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Functional Categories (functional + category)
Selected AbstractsSubjects: Grammatical Relations, Grammatical Functions and Functional CategoriesLINGUISTICS & LANGUAGE COMPASS (ELECTRONIC), Issue 9 2010Ileana Paul This paper presents an overview of how the notion of ,subject' has been defined in linguistic theory. Although the term developed out of Artistotelian logic, its use has been narrowed to refer to the grammatical relation (or function). Over the past 50 years, the definition of subject and its universality have been the source of much debate. Broadly Chomskian approaches claim that grammatical relations such as subject are not primitives of the grammar and can be derived from phrase structure. As such, testing for the subject involves constituency tests (more recent versions of Chomskian syntax, however, abstract away from constituency). Other approaches (Relational Grammar, Lexical-Function Grammar) posit grammatical relations as primitives of the grammar that are not necessarily related to constituency. And at the other extreme, certain linguists argue that subjects are not found in all languages and therefore the notion is not one of interest (e.g. Role and Reference Grammar). This paper reviews the various analyses of subjects and considers in some detail how the notion of subject has evolved within the Chomskian framework. [source] Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased coloniesENVIRONMENTAL MICROBIOLOGY, Issue 2 2010Nikole E. Kimes Summary A functional gene array (FGA), GeoChip 2.0, was used to assess the biogeochemical cycling potential of microbial communities associated with healthy and Caribbean yellow band diseased (YBD) Montastraea faveolata. Over 6700 genes were detected, providing evidence that the coral microbiome contains a diverse community of archaea, bacteria and fungi capable of fulfilling numerous functional niches. These included carbon, nitrogen and sulfur cycling, metal homeostasis and resistance, and xenobiotic contaminant degradation. A significant difference in functional structure was found between healthy and YBD M. faveolata colonies and those differences were specific to the physical niche examined. In the surface mucopolysaccharide layer (SML), only two of 31 functional categories investigated, cellulose degradation and nitrification, revealed significant differences, implying a very specific change in microbial functional potential. Coral tissue slurry, on the other hand, revealed significant changes in 10 of the 31 categories, suggesting a more generalized shift in functional potential involving various aspects of nutrient cycling, metal transformations and contaminant degradation. This study is the first broad screening of functional genes in coral-associated microbial communities and provides insights regarding their biogeochemical cycling capacity in healthy and diseased states. [source] Pyrosequencing and characterization of immune response genes from the American dog tick, Dermacentor variabilis (L.)INSECT MOLECULAR BIOLOGY, Issue 5 2010D. C. Jaworski Abstract Ticks continue to be a threat to animal and human health, and new and novel control strategies are needed for ticks and tick-borne pathogens. The characterization of the tick,pathogen interface and the tick immune response to microbial infections is fundamental toward the formulation of new control strategies for ticks and the pathogens they transmit. Our overall hypothesis for this research is that the tick immune system manages the maintenance of pathogens. Therefore, discovery of tick immune response genes may provide targets for novel control strategies directed toward reducing vector competency and pathogen transmission. In these studies, 454 pyrosequencing, a high-throughput genomic sequencing method was used to discover tick genes expressed in response to bacterial and fungal infections. Expressed sequence tags (ESTs) were analysed from Dermacentor variabilis ticks that had been injected with bacteria (Escherichia coli, Bacillus subtilis, Micrococcus luteus) or fungi (Saccharomyces cerevisiae and Candida albicans) and ticks that were naturally infected with the intracellular bacterium, Anaplasma marginale. By this approach, ESTs were assembled into 5995 contigs. Contigs fell into the five main functional categories of metabolism, genetic information processing, environmental information processing, cellular processes and human diseases. We identified more than 30 genes that are likely to encode for proteins involved in tick immune function. We further analysed by reverse transcriptase PCR (RT-PCR) the expression of 22 of these genes in each of our bacterial or fungal treatment groups and found that seven were up-regulated. Up-regulation of these seven genes was confirmed for bacterial, but not fungal treatment by quantitative PCR (qPCR). One of these products was novel, encoding a new tick defensin. Our results clearly demonstrate the complexities of the tick immune system and mark new directions for further study and characterization of proteins that modulate microbial infections in the American dog tick. [source] Molecular fingerprinting of TGFß-treated embryonic maxillary mesenchymal cellsORTHODONTICS & CRANIOFACIAL RESEARCH, Issue 4 2003M.M. Pisano Abstract The transforming growth factor-ß (TGFß) family represents a class of signaling molecules that plays a central role in normal embryonic development, specifically in development of the craniofacial region. Members of this family are vital to development of the secondary palate where they regulate maxillary and palate mesenchymal cell proliferation and extracellular matrix synthesis. The function of this growth factor family is particularly critical in that perturbation of either process results in a cleft of the palate. While the cellular and phenotypic effects of TGFß on embryonic craniofacial tissue have been extensively cataloged, the specific genes that function as downstream mediators of TGFß in maxillary/palatal development are poorly defined. Gene expression arrays offer the ability to conduct a rapid, simultaneous assessment of hundreds to thousands of differentially expressed genes in a single study. Inasmuch as the downstream sequelae of TGFß action are only partially defined, a complementary DNA (cDNA) expression array technology (Clontech's AtlasTM Mouse cDNA Expression Arrays), was utilized to delineate a profile of differentially expressed genes from TGFß-treated primary cultures of murine embryonic maxillary mesenchymal cells. Hybridization of a membrane-based cDNA array (1178 genes) was performed with 32P-labeled cDNA probes synthesized from RNA isolated from either TGFß-treated or vehicle-treated embryonic maxillary mesenchymal cells. Resultant phosphorimages were subject to AtlasImageTM analysis in order to determine differences in gene expression between control and TGFß-treated maxillary mesenchymal cells. Of the 1178 arrayed genes, 552 (47%) demonstrated detectable levels of expression. Steady state levels of 22 genes were up-regulated, while those of 8 other genes were down-regulated, by a factor of twofold or greater in response to TGFß. Affected genes could be grouped into three general functional categories: transcription factors and general DNA-binding proteins; growth factors/signaling molecules; and extracellular matrix and related proteins. The extent of hybridization of each gene was evaluated by comparison with the abundant, constitutively expressed mRNAs: ubiquitin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ornithine decarboxylase (ODC), cytoplasmic beta-actin and 40S ribosomal protein. No detectable changes were observed in the expression levels of these genes in response to TGFß treatment. Gene expression profiling results were verified by Real-Time quantitative polymerase chain reaction. Utilization of cDNA microarray technology has enabled us to delineate a preliminary transcriptional map of TGFß responsiveness in embryonic maxillary mesenchymal cells. The profile of differentially expressed genes offers revealing insights into potential molecular regulatory mechanisms employed by TGFß in orchestrating craniofacial ontogeny. [source] Transcriptomic study of apricot fruit (Prunus armeniaca) ripening among 13 006 expressed sequence tagsPHYSIOLOGIA PLANTARUM, Issue 3 2005Jérôme Grimplet To improve the knowledge of fruit ripening and to provide genomic resources for molecular breeding of apricot (Prunus armeniaca L), 13 006 expressed sequence tags (ESTs) were generated from three ,zap cDNA libraries of the pericarp tissues at different stages of development (Physiol Plant 105: 294,303), yielding 5219 (40%) Unigenes. At this stage, the very low interlibrary redundancy indicated that EST sampling of the transcriptome of apricot pericarp is still far from being saturated. Seventy-six percent of Unigenes displayed homologies with public sequences and were clustered into functional categories. The largest expressed categories were related to primary metabolism, stress response, and protein synthesis. Electronic Northern analysis revealed that stress-related proteins and cell wall modification-related enzymes strongly increased during ripening. Among 448 isoproteins (amino acid-level isogenes) detected in the Unigene set, 186 (42%) displayed significant homologies in their coding regions (nucleic acid-level isogenes). [source] Rapid analysis of Jatropha curcas gene functions by virus-induced gene silencingPLANT BIOTECHNOLOGY JOURNAL, Issue 9 2009Jian Ye Summary Jatropha curcas L. is a small, woody tree of the Euphorbiaceae family. This plant can grow on marginal land in the tropical and subtropical regions and produces seeds containing up to 30% oil. Several Asian countries have selected Jatropha for large scale planting as a biodiesel feedstock. Nevertheless, Jatropha also possesses several undesirable traits that may limit its wide adoption. An improved understanding of plant development and the regulation of fatty acid (FA) and triacylglyceride biosynthesis in Jatropha is particularly facilitative for the development of elite crops. Here, we show that a tobacco rattle virus (TRV) vector can trigger virus-induced gene silencing (VIGS) in Jatropha. Our optimized method produced robust and reliable gene silencing in plants agroinoculated with recombinant TRV harbouring Jatropha gene sequences. We used VIGS to investigate possible functions of 13 Jatropha genes of several functional categories, including FA biosynthesis, developmental regulation and toxin biosynthesis, etc. Based on the effects of VIGS on the FA composition of newly emerged leaves, we determined the function of several genes implicated in FA biosynthesis. Moreover, VIGS was able to discriminate independent functions of related gene family members. Our results show that VIGS can be used for high-throughput screening of Jatropha genes whose functions can be assayed in leaves. [source] Arabidopsis transcript and metabolite profiles: ecotype-specific responses to open-air elevated [CO2]PLANT CELL & ENVIRONMENT, Issue 11 2008PINGHUA LI ABSTRACT A Free-Air CO2 Enrichment (FACE) experiment compared the physiological parameters, transcript and metabolite profiles of Arabidopsis thaliana Columbia-0 (Col-0) and Cape Verde Island (Cvi-0) at ambient (,0.375 mg g,1) and elevated (,0.550 mg g,1) CO2 ([CO2]). Photoassimilate pool sizes were enhanced in high [CO2] in an ecotype-specific manner. Short-term growth at elevated [CO2] stimulated carbon gain irrespective of down-regulation of plastid functions and altered expression of genes involved in nitrogen metabolism resembling patterns observed under N-deficiency. The study confirmed well-known characteristics, but the use of a time course, ecotypic genetic differences, metabolite analysis and the focus on clusters of functional categories provided new aspects about responses to elevated [CO2]. Longer-term Cvi-0 responded by down-regulating functions favouring carbon accumulation, and both ecotypes showed altered expression of genes for defence, redox control, transport, signalling, transcription and chromatin remodelling. Overall, carbon fixation with a smaller commitment of resources in elevated [CO2] appeared beneficial, with the extra C only partially utilized possibly due to disturbance of the C : N ratio. To different degrees, both ecotypes perceived elevated [CO2] as a metabolic perturbation that necessitated increased functions consuming or storing photoassimilate, with Cvi-0 emerging as more capable of acclimating. Elevated [CO2] in Arabidopsis favoured adjustments in reactive oxygen species (ROS) homeostasis and signalling that defined genotypic markers. [source] Global gene expression profile of Orientia tsutsugamushiPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2010Bon-A Cho Abstract Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of Scrub typhus. The control mechanisms for bacterial gene expression are largely unknown. Here, the global gene expression of O. tsutsugamushi within eukaryotic cells was examined using a microarray and proteomic approaches for the first time. These approaches identified 643 genes, corresponding to approximately 30% of the genes encoded in the genome. The majority of expressed genes belonged to several functional categories including protein translation, protein processing/secretion, and replication/repair. We also searched the conserved sequence blocks (CSBs) in the O. tsutsugamushi genome which is unique in that up to 40% of its genome consists of dispersed repeated sequences. Although extensive shuffling of genomic sequences was observed between two different strains, 204 CSBs, covering 48% of the genome, were identified. When combining the data of CSBs and global gene expression, the CSBs correlates well with the location of expressed genes, suggesting the functional conservation between gene expression and genomic location. Finally, we compared the gene expression of the bacteria-infected fibroblasts and macrophages using microarray analysis. Some major changes were the downregulation of genes involved in translation, protein processing and secretion, which correlated with the reduction in bacterial translation rates and growth within macrophages. [source] The seminal fluid proteome of the honeybee Apis melliferaPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2009Boris Baer Dr. Abstract Ejaculates contain sperm but also seminal fluid, which is increasingly recognized to be of central importance for reproductive success. However, a detailed biochemical composition and physiological understanding of seminal fluid is still elusive. We have used MS to identify the 57 most abundant proteins within the ejaculated seminal fluid of the honeybee Apis mellifera. Their amino acid sequences revealed the presence of diverse functional categories of enzymes, regulators and structural proteins. A number have known or predicted roles in maintaining sperm viability, protecting sperm from microbial infections or interacting with the physiology of the female. A range of putative glycoproteins or glycosylation enzymes were detected among the 57, subsequent fluorescent staining of glycolysation revealed several prominant glycoproteins in seminal fluid, while no glycoproteins were detected in sperm samples. Many of the abundant proteins that accumulate in the seminal fluid did not contain predictable tags for secretion for the cell. Comparison of the honeybee seminal fluid proteins with Drosophila seminal fluid proteins (including secreted accessory gland proteins known as ACPs), and with the human seminal fluid proteome revealed the bee protein set contains a range of newly identified seminal fluid proteins and we noted more similarity of the bee protein set with the current human seminal fluid protein set than with the known Drosophila seminal fluid proteins. The honeybee seminal fluid proteome thus represents an important addition to available data for comparative studies of seminal fluid proteomes in insects. [source] A proteomic analysis of 14-3-3 binding proteins from developing barley grainsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2006Ross D. Alexander Abstract 14-3-3 proteins are important eukaryotic regulatory proteins. Barley (Hordeum vulgare,L.) 14-3-3A was over-expressed, immobilised and used to affinity purify 14-3-3 binding proteins from developing barley grains. Binding was shown to be phosphorylation-dependent. These proteins were fractionated by PAGE and identified by MALDI-TOF MS. In total, 54,14-3-3 binding proteins were identified, 49,of these interactions are novel to plants. These proteins fell into a number of functional categories. The largest category was for carbohydrate metabolism, including plastidic enzymes for starch synthesis and modification. 14-3-3 was shown to be present in isolated plastids. Four of five enzymes involved in sucrose biosynthesis from triose phosphates were identified, suggesting co-ordinated regulation of this pathway. Invertase and sucrose synthase, which break down sucrose to hexoses, were found. Sucrose synthase activity was shown to be inhibited by exogenous 14-3-3 in a dosage-dependent manner. The second-largest functional group was for proteins involved in stress and defence responses; for example, RGH2A, closely related to the MLA powdery mildew resistance protein, was found. This work illustrates the broad range of processes in which 14-3-3 may be involved, and augments previous data demonstrating key roles in carbohydrate metabolism and plant defence. [source] Large-scale analysis of the human ubiquitin-related proteomePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 16 2005Masaki Matsumoto Abstract Protein ubiquitylation contributes to the regulation of many cellular processes including protein degradation, receptor internalization, and repair of DNA damage. We now present a comprehensive characterization of ubiquitin-conjugated and ubiquitin-associated proteins in human cells. The proteins were purified by immunoaffinity chromatography under denaturing or native conditions. They were then digested with trypsin, and the resulting peptides were analyzed by 2-D LC and MS/MS. A total of 670 distinct proteins were identified; 345 proteins (51%) were classified as Urp-D (ubiquitin-related proteome under the denaturing condition) and comprised ubiquitin-conjugated molecules, whereas 325 proteins (49%) were classified as Urp-N (ubiquitin-related proteome only under the native condition) and included molecules that associated with ubiquitylated proteins. The proportions of proteins in various functional categories differed substantially between Urp-D and Urp-N. Many ribosomal subunits were detected in the Urp-D group of proteins and several of these subunits were directly shown to be ubiquitylated by mass spectrometric analysis, suggesting that ubiquitylation might play an important role in the regulation and/or quality control of ribosomal proteins. Our results demonstrate the potential of proteomics analysis of protein ubiquitylation to provide important insight into the regulation of protein stability and other ubiquitin-related cellular functions. [source] Developmentally induced changes of the proteome in the protozoan parasite Leishmania donovaniPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 9 2003Meike Bente Abstract In order to proceed through their life cycle, protozoan parasites of the genus Leishmania cycle between sandflies and mammals. This change of environment correlates with the differentiation from the promastigote stage (insect form) to the amastigote stage (intracellular mammalian form). The molecular basis underlying this major transformation is poorly understood so far; however, heat shock protein 90 (HSP90) appears to play a pivotal role. To further elucidate this process we identified proteins expressed preferentially in either of the two life cycle stages. By using two-dimensional (2-D) gel electrophoresis we observed defined changes in the protein pattern. A total of approximately 2000 protein spots were visualized. Of these, 31 proteins were present only in promastigotes. The abundance of 65 proteins increased during heat-induced in vitro amastigote differentiation, while a decreased abundance is observed for four proteins late in amastigote differentiation. Further analyses using matrix-assisted laser desorption/ionization-time of flight mass spectrometry and peptide mass fingerprinting 67 protein spots were identified representing 41 different proteins known from databases and eight hypothetical proteins. Further studies showed that most of the stage-specific proteins fall into five groups of functionally related proteins. These functional categories are: (i) stress response (e.g. heat, oxidative stress); (ii) cytoskeleton and cell membrane; (iii) energy metabolism and phosphorylation; (iv) cell cycle and proliferation; and (v) amino acid metabolism. Very similar changes in the 2-D protein pattern were obtained when in vitro amastigote differentiation was induced either by pharmacological inhibition of HSP90 or by a combination of heat stress and acidic pH supporting the critical role for HSP90 in life cycle control. [source] Molecular characterization of tumour heterogeneity and malignant mesothelioma cell differentiation by gene profilingTHE JOURNAL OF PATHOLOGY, Issue 1 2005Xiaojuan Sun Abstract Malignant mesothelioma is an aggressive tumour, characterized by a variable differentiation pattern and poor prognosis. At present, the clinical outcome in patients with malignant mesothelioma is mainly predicted by the morphological phenotype of the tumour. However, this conventional clinicopathological parameter is of limited value, partly because of the biological heterogeneity of this tumour and poor understanding of the regulatory mechanisms underlying the various patterns of growth. To elucidate the intrinsic molecular programmes that determine tumour differentiation, oligonucleotide arrays were used in an in vitro model of mesothelioma differentiation. The analysis of 2059 genes detected 102 genes that were significantly deregulated. Clustering of these genes into functional categories showed distinctive patterns for the two phenotypes, namely epithelioid and sarcomatoid. The molecular fingerprint of the sarcomatoid tumour component indicates overrepresentation of growth factor receptors and growth factor binding proteins, whereas epithelioid mesothelioma cells express other tumour-promoting factors involved in differentiation, metabolism, and regulation of apoptosis. These differences in the molecular phenotype may give a better basis for diagnosis and for designing novel therapies. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Differential display proteomic analysis of Picea meyeri pollen germination and pollen-tube growth after inhibition of actin polymerization by latrunculin BTHE PLANT JOURNAL, Issue 2 2006Yanmei Chen Summary To investigate roles of the actin cytoskeleton in growth of the pollen tube of Picea meyeri, we used the actin polymerization inhibitor latrunculin B (LATB) under quantitatively controlled conditions. At low concentrations, LATB inhibited polymerization of the actin cytoskeleton in the growing pollen tube, which rapidly inhibited tip growth. The proteomic approach was used to analyse protein expression-profile changes during pollen germination and subsequent pollen-tube development with disturbed organization of the actin cytoskeleton. Two-dimensional electrophoresis and staining with Coomassie Brilliant Blue revealed nearly 600 protein spots. A total of 84 of these were differentially displayed at different hours with varying doses of LATB, and 53 upregulated or downregulated proteins were identified by mass spectrometry. These proteins were grouped into distinct functional categories including signalling, actin cytoskeleton organization, cell expansion and carbohydrate metabolism. Moreover, actin disruption affected the morphology of Golgi stacks, mitochondria and amyloplasts, along with a differential expression of proteins involved in their functions. These findings provide new insights into the multifaceted mechanism of actin cytoskeleton functions and its interaction with signalling, cell-expansion machinery and energy-providing pathways. [source] Comparative Analysis of Muscle Architecture in Primate Arm and ForearmANATOMIA, HISTOLOGIA, EMBRYOLOGIA, Issue 2 2010Yasuhiro Kikuchi With 7 figures and 3 tables Summary A comparative study of myological morphology, i.e. muscle mass (MM), muscle fascicle length and muscle physiological cross-sectional area (an indicator of the force capacity of muscles), was conducted in nine primate species: human (Homo sapiens), chimpanzee (Pan troglodytes), gibbon (Hylobates spp.), papio (Papio hamadryas), lutong (Trachypithecus francoisi), green monkey (Chlorocebus aethiops), macaque monkey (Macaca spp.), capuchin monkey (Cebus albifrons) and squirrel monkey (Saimiri sciureus). The MM distributions and the percentages in terms of functional categories were calculated as the ratios of the muscle masses. Moreover, individual normalized data were compared directly amongst species, independent of size differences. The results show that the different ratios of forearm-rotation muscles between chimpanzee and gibbons may be related to the differences in their main positional behaviour, i.e. knuckle-walking in chimpanzees and brachiation in gibbons, and the different frequencies of arm-raising locomotion between these two species. Moreover, monkeys have larger normalized MM values for the elbow extensor muscles than apes, which may be attributed to the fact that almost all monkeys engage in quadrupedal locomotion. The characteristics of the muscle internal parameters of ape and human are discussed in comparison with those of monkey. [source] Twenty years after Baddeley (1988): Is the study of autobiographical memory fully functional?APPLIED COGNITIVE PSYCHOLOGY, Issue 8 2009David B. Pillemer Twenty years after Baddeley admonished memory researchers to examine the real-world relevance of their findings, research has informed a wide range of practical issues and it is increasingly guided by analyses of memory functions. Although broadly defined social, self and directive functional categories have provided an initial organizational framework for autobiographical memory research, the functional agenda will benefit from conceptual and methodological refinements and innovations. An especially valuable research strategy targets specific functions in carefully defined experimental and practical contexts. Promising research directions include comparing functions served by positive versus negative memories, tracking the early development of memory functions, and exploring individual and group differences. Although reconstructive memory processes contribute to inaccuracies in reproducing the past, functional analysis instead highlights the adaptive value of a flexible and constructive memory system. Copyright © 2009 John Wiley & Sons, Ltd. [source] Acoustic communication in crocodilians: from behaviour to brainBIOLOGICAL REVIEWS, Issue 3 2009A. L. Vergne ABSTRACT Crocodilians and birds are the modern representatives of Phylum Archosauria. Although there have been recent advances in our understanding of the phylogeny and ecology of ancient archosaurs like dinosaurs, it still remains a challenge to obtain reliable information about their behaviour. The comparative study of birds and crocodiles represents one approach to this interesting problem. One of their shared behavioural features is the use of acoustic communication, especially in the context of parental care. Although considerable data are available for birds, information concerning crocodilians is limited. The aim of this review is to summarize current knowledge about acoustic communication in crocodilians, from sound production to hearing processes, and to stimulate research in this field. Juvenile crocodilians utter a variety of communication sounds that can be classified into various functional categories: (1) "hatching calls", solicit the parents at hatching and fine-tune hatching synchrony among siblings; (2) "contact calls", thought to maintain cohesion among juveniles; (3) "distress calls", induce parental protection; and (4) "threat and disturbance calls", which perhaps function in defence. Adult calls can likewise be classified as follows: (1) "bellows", emitted by both sexes and believed to function during courtship and territorial defence; (2) "maternal growls", might maintain cohesion among offspring; and (3) "hisses", may function in defence. However, further experiments are needed to identify the role of each call more accurately as well as systematic studies concerning the acoustic structure of vocalizations. The mechanism of sound production and its control are also poorly understood. No specialized vocal apparatus has been described in detail and the motor neural circuitry remains to be elucidated. The hearing capabilities of crocodilians appear to be adapted to sound detection in both air and water. The ear functional anatomy and the auditory sensitivity of these reptiles are similar in many respects to those of birds. The crocodilian nervous system likewise shares many features with that of birds, especially regarding the neuroanatomy of the auditory pathways. However, the functional anatomy of the telencephalic auditory areas is less well understood in crocodilians compared to birds. [source] Positive selection in the evolution of cancerBIOLOGICAL REVIEWS, Issue 3 2006Bernard J. Grespi ABSTRACT We hypothesize that forms of antagonistic coevolution have forged strong links between positive selection at the molecular level and increased cancer risk. By this hypothesis, evolutionary conflict between males and females, mothers and foetuses, hosts and parasites, and other parties with divergent fitness interests has led to rapid evolution of genetic systems involved in control over fertilization and cellular resources. The genes involved in such systems promote cancer risk as a secondary effect of their roles in antagonistic coevolution, which generates evolutionary disequilibrium and maladaptation. Evidence from two sources: (1) studies on specific genes, including SPANX cancer/testis antigen genes, several Y-linked genes, the pem homebox gene, centromeric histone genes, the breast cancer gene BRCA1, the angiogenesis gene ANG, cadherin genes, cytochrome P450 genes, and viral oncogenes; and (2) large-scale database studies of selection on different functional categories of genes, supports our hypothesis. These results have important implications for understanding the evolutionary underpinnings of cancer and the dynamics of antagonistically-coevolving molecular systems. [source] Microarray analysis of changes in renal phenotype in the ethylene glycol rat model of urolithiasis: potential and pitfallsBJU INTERNATIONAL, Issue 4 2004Daniel H.-C. OBJECTIVES To investigate, in an initial study, the use of microarray analysis (MA) to develop an information base for urolithiasis. MA enables the screening of thousands of genes simultaneously making it the technique of choice for situations where the results are known, but the underlying mechanisms are not. Little is known about the pathological changes occurring in the kidney during urolithiasis and this has severely hampered efforts to develop effective therapeutics. MATERIALS AND METHODS Male rats were treated with 0.75% ethylene glycol for 2, 4 or 8 weeks; after death the kidneys were processed for RNA isolation and MA, conducted using a rat-based chip (one kidney/chip) and the results confirmed by reverse transcription-polymerase chain reaction (RT-PCR, 21 probe sets; control, four rats; treated, five rats). Targets were defined as different by the software if the fold change (FC) was ,,2, and sorted into functional categories using a data-mining tool. The repeatability of MA was investigated by subjecting the 4-week samples to MA in two independent runs. RESULTS The results for targets with a FC of , 2 were plotted (y = 1.01x , 0.75; r2 0.84). Comparing the results obtained by RT-PCR and MA showed a good qualitative correlation for those targets having a FC of ,,5 as determined by MA. Changes in the expression of genes associated with tubule function and regulation, oxidative damage, and inflammation were the most common in the functional categories. Changes in the expression of tubule-specific markers indicated that there was damage to the proximal (,-adducin, organic anion and cation transporters, sodium-hydrogen exchange protein-isoform 3) and distal tubules (,-adducin, kallikrein) at 2 and 4 weeks. Increased expression of mitochondrial uncoupling protein indicated that there were changes to the mitochondria and oxidative stress at 2 and 4 weeks. CONCLUSION This study shows the power of MA as an exploratory technique, and changes in the expression of several physiologically important genes whose expression has not previously been reported to be affected by hyperoxaluria or calcium oxalate crystalluria. [source] Electronic information resources in undergraduate education: an exploratory study of opportunities for student learning and independenceBRITISH JOURNAL OF EDUCATIONAL TECHNOLOGY, Issue 3 2002Liz McDowell The fast,growing array of electronic information resources is often viewed as a significant opportunity for change in education, with shifts towards increased student independence in learning. In order for this to happen students need to develop the capability to deal with information. This qualitative interview,based study examines lecturer perspectives on the roles of electronic information resources in undergraduate education. In line with the phenomenographic tradition, three functional categories of electronic information use are proposed. Firstly, the "electronic academic library" offers new opportunities for access to materials but lecturers indicated minimal change to their teaching approaches. Electronic resources were simply added to reading lists and the responsibility for developing students' information skills was seen to rest with librarians. Secondly, lecturers identified changes towards more constructivist approaches to learning, drawing upon new sources of primary data available electronically and described specific teaching approaches to assist students to develop the relevant information handling skills. Finally, lecturers were uncertain about the value of the wider information resources of the Internet/Web for students and were concerned about variable information quality and the possibilities of plagiarism. The research indicates that information use in student learning is a multi,faceted phenomenon. Much current discussion centres on the concept of information literacy which draws together information skills and subject-related skills and knowledge. Students do not merely require generic information skills but a knowledge of the discipline and the capability to handle complex information. Partnerships between academics and librarians are a way forward in helping students to develop as autonomous information users. Not only do the two professional groups offer different expertise, but they also bring different perspectives on the problematic balance between student autonomy and student support. [source] Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043FEBS JOURNAL, Issue 1 2008Ling-Ling Chen Over-annotation of hypothetical ORFs is a common phenomenon in bacterial genomes, which necessitates confirming the coding reliability of hypothetical ORFs and then predicting their functions. The important plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043 (Eca1043) is a typical case because more than a quarter of its annotated ORFs are hypothetical. Our analysis focuses on annotation of Eca1043 hypothetical ORFs, and comprises two efforts: (a) based on the Z-curve method, 49 originally annotated hypothetical ORFs are recognized as noncoding, this is further supported by principal components analysis and other evidence; and (b) using sequence-alignment tools and some functional resources, more than a half of the hypothetical genes were assigned functions. The potential functions of 427 hypothetical genes are summarized according to the cluster of orthologous groups functional category. Moreover, 114 and 86 hypothetical genes are recognized as putative ,membrane proteins' and ,exported proteins', respectively. Reannotation of Eca1043 hypothetical ORFs will benefit research into the lifestyle, metabolism and pathogenicity of the important plant pathogen. Also, our study proffers a model for the reannotation of hypothetical ORFs in microbial genomes. [source] | |||||||||||||||||||