a phosphatidylserine recognition receptor that can directly recruit a Rac-GEF complex to mediate the uptake of apoptotic cells.

8 typically slower than ϳ1 km s −1 ) might differ significantly from what is assumed by current modelling efforts 27 . The expected equation-of-state differences among small bodies (ice versus rock, for instance) presents another... more

8 typically slower than ϳ1 km s −1 ) might differ significantly from what is assumed by current modelling efforts 27 . The expected equation-of-state differences among small bodies (ice versus rock, for instance) presents another dimension of study; having recently adapted our code for massively parallel architectures (K. M. Olson and E.A, manuscript in preparation), we are now ready to perform a more comprehensive analysis.

by in situ X-ray observations based on the same pressure scale in the previous study . The overpressure was calculated using these boundaries. We observed the pressure to drop during the transformation by 1-2 GPa, but this would not... more

by in situ X-ray observations based on the same pressure scale in the previous study . The overpressure was calculated using these boundaries. We observed the pressure to drop during the transformation by 1-2 GPa, but this would not affect the transformation rate significantly because the overpressure is very large in the present study. This has been confirmed in the post-spinel transformation 7 .

Sir-Gottfried and Wilson 1 remark critically that "SSK [sociology of scientific knowledge] accounts often treat only the earliest phases of a scientific development, when the evidence is uncertain, and largely ignore subsequent convincing... more

Sir-Gottfried and Wilson 1 remark critically that "SSK [sociology of scientific knowledge] accounts often treat only the earliest phases of a scientific development, when the evidence is uncertain, and largely ignore subsequent convincing confirmations". This is true of controversy studies in SSK, but not of one of the books at issue, my own Constructing Quarks 2. There I documented and analysed the history of the establishment of the standard model as the 'new orthodoxy' in elementary particle physics. Ellis 3 makes a similar mistake, and adds that he would "also like [me] to document and compare more thoroughly the rejection by the scientific community of false 'discoveries'". I have published essays on discredited 'discoveries' of magnetic monopoles and isolated quarks, and on the ultimately unsuccessful theoretical arguments that the new particles (the J/psi and so on) were manifestations of quark colour rather than charm (see, for example, ref. 4). The analysis in those essays goes along the same lines as that of Constructing Quarks, and if Ellis wants to dispute it, I will be happy to respond. Capasso 5 is mistaken in asserting that successful technology "validates the specific theories on which it is founded". A machine works because it works, not because of what anybody thinks about it 6. And, as I believe Gottfried and Wilson recognize, Capasso's idea that technology owes everything to prior science is as historically misleading as its inverse. In short, the continuing criticism of science studies in your pages remains wide of its mark.

MicroRNAs (miRNAs) are small, highly conserved, non-coding RNAs that regulate gene expression of target mRNAs through cleavage or translational inhibition. miRNAs are most often identified through computational prediction from genome... more

MicroRNAs (miRNAs) are small, highly conserved, non-coding RNAs that regulate gene expression of target mRNAs through cleavage or translational inhibition. miRNAs are most often identified through computational prediction from genome sequences. The rainbow trout genome sequence is not available yet, which does not allow miRNA prediction for this species which is of great economic interest for aquaculture and sport fisheries, and is a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. To identify miRNAs from rainbow trout, we constructed a miRNA library from a pool of nine somatic tissues. Analysis of the library identified 210 unique sequences representing 54 distinct miRNAs; 50 with conserved sequences matching previously identified miRNAs and four novel miRNAs. In addition, 13 miRNAs were computationally predicted from the rainbow trout transcriptome. Real-time PCR was used to measure miRNA expression patterns in adult somatic tissues and unfertilized eggs. The majority of the miRNAs showed characteristic tissue-specific expression patterns suggesting potential roles in maintaining tissue identity. Potential miRNA-target interactions were computationally predicted and single nucleotide polymorphisms (SNPs) were identified in the miRNAs and their target sites in the rainbow trout transcripts. The rainbow trout miRNAs identified and characterized in this study provide a new tool for functional genome research in salmonids. Tissue-specific miRNAs may serve as molecular markers, predictive of specific functional and diagnostic implications. The data on genetic polymorphisms in miRNA-target interactions is particularly useful for rainbow trout breeding programs.

In many eukaryotic organisms, gender is determined by a pair of heteromorphic sex chromosomes. Degeneration of the non-recombining Y chromosome is a general facet of sex chromosome evolution. Selective pressure to restore expression... more

In many eukaryotic organisms, gender is determined by a pair of heteromorphic sex chromosomes. Degeneration of the non-recombining Y chromosome is a general facet of sex chromosome evolution. Selective pressure to restore expression levels of X-linked genes relative to autosomes accompanies Y-chromosome degeneration, thus driving the evolution of dosage compensation mechanisms. This review focuses on evolutionary aspects of dosage compensation, in light of recent advances in comparative and functional genomics that have substantially increased our understanding of the molecular mechanisms of dosage compensation and how it evolved. We review processes involved in sex chromosome evolution, and discuss the dynamic interaction between Y degeneration and the acquisition of dosage compensation. We compare mechanisms of dosage compensation and the origin of dosage compensation genes between different taxa and comment on sex chromosomes that apparently lack compensation mechanisms. Finally, we discuss how dosage compensation systems can also influence the evolution of well-established sex chromosomes.

A major challenge in the field of functional genomics is the development of computational techniques for organizing and interpreting large amounts of gene expression data. These methods will be critical for the discovery of new... more

A major challenge in the field of functional genomics is the development of computational techniques for organizing and interpreting large amounts of gene expression data. These methods will be critical for the discovery of new therapeutic drug targets. Here, we present a simple method for determining the most likely drug target candidates from temporal gene expression patterns assayed with reverse-transcription polymerase chain reaction (RT-PCR) and DNA microarrays.

I was appalled when I read a report in Nature last year about proposals by the Indian government to encourage universities to teach astrology (Nature 411, 227; 200110.1038/35077282), but never thought that anything similar might occur in... more

I was appalled when I read a report in Nature last year about proposals by the Indian government to encourage universities to teach astrology (Nature 411, 227; 200110.1038/35077282), but never thought that anything similar might occur in the West. ... To read this story in full you ...

Activated platelets bind numerous adhesive and procoagulant proteins by receptor-mediated processes. Although there is little evidence to suggest that these processes are heterogeneous in platelets, we previously found that platelets... more

Activated platelets bind numerous adhesive and procoagulant proteins by receptor-mediated processes. Although there is little evidence to suggest that these processes are heterogeneous in platelets, we previously found that platelets co-stimulated with collagen and thrombin express functional alpha-granule factor V only on a subpopulation of cells. Here we show that these cells, referred to as 'COAT-platelets', bind additional alpha-granule proteins, including fibrinogen, von Willebrand factor, thrombospondin, fibronectin and alpha2-antiplasmin. These proteins are all transglutaminase substrates, and inhibitors of transglutaminase prevent the production of COAT-platelets. A synthetic transglutaminase substrate (CP15) also binds to COAT-platelets, and analysis by high performance liquid chromatography/mass spectrometry shows that a product is formed with a relative molecular mass (Mr) equal to CP15 plus 176. Serotonin, an abundant component of platelet-dense granules, has an ...

El conocimiento derivado del genoma de Mycobacterium tuberculosis, junto con el desarrollo de sofisticados sistemas para la manipulación genética del bacilo, ofrece la mayor promesa para el desarrollo de herramientas nuevas y más... more

El conocimiento derivado del genoma de Mycobacterium tuberculosis, junto con el desarrollo de sofisticados sistemas para la manipulación genética del bacilo, ofrece la mayor promesa para el desarrollo de herramientas nuevas y más eficientes para prevenir y controlar la tuberculosis. Se han desarrollado métodos más eficientes para la inactivación de genes micobacterianos que se han convertido en el pilar de la genómica funcional micobacteriana. La generación de mutantes mediante la inactivación génica, apoyada directa o indirectamente por el desciframiento del genoma micobacteriano, ha permitido la generación de un número significativo de mutantes de M. tuberculosis. En algunos casos, el análisis de estas mutantes ha establecido relaciones entre los productos génicos y sus funciones en la fisiología y la patogenicidad de la micobacteria. En esta revisión se describen los estudios más representativos basados en dichas mutantes.

The diploid woodland strawberry (Fragaria vesca) is an attractive system for functional genomics studies. Its small stature, fast regeneration time, efficient transformability and small genome size, together with substantial EST and... more

The diploid woodland strawberry (Fragaria vesca) is an attractive system for functional genomics studies. Its small stature, fast regeneration time, efficient transformability and small genome size, together with substantial EST and genomic sequence resources make it an ideal reference plant for Fragaria and other herbaceous perennials. Most importantly, this species shares gene sequence similarity and genomic microcolinearity with other members of the Rosaceae family, including large-statured tree crops (such as apple, peach and cherry), and brambles and roses as well as with the cultivated octoploid strawberry, F. ×ananassa. F. vesca may be used to quickly address questions of gene function relevant to these valuable crop species. Although some F. vesca lines have been shown to be substantially homozygous, in our hands plants in purportedly homozygous populations exhibited a range of morphological and physiological variation, confounding phenotypic analyses. We also found the genotype of a named variety, thought to be well-characterized and even sold commercially, to be in question. An easy to grow, standardized, inbred diploid Fragaria line with documented genotype that is available to all members of the research community will facilitate comparison of results among laboratories and provide the research community with a necessary tool for functionally testing the large amount of sequence data that will soon be available for peach, apple, and strawberry.