RESUMO
One of the challenges of functional genomics is to create a better understanding of the biological system being studied so that the data produced are leveraged to provide gains for agriculture, human health, and the environment. Functional modeling enables researchers to make sense of these data as it reframes a long list of genes or gene products (mRNA, ncRNA, and proteins) by grouping based upon function, be it individual molecular functions or interactions between these molecules or broader biological processes, including metabolic and signaling pathways. However, poultry researchers have been hampered by a lack of functional annotation data, tools, and training to use these data and tools. Moreover, this lack is becoming more critical as new sequencing technologies enable us to generate data not only for an increasingly diverse range of species but also individual genomes and populations of individuals. We discuss the impact of these new sequencing technologies on poultry research, with a specific focus on what functional modeling resources are available for poultry researchers. We also describe key strategies for researchers who wish to functionally model their own data, providing background information about functional modeling approaches, the data and tools to support these approaches, and the strengths and limitations of each. Specifically, we describe methods for functional analysis using Gene Ontology (GO) functional summaries, functional enrichment analysis, and pathways and network modeling. As annotation efforts begin to provide the fundamental data that underpin poultry functional modeling (such as improved gene identification, standardized gene nomenclature, temporal and spatial expression data and gene product function), tool developers are incorporating these data into new and existing tools that are used for functional modeling, and cyberinfrastructure is being developed to provide the necessary extendibility and scalability for storing and analyzing these data. This process will support the efforts of poultry researchers to make sense of their functional genomics data sets, and we provide here a starting point for researchers who wish to take advantage of these tools.
Assuntos
Genoma , Genômica/métodos , Aves Domésticas/genética , Animais , Modelos GenéticosRESUMO
The equine genome sequence enables the use of high-throughput genomic technologies in equine research, but accurate identification of expressed gene products and interpreting their biological relevance require additional structural and functional genome annotation. Here, we employ the equine genome sequence to identify predicted and known proteins using proteomics and model these proteins into biological pathways, identifying 582 proteins in normal cell-free equine bronchoalveolar lavage fluid (BALF). We improved structural and functional annotation by directly confirming the in vivo expression of 558 (96%) proteins, which were computationally predicted previously, and adding Gene Ontology (GO) annotations for 174 proteins, 108 of which lacked functional annotation. Bronchoalveolar lavage is commonly used to investigate equine respiratory disease, leading us to model the associated proteome and its biological functions. Modelling of protein functions using Ingenuity Pathway Analysis identified carbohydrate metabolism, cell-to-cell signalling, cellular function, inflammatory response, organ morphology, lipid metabolism and cellular movement as key biological processes in normal equine BALF. Comparative modelling of protein functions in normal cell-free bronchoalveolar lavage proteomes from horse, human, and mouse, performed by grouping GO terms sharing common ancestor terms, confirms conservation of functions across species. Ninety-one of 92 human GO categories and 105 of 109 mouse GO categories were conserved in the horse. Our approach confirms the utility of the equine genome sequence to characterize protein networks without antibodies or mRNA quantification, highlights the need for continued structural and functional annotation of the equine genome and provides a framework for equine researchers to aid in the annotation effort.
Assuntos
Líquido da Lavagem Broncoalveolar/química , Genoma/genética , Cavalos/genética , Anotação de Sequência Molecular/métodos , Proteínas/genética , Animais , Humanos , Espectrometria de Massas , Camundongos , Modelos Biológicos , Proteínas/análise , Proteínas/fisiologia , Proteômica/métodosRESUMO
Tibial dyschondroplasia (TD) is a poultry leg problem that affects the proximal growth plate of the tibia, preventing its transition to bone. To understand the disease-induced proteomic changes, we compared the protein extracts of cartilage from normal and TD-affected growth plates. TD was induced by feeding thiram to chickens 2 wk before tissue harvest. Proteins were extracted from whole tissues and from conditioned media (CM) prepared by incubating appropriate growth plate tissues in serum-free culture medium for 48 hr. The extracts were prefractionated to contain proteins ranging between 10 and 100 kD. Equal amounts of proteins were subjected to 2D gel electrophoresis with three individual samples per group. The gels were silver stained, and digital images were compared and analyzed with Melanie software to determine differentially expressed protein spots. On comparison of two sets of gels, 47 matching spots were detected in tissue extracts and 27 in CM extracts. Among the matching spots, 12 were determined to be down-regulated in tissue extracts (P < or = 0.05) and two in CM extracts (P < or = 0.05) of TD-affected growth plates. Altogether, 32 protein spots could be identified in both tissue and CM extracts by in-gel trypsin digestion, followed by peptide mass fingerprinting and mass spectrometry (MS)/MS fragmentation. The down-regulated proteins included alpha-enolase, G protein, origin recognition complex, peptidyl prolyl isomerase, calumenin, type II collagen precursor, and the expressed sequence tag pgm2n.pk014.f20, a protein with homology to human reticulocalbin-3 (RCN3). Most of the downregulated proteins are associated with signal transduction, energy metabolism, and secretory functions that are integral to cell viability. Consistent with our earlier findings that the TD chondrocytes are nonviable, the current results suggest that thiram very likely interferes with basic metabolic functions of chondrocytes, leading to their death and, consequently, to the pathogenesis of TD.
Assuntos
Cartilagem/metabolismo , Regulação da Expressão Gênica/fisiologia , Lâmina de Crescimento/metabolismo , Osteocondrodisplasias/veterinária , Doenças das Aves Domésticas/metabolismo , Proteômica , Animais , Galinhas , Osteocondrodisplasias/metabolismoRESUMO
The chicken genome is sequenced and this, together with microarray and other functional genomics technologies, makes post-genomic research possible in the chicken. At this time, however, such research is hindered by a lack of genomic structural and functional annotations. Bio-ontologies have been developed for different annotation requirements, as well as to facilitate data sharing and computational analysis, but these are not yet optimally utilized in the chicken. Here we discuss genomic annotation and bio-ontologies. We focus specifically on the Gene Ontology (GO), chicken GO annotations and how these can facilitate functional genomics in the chicken. The GO is the most developed and widely used bio-ontology. It is the de facto standard for functional annotation. Despite its critical importance in analyzing microarray and other functional genomics data, relatively few chicken gene products have any GO annotation. When these are available, the average quality of chicken gene products annotations (defined using evidence code weight and annotation depth) is much less than in mouse. Moreover, tools allowing chicken researchers to easily and rapidly use the GO are either lacking or hard to use. To address all of these problems we developed ChickGO and AgBase. Chicken GO annotations are provided by complementary work at MSU-AgBase and EBI-GOA. The GO tools pipeline at AgBase uses GO to derive functional and biological significance from microarray and other functional genomics data. Not only will improved genomic annotation and tools to use these annotations benefit the chicken research community but they will also facilitate research in other avian species and comparative genomics.
Assuntos
Biologia/métodos , Genômica/métodos , Animais , Sequência de Bases , Genoma/genética , Humanos , InternetRESUMO
Professional antigen presenting cells (APC), dendritic cells (DC) and their myeloid progenitors, monocytes/macrophages are critical controllers of innate and adaptive immunity. Here we show that differential detergent fractionation (DDF) analysis of bovine monocytes reveals proteins related to antigen pattern recognition, uptake and presentation to immunocompetent lymphocytes. We identify 53 bovine proteins involved in immune function of professional APC. In particular, 13 adhesion molecules, three toll-like receptors (TLR1, 6 and 8), three antigen uptake-related proteins (including mannose receptor [MR] precursor), and eight actin-like proteins involved in active endocytosis were identified. In addition, MHC class I and II-related proteins, cytokines, active substances and growth factors have been identified. We conclude that the DDF approach can provide interpretable and meaningful functional information concerning protein expression profiles associated with monocyte activation, transformation into macrophages and/or immature DC, and maturation of monocyte-derived DC in the presence of multiple bovine pathogens.
Assuntos
Apresentação de Antígeno , Bovinos/imunologia , Células Dendríticas/imunologia , Leucócitos Mononucleares/imunologia , Proteômica/métodos , Sequência de Aminoácidos , Animais , Bovinos/sangue , Bovinos/genética , Moléculas de Adesão Celular/imunologia , Detergentes/química , Feminino , Cromatografia Gasosa-Espectrometria de Massas/veterinária , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Antígenos de Histocompatibilidade Classe II/genética , Antígenos de Histocompatibilidade Classe II/imunologia , Lectinas Tipo C/imunologia , Leucócitos Mononucleares/química , Receptores de Lipopolissacarídeos/análise , Receptores de Lipopolissacarídeos/imunologia , Receptor de Manose , Lectinas de Ligação a Manose/imunologia , Dados de Sequência Molecular , Receptores de Superfície Celular/imunologia , Alinhamento de Sequência , Espectrometria de Massas por Ionização por Electrospray/veterinária , Frações Subcelulares/química , Receptores Toll-Like/imunologiaRESUMO
In this study we report the full length (7.4 kb) sequence of two Australian bovine enterovirus (BEV) isolates, K2577 and SL305 and the partial sequence of a third isolate, 66/27, which are the prototypes of the three major serological groups of BEV in Australia. Australian BEV isolates have not previously been related to the international classification of BEV into the major serotypes BEV-1 and BEV-2. The sequences of the three representative Australian isolates were compared to the full length sequence of a Northern Ireland isolate (VG527) classified as BEV-1, as well as two partial sequences of isolates from the United States and the United Kingdom classified as BEV-2. All three Australian isolates were classified as BEV-1 on the basis of closer nucleotide and amino acid similarity to the 5'-UTR and capsid proteins of VG527 than to the BEV-2 isolates (79-81% versus 76-77% nucleotide identity in the 5-UTR, and 86-98% versus 65-77% amino acid identity in the capsid proteins). These results indicate that most if not all Australian BEV are BEV-1. The remainder of the genome, which encodes non-structural proteins involved in viral replication, showed high sequence homology as has been observed among such genes in other enteroviruses. A system for full-length amplification of BEV isolates was also developed and the K2577 isolate was cloned to obtain a full-length, infectious DNA copy of the BEV genome. When RNA transcripts of BEV amplification products were transfected into MDBK cells infectious particles were produced. These virus particles were identical to the original virus isolates. This system can be used as a basis for the development of BEV-vectored vaccines as well in further molecular studies of bovine enteroviruses.
Assuntos
Doenças dos Bovinos/virologia , Infecções por Enterovirus/veterinária , Enterovirus/genética , Sequência de Aminoácidos , Animais , Austrália , Sequência de Bases , Bovinos , Clonagem Molecular , Efeito Citopatogênico Viral , Primers do DNA/química , DNA Complementar/química , DNA Viral/química , Eletroforese em Gel de Ágar/veterinária , Enterovirus/química , Enterovirus/classificação , Infecções por Enterovirus/virologia , Dados de Sequência Molecular , Filogenia , RNA Viral/genética , RNA Viral/isolamento & purificação , Reação em Cadeia da Polimerase Via Transcriptase Reversa/veterinária , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Homologia de Sequência do Ácido Nucleico , Transfecção/genéticaRESUMO
Medical emergency preparedness in dentistry has become too complicated with far too many drugs, devices, and diagnostic/therapeutic routines being recommended by various authors. This review will target practicality in the real world of clinical practice. Only four drugs or devices are recommended for the general practitioner by this author.
Assuntos
Consultórios Odontológicos , Emergências , Serviços Médicos de Emergência , Epinefrina , Equipamentos e Provisões , Humanos , Nitroglicerina , Oxigenoterapia/instrumentação , Respiração com Pressão Positiva/instrumentaçãoRESUMO
Emergency drugs and devices in the dental office should be kept to a minimum. The minimum basics are defined as: positive-pressure ventilation capability; oxygen source; nitroglycerin tablets; and epinephrine syringes. Some emergency methods (airway patency maneuver and emesis/foreign body maneuver) also are described.
Assuntos
Consultórios Odontológicos , Medicina de Emergência/instrumentação , Primeiros Socorros/instrumentação , Obstrução das Vias Respiratórias/prevenção & controle , Medicina de Emergência/economia , Medicina de Emergência/métodos , Epinefrina/administração & dosagem , Equipamentos e Provisões , Humanos , Nitroglicerina , Oxigênio , Respiração com Pressão Positiva/instrumentação , Ressuscitação/instrumentação , SeringasRESUMO
A method of common risk disease recognition, physical status assessment and safe management of the medically compromised patient in dentistry is presented. This routine applies to all dentistry treatment, with special attention to pain/anxiety/stress control by any modality.
Assuntos
Assistência Odontológica para a Pessoa com Deficiência , Indicadores Básicos de Saúde , Idoso , Anestesia Dentária , Humanos , Isquemia , Anamnese , Fatores de Risco , Estresse FisiológicoRESUMO
Cocaine may induce totally unexpected cardiotoxicity in young individuals at some time distant from the cocaine ingestion. Commonly, such individuals are asymptomatic for coronary artery disease; some have no demonstrable coronary artery disease even after the cardiac event. Those who use cocaine must be considered at risk of cardiotoxicity at any time after recent cocaine ingestion. Guidelines are suggested for clinical management in oral and maxillofacial surgery.
Assuntos
Cocaína/intoxicação , Cardiopatias/induzido quimicamente , Coração/efeitos dos fármacos , Adulto , Feminino , Humanos , MasculinoRESUMO
No dental patient represents a greater risk of serious illness or sudden death related to the emotional and physical stresses of dental treatment than the patient who presents for emergency or routine care with a history of heart attack (acute myocardial infarction, MI). Yet most post-MI patients can be treated effectively with basic treatment modifications that reduce risk to a minor and acceptable level, allowing comprehensive care rather than the simple emergency treatment or basic esthetic care so often reserved for these patients. This article reviews methods of safe and complete care for the post-MI patient.
Assuntos
Anestesia Dentária/métodos , Anestesia Geral/métodos , Assistência Odontológica para a Pessoa com Deficiência , Infarto do Miocárdio/prevenção & controle , Estresse Psicológico/prevenção & controle , Humanos , Anamnese , Infarto do Miocárdio/etiologia , Oxigênio/administração & dosagem , Estresse Psicológico/complicaçõesRESUMO
An easily mastered safe treatment documentation system is presented. The routine consists of two parts, a comprehensive yet manageable medical history and a treatment modification record. Millions of medically compromised patients may now receive comprehensive care in safety.