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Functional Similarities (functional + similarity)
Selected AbstractsNutrients, diversity, and community structure of two phytotelm systems in a lower montane forest, Puerto RicoECOLOGICAL ENTOMOLOGY, Issue 3 2000Barbara A. Richardson Summary 1. Bromeliad and heliconia phytotelmata in the same forest area were compared in terms of their animal assemblages, nutrient inputs, and plant architecture. 2. For all major elements, nutrient inputs from canopy-derived debris and rainfall in bromeliads were significantly lower than those derived from decaying flower parts and plant secretions in heliconia bracts. Bromeliads contained significantly fewer organisms per unit volume of water and unit dry weight of organic matter than did heliconia inflorescences. They also contained a significantly lower animal biomass (199 mg DW from 15 bromeliads, 527 mg DW from 15 heliconia inflorescences). 3. Species richness was independent of abundance, demonstrating that, at least for small container habitats, higher abundance does not necessarily lead to a greater species richness. Communities were remarkably similar in patterns of relative abundance and species richness (23 spp. in bromeliads, 21 spp. in heliconia), probably due to functional similarities in plant architecture, with the two most abundant species comprising 60,62% of the total community. Coefficients of similarity were low because of marked differences in species assemblages. 4. Some taxa were phytotelm generalists but most showed a preference for one particular habitat, indicating differential selection in the choice of oviposition sites and larval development within the forest ecosystem. In common with many island communities, species richness was lower than that reported for these phytotelm habitats in mainland central and south America. [source] Comparative biochemical and functional studies of family I soluble inorganic pyrophosphatases from photosynthetic bacteriaFEBS JOURNAL, Issue 15 2007María R. Gómez-García Soluble inorganic pyrophosphatases (inorganic diphosphatases, EC 3.6.1.1) were isolated and characterized from three phylogenetically diverse cyanobacteria , Synechocystis sp. PCC 6803, Anabaena sp. PCC 7120, and Pseudanabaena sp. PCC 6903 , and one anoxygenic photosynthetic bacterium, Rhodopseudomonas viridis (purple nonsulfur). These enzymes were found to be family I soluble inorganic pyrophosphatases with c. 20 kDa subunits with diverse oligomeric structures. The corresponding ppa genes were cloned and functionally validated by heterologous expression. Cyanobacterial family I soluble inorganic pyrophosphatases were strictly Mg2+ -dependent enzymes. However, diverse cation cofactor dependence was observed for enzymes from other groups of photosynthetic bacteria. Immunochemical studies with antibodies to cyanobacterial soluble inorganic pyrophosphatases showed crossreaction with orthologs of other main groups of phototrophic prokaryotes and suggested a close relationship with the enzyme of heliobacteria, the nearest photosynthetic relatives of cyanobacteria. A slow-growing Escherichia coli JP5 mutant strain, containing a very low level of soluble inorganic pyrophosphatase activity, was functionally complemented up to wild-type growth rates with ppa genes from diverse photosynthetic prokaryotes expressed under their own promoters. Overall, these results suggest that the bacterial family I soluble inorganic pyrophosphatases described here have retained functional similarities despite their genealogies and their adaptations to diverse metabolic scenarios. [source] The initiator caspase, caspase-10,, and the BH-3-only molecule, Bid, demonstrate evolutionary conservation in Xenopus of their pro-apoptotic activities in the extrinsic and intrinsic pathwaysGENES TO CELLS, Issue 7 2006Katsuya Kominami Two major apoptotic signaling pathways have been defined in mammals, the extrinsic pathway, initiated by ligation of death receptors, and the intrinsic pathway, triggered by cytochrome c release from mitochondria. Here, we identified and characterized the Xenopus homologs of caspase-10 (xCaspase-10,), a novel initiator caspase, and Bid (xBid), a BH3-only molecule of the Bcl-2 family involved in both the extrinsic and intrinsic pathways. Exogenous expression of these molecules induced apoptosis of mammalian cells. By biochemical and cytological analyses, we clarified that xCaspase-10, and xBid exhibit structural and functional similarities to their mammalian orthologues. We also detected xCaspase-10, and xBid transcripts during embryogenesis by whole-mount in situ hybridization and RT-PCR analysis. Microinjection of mRNA encoding a protease-defect xCaspase-10, mutant into embryos resulted in irregular development. Enforced expression of active xBid induced cell death in developing embryos. Using transgenic frogs established to allow monitoring of caspase activation in vivo, we confirmed that this form of cell death is caspase-dependent apoptosis. Thus, we demonstrated that the machinery governing the extrinsic and intrinsic apoptotic pathways are already established in Xenopus embryos. Additionally, we propose that the functions of the initiator caspase and BH3-only molecule are evolutionarily conserved in vertebrates, functioning during embryonic development. [source] The adaptor molecule FADD from Xenopus laevis demonstrates evolutionary conservation of its pro-apoptotic activityGENES TO CELLS, Issue 12 2004Kazuhiro Sakamaki FADD is an adaptor protein that transmits apoptotic signals from death receptors such as Fas to downstream initiator caspases in mammals. We have identified and characterized the Xenopus orthologue of mammalian FADD (xFADD). xFADD contains both a death effector domain (DED) and a death domain (DD) that are structurally homologous to those of mammalian FADD. We observed xFADD binding to Xenopus caspase-8 and caspase-10 as well as to human caspase-8 and Fas through interactions with their homophilic DED and DD domains. When over-expressed, xFADD was also able to induce apoptosis in wild-type mouse embryonic fibroblasts (MEF), but not in caspase-8-deficient MEF cells. In contrast, DED-deficient xFADD (xFADDdn) acted as a dominant-negative mutant and prevented Fas-mediated apoptosis in mammalian cell lines. These results indicate that xFADD transmits apoptotic signals from Fas to caspase-8. Furthermore, we found that transgenic animals expressing xFADD in the developing heart or eye under the control of tissue-specific promoters show abnormal phenotypes. Taken together, these results suggest that xFADD can substitute functionally for its mammalian homologue in death receptor-mediated apoptosis, and we suggest that xFADD functions as a pro-apoptotic adaptor molecule in frogs. Thus, the structural and functional similarities between xFADD and mammalian FADD provide evidence that the apoptotic pathways are evolutionally conserved across vertebrate species. [source] CD1d-restricted natural killer T cells are potent targets for human immunodeficiency virus infectionIMMUNOLOGY, Issue 1 2003Richardson Fleuridor Summary Invariant human natural killer T cells (NKT) express a restricted T-cell receptor (TCR) V,24V,11 repertoire. These cells share both phenotypic and functional similarities between NK and T cells. Given the emerging role of NKT cells as critical cells in bridging the gap between innate and adaptive immunity, we examined their susceptibility to productive human immunodeficiency virus (HIV) infection by T-tropic, M-tropic, and primary isolates of HIV. We generated three human NKT cell clones (CA5, CA29, and CA31). Phenotypic characterization of these V,24+ V,11+ clones indicated that they were predominately positive for CD4, CD161, HLA-DR, CD38, CD45RO, and CD95 expression. The NKT cell clones expressed significantly more surface CCR5 molecules/cell and lower CXCR4 molecules/cell than phytohaemagglutinin-stimulated peripheral blood mononuclear cells (PBMC). Consistent with the surface expression of CCR5 and CXCR4, the NKT clones were also selectively susceptible to HIV M-tropic, T-tropic, and primary isolate infection, as evaluated by both HIV p24 enzyme-linked immunosorbent assay and intracellular staining of HIV proteins. The amount of p24 production was dependent on the NKT clone studied and the HIV strain used. Clones CA29 and CA31 were also susceptible to HIV IIIB infection. The virions produced by these clones were able to productively infect PHA-stimulated PBMCs with the same kinetics as for primary infection of CD4+ blast. Collectively, this data demonstrates that NKT cells can be a target for productive HIV infection but with a lag in the time to peak p24 production. [source] TRAF interactions with raft-like buoyant complexes, better than TRAF rates of degradation, differentiate signaling by CD40 and EBV latent membrane protein 1INTERNATIONAL JOURNAL OF CANCER, Issue 2 2005Hector Ardila-Osorio Abstract The CD40 receptor and the Epstein-Barr virus oncoprotein LMP1 are both members of the TNF-receptor family and share several signaling mediators, including TRAF2 and TRAF3. Depending on the cell lineage and stage of maturation, LMP1 and CD40 can have synergistic, antagonist or unrelated effects. Previous publications have suggested that both TRAF2 and TRAF3 move into lipid rafts upon LMP1 expression or CD40 activation, whereas their proteolysis is only enhanced by CD40. However CD40-induced proteolysis of TRAF2 has only been reported in murine cells, and there are conflicting data regarding translocation of TRAF2 into lipid rafts. We therefore investigated TRAF2 and TRAF3 modifications induced by CD40 and LMP1 signaling in a panel of human cell lines of lymphoid and epithelial origins. Upon CD40 stimulation, a marked redistribution of TRAF2 into the buoyant raft fraction was observed in all cell lines and was often associated with a similar redistribution of TRAF3. In contrast, only TRAF3 was redistributed into the raft fraction upon LMP1 expression. Moreover parallel changes in subcellular distribution of TRAF2 and TRAF3 were recorded by electron microscopy. A significant decrease in TRAF2 and TRAF3 concentrations triggered by CD40 ligation was observed in only 1 cell line and there was no evidence that this decrease was required for the negative feed-back on JNK activation. TRAF2 redistribution into raft-like complexes thus appears as the most significant event distinctive of CD40 and LMP1 signaling. On the other hand, the parallel influence of CD40 and LMP1 on TRAF3 redistribution is consistent with functional similarities between the CD40-TRAF3 and LMP1-TRAF3 axes. [source] A mycobacterial virulence gene cluster extending RD1 is required for cytolysis, bacterial spreading and ESAT-6 secretionMOLECULAR MICROBIOLOGY, Issue 6 2004Lian-Yong Gao Summary Initiation and maintenance of infection by mycobacteria in susceptible hosts are not well understood. A screen of Mycobacterium marinum transposon mutant library led to isolation of eight mutants that failed to cause haemolysis, all of which had transposon insertions in genes homologous to a region between Rv3866 and Rv3881c in Mycobacterium tuberculosis, which encompasses RD1 (Rv3871,Rv3879c), a known virulence gene cluster. The M. marinum mutants showed decreased virulence in vivo and failed to secrete ESAT-6, like M. tuberculosis RD1 mutants. M. marinum mutants in genes homologous to Rv3866-Rv3868 also failed to accumulate intracellular ESAT-6, suggesting a possible role for those genes in synthesis or stability of the protein. These transposon mutants and an ESAT-6/CFP-10 deletion mutant all showed reduced cytolysis and cytotoxicity to macrophages and significantly decreased intracellular growth at late stages of the infection only when the cells were infected at low multiplicity of infection, suggesting a defect in spreading. Direct evidence for cell-to-cell spread by wild-type M. marinum was obtained by microscopic detection in macrophage and epithelial monolayers, but the mutants all were defective in this assay. Expression of M. tuberculosis homologues complemented the corresponding M. marinum mutants, emphasizing the functional similarities between M. tuberculosis and M. marinum genes in this region that we designate extRD1 (extended RD1). We suggest that diminished membranolytic activity and defective spreading is a mechanism for the attenuation of the extRD1 mutants. These results extend recent findings on the genomic boundaries and functions of M. tuberculosis RD1 and establish a molecular cellular basis for the role that extRD1 plays in mycobacterial virulence. Disruption of the M. marinum homologue of Rv3881c, not previously implicated in virulence, led to a much more attenuated phenotype in macrophages and in vivo, suggesting that this gene plays additional roles in M. marinum survival in the host. [source] Comparison of conventional FASTA identity searches with the 80 amino acid sliding window FASTA search for the elucidation of potential identities to known allergensMOLECULAR NUTRITION & FOOD RESEARCH (FORMERLY NAHRUNG/FOOD), Issue 8 2007Gregory S. Ladics Abstract Food and Agriculture Organization/World Health Organization (FAO/WHO) recommended that IgE cross-reactivity between a transgenic protein and allergen be considered when there is ,F 35% identity over a sliding "window" of 80 amino acids. Our objective was to evaluate the false positive and negative rates observed using the FAO/WHO versus conventional FASTA analyses. Data used as queries against allergen databases and analyzed to assess false positive rates included: 1102 hypothetical corn ORFs; 907 randomly selected proteins; 89 randomly selected corn proteins; and 97 corn seed proteins. To evaluate false negative rates of both methods: Bet v 1a along with several crossreacting fruit/vegetable allergens and a bean ,-amylase inhibitor were used as queries. Both methods were also evaluated for their ability to detect a putative nonallergenic test protein containing a sequence derived from Ara h 1. FASTA versions 3.3t0 and 3.4t25 were utilized. Data indicate a conventional FASTA analysis produced fewer false positives and equivalent false negative rates. Conventional FASTA versus sliding window derived E scores were generally more significant. Results suggest a conventional FASTA search provides more relevant identity to the query protein and better reflects the functional similarities between proteins. It is recommended that the conventional FASTA analysis be conducted to compare identities of proteins to allergens. [source] An in vitro enzymatic assay coupled to proteomics analysis reveals a new DNA processing activity for Ewing sarcoma and TAF(II)68 proteinsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 22 2006Olivier Guipaud Abstract Based on structural and functional similarities, translocated in liposarcoma/fusion (TLS/FUS) protein, Ewing sarcoma,(EWS) protein and human TATA binding protein-associated factor (hTAF(II)68) have been grouped in the TLS-EWS-TAF(II)68 (TET) protein family. Translocations involving their genes lead to sarcomas. Polypyrimidine tract-binding protein-associated splicing factor,(PSF), although not grouped in this family, presents structural and functional similarities with TET proteins and is involved in translocation leading to carcinoma. Beside their role in RNA metabolism, the precise cellular functions of these multifunctional proteins are not yet fully elucidated. We previously showed that both TLS/FUS and PSF display activities able to pair homologous DNA on membrane in an in,vitro assay. In the present study, we address the question whether EWS and hTAF(II)68 also display pairing on membrane activities, and to a larger extent whether other proteins also exhibit such activity. We applied the pairing on membrane assay to 2-DE coupled to MS analysis for a global screening of DNA pairing on membrane activities. In addition to TLS/FUS and PSF, this test allowed us to identify EWS and hTAF(II)68, but no other proteins, indicating a feature specific to a protein family whose members share extensive structural similarities. This common activity suggests a role for TET proteins and PSF in genome plasticity control. [source] A Light and Scanning Electron Microscopic Study of the Closing Apparatus in Tintinnid Ciliates (Ciliophora, Spirotricha, Tintinnina): A Forgotten SynapomorphyTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2010SABINE AGATHA ABSTRACT. A membranous closing apparatus shuts the lorica opening in disturbed tintinnids of six genera belonging to four families. The homology of the apparatuses is investigated, using data from the literature and Mediterranean tintinnids studied in vivo and by scanning electron microscopy. Morphological and functional similarities indicate that the foldable closing apparatus is not only a synapomorphy of the genera Codonella (Codonellidae) and Dictyocysta (Dictyocystidae), as suggested 80 years ago, but also of Codonaria (Codonellidae) and Codonellopsis (Codonellopsidae). In Codonaria, Codonella, and Dictyocysta, the apparatuses merge posteriorly into membranous lorica sacs, which probably represent homologous structures. The diagnoses of these genera are improved according to the new findings. The close relationship of Codonella, Codonellopsis, and Dictyocysta is also inferred from small subunit rRNA phylogenies and the ultrastructure of the capsules. It contradicts the current lorica-based classification of the tintinnids. The assumption that the diaphragm-like apparatus in the genera Salpingacantha and Salpingella is not homologous to the foldable ones in the genera mentioned above is supported by molecular and cytological features. [source] Conserved features of type III secretionCELLULAR MICROBIOLOGY, Issue 9 2004A. P. Tampakaki Summary Type III secretion systems (TTSSs) are essential mediators of the interaction of many Gram-negative bacteria with human, animal or plant hosts. Extensive sequence and functional similarities exist between components of TTSS from bacteria as diverse as animal and plant pathogens. Recent crystal structure determinations of TTSS proteins reveal extensive structural homologies and novel structural motifs and provide a basis on which protein interaction networks start to be drawn within the TTSSs, that are consistent with and help rationalize genetic and biochemical data. Such studies, along with electron microscopy, also established common architectural design and function among the TTSSs of plant and mammalian pathogens, as well as between the TTSS injectisome and the flagellum. Recent comparative genomic analysis, bioinformatic genome mining and genome-wide functional screening have revealed an unsuspected number of newly discovered effectors, especially in plant pathogens and uncovered a wider distribution of TTSS in pathogenic, symbiotic and commensal bacteria. Functional proteomics and analysis further reveals common themes in TTSS effector functions across phylogenetic host and pathogen boundaries. Based on advances in TTSS biology, new diagnostics, crop protection and drug development applications, as well as new cell biology research tools are beginning to emerge. [source] Developmental Coordination Disorder and Joint Hypermobility Syndrome , overlapping disorders?CHILD: CARE, HEALTH AND DEVELOPMENT, Issue 5 2007Implications for research, clinical practice Abstract Background, Joint Hypermobility Syndrome (JHS) and Developmental Coordination Disorder (DCD) are two childhood disorders usually identified separately. DCD is a heterogeneous condition with little known of the underlying aetiology of the disorder. This paper examines the potential overlap between DCD and JHS and examines children with DCD for symptoms which may be consistent with a diagnosis of JHS. Implications for research and clinical practice are considered. Methods, A questionnaire covering a range of symptoms consistent with a diagnosis of JHS and related autonomic nervous systemic symptoms was completed by parents from 27 children with DCD and compared with responses from parents of 27 typically developing children. Results, Children with DCD showed a significant difference from the group of typically developing children on questions regarding hypermobility, pain and autonomic nervous system symptoms, typifying JHS. Conclusions, This study has shown a similarity in symptoms seen in some DCD children to those with a diagnosis of JHS. In addition, children are also presenting with multi-system symptomatology including those involving the autonomic nervous system. This study reinforces other recent work showing the reverse pattern of JHS children showing similar functional similarities to DCD children. This has implications for future research in DCD in order to understand the underlying aetiology of this complex disorder. In addition, it is important for clinicians to be aware of these findings in order to provide appropriate and tailored support and treatment for children presenting with differing patterns of co-ordination difficulties. Children with DCD and JHS may require appropriate podiatry as well as recognition of their symptoms of pain and how this may affect participation in physical activity. [source] Characterization and functional analysis of the ,-1,3-glucanosyltransferase 3 of the human pathogenic fungus Paracoccidioides brasiliensisFEMS YEAST RESEARCH, Issue 1 2009Nadya Da Silva Castro Abstract The fungus Paracoccidioides brasiliensis causes paracoccidioidomycosis, a systemic granulomatous mycosis prevalent in Latin America. In an effort to elucidate the molecular mechanisms involved in fungus cell wall assembly and morphogenesis, ,-1,3-glucanosyltransferase 3 (PbGel3p) is presented here. PbGel3p presented functional similarity to the glucan-elongating/glycophospholipid-anchored surface/pH-regulated /essential for pseudohyphal development protein families, which are involved in fungal cell wall biosynthesis and morphogenesis. The full-length cDNA and gene were obtained. Southern blot and in silico analysis suggested that there is one copy of the gene in P. brasiliensis. The recombinant PbGel3p was overexpressed in Escherichia coli, and a polyclonal antibody was obtained. The PbGEL3 mRNA, as well as the protein, was detected at the highest level in the mycelium phase. The protein was immunolocalized at the surface in both the mycelium and the yeast phases. We addressed the potential role of PbGel3p in cell wall biosynthesis and morphogenesis by assessing its ability to rescue the phenotype of the Saccharomyces cerevisiae gas1, mutant. The results indicated that PbGel3p is a cell wall-associated protein that probably works as a ,-1,3-glucan elongase capable of mediating fungal cell wall integrity. [source] Structural basis of MHC class I recognition by natural killer cell receptorsIMMUNOLOGICAL REVIEWS, Issue 1 2001Mark W. Sawicki Summary: Natural killer (NK)-cell function is regulated by NK receptors that recognize MHC class I (MHC-I) molecules on target cells. Two structurally distinct families of NK receptors have been identified, the immunoglobulin-like family (killer cell immunoglobulin-like receptors (KIRs), leukocyte immunoglobulin-like receptors (LIRs)) and the C-type lectin-like family (Ly49, CD94/NKG2A, NKG2D, CD69). Recently, the three-dimensional structures of several NK receptors were determined, in free form or bound to MHC-I. These include those of unbound KIRs, NKG2D, CD69, LIR-1 and the CD94 subunit of the CD94/NKG2A heterodimer. Together, these structures define the basic molecular architecture of both the immunoglobulin-like and C-type lectin-like families of NK receptors. In addition, crystal structures have been reported for the complex between Ly49A and H-2Dd, and for KIR2DL2 bound to HLA-Cw3. The complex structures provide a framework for understanding MHC-I recognition by NK receptors from both families and reveal striking differences in the nature of this recognition, despite the receptors' functional similarity. This research was supported, in part, by National Institutes of Health grants R01 AI47900 and R37 36900 (RAM) and a fellowship from the Cancer Research Institute (MWS). We are grateful to DW Wolan and IA Wilson for providing coordinates of NKG2D prior to publication, and to members of our laboratories for encouragement. [source] Intra- and intermuscular variation in human quadriceps femoris architecture assessed in vivoJOURNAL OF ANATOMY, Issue 3 2006Anthony J. Blazevich Abstract Despite the functional importance of the human quadriceps femoris in movements such as running, jumping, lifting and climbing, and the known effects of muscle architecture on muscle function, no research has fully described the complex architecture of this muscle group. We used ultrasound imaging techniques to measure muscle thickness, fascicle angle and fascicle length at multiple regions of the four quadriceps muscles in vivo in 31 recreationally active, but non-strength-trained adult men and women. Our analyses revealed a reasonable similarity in the superficial quadriceps muscles, which is suggestive of functional similarity (at least during the uni-joint knee extension task) given that they act via a common tendon. The deep vastus intermedius (VI) is architecturally dissimilar and therefore probably serves a different function(s). Architecture varies significantly along the length of the superficial muscles, which has implications for the accuracy of models that assume a constant intramuscular architecture. It might also have consequences for the efficiency of intra- and intermuscular force transmission. Our results provide some evidence that subjects with a given architecture of one superficial muscle, relative to the rest of the subject sample, also have a similar architecture in other superficial muscles. However, this is not necessarily true for vastus lateralis (VL), and was not the case for VI. Therefore, the relative architecture of one muscle cannot confidently be used to estimate the relative architecture of another. To confirm this, we calculated a value of whole quadriceps architecture by four different methods. Regardless of the method used, we found that the absolute or relative architecture of one muscle could not be used as an indicator of whole quadriceps architecture, although vastus medialis, possibly in concert with VL and the anterior portion of VI, could be used to provide a useful snapshot. Importantly, our estimates of whole quadriceps architecture show a gender difference in whole quadriceps muscle thickness, and that muscle thickness is positively correlated with fascicle angle whereas fascicle length is negatively, although weakly, correlated with fascicle angle. These results are supportive of the validity of estimates of whole quadriceps architecture. These data are interpreted with respect to their implications for neural control strategies, region-specific adaptations in muscle size in response to training, and gender-dependent differences in the response to exercise training. [source] Biotic homogenization: a new research agenda for conservation biogeographyJOURNAL OF BIOGEOGRAPHY, Issue 12 2006Julian D. Olden Abstract Aim, Biotic homogenization describes the process by which species invasions and extinctions increase the genetic, taxonomic or functional similarity of two or more biotas over a specified time interval. The study of biotic homogenization is a young and rapidly emerging research area in the budding field of conservation biogeography, and this paper aims to synthesize our current knowledge of this process and advocate a more systematic approach to its investigation. Methods, Based on a comprehensive examination of the primary literature this paper reviews the process of biotic homogenization, including its definition, quantification, underlying ecological mechanisms, environmental drivers, the empirical evidence for different taxonomic groups, and the potential ecological and evolutionary implications. Important gaps in our knowledge are then identified, and areas of new research that show the greatest promise for advancing our current thinking on biotic homogenization are highlighted. Results, Current knowledge of the patterns, mechanisms and implications of biotic homogenization is highly variable across taxonomic groups, but in general is incomplete. Quantitative estimates are almost exclusively limited to freshwater fishes and plants in the United States, and the principal mechanisms and drivers of homogenization remain elusive. To date research has focused on taxonomic homogenization, and genetic and functional homogenization has received inadequate attention. Trends over the past decade, however, suggest that biotic homogenization is emerging as a topic of greater research interest. Main conclusions, My investigation revealed a number of important knowledge gaps and priority research needs in the science of biotic homogenization. Future studies should examine the homogenization process for different community properties (species occurrence and abundance) at multiple spatial and temporal scales, with careful attention paid to the various biological mechanisms (invasions vs. extinctions) and environmental drivers (environmental alteration vs. biotic interactions) involved. Perhaps most importantly, this research should recognize that there are multiple possible outcomes resulting from the accumulation of species invasions and extinctions, including biotic differentiation whereby genetic, taxonomic or functional similarity of biotas decreases over time. [source] The Incidence and Structure of Conflict on the U.S. Court of Appeals for the Federal CircuitLAW & POLICY, Issue 1 2001Isaac Unah In 1982, Congress established the Court of Appeals for the Federal Circuit, a specialized court, with the objective of reducing judicial conflict and harmonizing circuit law in specific policy areas of special complexity. This article examines the incidence and determinants of judicial conflict on the U.S. courts of appeals, focusing specifically on the Federal Circuit. Using international trade and customs regulation cases decided during the 1982 to 1995 terms, the analysis reviews three possible explanations of judicial conflict: policy-oriented, sociolegal, and organizational. The analysis shows that conflict appears in 8.4 percent of the trade and customs regulation decisions rendered by the Federal Circuit during the period of study. The policy direction of Federal Circuit decisions and the court's hierarchical relationship with lower specialized courts provide the strongest explanation for the emergence of conflict on the court. Organizational factors such as panel composition evinced rather anemic explanatory capacity. The results raise an important functional similarity between the Federal Circuit and the generalist courts of appeals. Contrary to the laments of legal practitioners that conflict on the Federal Circuit is excessive relative to conflict on the generalist circuit courts, this analysis finds little support for that claim. Rather, the level of overt conflict on the court is actually low and corroborates conflict levels that have been reported for other U.S. courts of appeals. [source] Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedlingTHE PLANT JOURNAL, Issue 4 2007Ralf Stracke Summary The genes MYB11, MYB12 and MYB111 share significant structural similarity and form subgroup 7 of the Arabidopsis thaliana R2R3-MYB gene family. To determine the regulatory potential of these three transcription factors, we used a combination of genetic, functional genomics and metabolite analysis approaches. MYB11, MYB12 and MYB111 show a high degree of functional similarity and display very similar target gene specificity for several genes of flavonoid biosynthesis, including CHALCONE SYNTHASE, CHALCONE ISOMERASE, FLAVANONE 3-HYDROXYLASE and FLAVONOL SYNTHASE1. Seedlings of the triple mutant myb11 myb12 myb111, which genetically lack a complete subgroup of R2R3-MYB genes, do not form flavonols while the accumulation of anthocyanins is not affected. In developing seedlings, MYB11, MYB12 and MYB111 act in an additive manner due to their differential spatial activity; MYB12 controls flavonol biosynthesis mainly in the root, while MYB111 controls flavonol biosynthesis primarily in cotyledons. We identified and confirmed additional target genes of the R2R3-MYB subgroup 7 factors, including the UDP-glycosyltransferases UGT91A1 and UGT84A1, and we demonstrate that the accumulation of distinct and structurally identified flavonol glycosides in seedlings correlates with the expression domains of the different R2R3-MYB factors. Therefore, we refer to these genes as PFG1,3 for ,PRODUCTION OF FLAVONOL GLYCOSIDES'. [source] Crystallization and preliminary X-ray analysis of the matrix protein from Ebola virusACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2000Andréa Dessen The matrix protein from Ebola virus is a membrane-associated molecule that plays a role in viral budding. Despite its functional similarity to other viral matrix proteins, it displays no sequence similarity and hence may have a distinct fold. X-ray diffraction quality crystals of the Ebola VP40 matrix protein were grown by the hanging-drop vapour-diffusion method. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 64.4, b = 91.1, c = 47.9,Å, , = 96.3°. A data set to 1.9,Å resolution has been collected using synchrotron radiation. The unit cell contains one molecule of molecular weight 35,kDa per asymmetric unit, with a corresponding volume solvent content of 35%. [source] Differential Expression and Network Inferences through Functional Data ModelingBIOMETRICS, Issue 3 2009Donatello Telesca Summary Time course microarray data consist of mRNA expression from a common set of genes collected at different time points. Such data are thought to reflect underlying biological processes developing over time. In this article, we propose a model that allows us to examine differential expression and gene network relationships using time course microarray data. We model each gene-expression profile as a random functional transformation of the scale, amplitude, and phase of a common curve. Inferences about the gene-specific amplitude parameters allow us to examine differential gene expression. Inferences about measures of functional similarity based on estimated time-transformation functions allow us to examine gene networks while accounting for features of the gene-expression profiles. We discuss applications to simulated data as well as to microarray data on prostate cancer progression. [source] | ||||||||||||||||||||||