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Sample records for functionally diverse proteins

  1. Diversity and functions of protein glycosylation in insects.

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    Walski, Tomasz; De Schutter, Kristof; Van Damme, Els J M; Smagghe, Guy

    2017-04-01

    The majority of proteins is modified with carbohydrate structures. This modification, called glycosylation, was shown to be crucial for protein folding, stability and subcellular location, as well as protein-protein interactions, recognition and signaling. Protein glycosylation is involved in multiple physiological processes, including embryonic development, growth, circadian rhythms, cell attachment as well as maintenance of organ structure, immunity and fertility. Although the general principles of glycosylation are similar among eukaryotic organisms, insects synthesize a distinct repertoire of glycan structures compared to plants and vertebrates. Consequently, a number of unique insect glycans mediate functions specific to this class of invertebrates. For instance, the core α1,3-fucosylation of N-glycans is absent in vertebrates, while in insects this modification is crucial for the development of wings and the nervous system. At present, most of the data on insect glycobiology comes from research in Drosophila. Yet, progressively more information on the glycan structures and the importance of glycosylation in other insects like beetles, caterpillars, aphids and bees is becoming available. This review gives a summary of the current knowledge and recent progress related to glycan diversity and function(s) of protein glycosylation in insects. We focus on N- and O-glycosylation, their synthesis, physiological role(s), as well as the molecular and biochemical basis of these processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Evolutionary and functional diversity of green fluorescent proteins in cephalochordates.

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    Li, Guang; Zhang, Qiu-Jin; Zhong, Jing; Wang, Yi-Quan

    2009-10-01

    Green fluorescent protein (GFP) has been widely used as a molecular marker in modern biological research. Before the recent report of one GFP gene in Branchiostoma floridae, GFP family members were cloned only from other two groups of species: Cnidaria and Copepoda. Here we describe the complete GFP gene repertoire of B. floridae which includes 13 functional genes and 2 pseudogenes, representing the largest GFP family found so far. Coupling with nine other GFP sequences from another two species of genus Branchiostoma and the sequences from Cnidaria and Copepoda, we made a deep-level phylogenetic analysis for GFP genes in cephalochordates and found: 1) GFP genes have experienced a divergent evolution in cephalochordates; 2) all amphioxus GFP genes form four main clades on the tree which had diverged before the radiation of the last common ancestor of all extant cephalochordates; 3) GFP genes in amphioxus shared a common ancestor with that in Copepoda rather than being derived from horizontal gene transfer, which indicates that our ancestor was derived from a fluorescent organism and lost this ability after its separation from Cephalochordata, and also makes GFP a rare gene which has a rather unusual evolutionary path. In addition, we also provided evidence indicating that GFP genes have evolved divergent functions by specializing their expression profile, and different fluorescent spectra by changing their emission peaks. These findings spark two interesting issues: what are GFP in vivo functions in cephalochordates and why they are lost in other examined deuterostomes?

  3. Protein variety and functional diversity: Swiss-Prot annotation in its biological context.

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    Boeckmann, Brigitte; Blatter, Marie-Claude; Famiglietti, Livia; Hinz, Ursula; Lane, Lydie; Roechert, Bernd; Bairoch, Amos

    2005-01-01

    We all know that the dogma 'one gene, one protein' is obsolete. A functional protein and, likewise, a protein's ultimate function depend not only on the underlying genetic information but also on the ongoing conditions of the cellular system. Frequently the transcript, like the polypeptide, is processed in multiple ways, but only one or a few out of a multitude of possible variants are produced at a time. An overview on processes that can lead to sequence variety and structural diversity in eukaryotes is given. The UniProtKB/Swiss-Prot protein knowledgebase provides a wealth of information regarding protein variety, function and associated disorders. Examples for such annotation are shown and further ones are available at http://www.expasy.org/sprot/tutorial/examples_CRB.

  4. Functional diversity of human protein kinase splice variants marks significant expansion of human kinome

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    Anamika Krishanpal

    2009-12-01

    Full Text Available Abstract Background Protein kinases are involved in diverse spectrum of cellular processes. Availability of draft version of the human genomic data in the year 2001 enabled recognition of repertoire of protein kinases. However, over the years the human genomic data is being refined and the current release of human genomic data has helped us to recognize a larger repertoire of over 900 human protein kinases represented mainly by splice variants. Results Many of these identified protein kinases are alternatively spliced products. Interestingly, some of the human kinase splice variants appear to be significantly diverged in terms of their functional properties as represented by incorporation or absence of one or more domains. Many sets of protein kinase splice variants have substantially different domain organization and in a few sets of splice variants kinase domains belong to different subfamilies of kinases suggesting potential participation in different signal transduction pathways. Conclusions Addition or deletion of a domain between splice variants of multi-domain kinases appears to be a means of generating differences in the functional features of otherwise similar kinases. It is intriguing that marked sequence diversity within the catalytic regions of some of the splice variant kinases result in kinases belonging to different subfamilies. These human kinase splice variants with different functions might contribute to diversity of eukaryotic cellular signaling.

  5. Post-translational processing targets functionally diverse proteins in Mycoplasma hyopneumoniae.

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    Tacchi, Jessica L; Raymond, Benjamin B A; Haynes, Paul A; Berry, Iain J; Widjaja, Michael; Bogema, Daniel R; Woolley, Lauren K; Jenkins, Cheryl; Minion, F Chris; Padula, Matthew P; Djordjevic, Steven P

    2016-02-01

    Mycoplasma hyopneumoniae is a genome-reduced, cell wall-less, bacterial pathogen with a predicted coding capacity of less than 700 proteins and is one of the smallest self-replicating pathogens. The cell surface of M. hyopneumoniae is extensively modified by processing events that target the P97 and P102 adhesin families. Here, we present analyses of the proteome of M. hyopneumoniae-type strain J using protein-centric approaches (one- and two-dimensional GeLC-MS/MS) that enabled us to focus on global processing events in this species. While these approaches only identified 52% of the predicted proteome (347 proteins), our analyses identified 35 surface-associated proteins with widely divergent functions that were targets of unusual endoproteolytic processing events, including cell adhesins, lipoproteins and proteins with canonical functions in the cytosol that moonlight on the cell surface. Affinity chromatography assays that separately used heparin, fibronectin, actin and host epithelial cell surface proteins as bait recovered cleavage products derived from these processed proteins, suggesting these fragments interact directly with the bait proteins and display previously unrecognized adhesive functions. We hypothesize that protein processing is underestimated as a post-translational modification in genome-reduced bacteria and prokaryotes more broadly, and represents an important mechanism for creating cell surface protein diversity. © 2016 The Authors.

  6. Function and diversity of P0 proteins among cotton leafroll dwarf virus isolates.

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    Cascardo, Renan S; Arantes, Ighor L G; Silva, Tatiane F; Sachetto-Martins, Gilberto; Vaslin, Maité F S; Corrêa, Régis L

    2015-08-12

    The RNA silencing pathway is an important anti-viral defense mechanism in plants. As a counter defense, some members of the viral family Luteoviridae are able to evade host immunity by encoding the P0 RNA silencing suppressor protein. Here we explored the functional diversity of P0 proteins among eight cotton leafroll dwarf virus (CLRDV) isolates, a virus associated with a worldwide cotton disease known as cotton blue disease (CBD). CLRDV-infected cotton plants of different varieties were collected from five growing fields in Brazil and their P0 sequences compared to three previously obtained isolates. P0's silencing suppression activities were scored based on transient expression experiments in Nicotiana benthamiana leaves. High sequence diversity was observed among CLRDV P0 proteins, indicating that some isolates found in cotton varieties formerly resistant to CLRDV should be regarded as new genotypes within the species. All tested proteins were able to suppress local and systemic silencing, but with significantly variable degrees. All P0 proteins were able to mediate the decay of ARGONAUTE proteins, a key component of the RNA silencing machinery. The sequence diversity observed in CLRDV P0s is also reflected in their silencing suppression capabilities. However, the strength of local and systemic silencing suppression was not correlated for some proteins.

  7. FLORA: a novel method to predict protein function from structure in diverse superfamilies.

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    Oliver C Redfern

    2009-08-01

    Full Text Available Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA that automatically generates structural motifs associated with different functional sub-families (FSGs within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2-3 fold increase in coverage at low error rates popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (alpha, beta, alphabeta and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues.

  8. Scaffolds, levers, rods and springs: diverse cellular functions of long coiled-coil proteins.

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    Rose, A; Meier, I

    2004-08-01

    Long alpha-helical coiled-coil proteins are involved in a variety of organizational and regulatory processes in eukaryotic cells. They provide cables and networks in the cyto- and nucleoskeleton, molecular scaffolds that organize membrane systems, motors, levers, rotating arms and possibly springs. A growing number of human diseases are found to be caused by mutations in long coiled-coil proteins. This review summarizes our current understanding of the multifaceted group of long coiled-coil proteins in the cytoskeleton, nucleus, Golgi and cell division apparatus. The biophysical features of coiled-coil domains provide first clues toward their contribution to the diverse protein functions and promise potential future applications in the area of nanotechnology. Combining the power of fully sequenced genomes and structure prediction algorithms, it is now possible to comprehensively summarize and compare the complete inventory of coiled-coil proteins of different organisms.

  9. Distinct expression patterns of ICK/MAK/MOK protein kinases in the intestine implicate functional diversity.

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    Tufeng Chen

    Full Text Available ICK/MRK (intestinal cell kinase/MAK-related kinase, MAK (male germ cell-associated kinase, and MOK (MAPK/MAK/MRK-overlapping kinase are closely related serine/threonine protein kinases in the protein kinome. The biological functions and regulatory mechanisms of the ICK/MAK/MOK family are still largely elusive. Despite significant similarities in their catalytic domains, they diverge markedly in the sequence and structural organization of their C-terminal non-catalytic domains, raising the question as to whether they have distinct, overlapping, or redundant biological functions. In order to gain insights into their biological activities and lay a fundamental groundwork for functional studies, we investigated the spatio-temporal distribution patterns and the expression dynamics of ICK/MAK/MOK protein kinases in the intestine. We found that ICK/MAK/MOK proteins display divergent expression patterns along the duodenum-to-colon axis and during postnatal murine development. Furthermore, they are differentially partitioned between intestinal epithelium and mesenchyme. A significant increase in the protein level of ICK, but not MAK, was induced in human primary colon cancer specimens. ICK protein level was up-regulated whereas MOK protein level was down-regulated in mouse intestinal adenomas as compared with their adjacent normal intestinal mucosa. These data suggest distinct roles for ICK/MAK/MOK protein kinases in the regulation of intestinal neoplasia. Taken together, our findings demonstrate that the expressions of ICK/MAK/MOK proteins in the intestinal tract can be differentially and dynamically regulated, implicating a significant functional diversity within this group of protein kinases.

  10. Unanticipated functional diversity among the TatA-type components of the Tat protein translocase.

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    Eimer, Ekaterina; Kao, Wei-Chun; Fröbel, Julia; Blümmel, Anne-Sophie; Hunte, Carola; Müller, Matthias

    2018-01-22

    Twin-arginine translocation (Tat) systems transport folded proteins that harbor a conserved arginine pair in their signal peptides. They assemble from hexahelical TatC-type and single-spanning TatA-type proteins. Many Tat systems comprise two functionally diverse, TatA-type proteins, denominated TatA and TatB. Some bacteria in addition express TatE, which thus far has been characterized as a functional surrogate of TatA. For the Tat system of Escherichia coli we demonstrate here that different from TatA but rather like TatB, TatE contacts a Tat signal peptide independently of the proton-motive force and restricts the premature processing of a Tat signal peptide. Furthermore, TatE embarks at the transmembrane helix five of TatC where it becomes so closely spaced to TatB that both proteins can be covalently linked by a zero-space cross-linker. Our results suggest that in addition to TatB and TatC, TatE is a further component of the Tat substrate receptor complex. Consistent with TatE being an autonomous TatAB-type protein, a bioinformatics analysis revealed a relatively broad distribution of the tatE gene in bacterial phyla and highlighted unique protein sequence features of TatE orthologs.

  11. Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironment.

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    Viju Vijayan Pillai

    Full Text Available The oviductal microenvironment is a site for key events that involve gamete maturation, fertilization and early embryo development. Secretions into the oviductal lumen by either the lining epithelium or by transudation of plasma constituents are known to contain elements conducive for reproductive success. Although previous studies have identified some of these factors involved in reproduction, knowledge of secreted proteins in the oviductal fluid remains rudimentary with limited definition of function even in extensively studied species like cattle. In this study, we used a shotgun proteomics approach followed by bioinformatics sequence prediction to identify secreted proteins present in the bovine oviductal fluid (ex vivo and secretions from the bovine oviductal epithelial cells (in vitro. From a total of 2087 proteins identified, 266 proteins could be classified as secreted, 109 (41% of which were common for both in vivo and in vitro conditions. Pathway analysis indicated different classes of proteins that included growth factors, metabolic regulators, immune modulators, enzymes, and extracellular matrix components. Functional analysis revealed mechanisms in the oviductal lumen linked to immune homeostasis, gamete maturation, fertilization and early embryo development. These results point to several novel components that work together with known elements mediating functional homeostasis, and highlight the diversity of machinery associated with oviductal physiology and early events in cattle fertility.

  12. Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironment.

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    Pillai, Viju Vijayan; Weber, Darren M; Phinney, Brett S; Selvaraj, Vimal

    2017-01-01

    The oviductal microenvironment is a site for key events that involve gamete maturation, fertilization and early embryo development. Secretions into the oviductal lumen by either the lining epithelium or by transudation of plasma constituents are known to contain elements conducive for reproductive success. Although previous studies have identified some of these factors involved in reproduction, knowledge of secreted proteins in the oviductal fluid remains rudimentary with limited definition of function even in extensively studied species like cattle. In this study, we used a shotgun proteomics approach followed by bioinformatics sequence prediction to identify secreted proteins present in the bovine oviductal fluid (ex vivo) and secretions from the bovine oviductal epithelial cells (in vitro). From a total of 2087 proteins identified, 266 proteins could be classified as secreted, 109 (41%) of which were common for both in vivo and in vitro conditions. Pathway analysis indicated different classes of proteins that included growth factors, metabolic regulators, immune modulators, enzymes, and extracellular matrix components. Functional analysis revealed mechanisms in the oviductal lumen linked to immune homeostasis, gamete maturation, fertilization and early embryo development. These results point to several novel components that work together with known elements mediating functional homeostasis, and highlight the diversity of machinery associated with oviductal physiology and early events in cattle fertility.

  13. Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironment

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    Pillai, Viju Vijayan; Weber, Darren M.; Phinney, Brett S.

    2017-01-01

    The oviductal microenvironment is a site for key events that involve gamete maturation, fertilization and early embryo development. Secretions into the oviductal lumen by either the lining epithelium or by transudation of plasma constituents are known to contain elements conducive for reproductive success. Although previous studies have identified some of these factors involved in reproduction, knowledge of secreted proteins in the oviductal fluid remains rudimentary with limited definition of function even in extensively studied species like cattle. In this study, we used a shotgun proteomics approach followed by bioinformatics sequence prediction to identify secreted proteins present in the bovine oviductal fluid (ex vivo) and secretions from the bovine oviductal epithelial cells (in vitro). From a total of 2087 proteins identified, 266 proteins could be classified as secreted, 109 (41%) of which were common for both in vivo and in vitro conditions. Pathway analysis indicated different classes of proteins that included growth factors, metabolic regulators, immune modulators, enzymes, and extracellular matrix components. Functional analysis revealed mechanisms in the oviductal lumen linked to immune homeostasis, gamete maturation, fertilization and early embryo development. These results point to several novel components that work together with known elements mediating functional homeostasis, and highlight the diversity of machinery associated with oviductal physiology and early events in cattle fertility. PMID:29155854

  14. The signaling helix: a common functional theme in diverse signaling proteins

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    Aravind L

    2006-09-01

    Full Text Available Abstract Background The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. Results Using sensitive sequence analysis methods we identify a conserved helical segment of around 40 residues in a wide range of signaling proteins, including numerous sensor histidine kinases such as Sln1p, and receptor guanylyl cyclases such as the atrial natriuretic peptide receptor and nitric oxide receptors. We term this helical segment the signaling (S-helix and present evidence that it forms a novel parallel coiled-coil element, distinct from previously known helical segments in signaling proteins, such as the Dimerization-Histidine phosphotransfer module of histidine kinases, the intra-cellular domains of the chemotaxis receptors, inter-GAF domain helical linkers and the α-helical HAMP module. Analysis of domain architectures allowed us to reconstruct the domain-neighborhood graph for the S-helix, which showed that the S-helix almost always occurs between two signaling domains. Several striking patterns in the domain neighborhood of the S-helix also became evident from the graph. It most often separates diverse N-terminal sensory domains from various C-terminal catalytic signaling domains such as histidine kinases, cNMP cyclase, PP2C phosphatases, NtrC-like AAA+ ATPases and diguanylate cyclases. It might also occur between two sensory domains such as PAS domains and occasionally between a DNA-binding HTH domain and a sensory domain. The sequence conservation pattern of the S-helix revealed the presence of a unique constellation of polar residues in the dimer-interface positions within the central heptad of the coiled-coil formed by the S-helix. Conclusion Combining these observations with previously reported mutagenesis studies on different S-helix-containing proteins we suggest that it functions as a switch that prevents constitutive activation of linked downstream

  15. Evolutionary Conservation and Emerging Functional Diversity of the Cytosolic Hsp70:J Protein Chaperone Network of Arabidopsis thaliana.

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    Verma, Amit K; Diwan, Danish; Raut, Sandeep; Dobriyal, Neha; Brown, Rebecca E; Gowda, Vinita; Hines, Justin K; Sahi, Chandan

    2017-06-07

    Heat shock proteins of 70 kDa (Hsp70s) partner with structurally diverse Hsp40s (J proteins), generating distinct chaperone networks in various cellular compartments that perform myriad housekeeping and stress-associated functions in all organisms. Plants, being sessile, need to constantly maintain their cellular proteostasis in response to external environmental cues. In these situations, the Hsp70:J protein machines may play an important role in fine-tuning cellular protein quality control. Although ubiquitous, the functional specificity and complexity of the plant Hsp70:J protein network has not been studied. Here, we analyzed the J protein network in the cytosol of Arabidopsis thaliana and, using yeast genetics, show that the functional specificities of most plant J proteins in fundamental chaperone functions are conserved across long evolutionary timescales. Detailed phylogenetic and functional analysis revealed that increased number, regulatory differences, and neofunctionalization in J proteins together contribute to the emerging functional diversity and complexity in the Hsp70:J protein network in higher plants. Based on the data presented, we propose that higher plants have orchestrated their "chaperome," especially their J protein complement, according to their specialized cellular and physiological stipulations. Copyright © 2017 Verma et al.

  16. Cyanobacterial Sfp-type phosphopantetheinyl transferases functionalize carrier proteins of diverse biosynthetic pathways.

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    Yang, Guang; Zhang, Yi; Lee, Nicholas K; Cozad, Monica A; Kearney, Sara E; Luesch, Hendrik; Ding, Yousong

    2017-09-19

    Cyanobacteria produce structurally and functionally diverse polyketides, nonribosomal peptides and their hybrids. Sfp-type phosphopantetheinyl transferases (PPTases) are essential to the production of these compounds via functionalizing carrier proteins (CPs) of biosynthetic megaenzymes. However, cyanobacterial Sfp-type PPTases remain poorly characterized, posing a significant barrier to the exploitation of cyanobacteria for biotechnological and biomedical applications. Herein, we describe the detailed characterization of multiple cyanobacterial Sfp-type PPTases that were rationally selected. Biochemical characterization of these enzymes along with the prototypic enzyme Sfp from Bacillus subtilis demonstrated their varying specificities toward 11 recombinant CPs of different types of biosynthetic pathways from cyanobacterial and Streptomyces strains. Kinetic analysis further indicated that PPTases possess the higher binding affinity and catalytic efficiency toward their cognate CPs in comparison with noncognate substrates. Moreover, when chromosomally replacing the native PPTase gene of Synechocystis sp. PCC6803, two selected cyanobacterial PPTases and Sfp supported the growth of resulted mutants. Cell lysates of the cyanobacterial mutants further functionalized recombinant CP substrates. Collectively, these studies reveal the versatile catalysis of selected cyanobacterial PPTases and provide new tools to synthesize cyanobacterial natural products using in vitro and in vivo synthetic biology approaches.

  17. Functional and structural diversities of C-reactive proteins present in horseshoe crab hemolymph plasma.

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    Iwaki, D; Osaki, T; Mizunoe, Y; Wai, S N; Iwanaga, S; Kawabata, S

    1999-09-01

    CRPs and with templates including genomic DNA and cDNA of hemocytes or hepatopancreas derived from one individual. The translation products of the tCRP clones possess high molecular diversity which falls into three related groups, consistent with classification based on their biological activities. Only tCRP-3 contained a unique hydrophobic nonapeptide sequence that appears in the transmembrane domain of a major histocompatibility complex class I heavy chain of rainbow trout, suggesting the importance of the hydrophobic patch to the hemolytic activity of tCRP-3. The structural and functional diversities of tCRPs provide a good model for studying the properties of innate immunity in invertebrates, which survive without the benefit of acquired immunity.

  18. Food proteins as a source of bioactive peptides with diverse functions.

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    Rutherfurd-Markwick, Kay J

    2012-08-01

    In addition to supplying essential nutrients, some food proteins can confer additional health benefits beyond nutrition. The presence of bioactive proteins and peptides in different foods is a factor not currently taken into consideration when assessing the dietary quality of food proteins. The range of described physiological benefits attributed to bioactive proteins and peptides is diverse. Multiple factors can potentially impact on the ability of a bioactive peptide or protein to elicit an effect. Although some food proteins act directly in their intact form to elicit their effects, generally it is peptides derived from digestion, hydrolysis or fermentation that are of most interest. The levels of bioactive peptides generated must be sufficient to elicit a response, but should not be so high as to be unsafe, thus causing negative effects. In addition, some peptides cause systemic effects and therefore must be absorbed, again in sufficient amounts to elicit their action. Many studies to date have been carried out in vitro; therefore it is important that further trials are conducted in vivo to assess efficacy, dose response and safety of the peptides, particularly if health related claims are to be made. Therefore, methods must be developed and standardised that enable the measurement of health benefits and also the level of bioactive peptides which are absorbed into the bloodstream. Once standardised, such methods may provide a new perspective and an additional mechanism for analysing protein quality which is currently not encompassed by the use of the protein digestibility-corrected amino acid score (PDCAAS).

  19. Protein secretion systems in Pseudomonas aeruginosa: an essay on diversity, evolution and function

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    Alain eFILLOUX

    2011-07-01

    Full Text Available Protein secretion systems are molecular nanomachines used by Gram-negative bacteria to thrive within their environment. They are used to release enzymes that hydrolyze complex carbon sources into usable compounds, or to release proteins that capture essential ions such as iron. They are also used to colonize and survive within eukaryotic hosts, causing acute or chronic infections, subverting the host cell response and escaping the immune system. In this article, the opportunistic human pathogen Pseudomonas aeruginosa is used as a model to review the diversity of secretion systems that bacteria have evolved to achieve these goals. This diversity may result from a progressive transformation of cell envelope complexes that initially may not have been dedicated to secretion. The striking similarities between secretion systems and type IV pili, flagella, bacteriophage tail or efflux pumps is a nice illustration of this evolution. Differences are also needed since various secretion configurations calls for diversity. For example, some proteins are released in the extracellular medium while others are directly injected into the cytosol of eukaryotic cells. Some proteins are folded before being released and transit into the periplasm. Other proteins cross the whole cell envelope at once in an unfolded state. However, the secretion system requires conserved basic elements or features. For example, there is a need for an energy source or for an outer membrane channel. The structure of this review is thus quite unconventional. Instead of listing secretion types one after each other, it presents a melting pot of concepts indicating that secretion types are in constant evolution and use basic principles. In other words, emergence of new secretion systems could be predicted the way Mendeleïev had anticipated characteristics of yet unknown elements.

  20. Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.

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    Stubenrauch, Christopher J; Dougan, Gordon; Lithgow, Trevor; Heinz, Eva

    2017-11-01

    Fimbriae are long, adhesive structures widespread throughout members of the family Enterobacteriaceae. They are multimeric extrusions, which are moved out of the bacterial cell through an integral outer membrane protein called usher. The complex folding mechanics of the usher protein were recently revealed to be catalysed by the membrane-embedded translocation and assembly module (TAM). Here, we examine the diversity of usher proteins across a wide range of extraintestinal (ExPEC) and enteropathogenic (EPEC) Escherichia coli , and further focus on a so far undescribed chaperone-usher system, with this usher referred to as UshC. The fimbrial system containing UshC is distributed across a discrete set of EPEC types, including model strains like E2348/67, as well as ExPEC ST131, currently the most prominent multi-drug-resistant uropathogenic E. coli strain worldwide. Deletion of the TAM from a naive strain of E. coli results in a drastic time delay in folding of UshC, which can be observed for a protein from EPEC as well as for two introduced proteins from related organisms, Yersinia and Enterobacter We suggest that this models why the TAM machinery is essential for efficient folding of proteins acquired via lateral gene transfer. © 2017 The Authors.

  1. Evolution and functional diversity of the Calcium Binding Proteins (CaBPs

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    Lee P Haynes

    2012-02-01

    Full Text Available The mammalian central nervous system (CNS exhibits a remarkable ability to process, store and transfer information. Key to these activities is the use of highly regulated and unique patterns of calcium signals encoded by calcium channels and decoded by families of specific calcium-sensing proteins. The largest family of eukaryotic calcium sensors are those related to the small EF-hand containing protein calmodulin (CaM. In order to maximise the usefulness of calcium as a signalling species and to permit the evolution and fine tuning of the mammalian CNS, families of related proteins have arisen that exhibit characteristic calcium binding properties and tissue-, cellular- and sub-cellular distribution profiles. The Calcium Binding Proteins (CaBPs represent one such family of vertebrate specific calmodulin like proteins that have emerged in recent years as important regulators of essential neuronal target proteins. Bioinformatic analyses indicate that the CaBPs consist of two subfamilies and that the ancestral members of these are CaBP1 and CaBP8. The CaBPs have distinct intracellular localisations based on different targeting mechanisms including a novel type-II transmembrane domain in CaBPs 7 and 8. Recent work has led to the identification of new target interactions and possible functions for the CaBPs suggesting that they have multiple physiological roles with relevance for the normal functioning of the CNS.

  2. Molecular properties of Zic4 and Zic5 proteins: functional diversity within Zic family

    International Nuclear Information System (INIS)

    Ishiguro, Akira; Inoue, Takashi; Mikoshiba, Katuhiko; Aruga, Jun

    2004-01-01

    The Zic-family proteins control various developmental processes. Previous studies have shown that Zic1, Zic2, and Zic3 can act as transcriptional regulators, and that their functions are repressed by I-mfa, which has been identified as a repressor for basic helix-loop-helix-type transcriptional factors. Here, we investigated the molecular properties of the Zic4 and Zic5 proteins. Zic4/Zic5 showed DNA-binding activity to the Gli-binding sequence, similar to Zic1/Zic2/Zic3 proteins. However, Zic4/Zic5 did not exhibit any significant transcriptional activation ability nor they bind to I-mfa differently from Zic1/Zic2/Zic3. The nuclear localization of Zic4/Zic5 was not affected by the presence of the I-mfa protein, whereas the Zic1/Zic2/Zic3 proteins were translocated to the cytoplasmic compartment in the presence of I-mfa. The difference may be attributable to the dissimilarity of the N-terminal region between the Zic1/Zic2/Zic3 and Zic4/Zic5 proteins, since the binding of the Zic1/Zic2/Zic3 proteins to I-mfa occurs through their N-terminal regions

  3. The structure of a haemopexin-fold protein from cow pea (Vigna unguiculata) suggests functional diversity of haemopexins in plants

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    Gaur, Vineet; Chanana, Veenu; Jain, Abha; Salunke, Dinakar M.

    2011-01-01

    The structure of CP4, a haemopexin-fold protein from cow pea (Vigna unguiculata), has been determined at 2.1 Å resolution. The haemopexin fold is present in almost all life forms and is utilized for carrying out diverse physiological functions. The structure of CP4, a haemopexin-fold protein from cow pea (Vigna unguiculata), was determined at 2.1 Å resolution. The protein exists as a monomer both in solution and in the crystal. The structure revealed a typical four-bladed β-propeller topology. The protein exhibits 42% sequence similarity to LS-24 from Lathyrus sativus, with substantial differences in the surface-charge distribution and in the oligomeric state. A structure-based sequence analysis of haemopexin-fold proteins of plant and mammalian origin established a sequence signature associated with the haemopexin motif. This signature sequence enabled the identification of other proteins with possible haemopexin-like topology of both plant and animal origin. Although CP4 shares a structural fold with LS-24 and other haemopexins, biochemical studies indicated possible functional differences between CP4 and LS-24. While both of these proteins exhibit spermine-binding potential, CP4 does not bind to haem, unlike LS-24

  4. Diverse mitotic functions of the cytoskeletal cross-linking protein Shortstop suggest a role in Dynein/Dynactin activity

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    Dewey, Evan B.; Johnston, Christopher A.

    2017-01-01

    Proper assembly and orientation of the bipolar mitotic spindle is critical to the fidelity of cell division. Mitotic precision fundamentally contributes to cell fate specification, tissue development and homeostasis, and chromosome distribution within daughter cells. Defects in these events are thought to contribute to several human diseases. The underlying mechanisms that function in spindle morphogenesis and positioning remain incompletely defined, however. Here we describe diverse roles for the actin-microtubule cross-linker Shortstop (Shot) in mitotic spindle function in Drosophila. Shot localizes to mitotic spindle poles, and its knockdown results in an unfocused spindle pole morphology and a disruption of proper spindle orientation. Loss of Shot also leads to chromosome congression defects, cell cycle progression delay, and defective chromosome segregation during anaphase. These mitotic errors trigger apoptosis in Drosophila epithelial tissue, and blocking this apoptotic response results in a marked induction of the epithelial–mesenchymal transition marker MMP-1. The actin-binding domain of Shot directly interacts with Actin-related protein-1 (Arp-1), a key component of the Dynein/Dynactin complex. Knockdown of Arp-1 phenocopies Shot loss universally, whereas chemical disruption of F-actin does so selectively. Our work highlights novel roles for Shot in mitosis and suggests a mechanism involving Dynein/Dynactin activation. PMID:28747439

  5. Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity.

    Science.gov (United States)

    Lopes Cardoso, Daniela; Sharpe, Colin

    2017-01-01

    Organismal complexity broadly relates to the number of different cell types within an organism and generally increases across a phylogeny. Whilst gene expression will underpin organismal complexity, it has long been clear that a simple count of gene number is not a sufficient explanation. In this paper, we use open-access information from the Ensembl databases to quantify the functional diversity of human genes that are broadly involved in transcription. Functional diversity is described in terms of the numbers of paralogues, protein isoforms and structural domains for each gene. The change in functional diversity is then calculated for up to nine orthologues from the nematode worm to human and correlated to the change in cell-type number. Those with the highest correlation are subject to gene ontology term enrichment and interaction analyses. We found that a range of genes that encode proteins associated with dynamic changes to chromatin are good candidates to contribute to organismal complexity.

  6. Comparative proteomics reveal diverse functions and dynamic changes of Bombyx mori silk proteins spun from different development stages.

    Science.gov (United States)

    Dong, Zhaoming; Zhao, Ping; Wang, Chen; Zhang, Yan; Chen, Jianping; Wang, Xin; Lin, Ying; Xia, Qingyou

    2013-11-01

    Silkworms (Bombyx mori) produce massive amounts of silk proteins to make cocoons during the final stages of larval development. Although the major components, fibroin and sericin, have been the focus for a long time, few researchers have realized the complexity of the silk proteome. We collected seven kinds of silk fibers spun by silkworm larvae at different developmental stages: the silks spun by new hatched larvae, second instar day 0 larvae, third instar day 0 larvae, fourth instar day 0 larvae, and fourth instar molting larvae, the scaffold silk used to attach the cocoon to the substrate and the cocoon silk. Analysis by liquid chromatography-tandem mass spectrometry identified 500 proteins from the seven silks. In addition to the expected fibroins, sericins, and some known protease inhibitors, we also identified further protease inhibitors, enzymes, proteins of unknown function, and other proteins. Unsurprisingly, our quantitative results showed fibroins and sericins were the most abundant proteins in all seven silks. Except for fibroins and sericins, protease inhibitors, enzymes, and proteins of unknown function were more abundant than other proteins. We found significant change in silk protein compositions through development, being consistent with their different biological functions and complicated formation.

  7. Evidence for functional diversity between the voltage-gated proton channel Hv1 and its closest related protein HVRP1.

    Directory of Open Access Journals (Sweden)

    Iris H Kim

    Full Text Available The Hv1 channel and voltage-sensitive phosphatases share with voltage-gated sodium, potassium, and calcium channels the ability to detect changes in membrane potential through voltage-sensing domains (VSDs. However, they lack the pore domain typical of these other channels. NaV, KV, and CaV proteins can be found in neurons and muscles, where they play important roles in electrical excitability. In contrast, VSD-containing proteins lacking a pore domain are found in non-excitable cells and are not involved in neuronal signaling. Here, we report the identification of HVRP1, a protein related to the Hv1 channel (from which the name Hv1 Related Protein 1 is derived, which we find to be expressed primarily in the central nervous system, and particularly in the cerebellum. Within the cerebellar tissue, HVRP1 is specifically expressed in granule neurons, as determined by in situ hybridization and immunohistochemistry. Analysis of subcellular distribution via electron microscopy and immunogold labeling reveals that the protein localizes on the post-synaptic side of contacts between glutamatergic mossy fibers and the granule cells. We also find that, despite the similarities in amino acid sequence and structural organization between Hv1 and HVRP1, the two proteins have distinct functional properties. The high conservation of HVRP1 in vertebrates and its cellular and subcellular localizations suggest an important function in the nervous system.

  8. The diversity challenge in directed protein evolution.

    Science.gov (United States)

    Wong, Tuck Seng; Zhurina, Daria; Schwaneberg, Ulrich

    2006-05-01

    Over the past decade, we have witnessed a bloom in the field of evolutive protein engineering which is fueled by advances in molecular biology techniques and high-throughput screening technology. Directed protein evolution is a powerful algorithm using iterative cycles of random mutagenesis and screening for tailoring protein properties to our needs in industrial applications and for elucidating proteins' structure function relationships. This review summarizes, categorizes and discusses advantages and disadvantages of random mutagenesis methods used for generating genetic diversity. These random mutagenesis methods have been classified into four main categories depending on the method employed for nucleotide substitutions: enzyme based methods (Category I), synthetic chemistry based methods (Category II), whole cell methods (Category III) and combined methods (Category I-II, I-III and II-III). The basic principle of each method is discussed and varied mutagenic conditions are summarized in Tables and compared (benchmarked) to each other in terms of: mutational bias, controllable mutation frequency, ability to generate consecutive nucleotide substitutions and subset diversity, dependency on gene length, technical simplicity/robustness and cost-effectiveness. The latter comparison shows how highly-biased and limited current diversity creating methods are. Based on these limitations, strategies for generating diverse mutant libraries are proposed and discussed (RaMuS-Flowchart; KISS principle). We hope that this review provides, especially for researchers just entering the field of directed evolution, a guide for developing successful directed evolution strategies by selecting complementary methods for generating diverse mutant libraries.

  9. Diversity in fosfomycin resistance proteins

    Directory of Open Access Journals (Sweden)

    Matthew K. Thompson

    2015-03-01

    Full Text Available Certain strains of the soil microorganism Streptomyces produce an antibiotic, fosfomycin [(1 R,2 S-epoxypropylphosphonic acid], which is effective against both Gram-positive and Gram-negative pathogens by inhibiting the first committed step in cell-wall biosynthesis. Fosfomycin resistance proteins are metallo-enzymes that are known to inactivate the antibiotic by the addition of nucleophiles such as water, glutathione (GSH, l-cysteine and bacillithiol (BSH to the oxirane ring of the molecule. Progress in the characterisation of FosB-type fosfomycin resistance proteins found in many Gram-positive organisms has been slow. This paper provides a brief description of the diversity of fosfomycin resistance proteins in general and, more specifically, new data characterising the substrate selectivity, structure, mechanism and metal-ion dependence of FosB enzymes from pathogenic strains of Staphylococcus and Bacillus. These new findings include the high-resolution X-ray diffraction structures of FosB enzymes from Staphylococcus aureus and Bacillus cereus in various liganded states and kinetic data that suggest that Mn(II and BSH are the preferred divalent cation and thiol substrate for the reaction, respectively. The discovery of the inhibition of the enzyme by Zn(II led to the determination of a ternary structure of the FosB·Zn(II·fosfomycin·l-Cys complex which reveals both substrates present in a pose prior to reaction.

  10. Functional diversity of aquatic ciliates.

    Science.gov (United States)

    Weisse, Thomas

    2017-10-01

    This paper first reviews the concept of functional diversity in general terms and then applies it to free-living aquatic ciliates. Ciliates are extremely versatile organisms and display an enormous functional diversity as key elements of pelagic food webs, acting as predators of bacteria, algae, other protists and even some metazoans. Planktonic ciliates are important food for zooplankton, and mixotrophic and functionally autotrophic species may significantly contribute to primary production in the ocean and in lakes. The co-occurrence of many ciliate species in seemingly homogenous environments indicates a wide range of their ecological niches. Variation in space and time may foster co-occurrence and prevent violating the competitive exclusion principle among ciliates using the same resources. Considering that many ciliates may be dormant and/or rare in many habitats, ciliate species diversity must be higher than can be deduced from simple sampling techniques; molecular methods of identification clearly point to this hidden diversity. From a functional point of view, the question is how much of this diversity represents redundancy. A key challenge for future research is to link the ecophysiological performance of naturally co-occurring ciliates to their functional genes. To this end, more experimental research is needed with with functionally different species. Copyright © 2017 The Author. Published by Elsevier GmbH.. All rights reserved.

  11. Biased μ-opioid receptor agonists diversely regulate lateral mobility and functional coupling of the receptor to its cognate G proteins.

    Science.gov (United States)

    Melkes, Barbora; Hejnova, Lucie; Novotny, Jiri

    2016-12-01

    There are some indications that biased μ-opioid ligands may diversely affect μ-opioid receptor (MOR) properties. Here, we used confocal fluorescence recovery after photobleaching (FRAP) to study the regulation by different MOR agonists of receptor movement within the plasma membrane of HEK293 cells stably expressing a functional yellow fluorescent protein (YFP)-tagged μ-opioid receptor (MOR-YFP). We found that the lateral mobility of MOR-YFP was increased by (D-Ala 2 ,N-MePhe 4 ,Gly 5 -ol)-enkephalin (DAMGO) and to a lesser extent also by morphine but decreased by endomorphin-2. Interestingly, cholesterol depletion strongly enhanced the ability of morphine to elevate receptor mobility but significantly reduced or even eliminated the effect of DAMGO and endomorphin-2, respectively. Moreover, the ability of DAMGO and endomorphin-2 to influence MOR-YFP movement was diminished by pertussis toxin treatment. The results obtained by agonist-stimulated [ 35 S]GTPγS binding assays indicated that DAMGO exhibited higher efficacy than morphine and endomorphin-2 did and that the efficacy of DAMGO, contrary to the latter agonists, was enhanced by cholesterol depletion. Overall, our study provides clear evidence that biased MOR agonists diversely affect receptor mobility in plasma membranes as well as MOR/G protein coupling and that the regulatory effect of different ligands depends on the membrane cholesterol content. These findings help to delineate the fundamental properties of MOR regarding their interaction with biased MOR ligands and cognate G proteins.

  12. A user's guide to functional diversity indices

    OpenAIRE

    Schleuter , D.; Daufresne , M.; Massol , F.; Argillier , C.

    2010-01-01

    Functional diversity is the diversity of species traits in ecosystems. This concept is increasingly used in ecological research, yet its formal definition and measurements are currently under discussion. As the overall behaviour and consistency of functional diversity indices have not been described so far, the novice user risks choosing an inaccurate index or a set of redundant indices to represent functional diversity. In our study we closely examine functional diversity indices to clari...

  13. Diversity and functional properties of bistable pigments.

    Science.gov (United States)

    Tsukamoto, Hisao; Terakita, Akihisa

    2010-11-01

    Rhodopsin and related opsin-based pigments, which are photosensitive membrane proteins, have been extensively studied using a wide variety of techniques, with rhodopsin being the most understood G protein-coupled receptor (GPCR). Animals use various opsin-based pigments for vision and a wide variety of non-visual functions. Many functionally varied pigments are roughly divided into two kinds, based on their photoreaction: bistable and monostable pigments. Bistable pigments are thermally stable before and after photo-activation, but monostable pigments are stable only before activation. Here, we review the diversity of bistable pigments and their molecular characteristics. We also discuss the mechanisms underlying different molecular characteristics of bistable and monostable pigments. In addition, the potential of bistable pigments as a GPCR model is proposed.

  14. Protein Functionalized Nanodiamond Arrays

    Directory of Open Access Journals (Sweden)

    Liu YL

    2010-01-01

    Full Text Available Abstract Various nanoscale elements are currently being explored for bio-applications, such as in bio-images, bio-detection, and bio-sensors. Among them, nanodiamonds possess remarkable features such as low bio-cytotoxicity, good optical property in fluorescent and Raman spectra, and good photostability for bio-applications. In this work, we devise techniques to position functionalized nanodiamonds on self-assembled monolayer (SAMs arrays adsorbed on silicon and ITO substrates surface using electron beam lithography techniques. The nanodiamond arrays were functionalized with lysozyme to target a certain biomolecule or protein specifically. The optical properties of the nanodiamond-protein complex arrays were characterized by a high throughput confocal microscope. The synthesized nanodiamond-lysozyme complex arrays were found to still retain their functionality in interacting with E. coli.

  15. Functional & phylogenetic diversity of copepod communities

    Science.gov (United States)

    Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.

    2016-02-01

    The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.

  16. Functional diversity in resource use by fungi.

    Science.gov (United States)

    McGuire, Krista L; Bent, Elizabeth; Borneman, James; Majumder, Arundhati; Allison, Steven D; Tresederi, Kathleen K

    2010-08-01

    Fungi influence nutrient cycling in terrestrial ecosystems, as they are major regulators of decomposition and soil respiration. However, little is known about the substrate preferences of individual fungal species outside of laboratory culture studies. If active fungi differ in their substrate preferences in situ, then changes in fungal diversity due to global change may dramatically influence nutrient cycling in ecosystems. To test the responses of individual fungal taxa to specific substrates, we used a nucleotide-analogue procedure in the boreal forest of Alaska (USA). Specifically, we added four organic N compounds commonly found in plant litter (arginine, glutamate, lignocellulose, and tannin-protein) to litterbags filled with decomposed leaf litter (black spruce and aspen) and assessed the responses of active fungal species using qPCR (quantitative polymerase chain reaction), oligonucleotide fingerprinting of rRNA genes, and sequencing. We also compared the sequences from our experiment with a concurrent warming experiment to see if active fungi that targeted more recalcitrant compounds would respond more positively to soil warming. We found that individual fungal taxa responded differently to substrate additions and that active fungal communities were different across litter types (spruce vs. aspen). Active fungi that targeted lignocellulose also responded positively to experimental warming. Additionally, resource-use patterns in different fungal taxa were genetically correlated, suggesting that it may be possible to predict the ecological function of active fungal communities based on genetic information. Together, these results imply that fungi are functionally diverse and that reductions in fungal diversity may have consequences for ecosystem functioning.

  17. Esterase, total protein and seed storage protein diversity in Okra ...

    African Journals Online (AJOL)

    Twenty-two accessions of okra (Abelmoschus esculentus), maintained at the Plant Genetic Resources Centre, Bunso, Ghana, were assayed for diversity in esterases, and total and storage proteins. A total of 34 reproducible and easily scorable bands were exposed with the number of bands per accession ranging from one ...

  18. Individual diversity management and salutogenic functioning.

    Science.gov (United States)

    Cilliers, Frans

    2011-12-01

    Individual diversity management was framed as how individual managers engage with and experience diversity situations. Salutogenesis was chosen as the psychological model to understand individual' management of diversity. The aim of the research was to investigate whether and how sense of coherence (SOC) acts as differentiator between ineffective and effective diversity management amongst managers. Based on their quantitatively measured SOC scores, 33 managers in a financial services organization were divided into a (statistically significantly different) low and high functioning subgroup. This was followed by a qualitative interview based on their experienced comprehension, manageability and meaningfulness of diversity experiences. Compared to the low subgroup, the high SOC subgroup reported understanding of the necessity of diversity discussions, managing themselves as representatives of a specific race, gender and age group, and finding diversity experiences meaningful towards identity forming and effective interpersonal relationships. Their SOC was linked to other salutogenic constructs. It was recommended that this organization design its diversity programme based on salutogenesis as theoretical model.

  19. Tree species diversity promotes aboveground carbon storage through functional diversity and functional dominance.

    Science.gov (United States)

    Mensah, Sylvanus; Veldtman, Ruan; Assogbadjo, Achille E; Glèlè Kakaï, Romain; Seifert, Thomas

    2016-10-01

    The relationship between biodiversity and ecosystem function has increasingly been debated as the cornerstone of the processes behind ecosystem services delivery. Experimental and natural field-based studies have come up with nonconsistent patterns of biodiversity-ecosystem function, supporting either niche complementarity or selection effects hypothesis. Here, we used aboveground carbon (AGC) storage as proxy for ecosystem function in a South African mistbelt forest, and analyzed its relationship with species diversity, through functional diversity and functional dominance. We hypothesized that (1) diversity influences AGC through functional diversity and functional dominance effects; and (2) effects of diversity on AGC would be greater for functional dominance than for functional diversity. Community weight mean (CWM) of functional traits (wood density, specific leaf area, and maximum plant height) were calculated to assess functional dominance (selection effects). As for functional diversity (complementarity effects), multitrait functional diversity indices were computed. The first hypothesis was tested using structural equation modeling. For the second hypothesis, effects of environmental variables such as slope and altitude were tested first, and separate linear mixed-effects models were fitted afterward for functional diversity, functional dominance, and both. Results showed that AGC varied significantly along the slope gradient, with lower values at steeper sites. Species diversity (richness) had positive relationship with AGC, even when slope effects were considered. As predicted, diversity effects on AGC were mediated through functional diversity and functional dominance, suggesting that both the niche complementarity and the selection effects are not exclusively affecting carbon storage. However, the effects were greater for functional diversity than for functional dominance. Furthermore, functional dominance effects were strongly transmitted by CWM of

  20. Functional diversity of resilin in Arthropoda

    Directory of Open Access Journals (Sweden)

    Jan Michels

    2016-09-01

    Full Text Available Resilin is an elastomeric protein typically occurring in exoskeletons of arthropods. It is composed of randomly orientated coiled polypeptide chains that are covalently cross-linked together at regular intervals by the two unusual amino acids dityrosine and trityrosine forming a stable network with a high degree of flexibility and mobility. As a result of its molecular prerequisites, resilin features exceptional rubber-like properties including a relatively low stiffness, a rather pronounced long-range deformability and a nearly perfect elastic recovery. Within the exoskeleton structures, resilin commonly forms composites together with other proteins and/or chitin fibres. In the last decades, numerous exoskeleton structures with large proportions of resilin and various resilin functions have been described. Today, resilin is known to be responsible for the generation of deformability and flexibility in membrane and joint systems, the storage of elastic energy in jumping and catapulting systems, the enhancement of adaptability to uneven surfaces in attachment and prey catching systems, the reduction of fatigue and damage in reproductive, folding and feeding systems and the sealing of wounds in a traumatic reproductive system. In addition, resilin is present in many compound eye lenses and is suggested to be a very suitable material for optical elements because of its transparency and amorphousness. The evolution of this remarkable functional diversity can be assumed to have only been possible because resilin exhibits a unique combination of different outstanding properties.

  1. Functional Diversity of AAA+ Protease Complexes in Bacillus subtilis

    Science.gov (United States)

    Elsholz, Alexander K. W.; Birk, Marlene S.; Charpentier, Emmanuelle; Turgay, Kürşad

    2017-01-01

    Here, we review the diverse roles and functions of AAA+ protease complexes in protein homeostasis, control of stress response and cellular development pathways by regulatory and general proteolysis in the Gram-positive model organism Bacillus subtilis. We discuss in detail the intricate involvement of AAA+ protein complexes in controlling sporulation, the heat shock response and the role of adaptor proteins in these processes. The investigation of these protein complexes and their adaptor proteins has revealed their relevance for Gram-positive pathogens and their potential as targets for new antibiotics. PMID:28748186

  2. Architectures and Functional Coverage of Protein-Protein Interfaces

    Science.gov (United States)

    Tuncbag, Nurcan; Gursoy, Attila; Guney, Emre; Nussinov, Ruth; Keskin, Ozlem

    2008-01-01

    The diverse range of cellular functions is performed by a limited number of protein folds existing in nature. One may similarly expect that cellular functional diversity would be covered by a limited number of protein-protein interface architectures. Here, we present 8205 interface clusters, each representing unique interface architecture. This dataset of protein-protein interfaces is analyzed and compared with older datasets. We observe that the number of both biological and crystal interfaces increase significantly compared to the number of PDB entries. Further, we find that the number of distinct interface architectures grows at a much faster rate than the number of folds and is yet to level off. We further analyze the growth trend of the functional coverage by constructing functional interaction networks from interfaces. The functional coverage is also found to steadily increase. Interestingly, we also observe that despite the diversity of interface architectures, some are more favorable and frequently used, and of particular interest, those are the ones which are also preferred in single chains. PMID:18620705

  3. Zinc-Binding Cysteines: Diverse Functions and Structural Motifs

    Science.gov (United States)

    Pace, Nicholas J.; Weerapana, Eranthie

    2014-01-01

    Cysteine residues are known to perform essential functions within proteins, including binding to various metal ions. In particular, cysteine residues can display high affinity toward zinc ions (Zn2+), and these resulting Zn2+-cysteine complexes are critical mediators of protein structure, catalysis and regulation. Recent advances in both experimental and theoretical platforms have accelerated the identification and functional characterization of Zn2+-bound cysteines. Zn2+-cysteine complexes have been observed across diverse protein classes and are known to facilitate a variety of cellular processes. Here, we highlight the structural characteristics and diverse functional roles of Zn2+-cysteine complexes in proteins and describe structural, computational and chemical proteomic technologies that have enabled the global discovery of novel Zn2+-binding cysteines. PMID:24970223

  4. Soil eukaryotic functional diversity, a metatranscriptomic approach.

    Science.gov (United States)

    Bailly, Julie; Fraissinet-Tachet, Laurence; Verner, Marie-Christine; Debaud, Jean-Claude; Lemaire, Marc; Wésolowski-Louvel, Micheline; Marmeisse, Roland

    2007-11-01

    To appreciate the functional diversity of communities of soil eukaryotic micro-organisms we evaluated an experimental approach based on the construction and screening of a cDNA library using polyadenylated mRNA extracted from a forest soil. Such a library contains genes that are expressed by each of the different organisms forming the community and represents its metatranscriptome. The diversity of the organisms that contributed to this library was evaluated by sequencing a portion of the 18S rDNA gene amplified from either soil DNA or reverse-transcribed RNA. More than 70% of the sequences were from fungi and unicellular eukaryotes (protists) while the other most represented group was the metazoa. Calculation of richness estimators suggested that more than 180 species could be present in the soil samples studied. Sequencing of 119 cDNA identified genes with no homologues in databases (32%) and genes coding proteins involved in different biochemical and cellular processes. Surprisingly, the taxonomic distribution of the cDNA and of the 18S rDNA genes did not coincide, with a marked under-representation of the protists among the cDNA. Specific genes from such an environmental cDNA library could be isolated by expression in a heterologous microbial host, Saccharomyces cerevisiae. This is illustrated by the functional complementation of a histidine auxotrophic yeast mutant by two cDNA originating possibly from an ascomycete and a basidiomycete fungal species. Study of the metatranscriptome has the potential to uncover adaptations of whole microbial communities to local environmental conditions. It also gives access to an abundant source of genes of biotechnological interest.

  5. A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces.

    Science.gov (United States)

    Gilbreth, Ryan N; Esaki, Kaori; Koide, Akiko; Sidhu, Sachdev S; Koide, Shohei

    2008-08-29

    Recent studies have shown that highly simplified interaction surfaces consisting of combinations of just two amino acids, Tyr and Ser, exhibit high affinity and specificity. The high functional levels of such minimalist interfaces might thus indicate small contributions of greater amino acid diversity seen in natural interfaces. Toward addressing this issue, we have produced a pair of binding proteins built on the fibronectin type III scaffold, termed "monobodies." One monobody contains the Tyr/Ser binary-code interface (termed YS) and the other contains an expanded amino acid diversity interface (YSX), but both bind to an identical target, maltose-binding protein. The YSX monobody bound with higher affinity, a slower off rate and a more favorable enthalpic contribution than the YS monobody. High-resolution X-ray crystal structures revealed that both proteins bound to an essentially identical epitope, providing a unique opportunity to directly investigate the role of amino acid diversity in a protein interaction interface. Surprisingly, Tyr still dominates the YSX paratope and the additional amino acid types are primarily used to conformationally optimize contacts made by tyrosines. Scanning mutagenesis showed that while all contacting Tyr side chains are essential in the YS monobody, the YSX interface was more tolerant to mutations. These results suggest that the conformational, not chemical, diversity of additional types of amino acids provided higher functionality and evolutionary robustness, supporting the dominant role of Tyr and the importance of conformational diversity in forming protein interaction interfaces.

  6. Functional diversity changes during tropical forest succession.

    NARCIS (Netherlands)

    Lohbeck, M.W.M.; Poorter, L.; Paz, H.; Breugel, van M.; Martinez-Ramos, M.; Bongers, F.

    2012-01-01

    Functional diversity (FD) ‘those components of biodiversity that influence how an ecosystem operates or functions’ is a promising tool to assess the effect of biodiversity loss on ecosystem functioning. FD has received ample theoretical attention, but empirical studies are limited. We evaluate

  7. Functional aspects of protein flexibility

    DEFF Research Database (Denmark)

    Teilum, Kaare; Olsen, Johan G; Kragelund, Birthe B

    2009-01-01

    . The thermodynamics involved are reviewed, and examples of structure-function studies involving experimentally determined flexibility descriptions are presented. While much remains to be understood about protein flexibility, it is clear that it is encoded within their amino acid sequence and should be viewed......Proteins are dynamic entities, and they possess an inherent flexibility that allows them to function through molecular interactions within the cell, among cells and even between organisms. Appreciation of the non-static nature of proteins is emerging, but to describe and incorporate...... this into an intuitive perception of protein function is challenging. Flexibility is of overwhelming importance for protein function, and the changes in protein structure during interactions with binding partners can be dramatic. The present review addresses protein flexibility, focusing on protein-ligand interactions...

  8. FUNCTIONAL DIVERSITY AND OPTOGENETIC POTENTIALS OF MICROBIAL RHODOPSINS

    Directory of Open Access Journals (Sweden)

    Mayanka Awasthi

    2011-12-01

    Full Text Available Microbial or type-1 rhodopsins are light sensitive proteins that utilize all-trans retinal as chromophore. Microbial rhodopsins are present in archaea, eubacteria and eukaryotes. Their broad and patchy distribution among the three domains of life is attributed to the lateral gene transfer mechanism of evolution. Microbial rhodopsins function as sensory rhodopsins, light-gated ion pumps and light-activated ion channels in nature. In this review, we present functional diversity and optogenetics applications of microbial rhodopsins.

  9. Diversity and evolution of coral fluorescent proteins.

    Directory of Open Access Journals (Sweden)

    Naila O Alieva

    2008-07-01

    Full Text Available GFP-like fluorescent proteins (FPs are the key color determinants in reef-building corals (class Anthozoa, order Scleractinia and are of considerable interest as potential genetically encoded fluorescent labels. Here we report 40 additional members of the GFP family from corals. There are three major paralogous lineages of coral FPs. One of them is retained in all sampled coral families and is responsible for the non-fluorescent purple-blue color, while each of the other two evolved a full complement of typical coral fluorescent colors (cyan, green, and red and underwent sorting between coral groups. Among the newly cloned proteins are a "chromo-red" color type from Echinopora forskaliana (family Faviidae and pink chromoprotein from Stylophora pistillata (Pocilloporidae, both evolving independently from the rest of coral chromoproteins. There are several cyan FPs that possess a novel kind of excitation spectrum indicating a neutral chromophore ground state, for which the residue E167 is responsible (numeration according to GFP from A. victoria. The chromoprotein from Acropora millepora is an unusual blue instead of purple, which is due to two mutations: S64C and S183T. We applied a novel probabilistic sampling approach to recreate the common ancestor of all coral FPs as well as the more derived common ancestor of three main fluorescent colors of the Faviina suborder. Both proteins were green such as found elsewhere outside class Anthozoa. Interestingly, a substantial fraction of the all-coral ancestral protein had a chromohore apparently locked in a non-fluorescent neutral state, which may reflect the transitional stage that enabled rapid color diversification early in the history of coral FPs. Our results highlight the extent of convergent or parallel evolution of the color diversity in corals, provide the foundation for experimental studies of evolutionary processes that led to color diversification, and enable a comparative analysis of

  10. Assessing functional diversity by program slicing

    International Nuclear Information System (INIS)

    Wallace, D.R.; Lyle, J.R.; Gallagher, K.B.; Ippolito, L.M.

    1994-01-01

    A responsibility of the Nuclear Regulatory Commission auditors is to provide assessments of the quality of the safety systems. For software, the audit process as currently implemented is a slow, tedious, manual process prone to human errors. While auditors cannot possibly examine all components of the system in complete detail, they do check for implementation of specific principles like functional diversity. This paper describes an experimental prototype Computer Aided Software Engineering (CASE) tool, UNRAVEL, designed to enable auditors to check for functional diversity and aid an auditor in examining software by extracting all code relevant to a computation identified for detailed inspection

  11. NAC transcription factors: structurally distinct, functionally diverse

    DEFF Research Database (Denmark)

    Olsen, Addie Nina; Ernst, Heidi A; Leggio, Leila Lo

    2005-01-01

    level and localization, and to the first indications of NAC participation in transcription factor networks. The recent determination of the DNA and protein binding NAC domain structure offers insight into the molecular functions of the protein family. Research into NAC transcription factors has...

  12. Nutritional and functional properties of whey proteins concentrate and isolate

    OpenAIRE

    Zoran Herceg; Anet Režek

    2006-01-01

    Whey protein fractions represent 18 - 20 % of total milk nitrogen content. Nutritional value in addition to diverse physico - chemical and functional properties make whey proteins highly suitable for application in foodstuffs. In the most cases, whey proteins are used because of their functional properties. Whey proteins possess favourable functional characteristics such as gelling, water binding, emulsification and foaming ability. Due to application of new process techniques (membrane fract...

  13. Soil-borne microbiome: linking diversity to function

    NARCIS (Netherlands)

    Mendes, L.M.; Tsai, S.M.; Navarrete, Acácio A.; De Hollander, Mattias; Van Veen, J.A.; Kuramae, Eiko E.

    2015-01-01

    Soil microorganisms are sensitive to environment disturbances, and such alterations have consequences on microbial diversity and functions. Our hypothesis is that alpha diversity of microbial communities and functional diversity decrease from undisturbed to disturbed soils, with consequences for

  14. Protein dynamics and the diversity of an antibody response.

    Science.gov (United States)

    Adhikary, Ramkrishna; Yu, Wayne; Oda, Masayuki; Zimmermann, Jörg; Romesberg, Floyd E

    2012-08-03

    The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved.

  15. Protein Dynamics and the Diversity of an Antibody Response*

    Science.gov (United States)

    Adhikary, Ramkrishna; Yu, Wayne; Oda, Masayuki; Zimmermann, Jörg; Romesberg, Floyd E.

    2012-01-01

    The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved. PMID:22685303

  16. Protein stability, flexibility and function

    DEFF Research Database (Denmark)

    Teilum, Kaare; Olsen, Johan G; Kragelund, Birthe B

    2011-01-01

    Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests...... for a delineation of the molecular details of their function. Several of these mutations interfered with the binding of a specific ligand with a concomitant effect on the stability of the protein scaffold. It has been ambiguous and not straightforward to recognize if any relationships exist between the stability...... of a protein and the affinity for its ligand. In this review, we present examples of proteins where changes in stability results in changes in affinity and of proteins where stability and affinity are uncorrelated. We discuss the possibility for a relationship between stability and binding. From the data...

  17. Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

    Science.gov (United States)

    He, Zhili; Zhang, Ping; Wu, Linwei; Rocha, Andrea M; Tu, Qichao; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D; Wu, Liyou; Yang, Yunfeng; Elias, Dwayne A; Watson, David B; Adams, Michael W W; Fields, Matthew W; Alm, Eric J; Hazen, Terry C; Adams, Paul D; Arkin, Adam P; Zhou, Jizhong

    2018-02-20

    Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly ( P contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as

  18. Protein landmarks for diversity assessment in wheat genotypes

    African Journals Online (AJOL)

    jai ganesha

    2013-07-17

    Jul 17, 2013 ... Grain proteins from 20 Indian wheat genotypes were evaluated for diversity assessment based seed storage protein profiling on sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE). Genetic diversity was evaluated using Nei's index, Shannon index and Unweighted pair group method.

  19. Protein landmarks for diversity assessment in wheat genotypes ...

    African Journals Online (AJOL)

    Grain proteins from 10 Pakistani registered wheat genotypes were evaluated for diversity assessment based on sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE). Genetic diversity was evaluated via UPGMA cluster analysis by constructing dendrogram of fractions of proteins, which were used for the ...

  20. Exploring the diversity of protein modifications: special bacterial phosphorylation systems

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Grangeasse, Christophe; Turgay, Kürşad

    2016-01-01

    Protein modifications not only affect protein homeostasis but can also establish new cellular protein functions and are important components of complex cellular signal sensing and transduction networks. Among these post-translational modifications, protein phosphorylation represents the one that ...

  1. Does the Cave Environment Reduce Functional Diversity?

    Science.gov (United States)

    Fernandes, Camile Sorbo; Batalha, Marco Antonio; Bichuette, Maria Elina

    2016-01-01

    Caves are not colonised by all taxa present in the surface species pool, due to absence of light and the tendency to food limitation when compared to surface communities. Under strong species sorting during colonisation and later by the restrictive environmental filter, traits that are not adaptive in subterranean habitats may be filtered out. We tested whether cave communities were assembled by the restrictive regime propitiated by permanent darkness or by competitive exclusion due to resource scarcity. When compared to surface communities, the restrictive subterranean regime would lead to lower functional diversity and phenotypic clustering inside the caves, and the opposite should be expected in the case of competitive exclusion. Using isopods (Oniscidea) as model taxa, we measured several niche descriptors of taxa from surface and cave habitats, used a multivariate measure of functional diversity, and compared their widths. We found phenotypic overdispersion and higher functional diversity in cave taxa when compared to surface taxa. On the one hand, the dry climate outside of caves hampered the survival of several taxa and their ecological strategies, not viable under severe desiccation risk, culminating in the clustering of functional traits. In contrast, this restriction does not occur inside of caves, where isopods find favourable conditions under lower predation pressures and more amenable environmental parameters that allow occupation and subsequent diversification. Our results showed that, at least for some taxa, caves may not be such a harsh environment as previously thought. The high functional diversity we found inside caves adds an additional reason for the conservation of these sensitive environments.

  2. Nutritional and functional properties of whey proteins concentrate and isolate

    Directory of Open Access Journals (Sweden)

    Zoran Herceg

    2006-12-01

    Full Text Available Whey protein fractions represent 18 - 20 % of total milk nitrogen content. Nutritional value in addition to diverse physico - chemical and functional properties make whey proteins highly suitable for application in foodstuffs. In the most cases, whey proteins are used because of their functional properties. Whey proteins possess favourable functional characteristics such as gelling, water binding, emulsification and foaming ability. Due to application of new process techniques (membrane fractionation techniques, it is possible to produce various whey - protein based products. The most important products based on the whey proteins are whey protein concentrates (WPC and whey protein isolates (WPI. The aim of this paper was to give comprehensive review of nutritional and functional properties of the most common used whey proteins (whey protein concentrate - WPC and whey protein isolate - WPI in the food industry.

  3. Enterovirus A71 Proteins: Structure and Function

    Directory of Open Access Journals (Sweden)

    Jingjing Yuan

    2018-02-01

    Full Text Available Enterovirus A71 (EV-A71 infection has grown to become a serious threat to global public health. It is one of the major causes of hand, foot, and mouth disease (HFMD in infants and young children. EV-A71 can also infect the central nervous system (CNS and induce diverse neurological complications, such as brainstem encephalitis, aseptic meningitis, and acute flaccid paralysis, or even death. Viral proteins play a crucial role in EV-A71 infection. Many recent studies have discussed the structure and function of EV-A71 proteins, and the findings reported will definitely aid the development of vaccines and therapeutic approaches. This article reviews the progress in the research on the structure and function of EV-A71 proteins. Available literature can provide a basis for studying the pathogenesis of EV-A71 infection in detail.

  4. Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

    Science.gov (United States)

    Zhang, Ping; Wu, Linwei; Rocha, Andrea M.; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D.; Wu, Liyou; Watson, David B.; Adams, Michael W. W.; Alm, Eric J.; Adams, Paul D.; Arkin, Adam P.

    2018-01-01

    ABSTRACT Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. PMID:29463661

  5. Diversity and functions of intestinal mononuclear phagocytes

    DEFF Research Database (Denmark)

    Joeris, Thorsten; Müller-Luda, K; Agace, William Winston

    2017-01-01

    The intestinal lamina propria (LP) contains a diverse array of mononuclear phagocyte (MNP) subsets, including conventional dendritic cells (cDC), monocytes and tissue-resident macrophages (mφ) that collectively play an essential role in mucosal homeostasis, infection and inflammation. In the curr......The intestinal lamina propria (LP) contains a diverse array of mononuclear phagocyte (MNP) subsets, including conventional dendritic cells (cDC), monocytes and tissue-resident macrophages (mφ) that collectively play an essential role in mucosal homeostasis, infection and inflammation....... In the current review we discuss the function of intestinal cDC and monocyte-derived MNP, highlighting how these subsets play several non-redundant roles in the regulation of intestinal immune responses. While much remains to be learnt, recent findings also underline how the various populations of MNP adapt...

  6. The SpTransformer Gene Family (Formerly Sp185/333 in the Purple Sea Urchin and the Functional Diversity of the Anti-Pathogen rSpTransformer-E1 Protein

    Directory of Open Access Journals (Sweden)

    L. Courtney Smith

    2017-06-01

    Full Text Available The complex innate immune system of sea urchins is underpinned by several multigene families including the SpTransformer family (SpTrf; formerly Sp185/333 with estimates of ~50 members, although the family size is likely variable among individuals of Strongylocentrotus purpuratus. The genes are small with similar structure, are tightly clustered, and have several types of repeats in the second of two exons and that surround each gene. The density of repeats suggests that the genes are positioned within regions of genomic instability, which may be required to drive sequence diversification. The second exon encodes the mature protein and is composed of blocks of sequence called elements that are present in mosaics of defined element patterns and are the major source of sequence diversity. The SpTrf genes respond swiftly to immune challenge, but only a single gene is expressed per phagocyte. Many of the mRNAs appear to be edited and encode proteins with altered and/or missense sequence that are often truncated, of which some may be functional. The standard SpTrf protein structure is an N-terminal glycine-rich region, a central RGD motif, a histidine-rich region, and a C-terminal region. Function is predicted from a recombinant protein, rSpTransformer-E1 (rSpTrf-E1, which binds to Vibrio and Saccharomyces, but not to Bacillus, and binds tightly to lipopolysaccharide, β-1,3-glucan, and flagellin, but not to peptidoglycan. rSpTrf-E1 is intrinsically disordered but transforms to α helical structure in the presence of binding targets including lipopolysaccharide, which may underpin the characteristics of binding to multiple targets. SpTrf proteins associate with coelomocyte membranes, and rSpTrf-E1 binds specifically to phosphatidic acid (PA. When rSpTrf-E1 is bound to PA in liposome membranes, it induces morphological changes in liposomes that correlate with PA clustering and leakage of luminal contents, and it extracts or removes PA from the bilayer

  7. TheSpTransformerGene Family (FormerlySp185/333) in the Purple Sea Urchin and the Functional Diversity of the Anti-Pathogen rSpTransformer-E1 Protein.

    Science.gov (United States)

    Smith, L Courtney; Lun, Cheng Man

    2017-01-01

    The complex innate immune system of sea urchins is underpinned by several multigene families including the SpTransformer family ( SpTrf ; formerly Sp185/333 ) with estimates of ~50 members, although the family size is likely variable among individuals of Strongylocentrotus purpuratus . The genes are small with similar structure, are tightly clustered, and have several types of repeats in the second of two exons and that surround each gene. The density of repeats suggests that the genes are positioned within regions of genomic instability, which may be required to drive sequence diversification. The second exon encodes the mature protein and is composed of blocks of sequence called elements that are present in mosaics of defined element patterns and are the major source of sequence diversity. The SpTrf genes respond swiftly to immune challenge, but only a single gene is expressed per phagocyte. Many of the mRNAs appear to be edited and encode proteins with altered and/or missense sequence that are often truncated, of which some may be functional. The standard SpTrf protein structure is an N-terminal glycine-rich region, a central RGD motif, a histidine-rich region, and a C-terminal region. Function is predicted from a recombinant protein, rSpTransformer-E1 (rSpTrf-E1), which binds to Vibrio and Saccharomyces , but not to Bacillus , and binds tightly to lipopolysaccharide, β-1,3-glucan, and flagellin, but not to peptidoglycan. rSpTrf-E1 is intrinsically disordered but transforms to α helical structure in the presence of binding targets including lipopolysaccharide, which may underpin the characteristics of binding to multiple targets. SpTrf proteins associate with coelomocyte membranes, and rSpTrf-E1 binds specifically to phosphatidic acid (PA). When rSpTrf-E1 is bound to PA in liposome membranes, it induces morphological changes in liposomes that correlate with PA clustering and leakage of luminal contents, and it extracts or removes PA from the bilayer. The

  8. The SpTransformer Gene Family (Formerly Sp185/333) in the Purple Sea Urchin and the Functional Diversity of the Anti-Pathogen rSpTransformer-E1 Protein

    Science.gov (United States)

    Smith, L. Courtney; Lun, Cheng Man

    2017-01-01

    The complex innate immune system of sea urchins is underpinned by several multigene families including the SpTransformer family (SpTrf; formerly Sp185/333) with estimates of ~50 members, although the family size is likely variable among individuals of Strongylocentrotus purpuratus. The genes are small with similar structure, are tightly clustered, and have several types of repeats in the second of two exons and that surround each gene. The density of repeats suggests that the genes are positioned within regions of genomic instability, which may be required to drive sequence diversification. The second exon encodes the mature protein and is composed of blocks of sequence called elements that are present in mosaics of defined element patterns and are the major source of sequence diversity. The SpTrf genes respond swiftly to immune challenge, but only a single gene is expressed per phagocyte. Many of the mRNAs appear to be edited and encode proteins with altered and/or missense sequence that are often truncated, of which some may be functional. The standard SpTrf protein structure is an N-terminal glycine-rich region, a central RGD motif, a histidine-rich region, and a C-terminal region. Function is predicted from a recombinant protein, rSpTransformer-E1 (rSpTrf-E1), which binds to Vibrio and Saccharomyces, but not to Bacillus, and binds tightly to lipopolysaccharide, β-1,3-glucan, and flagellin, but not to peptidoglycan. rSpTrf-E1 is intrinsically disordered but transforms to α helical structure in the presence of binding targets including lipopolysaccharide, which may underpin the characteristics of binding to multiple targets. SpTrf proteins associate with coelomocyte membranes, and rSpTrf-E1 binds specifically to phosphatidic acid (PA). When rSpTrf-E1 is bound to PA in liposome membranes, it induces morphological changes in liposomes that correlate with PA clustering and leakage of luminal contents, and it extracts or removes PA from the bilayer. The

  9. Protein landmarks for diversity assessment in wheat genotypes ...

    African Journals Online (AJOL)

    Genetic diversity was evaluated using Nei's index, Shannon index and Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis by constructing dendrogram of fractions of proteins, which were used for the calculation of similarity coefficients between these varieties. Diversity analysis attributes ...

  10. Functional diversity in coral-dinoflagellate symbiosis.

    Science.gov (United States)

    Stat, Michael; Morris, Emily; Gates, Ruth D

    2008-07-08

    Symbioses are widespread in nature and occur along a continuum from parasitism to mutualism. Coral-dinoflagellate symbioses are defined as mutualistic because both partners receive benefit from the association via the exchange of nutrients. This successful interaction underpins the growth and formation of coral reefs. The symbiotic dinoflagellate genus Symbiodinium is genetically diverse containing eight divergent lineages (clades A-H). Corals predominantly associate with clade C Symbiodinium and to a lesser extent with clades A, B, D, F, and G. Variation in the function and interactive physiology of different coral-dinoflagellate assemblages is virtually unexplored but is an important consideration when developing the contextual framework of factors that contribute to coral reef resilience. In this study, we present evidence that clade A Symbiodinium are functionally less beneficial to corals than the dominant clade C Symbiodinium and may represent parasitic rather than mutualistic symbionts. Our hypothesis is supported by (i) a significant correlation between the presence of Symbiodinium clade A and health-compromised coral; (ii) a phylogeny and genetic diversity within Symbiodinium that suggests a different evolutionary trajectory for clade A compared with the other dominant Symbiodinium lineages; and (iii) a significantly lower amount of carbon fixed and released by clade A in the presence of a coral synthetic host factor as compared with the dominant coral symbiont lineage, clade C. Collectively, these data suggest that along the symbiotic continuum the interaction between clade A Symbiodinium and corals may be closer to parasitism than mutualism.

  11. Protein landmarks for diversity assessment in wheat genotypes ...

    African Journals Online (AJOL)

    Grain proteins from 20 Indian wheat genotypes were evaluated for diversity assessment based seed storage protein profiling on sodium dodecylsulphate ... to plant protection regulatory systems, especially for plant variety identification and registration of new plant varieties, breeding programs and protection purposes.

  12. Functional dominance rather than taxonomic diversity and functional diversity mainly affects community aboveground biomass in the Inner Mongolia grassland.

    Science.gov (United States)

    Zhang, Qing; Buyantuev, Alexander; Li, Frank Yonghong; Jiang, Lin; Niu, Jianming; Ding, Yong; Kang, Sarula; Ma, Wenjing

    2017-03-01

    The relationship between biodiversity and productivity has been a hot topic in ecology. However, the relative importance of taxonomic diversity and functional characteristics (including functional dominance and functional diversity) in maintaining community productivity and the underlying mechanisms (including selection and complementarity effects) of the relationship between diversity and community productivity have been widely controversial. In this study, 194 sites were surveyed in five grassland types along a precipitation gradient in the Inner Mongolia grassland of China. The relationships between taxonomic diversity (species richness and the Shannon-Weaver index), functional dominance (the community-weighted mean of four plant traits), functional diversity (Rao's quadratic entropy), and community aboveground biomass were analyzed. The results showed that (1) taxonomic diversity, functional dominance, functional diversity, and community aboveground biomass all increased from low to high precipitation grassland types; (2) there were significant positive linear relationships between taxonomic diversity, functional dominance, functional diversity, and community aboveground biomass; (3) the effect of functional characteristics on community aboveground biomass is greater than that of taxonomic diversity; and (4) community aboveground biomass depends on the community-weighted mean plant height, which explained 57.1% of the variation in the community aboveground biomass. Our results suggested that functional dominance rather than taxonomic diversity and functional diversity mainly determines community productivity and that the selection effect plays a dominant role in maintaining the relationship between biodiversity and community productivity in the Inner Mongolia grassland.

  13. Fungal endophytes: diversity and functional roles

    Science.gov (United States)

    Rodriguez, R.J.; White, J.F.; Arnold, A.E.; Redman, R.S.

    2009-01-01

    All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.

  14. Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity.

    Science.gov (United States)

    Wright, Tom H; Bower, Ben J; Chalker, Justin M; Bernardes, Gonçalo J L; Wiewiora, Rafal; Ng, Wai-Lung; Raj, Ritu; Faulkner, Sarah; Vallée, M Robert J; Phanumartwiwath, Anuchit; Coleman, Oliver D; Thézénas, Marie-Laëtitia; Khan, Maola; Galan, Sébastien R G; Lercher, Lukas; Schombs, Matthew W; Gerstberger, Stefanie; Palm-Espling, Maria E; Baldwin, Andrew J; Kessler, Benedikt M; Claridge, Timothy D W; Mohammed, Shabaz; Davis, Benjamin G

    2016-11-04

    Posttranslational modification of proteins expands their structural and functional capabilities beyond those directly specified by the genetic code. However, the vast diversity of chemically plausible (including unnatural but functionally relevant) side chains is not readily accessible. We describe C (sp 3 )-C (sp 3 ) bond-forming reactions on proteins under biocompatible conditions, which exploit unusual carbon free-radical chemistry, and use them to form Cβ-Cγ bonds with altered side chains. We demonstrate how these transformations enable a wide diversity of natural, unnatural, posttranslationally modified (methylated, glycosylated, phosphorylated, hydroxylated), and labeled (fluorinated, isotopically labeled) side chains to be added to a common, readily accessible dehydroalanine precursor in a range of representative protein types and scaffolds. This approach, outside of the rigid constraints of the ribosome and enzymatic processing, may be modified more generally for access to diverse proteins. Copyright © 2016, American Association for the Advancement of Science.

  15. Junctional adhesion molecule-A: functional diversity through molecular promiscuity.

    Science.gov (United States)

    Steinbacher, Tim; Kummer, Daniel; Ebnet, Klaus

    2017-12-14

    Cell adhesion molecules (CAMs) of the immunoglobulin superfamily (IgSF) regulate important processes such as cell proliferation, differentiation and morphogenesis. This activity is primarily due to their ability to initiate intracellular signaling cascades at cell-cell contact sites. Junctional adhesion molecule-A (JAM-A) is an IgSF-CAM with a short cytoplasmic tail that has no catalytic activity. Nevertheless, JAM-A is involved in a variety of biological processes. The functional diversity of JAM-A resides to a large part in a C-terminal PDZ domain binding motif which directly interacts with nine different PDZ domain-containing proteins. The molecular promiscuity of its PDZ domain motif allows JAM-A to recruit protein scaffolds to specific sites of cell-cell adhesion and to assemble signaling complexes at those sites. Here, we review the molecular characteristics of JAM-A, including its dimerization, its interaction with scaffolding proteins, and the phosphorylation of its cytoplasmic domain, and we describe how these characteristics translate into diverse biological activities.

  16. Functional diversity: a tool for answering challenging ecological questions

    Czech Academy of Sciences Publication Activity Database

    Mason, N. W. H.; de Bello, Francesco

    2013-01-01

    Roč. 24, č. 5 (2013), s. 777-780 ISSN 1100-9233 Institutional support: RVO:67985939 Keywords : Beta diversity * Ecosystem function * Phylogenetic diversity Subject RIV: EH - Ecology, Behaviour Impact factor: 3.372, year: 2013

  17. The Drosophila CLAMP protein associates with diverse proteins on chromatin.

    Science.gov (United States)

    Urban, Jennifer A; Urban, John M; Kuzu, Guray; Larschan, Erica N

    2017-01-01

    Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to equalize gene expression between XY males and XX females. We previously identified a zinc finger protein in Drosophila melanogaster that plays a sex-specific role in targeting the Male-specific lethal (MSL) dosage compensation complex to the male X-chromosome, called the Chromatin-Linked Adapter for MSL Proteins (CLAMP). More recently, we established that CLAMP has non-sex-specific roles as an essential protein that regulates chromatin accessibility at promoters genome-wide. To identify associations between CLAMP and other factors in both male and female cells, we used two complementary mass spectrometry approaches. We demonstrate that CLAMP associates with the transcriptional regulator complex Negative Elongation Factor (NELF) in both sexes and determine that CLAMP reduces NELF recruitment to several target genes. In sum, we have identified many new CLAMP-associated factors and provide a resource for further study of this little understood essential protein.

  18. Modeling the SHG activities of diverse protein crystals

    International Nuclear Information System (INIS)

    Haupert, Levi M.; DeWalt, Emma L.; Simpson, Garth J.

    2012-01-01

    The origins of the diversity in the SHG signal from protein crystals are investigated and potential protein-crystal coverage by SHG microscopy is assessed. A symmetry-additive ab initio model for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine point-group symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much of the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within the crystal lattice. Two or more orders-of-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of ∼84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices

  19. Diverse Functions of Plasma PAF-AH in Tumorigenesis.

    Science.gov (United States)

    Stafforini, Diana M

    2015-01-01

    This chapter is focused on the role of the plasma form of platelet-activating factor-acetylhydrolase (PAF-AH), heretofore referred to as PAF-AH, in tumorigenic responses. Biochemical and other properties of this enzyme were discussed in detail in chapter "Plasma PAF-AH (PLA2G7): Biochemical Properties, Association with LDLs and HDLs, and Regulation of Expression" by Stafforini and in other chapters. Although phospholipases tend not to be drivers of tumorigenesis themselves, these enzymes and the lipid mediators whose levels they regulate interact with a variety of oncogenes and tumor suppressors [1]. Like other phospholipases, the functions of PAF-AH in cancer likely are related to its ability to regulate the levels of lipid mediators that participate in cellular processes related to initial tumorigenic events (e.g., proliferation, growth, inflammation) and/or spreading of the disease (e.g., matrix metalloproteinase secretion, actin cytoskeleton reorganization, migration, and angiogenesis) [1]. The importance of substrates and products of PAF-AH on key cellular functions has been evaluated in cell-based analyses which revealed that these metabolites can have pro- and antitumorigenic functions. Studies in genetically engineered mice lacking PAF-AH expression and genetic manipulation of PAF-AH levels in cancer cells demonstrated diverse functions of the protein in models of melanoma, prostate cancer, colon cancer, and others. The following sections highlight lessons learned from studies in cell lines and in mouse models regarding the diversity of functions of PAF-AH in cancer, and the potential of PAFAH transcripts, protein, and/or activity levels to become cancer biomarkers and therapeutic targets. © 2015 Elsevier Inc. All rights reserved.

  20. Sphingolipids in the function of G protein-coupled receptors.

    Science.gov (United States)

    Jafurulla, Mohammad; Chattopadhyay, Amitabha

    2015-09-15

    G protein-coupled receptors (GPCRs) constitute the largest and most diverse protein family in mammals and are involved in information transfer across cellular membranes. GPCRs are known to regulate multiple physiological functions and therefore represent major drug targets in all clinical areas. The fact that GPCRs are integral membrane proteins raises the possibility of their interaction with functionally important membrane lipids such as sphingolipids. Sphingolipids are essential membrane components and are recognized as diverse and dynamic regulators of a multitude of cellular processes. Interaction with sphingolipids could lead to modulation of GPCR structure and function. In this review, we highlight the role of sphingolipids in the function of GPCRs with specific examples. A comprehensive understanding of molecular events involved in GPCR-lipid interaction would provide better insight into GPCR function in health and disease. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Esterase, Total Protein and Seed Storage Protein Diversity in Okra ...

    African Journals Online (AJOL)

    USER

    The protein content of okra seeds varies between 15% and 26%, and edible oil content of more than 14% has been reported (NARP, 1993). A mucilaginous preparation from the pod can be used as a plasma replacement or blood volume expander. Also, mucilage from the stem and roots is used for clarifying sugar juice in.

  2. Functional diversity in plant communities: Theory and analysis ...

    African Journals Online (AJOL)

    Plant functional diversity in community has become a key point in ecology studies recently. The development of species functional diversity was reviewed in the present work. Based on the former original research papers and reviews, we discussed the concept and connotation and put forward a new definition of functional ...

  3. A dominant conformational role for amino acid diversity in minimalist protein–protein interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Gilbreth, Ryan N. [Univ. of Chicago, Chicago, IL (United States); Esaki, Kaori [Univ. of Chicago, Chicago, IL (United States); Koide, Akiko [Univ. of Chicago, Chicago, IL (United States); Sidhu, Sachdev S. [Genentech, San Francisco, CA (United States); Koide, Shohei [Univ. of Chicago, Chicago, IL (United States)

    2008-08-01

    Recent studies have shown that highly simplified interaction surfaces consisting of combinations of just two amino acids, Tyr and Ser, exhibit high affinity and specificity. The high functional levels of such minimalist interfaces might thus indicate small contributions of greater amino acid diversity seen in natural interfaces. Toward addressing this issue, we have produced a pair of binding proteins built on the fibronectin type III scaffold, termed “monobodies.” One monobody contains the Tyr/Ser binary-code interface (termed YS) and the other contains an expanded amino acid diversity interface (YSX), but both bind to an identical target, maltose-binding protein. The YSX monobody bound with higher affinity, a slower off rate and a more favorable enthalpic contribution than the YS monobody. High-resolution X-ray crystal structures revealed that both proteins bound to an essentially identical epitope, providing a unique opportunity to directly investigate the role of amino acid diversity in a protein interaction interface. Surprisingly, Tyr still dominates the YSX paratope and the additional amino acid types are primarily used to conformationally optimize contacts made by tyrosines. Scanning mutagenesis showed that while all contacting Tyr side chains are essential in the YS monobody, the YSX interface was more tolerant to mutations. These results suggest that the conformational, not chemical, diversity of additional types of amino acids provided higher functionality and evolutionary robustness, supporting the dominant role of Tyr and the importance of conformational diversity in forming protein interaction interfaces.

  4. Disturbance effects on species diversity and functional diversity in riparian and upland plant communities.

    Science.gov (United States)

    Biswas, Shekhar R; Mallik, Azim U

    2010-01-01

    Understanding disturbance effects on species diversity and functional diversity is fundamental to conservation planning but remains elusive. We quantified species richness, diversity, and evenness and functional richness, diversity, and evenness of riparian and upland plants along 24 small streams subjected to a range of anthropogenic disturbances in the boreal forest of northwestern Ontario, Canada. We included a total of 36 functional traits related to productivity, competitive ability, reproduction, disturbance tolerance, life history, and tolerance to habitat instability. Using nested ANOVA, we examined the response of diversity indices to disturbance and whether it followed the intermediate disturbance hypothesis (IDH) and varied with habitat stability. We found that, like species richness and diversity, functional richness and diversity reached peaks at moderate disturbance intensity; functional diversity followed the predictions of the IDH. Second, disturbance-habitat-stability coupling has very little effect on overall species and functional diversity, but the effect on particular life forms and functions may be significant. Since species richness and diversity patterns are context and system dependent, our findings should be most applicable to similar temperate riparian systems.

  5. Functional diversity of terrestrial microbial decomposers and their substrates.

    Science.gov (United States)

    Hättenschwiler, Stephan; Fromin, Nathalie; Barantal, Sandra

    2011-05-01

    The relationship between biodiversity and biogeochemical processes gained much interest in light of the rapidly decreasing biodiversity worldwide. In this article, we discuss the current status, challenges and prospects of functional concepts to plant litter diversity and microbial decomposer diversity. We also evaluate whether these concepts permit a better understanding of how biodiversity is linked to litter decomposition as a key ecosystem process influencing carbon and nutrient cycles. Based on a literature survey, we show that plant litter and microbial diversity matters for decomposition, but that considering numbers of taxonomic units appears overall as little relevant and less useful than functional diversity. However, despite easily available functional litter traits and the well-established theoretical framework for functional litter diversity, the impact of functional litter diversity on decomposition is not yet well enough explored. Defining functional diversity of microorganisms remains one of the biggest challenges for functional approaches to microbial diversity. Recent developments in microarray and metagenomics technology offer promising possibilities in the assessment of the functional structure of microbial communities. This might allow significant progress in measuring functional microbial diversity and ultimately in our ability to predict consequences of biodiversity loss in the decomposer system for biogeochemical processes. Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  6. A note on reliability estimation of functionally diverse systems

    International Nuclear Information System (INIS)

    Littlewood, B.; Popov, P.; Strigini, L.

    1999-01-01

    It has been argued that functional diversity might be a plausible means of claiming independence of failures between two versions of a system. We present a model of functional diversity, in the spirit of earlier models of diversity such as those of Eckhardt and Lee, and Hughes. In terms of the model, we show that the claims for independence between functionally diverse systems seem rather unrealistic. Instead, it seems likely that functionally diverse systems will exhibit positively correlated failures, and thus will be less reliable than an assumption of independence would suggest. The result does not, of course, suggest that functional diversity is not worthwhile; instead, it places upon the evaluator of such a system the onus to estimate the degree of dependence so as to evaluate the reliability of the system

  7. Site‐Selective Disulfide Modification of Proteins: Expanding Diversity beyond the Proteome

    OpenAIRE

    Kuan, Seah Ling; Wang, Tao; Weil, Tanja

    2016-01-01

    Abstract The synthetic transformation of polypeptides with molecular accuracy holds great promise for providing functional and structural diversity beyond the proteome. Consequently, the last decade has seen an exponential growth of site‐directed chemistry to install additional features into peptides and proteins even inside living cells. The disulfide rebridging strategy has emerged as a powerful tool for site‐selective modifications since most proteins contain disulfide bonds. In this Revie...

  8. Regulation, Signaling, and Physiological Functions of G-Proteins.

    Science.gov (United States)

    Syrovatkina, Viktoriya; Alegre, Kamela O; Dey, Raja; Huang, Xin-Yun

    2016-09-25

    Heterotrimeric guanine-nucleotide-binding regulatory proteins (G-proteins) mainly relay the information from G-protein-coupled receptors (GPCRs) on the plasma membrane to the inside of cells to regulate various biochemical functions. Depending on the targeted cell types, tissues, and organs, these signals modulate diverse physiological functions. The basic schemes of heterotrimeric G-proteins have been outlined. In this review, we briefly summarize what is known about the regulation, signaling, and physiological functions of G-proteins. We then focus on a few less explored areas such as the regulation of G-proteins by non-GPCRs and the physiological functions of G-proteins that cannot be easily explained by the known G-protein signaling pathways. There are new signaling pathways and physiological functions for G-proteins to be discovered and further interrogated. With the advancements in structural and computational biological techniques, we are closer to having a better understanding of how G-proteins are regulated and of the specificity of G-protein interactions with their regulators. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Land use change has stronger effects on functional diversity than taxonomic diversity in tropical Andean hummingbirds.

    Science.gov (United States)

    Tinoco, Boris A; Santillán, Vinicio E; Graham, Catherine H

    2018-03-01

    Land use change modifies the environment at multiple spatial scales, and is a main driver of species declines and deterioration of ecosystem services. However, most of the research on the effects of land use change has focused on taxonomic diversity, while functional diversity, an important predictor of ecosystem services, is often neglected. We explored how local and landscape scale characteristics influence functional and taxonomic diversity of hummingbirds in the Andes Mountains in southern Ecuador. Data was collected in six landscapes along a land use gradient, from an almost intact landscape to one dominated by cattle pastures. We used point counts to sample hummingbirds from 2011 to 2012 to assessed how local factors (i.e., vegetation structure, flowering plants richness, nectar availability) and landscape factors (i.e., landscape heterogeneity, native vegetation cover) influenced taxonomic and functional diversity. Then, we analyzed environment - trait relationships (RLQ test) to explore how different hummingbird functional traits influenced species responses to these factors. Taxonomic and functional diversity of hummingbirds were positively associated with landscape heterogeneity but only functional diversity was positively related to native vegetation coverage. We found a weak response of taxonomic and functional diversity to land use change at the local scale. Environment-trait associations showed that body mass of hummingbirds likely influenced species sensitivity to land use change. In conclusion, landscape heterogeneity created by land use change can positively influence hummingbird taxonomic and functional diversity; however, a reduction of native vegetation cover could decrease functional diversity. Given that functional diversity can mediate ecosystem services, the conservation of native vegetation cover could play a key role in the maintenance of hummingbird pollination services in the tropical Andes. Moreover, there are particular functional

  10. Low Functional β-Diversity Despite High Taxonomic β-Diversity among Tropical Estuarine Fish Communities

    Science.gov (United States)

    Villéger, Sébastien; Miranda, Julia Ramos; Hernandez, Domingo Flores; Mouillot, David

    2012-01-01

    The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

  11. Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View

    Science.gov (United States)

    Koehorst, Jasper J.; Martins dos Santos, Vitor A. P.; Schaap, Peter J.

    2015-01-01

    Understanding the diversity and robustness of the metabolism of bacteria is fundamental for understanding how bacteria evolve and adapt to different environments. In this study, we characterised 121 Streptococcus strains and studied metabolic diversity from a protein domain perspective. Metabolic pathways were described in terms of the promiscuity of domains participating in metabolic pathways that were inferred to be functional. Promiscuity was defined by adapting existing measures based on domain abundance and versatility. The approach proved to be successful in capturing bacterial metabolic flexibility and species diversity, indicating that it can be described in terms of reuse and sharing functional domains in different proteins involved in metabolic activity. Additionally, we showed striking differences among metabolic organisation of the pathogenic serotype 2 Streptococcus suis and other strains. PMID:26366735

  12. The structure and function of G-protein-coupled receptors

    DEFF Research Database (Denmark)

    Rosenbaum, Daniel M; Rasmussen, Søren Gøgsig Faarup; Kobilka, Brian K

    2009-01-01

    -protein structure and biology. Great progress has been made over the past three decades in understanding diverse GPCRs, from pharmacology to functional characterization in vivo. Recent high-resolution structural studies have provided insights into the molecular mechanisms of GPCR activation and constitutive...

  13. Genetic diversity of coastal bottlenose dolphins revealed by structurally and functionally diverse hemoglobins.

    Science.gov (United States)

    Remington, Nicole; Stevens, Robert D; Wells, Randall S; Holn, Aleta; Dhungana, Suraj; Taboy, Celine H; Crumbliss, Alvin L; Henkens, Robert; Bonaventura, Celia

    2007-08-15

    Studies of structure-function relationships in the respiratory proteins of marine mammals revealed unexpected variations in the number and types of hemoglobins (Hbs) present in coastal bottlenose dolphins, Tursiops truncatus. We obtained blood samples from free-ranging coastal bottlenose dolphins as a component of capture-release studies. We found that the oxygen-binding functions of bottlenose dolphin blood are poised between effector-saturated and unsaturated levels, enabling exercise-dependent shifts in oxygen transfer functions. Isolated bottlenose dolphin Hbs showed elevated pH sensitivities (Bohr effects) and appreciably lower oxygen affinities than adult human Hb in the absence of allosteric effectors. These properties may be an adaptive modification that enhances oxygen delivery during diving episodes when oxygen tensions and effector levels are low. The Hbs of individual dolphins showed similar oxygen affinities, responses to effectors, and expression of heme-heme interaction in oxygen binding, but differed in their redox potentials and rates of autoxidation. The heterogeneity suggested by these functional variations in Hbs of individual dolphins was born out by variations in the molecular weights and numbers of their alpha and beta globin chains. Although coastal bottlenose dolphins were expected to have a single type of Hb, the mass differences observed revealed considerable genetic diversity. There were multiple Hb forms in some individuals and differences in Hb patterns among individuals within the same community.

  14. Interaction and localization diversities of global and local hubs in human protein-protein interaction networks.

    Science.gov (United States)

    Kiran, M; Nagarajaram, H A

    2016-08-16

    Hubs, the highly connected nodes in protein-protein interaction networks (PPINs), are associated with several characteristic properties and are known to perform vital roles in cells. We defined two classes of hubs, global (housekeeping) and local (tissue-specific) hubs. These two categories of hubs are distinct from each other with respect to their abundance, structure and function. However, how distinct are the spatial expression pattern and other characteristics of their interacting partners is still not known. Our investigations revealed that the partners of the local hubs compared with those of global hubs are conserved across the tissues in which they are expressed. Partners of local hubs show diverse subcellular localizations as compared with the partners of global hubs. We examined the nature of interacting domains in both categories of hubs and found that they are promiscuous in global hubs but not so in local hubs. Deletion of some of the local and global hubs has an impact on the characteristic path length of the network indicating that those hubs are inter-modular in nature. Our present study has, therefore, shed further light on the characteristic features of the local and global hubs in human PPIN. This knowledge of different topological aspects of hubs with regard to their types and subtypes is essential as it helps in better understanding of roles of hub proteins in various cellular processes under various conditions including those caused by host-pathogen interactions and therefore useful in prioritizing targets for drug design and repositioning.

  15. The S100 proteins in epidermis: Topology and function.

    Science.gov (United States)

    Leśniak, Wiesława; Graczyk-Jarzynka, Agnieszka

    2015-12-01

    S100 proteins are small calcium binding proteins encoded by genes located in the epidermal differentiation complex (EDC). Differently to other proteins encoded by EDC genes, which are indispensable for normal epidermal differentiation, the role of S100 proteins in the epidermis remains largely unknown. Particular S100 proteins differ in their distribution in epidermal layers, skin appendages, melanocytes and Langerhans cells. Taking into account that each epidermal component consists of specialized cells with well-defined functions, such differential distribution may be indicative of the function of a given S100 protein. We used this criterion together with the survey of the current experimental data pertinent to epidermis to provide a fairly comprehensive view on the possible function of individual S100 proteins in this tissue. S100 proteins are differently expressed and, despite extensive structural homology, perform diverse functions in the epidermis. Certain S100 proteins probably ensure constant epidermal renewal and support wound healing while others act in epidermal differentiation or have a protective role. As their expression is differently affected in various skin pathologies, particular S100 proteins could be valuable diagnostic markers. S100 proteins seem to be important although not yet fully recognized epidermal constituents. Better understanding of their role in the epidermis might be helpful in designing therapies to various skin diseases. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Emergence of Complexity in Protein Functions and Metabolic Networks

    Science.gov (United States)

    Pohorille, Andzej

    2009-01-01

    In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis of very large libraries of random amino acid sequences and subsequently subjecting them to in vitro evolution. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions, important clues have been uncovered. Considerable progress has been also achieved in understanding the origins of membrane proteins. We will address this issue in the example of ion channels - proteins that mediate transport of ions across cell walls. Remarkably, despite overall complexity of these proteins in contemporary cells, their structural motifs are quite simple, with -helices being most common. By combining results of experimental and computer simulation studies on synthetic models and simple, natural channels, I will show that, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during

  17. Contrasting responses of functional diversity to major losses in taxonomic diversity.

    Science.gov (United States)

    Edie, Stewart M; Jablonski, David; Valentine, James W

    2018-01-23

    Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.

  18. Integration of latex protein sequence data provides comprehensive functional overview of latex proteins.

    Science.gov (United States)

    Cho, Won Kyong; Jo, Yeonhwa; Chu, Hyosub; Park, Sang-Ho; Kim, Kook-Hyung

    2014-03-01

    The laticiferous system is one of the most important conduit systems in higher plants, which produces a milky-like sap known as latex. Latex contains diverse secondary metabolites with various ecological functions. To obtain a comprehensive overview of the latex proteome, we integrated available latex proteins sequences and constructed a comprehensive dataset composed of 1,208 non-redundant latex proteins from 20 various latex-bearing plants. The results of functional analyses revealed that latex proteins are involved in various biological processes, including transcription, translation, protein degradation and the plant response to environmental stimuli. The results of the comparative analysis showed that the functions of the latex proteins are similar to those of phloem, suggesting the functional conservation of plant vascular proteins. The presence of latex proteins in mitochondria and plastids suggests the production of diverse secondary metabolites. Furthermore, using a BLAST search, we identified 854 homologous latex proteins in eight plant species, including three latex-bearing plants, such as papaya, caster bean and cassava, suggesting that latex proteins were newly evolved in vascular plants. Taken together, this study is the largest and most comprehensive in silico analysis of the latex proteome. The results obtained here provide useful resources and information for characterizing the evolution of the latex proteome.

  19. Functional diversity: back to basics and looking forward.

    Science.gov (United States)

    Petchey, Owen L; Gaston, Kevin J

    2006-06-01

    Functional diversity is a component of biodiversity that generally concerns the range of things that organisms do in communities and ecosystems. Here, we review how functional diversity can explain and predict the impact of organisms on ecosystems and thereby provide a mechanistic link between the two. Critical points in developing predictive measures of functional diversity are the choice of functional traits with which organisms are distinguished, how the diversity of that trait information is summarized into a measure of functional diversity, and that the measures of functional diversity are validated through quantitative analyses and experimental tests. There is a vast amount of trait information available for plant species and a substantial amount for animals. Choosing which traits to include in a particular measure of functional diversity will depend on the specific aims of a particular study. Quantitative methods for choosing traits and for assigning weighting to traits are being developed, but need much more work before we can be confident about trait choice. The number of ways of measuring functional diversity is growing rapidly. We divide them into four main groups. The first, the number of functional groups or types, has significant problems and researchers are more frequently using measures that do not require species to be grouped. Of these, some measure diversity by summarizing distances between species in trait space, some by estimating the size of the dendrogram required to describe the difference, and some include information about species' abundances. We show some new and important differences between these, as well as what they indicate about the responses of assemblages to loss of individuals. There is good experimental and analytical evidence that functional diversity can provide a link between organisms and ecosystems but greater validation of measures is required. We suggest that non-significant results have a range of alternate explanations

  20. Hydrophobicity diversity in globular and nonglobular proteins measured with the Gini index.

    Science.gov (United States)

    Carugo, Oliviero

    2017-12-01

    Amino acids and their properties are variably distributed in proteins and different compositions determine all protein features, ranging from solubility to stability and functionality. Gini index, a tool to estimate distribution uniformity, is widely used in macroeconomics and has numerous statistical applications. Here, Gini index is used to analyze the distribution of hydrophobicity in proteins and to compare hydrophobicity distribution in globular and intrinsically disordered proteins. Based on the analysis of carefully selected high-quality data sets of proteins extracted from the Protein Data Bank (http://www.rcsb.org) and from the DisProt database (http://www.disprot.org/), it is observed that hydrophobicity is distributed in a more diverse way in intrinsically disordered proteins than in folded and soluble globular proteins. This correlates with the observation that the amino acid composition deviates from the uniformity (estimate with the Shannon and the Gini-Simpson indices) more in intrinsically disordered proteins than in globular and soluble proteins. Although statistical tools tike the Gini index have received little attention in molecular biology, these results show that they allow one to estimate sequence diversity and that they are useful to delineate trends that can hardly be described, otherwise, in simple and concise ways. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. Classification of sequence signatures: a guide to Hox protein function.

    Science.gov (United States)

    Merabet, Samir; Hudry, Bruno; Saadaoui, Mehdi; Graba, Yacine

    2009-05-01

    Hox proteins are part of the conserved superfamily of homeodomain-containing transcription factors and play fundamental roles in shaping animal body plans in development and evolution. However, molecular mechanisms underlying their diverse and specific biological functions remain largely enigmatic. Here, we have analyzed Hox sequences from the main evolutionary branches of the Bilateria group. We have found that four classes of Hox protein signatures exist, which together provide sufficient support to explain how different Hox proteins differ in their control and function. The homeodomain and its surrounding sequences accumulate nearly all signatures, constituting an extended module where most of the information distinguishing Hox proteins is concentrated. Only a small fraction of these signatures has been investigated at the functional level, but these show that approaches relying on Hox protein alterations still have a large potential for deciphering molecular mechanisms of Hox differential control.

  2. Phylogenetic and functional diversity in large carnivore assemblages.

    Science.gov (United States)

    Dalerum, F

    2013-06-07

    Large terrestrial carnivores are important ecological components and prominent flagship species, but are often extinction prone owing to a combination of biological traits and high levels of human persecution. This study combines phylogenetic and functional diversity evaluations of global and continental large carnivore assemblages to provide a framework for conservation prioritization both between and within assemblages. Species-rich assemblages of large carnivores simultaneously had high phylogenetic and functional diversity, but species contributions to phylogenetic and functional diversity components were not positively correlated. The results further provide ecological justification for the largest carnivore species as a focus for conservation action, and suggests that range contraction is a likely cause of diminishing carnivore ecosystem function. This study highlights that preserving species-rich carnivore assemblages will capture both high phylogenetic and functional diversity, but that prioritizing species within assemblages will involve trade-offs between optimizing contemporary ecosystem function versus the evolutionary potential for future ecosystem performance.

  3. Functional diversity increases ecological stability in a grazed grassland.

    Science.gov (United States)

    Hallett, Lauren M; Stein, Claudia; Suding, Katharine N

    2017-03-01

    Understanding the factors governing ecological stability in variable environments is a central focus of ecology. Functional diversity can stabilize ecosystem function over time if one group of species compensates for an environmentally driven decline in another. Although intuitively appealing, evidence for this pattern is mixed. We hypothesized that diverse functional responses to rainfall will increase the stability of vegetation cover and biomass across rainfall conditions, but that this effect depends on land-use legacies that maintain functional diversity. We experimentally manipulated grazing in a California grassland to create land-use legacies of low and moderate grazing, across which we implemented rainout shelters and irrigation to create dry and wet conditions over 3 years. We found that the stability of the vegetation cover was greatly elevated and the stability of the biomass was slightly elevated across rainfall conditions in areas with histories of moderate grazing. Initial functional diversity-both in the seed bank and aboveground-was also greater in areas that had been moderately grazed. Rainfall conditions in conjunction with this grazing legacy led to different functional diversity patterns over time. Wet conditions led to rapid declines in functional diversity and a convergence on resource-acquisitive traits. In contrast, consecutively dry conditions maintained but did not increase functional diversity over time. As a result, grazing practices and environmental conditions that decrease functional diversity may be associated with lasting effects on the response of ecosystem functions to drought. Our results demonstrate that theorized relationships between diversity and stability are applicable and important in the context of working grazed landscapes.

  4. Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

    Science.gov (United States)

    Merabet, Samir; Litim-Mecheri, Isma; Karlsson, Daniel; Dixit, Richa; Saadaoui, Mehdi; Monier, Bruno; Brun, Christine; Thor, Stefan; Vijayraghavan, K; Perrin, Laurent; Pradel, Jacques; Graba, Yacine

    2011-10-01

    Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.

  5. Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

    Directory of Open Access Journals (Sweden)

    Samir Merabet

    2011-10-01

    Full Text Available Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA, we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.

  6. Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes

    OpenAIRE

    Garc?a-Morales, Rodrigo; Moreno, Claudia E.; Badano, Ernesto I.; Zuria, Iriana; Galindo-Gonz?lez, Jorge; Rojas-Mart?nez, Alberto E.; ?vila-G?mez, Eva S.

    2016-01-01

    Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the...

  7. Metals affect soil bacterial and fungal functional diversity differently.

    Science.gov (United States)

    Stefanowicz, Anna M; Niklińska, Maria; Laskowski, Ryszard

    2008-03-01

    Heavy metals can cause a decrease in the taxonomic diversity of soil communities. Because of functional redundancy, it remains unclear to what extent different functions performed by the soil microbial communities may be affected by pollution. We studied the impact of metal contamination on soil bacterial and fungal functional diversity, active microbial biomass, and soil respiration rate. Soil samples were collected from 39 sites along three forest and five meadow pollution transects near an abandoned Pb/Zn smelter in Avonmouth (UK) and Ni smelter in Clydach (UK), in a Cu mining and smelting region near Glogów (Poland), and in a Zn/Pb mining and smelting region near Olkusz (Poland). Biolog GN2 and SFN2 plates were used to study the bacterial and fungal functional diversity, which subsequently was expressed as Shannon's diversity index (H'). The active microbial biomass was measured as substrate-induced respiration. We found that the bacterial functional diversity significantly decreased, whereas the fungal functional diversity slightly increased, with increasing metal concentration. We also observed a slight negative effect of metal pollution on the active microbial biomass. No relationship was found between metal contamination and total soil respiration rate. This suggests a higher sensitivity of bacterial functional diversity as an indicator for the effects of metal pollution compared with overall soil respiration. All microbial parameters were affected by nutrient concentrations and/or soil pH.

  8. Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins.

    Science.gov (United States)

    Khan, Ishita; Chitale, Meghana; Rayon, Catherine; Kihara, Daisuke

    2012-11-13

    Advancements in function prediction algorithms are enabling large scale computational annotation for newly sequenced genomes. With the increase in the number of functionally well characterized proteins it has been observed that there are many proteins involved in more than one function. These proteins characterized as moonlighting proteins show varied functional behavior depending on the cell type, localization in the cell, oligomerization, multiple binding sites, etc. The functional diversity shown by moonlighting proteins may have significant impact on the traditional sequence based function prediction methods. Here we investigate how well diverse functions of moonlighting proteins can be predicted by some existing function prediction methods. We have analyzed the performances of three major sequence based function prediction methods,PSI-BLAST, the Protein Function Prediction (PFP), and the Extended Similarity Group (ESG) on predicting diverse functions of moonlighting proteins. In predicting discrete functions of a set of 19 experimentally identified moonlighting proteins, PFP showed overall highest recall among the three methods. Although ESG showed the highest precision, its recall was lower than PSI-BLAST. Recall by PSI-BLAST greatly improved when BLOSUM45 was used instead of BLOSUM62. We have analyzed the performances of PFP, ESG, and PSI-BLAST in predicting the functional diversity of moonlighting proteins. PFP shows overall better performance in predicting diverse moonlighting functions as compared with PSI-BLAST and ESG. Recall by PSI-BLAST greatly improved when BLOSUM45 was used. This analysis indicates that considering weakly similar sequences in prediction enhances the performance of sequence based AFP methods in predicting functional diversity of moonlighting proteins. The current study will also motivate development of novel computational frameworks for automatic identification of such proteins.

  9. Functional Foods Containing Whey Proteins

    Science.gov (United States)

    Whey proteins, modified whey proteins, and whey components are useful as nutrients or supplements for health maintenance. Extrusion modified whey proteins can easily fit into new products such as beverages, confectionery items (e.g., candies), convenience foods, desserts, baked goods, sauces, and in...

  10. Plant diversity and functional trait composition during mire development

    Directory of Open Access Journals (Sweden)

    A.M. Laine

    2018-02-01

    Full Text Available During succession, plant species composition undergoes changes that may have implications for ecosystem functions. Here we aimed to study changes in plant species diversity, functional diversity and functional traits associated with mire development. We sampled vegetation from 22 mires on the eastern shore of the Gulf of Bothnia (west coast of Finland that together represent seven different time steps along a mire chronosequence resulting from post-glacial rebound. This chronosequence spans a time period of almost 2500 years. Information about 15 traits of vascular plants and 17 traits of mosses was collected, mainly from two different databases. In addition to species richness and Shannon diversity index, we measured functional diversity and community weighted means of functional traits. We found that plant species diversity increased from the early succession stages towards the fen–bog transition. The latter stage also has the most diverse surface structure, consisting of pools and hummocks. Functional diversity increased linearly with species richness, suggesting a lack of functional redundancy during mire succession. On the other hand, Rao’s quadratic entropy, another index of functional diversity, remained rather constant throughout the succession. The changes in functional traits indicate a trade-off between acquisitive and conservative strategies. The functional redundancy, i.e. the lack of overlap between similarly functioning species, may indicate that the resistance to environmental disturbances such as drainage or climate change does not change during mire succession. However, the trait trade-off towards conservative strategy, together with the developing microtopography of hummocks and hollows with strongly differing vegetation composition, could increase resistance during mire succession.

  11. Antifreeze Proteins from Diverse Organisms and their Applications: An Overview.

    Science.gov (United States)

    Cheung, Randy Chi Fai; Ng, Tzi Bun; Wong, Jack Ho

    2017-01-01

    Antifreeze proteins are ice-binding or ice-structuring proteins that prevent water from freezing by adsorbing to the ice surface and stopping the growth of minute ice crystals to large crystals in a non-colligative manner. The antifreeze proteins are found in species like fish, arthropods, plants, algae, fungi, yeasts and bacteria. The diversity, distribution and classification of antifreeze proteins were highlighted in this review. Antifreeze proteins help the organisms adapt to and survive in subzero temperature environments. The distribution of antifreeze proteins in different species appears to be the outcome of a combination of independent evolutionary events, probably the convergent evolution or horizontal gene transfer. Benefits can be derived from the frost resistance of these organisms. Their potential applications have been recognized in food processing, cryopreservation, cryosurgery, fishery and agricultural industries and anti-icing materials development. This review includes information on the current understanding of antifreeze proteins. A discussion on interactions and mechanisms involving ice recognition and adsorption was also included. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  12. Phytochemicals perturb membranes and promiscuously alter protein function.

    Science.gov (United States)

    Ingólfsson, Helgi I; Thakur, Pratima; Herold, Karl F; Hobart, E Ashley; Ramsey, Nicole B; Periole, Xavier; de Jong, Djurre H; Zwama, Martijn; Yilmaz, Duygu; Hall, Katherine; Maretzky, Thorsten; Hemmings, Hugh C; Blobel, Carl; Marrink, Siewert J; Koçer, Armağan; Sack, Jon T; Andersen, Olaf S

    2014-08-15

    A wide variety of phytochemicals are consumed for their perceived health benefits. Many of these phytochemicals have been found to alter numerous cell functions, but the mechanisms underlying their biological activity tend to be poorly understood. Phenolic phytochemicals are particularly promiscuous modifiers of membrane protein function, suggesting that some of their actions may be due to a common, membrane bilayer-mediated mechanism. To test whether bilayer perturbation may underlie this diversity of actions, we examined five bioactive phenols reported to have medicinal value: capsaicin from chili peppers, curcumin from turmeric, EGCG from green tea, genistein from soybeans, and resveratrol from grapes. We find that each of these widely consumed phytochemicals alters lipid bilayer properties and the function of diverse membrane proteins. Molecular dynamics simulations show that these phytochemicals modify bilayer properties by localizing to the bilayer/solution interface. Bilayer-modifying propensity was verified using a gramicidin-based assay, and indiscriminate modulation of membrane protein function was demonstrated using four proteins: membrane-anchored metalloproteases, mechanosensitive ion channels, and voltage-dependent potassium and sodium channels. Each protein exhibited similar responses to multiple phytochemicals, consistent with a common, bilayer-mediated mechanism. Our results suggest that many effects of amphiphilic phytochemicals are due to cell membrane perturbations, rather than specific protein binding.

  13. Firm size diversity, functional richness, and resilience

    Science.gov (United States)

    Garmestani, A.S.; Allen, Craig R.; Mittelstaedt, J.D.; Stow, C.A.; Ward, W.A.

    2006-01-01

    This paper applies recent advances in ecology to our understanding of firm development, sustainability, and economic development. The ecological literature indicates that the greater the functional richness of species in a system, the greater its resilience - that is, its ability to persist in the face of substantial changes in the environment. This paper focuses on the effects of functional richness across firm size on the ability of industries to survive in the face of economic change. Our results indicate that industries with a richness of industrial functions are more resilient to employment volatility. ?? 2006 Cambridge University Press.

  14. Topology-function conservation in protein-protein interaction networks.

    Science.gov (United States)

    Davis, Darren; Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Stojmirovic, Aleksandar; Pržulj, Nataša

    2015-05-15

    Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. © The Author 2015. Published by Oxford University Press.

  15. High functional diversity stimulates diversification in experimental microbial communities

    NARCIS (Netherlands)

    Jousset, Alexandre; Eisenhauer, Nico; Merker, Monika; Mouquet, Nicolas; Scheu, Stefan

    There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can

  16. Ecosystem functions across trophic levels are linked to functional and phylogenetic diversity.

    Directory of Open Access Journals (Sweden)

    Patrick L Thompson

    Full Text Available In experimental systems, it has been shown that biodiversity indices based on traits or phylogeny can outperform species richness as predictors of plant ecosystem function. However, it is unclear whether this pattern extends to the function of food webs in natural ecosystems. Here we tested whether zooplankton functional and phylogenetic diversity explains the functioning of 23 natural pond communities. We used two measures of ecosystem function: (1 zooplankton community biomass and (2 phytoplankton abundance (Chl a. We tested for diversity-ecosystem function relationships within and across trophic levels. We found a strong correlation between zooplankton diversity and ecosystem function, whereas local environmental conditions were less important. Further, the positive diversity-ecosystem function relationships were more pronounced for measures of functional and phylogenetic diversity than for species richness. Zooplankton and phytoplankton biomass were best predicted by different indices, suggesting that the two functions are dependent upon different aspects of diversity. Zooplankton community biomass was best predicted by zooplankton trait-based functional richness, while phytoplankton abundance was best predicted by zooplankton phylogenetic diversity. Our results suggest that the positive relationship between diversity and ecosystem function can extend across trophic levels in natural environments, and that greater insight into variation in ecosystem function can be gained by combining functional and phylogenetic diversity measures.

  17. Ecosystem functions across trophic levels are linked to functional and phylogenetic diversity.

    Science.gov (United States)

    Thompson, Patrick L; Davies, T Jonathan; Gonzalez, Andrew

    2015-01-01

    In experimental systems, it has been shown that biodiversity indices based on traits or phylogeny can outperform species richness as predictors of plant ecosystem function. However, it is unclear whether this pattern extends to the function of food webs in natural ecosystems. Here we tested whether zooplankton functional and phylogenetic diversity explains the functioning of 23 natural pond communities. We used two measures of ecosystem function: (1) zooplankton community biomass and (2) phytoplankton abundance (Chl a). We tested for diversity-ecosystem function relationships within and across trophic levels. We found a strong correlation between zooplankton diversity and ecosystem function, whereas local environmental conditions were less important. Further, the positive diversity-ecosystem function relationships were more pronounced for measures of functional and phylogenetic diversity than for species richness. Zooplankton and phytoplankton biomass were best predicted by different indices, suggesting that the two functions are dependent upon different aspects of diversity. Zooplankton community biomass was best predicted by zooplankton trait-based functional richness, while phytoplankton abundance was best predicted by zooplankton phylogenetic diversity. Our results suggest that the positive relationship between diversity and ecosystem function can extend across trophic levels in natural environments, and that greater insight into variation in ecosystem function can be gained by combining functional and phylogenetic diversity measures.

  18. Soil Protists Diversity, Distribution and Ecological Functioning

    OpenAIRE

    Geisen, Stefan

    2014-01-01

    Soil protists occupy key nodes in soil food webs due to their high abundance, fast turnover and functional importance as bacterial grazers. However, methodological drawbacks obscure the knowledge of soil protists, so that many taxa remain unknown. The structure of natural protist communities and taxa-specific ecological functions are also largely unknown. This thesis aims to increase the knowledge on soil protists using a variety of approaches. In the first part, naked amoebae being pres...

  19. Hybrid diversity method utilizing adaptive diversity function for recovering unknown aberrations in an optical system

    Science.gov (United States)

    Dean, Bruce H. (Inventor)

    2009-01-01

    A method of recovering unknown aberrations in an optical system includes collecting intensity data produced by the optical system, generating an initial estimate of a phase of the optical system, iteratively performing a phase retrieval on the intensity data to generate a phase estimate using an initial diversity function corresponding to the intensity data, generating a phase map from the phase retrieval phase estimate, decomposing the phase map to generate a decomposition vector, generating an updated diversity function by combining the initial diversity function with the decomposition vector, generating an updated estimate of the phase of the optical system by removing the initial diversity function from the phase map. The method may further include repeating the process beginning with iteratively performing a phase retrieval on the intensity data using the updated estimate of the phase of the optical system in place of the initial estimate of the phase of the optical system, and using the updated diversity function in place of the initial diversity function, until a predetermined convergence is achieved.

  20. Traits Without Borders:Integrating Functional Diversity Across Scales

    Czech Academy of Sciences Publication Activity Database

    Carmona, C. P.; de Bello, Francesco; Mason, N. W. H.; Lepš, Jan

    2016-01-01

    Roč. 31, č. 5 (2016), s. 382-394 ISSN 0169-5347 R&D Projects: GA ČR GAP505/12/1296; GA ČR GB14-36079G Institutional support: RVO:67985939 ; RVO:60077344 Keywords : functional trait * functional diversity * functional niche Subject RIV: EH - Ecology, Behaviour Impact factor: 15.268, year: 2016

  1. Structural and functional diversity in rangelands: integrating different ...

    African Journals Online (AJOL)

    Many rangelands exist as dynamic systems where structural and functional diversity of the community is a function of several interacting factors. Understanding the effects of these factors in rangelands requires an understanding of component functioning at different scales. Integrating the range of levels from ecophysiology ...

  2. Functionally diverse reef-fish communities ameliorate coral disease

    OpenAIRE

    Raymundo, Laurie J.; Halford, Andrew R.; Maypa, Aileen P.; Kerr, Alexander M.

    2009-01-01

    Coral reefs, the most diverse of marine ecosystems, currently experience unprecedented levels of degradation. Diseases are now recognized as a major cause of mortality in reef-forming corals and are complicit in phase shifts of reef ecosystems to algal-dominated states worldwide. Even so, factors contributing to disease occurrence, spread, and impact remain poorly understood. Ecosystem resilience has been linked to the conservation of functional diversity, whereas overfishing reduces function...

  3. CATH FunFHMMer web server: protein functional annotations using functional family assignments.

    Science.gov (United States)

    Das, Sayoni; Sillitoe, Ian; Lee, David; Lees, Jonathan G; Dawson, Natalie L; Ward, John; Orengo, Christine A

    2015-07-01

    The widening function annotation gap in protein databases and the increasing number and diversity of the proteins being sequenced presents new challenges to protein function prediction methods. Multidomain proteins complicate the protein sequence-structure-function relationship further as new combinations of domains can expand the functional repertoire, creating new proteins and functions. Here, we present the FunFHMMer web server, which provides Gene Ontology (GO) annotations for query protein sequences based on the functional classification of the domain-based CATH-Gene3D resource. Our server also provides valuable information for the prediction of functional sites. The predictive power of FunFHMMer has been validated on a set of 95 proteins where FunFHMMer performs better than BLAST, Pfam and CDD. Recent validation by an independent international competition ranks FunFHMMer as one of the top function prediction methods in predicting GO annotations for both the Biological Process and Molecular Function Ontology. The FunFHMMer web server is available at http://www.cathdb.info/search/by_funfhmmer. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Contrasting biodiversity-ecosystem functioning relationships in phylogenetic and functional diversity.

    Science.gov (United States)

    Steudel, Bastian; Hallmann, Christine; Lorenz, Maike; Abrahamczyk, Stefan; Prinz, Kathleen; Herrfurth, Cornelia; Feussner, Ivo; Martini, Johannes W R; Kessler, Michael

    2016-10-01

    It is well known that ecosystem functioning is positively influenced by biodiversity. Most biodiversity-ecosystem functioning experiments have measured biodiversity based on species richness or phylogenetic relationships. However, theoretical and empirical evidence suggests that ecosystem functioning should be more closely related to functional diversity than to species richness. We applied different metrics of biodiversity in an artificial biodiversity-ecosystem functioning experiment using 64 species of green microalgae in combinations of two to 16 species. We found that phylogenetic and functional diversity were positively correlated with biomass overyield, driven by their strong correlation with species richness. At low species richness, no significant correlation between overyield and functional and phylogenetic diversity was found. However, at high species richness (16 species), we found a positive relationship of overyield with functional diversity and a negative relationship with phylogenetic diversity. We show that negative phylogenetic diversity-ecosystem functioning relationships can result from interspecific growth inhibition. The opposing performances of facilitation (functional diversity) and inhibition (phylogenetic diversity) we observed at the 16 species level suggest that phylogenetic diversity is not always a good proxy for functional diversity and that results from experiments with low species numbers may underestimate negative species interactions. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  5. Global functional diversity of freshwater fish is concentrated in the Neotropics while functional vulnerability is widespread.

    Science.gov (United States)

    Toussaint, A; Charpin, N; Brosse, S; Villéger, S

    2016-03-16

    Worldwide biodiversity assessments have mainly focused on species richness but little is known about the diversity of species roles, i.e. functional diversity, while this is a key facet to understanding the consequences of global changes on the ecosystem services to human societies. Here, we report the world pattern of functional diversity of freshwater fish using a database encompassing morphological characteristics of more than 9,000 species. The Neotropical realm hosts more than 75% of global functional diversity while other realms each host less than 25%. This discrepancy is mediated by high functional uniqueness in some diversified Neotropical fish orders. Surprisingly, functional diversity patterns were weakly related to functional vulnerability. In the Neotropics the loss of threatened species will cause a limited loss of functional diversity (functional diversity will reach 43% and 33%, respectively, conferring a high functional vulnerability to these realms. Conservation of the Neotropical fish diversity is a key target to maintain world fish functional diversity, but this should not hide the pressing need to conserve the vulnerable fish faunas of the rest of the world, in which functional diversity is to a large extent supported by threatened species.

  6. Protein kinase substrate identification on functional protein arrays

    Directory of Open Access Journals (Sweden)

    Zhou Fang

    2008-02-01

    Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

  7. Origins of Protein Functions in Cells

    Science.gov (United States)

    Seelig, Burchard; Pohorille, Andrzej

    2011-01-01

    In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis and in vitro evolution of very large libraries of random amino acid sequences. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions yet, important clues have been uncovered. In one example (Keefe and Szostak, 2001), novel ATP binding proteins were identified that appear to be unrelated in both sequence and structure to any known ATP binding proteins. One of these proteins was subsequently redesigned computationally to bind GTP through introducing several mutations that introduce targeted structural changes to the protein, improve its binding to guanine and prevent water from accessing the active center. This study facilitates further investigations of individual evolutionary steps that lead to a change of function in primordial proteins. In a second study (Seelig and Szostak, 2007), novel enzymes were generated that can join two pieces of RNA in a reaction for which no natural enzymes are known

  8. The construction of an amino acid network for understanding protein structure and function.

    Science.gov (United States)

    Yan, Wenying; Zhou, Jianhong; Sun, Maomin; Chen, Jiajia; Hu, Guang; Shen, Bairong

    2014-06-01

    Amino acid networks (AANs) are undirected networks consisting of amino acid residues and their interactions in three-dimensional protein structures. The analysis of AANs provides novel insight into protein science, and several common amino acid network properties have revealed diverse classes of proteins. In this review, we first summarize methods for the construction and characterization of AANs. We then compare software tools for the construction and analysis of AANs. Finally, we review the application of AANs for understanding protein structure and function, including the identification of functional residues, the prediction of protein folding, analyzing protein stability and protein-protein interactions, and for understanding communication within and between proteins.

  9. Soil-borne microbiome: linking diversity to function.

    Science.gov (United States)

    Mendes, Lucas W; Tsai, Siu M; Navarrete, Acácio A; de Hollander, Mattias; van Veen, Johannes A; Kuramae, Eiko E

    2015-07-01

    Soil microorganisms are sensitive to environment disturbances, and such alterations have consequences on microbial diversity and functions. Our hypothesis is that alpha diversity of microbial communities and functional diversity decrease from undisturbed to disturbed soils, with consequences for functional redundancy in the soil ecosystem. To test this hypothesis, we used soil DNA shotgun metagenomics approach to assess the soil microbiome in a chronosequence of land-use from a native tropical forest, followed by deforestation and cultivation of soybean croplands and pasture in different seasons. Agriculture and pasture soils were among the most diverse and presented higher functional redundancy, which is important to maintain the ecosystem functioning after the forest conversion. On the other hand, the ecosystem equilibrium in forest is maintained based on a lower alpha diversity but higher abundance of microorganisms. Our results indicate that land-use change alters the structure and composition of microbial communities; however, ecosystem functionality is overcome by different strategies based on the abundance and diversity of the communities.

  10. Diverse gene functions in a soil mobilome

    DEFF Research Database (Denmark)

    Luo, Wenting; Xu, Zhuofei; Riber, Leise

    2016-01-01

    , the soil mobilome sampled from a well-characterized field in Hygum, Denmark. Soil bacterial cells were obtained by Nycodenz extraction, total DNA was purified by removing sheared chromosomal DNA using exonuclease digestion, and the remaining circular DNA was amplified with the phi29 polymerase and finally...... sequenced. The soil mobilome represented a wide range of known bacterial gene functions and highlighted the enrichment of plasmids, transposable elements and phages when compared to a well-characterized soil metagenome that, on the other hand, was dominated by basic biosynthesis and metabolism functions....... Approximately one eighth of the gene set was of plasmid-intrinsic traits, including replication, conjugation, mobilization and stability based on Pfam database analysis. Resistance determinants toward aminoglycosides, beta-lactams and glycopeptides as well as multi-drug functions indicated that a substantial...

  11. Testing the Link between Functional Diversity and Ecosystem Functioning in a Minnesota Grassland Experiment

    OpenAIRE

    Clark, Christopher M; Flynn, Dan F B; Butterfield, Bradley J; Reich, Peter B

    2012-01-01

    The functional diversity of a community can influence ecosystem functioning and reflects assembly processes. The large number of disparate metrics used to quantify functional diversity reflects the range of attributes underlying this concept, generally summarized as functional richness, functional evenness, and functional divergence. However, in practice, we know very little about which attributes drive which ecosystem functions, due to a lack of field-based tests. Here we test the associatio...

  12. Year 2 Report: Protein Function Prediction Platform

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C E

    2012-04-27

    Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.

  13. [Soil microbial functional diversity of different altitude Pinus koraiensis forests].

    Science.gov (United States)

    Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan

    2015-12-01

    In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity.

  14. Functional group diversity increases with modularity in complex food webs.

    Science.gov (United States)

    Montoya, D; Yallop, M L; Memmott, J

    2015-06-10

    Biodiversity increases the ability of ecosystems to provide multiple functions. Most studies report a positive relationship between species richness and the number of ecosystem functions. However, it is not known whether the number of functional groups is related to the structure of the underlying species interaction network. Here we present food web data from 115 salt marsh islands and show that network structure is associated with the number of functional groups present. Functional group diversity is heterogeneously distributed across spatial scales, with some islands hosting more functional groups than others. Functional groups form modules within the community so that food webs with more modular architectures have more functional group diversity. Further, in communities with different interaction types, modularity can be seen as the multifunctional equivalent of trophic complementarity. Collectively, these findings reveal spatial heterogeneity in the number of functional groups that emerges from patterns in the structure of the food web.

  15. On the Functional Diversity of Phonological Rules

    Science.gov (United States)

    Brasington, R. W. P.

    1976-01-01

    Shows that a phonological description that recognizes the functional variety of phonological rules is more illuminating than one in which data are handled merely as the output of a set of completely undifferentiated processes. Emphasizes the value of distinguishing motivated and unmotivated processes in phonology. (Author/RM)

  16. Moderate land use changes plant functional composition without loss of functional diversity in India's Western Ghats.

    Science.gov (United States)

    Mandle, Lisa; Ticktin, Tamara

    2015-09-01

    The fields of ecology and conservation science increasingly recognize the importance of managing for functional composition and functional diversity to maintain critical ecosystem processes and services. However, little is known about the degree to which widespread but moderate forms of land use that maintain overall vegetation structure are compatible with the conservation of functional diversity. We assessed differences in plani functional composition and functional diversity across savanna woodlands in the Western Ghats, India, managed with varying degrees of biomass extraction, livestock grazing, and ground fire. Across the gradient of moderate land uses, we found shifts in functional composition but no overall decline in functional diversity with land, use intensification. Biomass extraction was associated with changes in dispersal mode, reduced seed mass, and lower overstory functional diversity. Livestock grazing was associated with shorter overstory species, reduced seed mass, and increased understory functional diversity. Nonnative invasive species contributed to shifts in understory functional composition with livestock grazing and increased functional diversity with more intensive land use. Our study highlights both the utility and some limitations of assessing conservation value with functional diversity. These results suggest that moderate-intensity local land use can be compatible with maintenance of functional diversity in savanna woodlands of the Western Ghats, and further efforts to maximize this compatibility would benefit conservation in South India's extensive human-managed landscapes. However, using functional diversity as the sole metric by which to gauge conservation value can mask threats from invasive species and loss of diversity within categories of biotic dispersal. Therefore, functional diversity metrics are likely to provide a valuable complement to, but not replacement for, other management targets such as species composition.

  17. Predicting protein function from biomedical text.

    Science.gov (United States)

    Taha, Kamal; Yoo, Paul D

    2015-01-01

    We propose a classifier system called PFPBT that predicts the functions of un-annotated proteins. PFPBT assigns an un-annotated protein p the functional category of annotated proteins that are semantically similar to p. Each protein p is represented by a vector of weights. Each weight reflects the significance of a molecule m in the biomedical abstracts associated with p. That is, each weight quantifies the likelihood of the association between m and p. This is because all proteins bind to other molecules, which are highly predictive of the functions of the proteins. Let S be the set of proteins that is semantically similar to an un-annotated protein p. p is annotated with the functional category f, if its occurrence probability in abstracts associated with S whose functional category is f is statistically significantly different than its occurrences in abstracts associated with S that belong to all other functional categories. PFPBT automatically extracts each co-occurrence of a protein-molecule pair that represents semantic relationship between the pair. We present novel semantic rules based on the syntactic structures of sentences for identifying the semantic relationships between each co-occurrence of a protein-molecule pair in a sentence. We evaluated PFPBT by comparing it experimentally with two systems. Results showed improvement.

  18. Opposing Responses of Bird Functional Diversity to Vegetation Structural Diversity in Wet and Dry Forest.

    Science.gov (United States)

    Sitters, Holly; York, Alan; Swan, Matthew; Christie, Fiona; Di Stefano, Julian

    2016-01-01

    Disturbance regimes are changing worldwide, and the consequences for ecosystem function and resilience are largely unknown. Functional diversity (FD) provides a surrogate measure of ecosystem function by capturing the range, abundance and distribution of trait values in a community. Enhanced understanding of the responses of FD to measures of vegetation structure at landscape scales is needed to guide conservation management. To address this knowledge gap, we used a whole-of-landscape sampling approach to examine relationships between bird FD, vegetation diversity and time since fire. We surveyed birds and measured vegetation at 36 landscape sampling units in dry and wet forest in southeast Australia during 2010 and 2011. Four uncorrelated indices of bird FD (richness, evenness, divergence and dispersion) were derived from six bird traits, and we investigated responses of these indices and species richness to both vertical and horizontal vegetation diversity using linear mixed models. We also considered the extent to which the mean and diversity of time since fire were related to vegetation diversity. Results showed opposing responses of FD to vegetation diversity in dry and wet forest. In dry forest, where fire is frequent, species richness and two FD indices (richness and dispersion) were positively related to vertical vegetation diversity, consistent with theory relating to environmental variation and coexistence. However, in wet forest subject to infrequent fire, the same three response variables were negatively associated with vertical diversity. We suggest that competitive dominance by species results in lower FD as vegetation diversity increases in wet forest. The responses of functional evenness were opposite to those of species richness, functional richness and dispersion in both forest types, highlighting the value of examining multiple FD metrics at management-relevant scales. The mean and diversity of time since fire were uncorrelated with vegetation

  19. Opposing Responses of Bird Functional Diversity to Vegetation Structural Diversity in Wet and Dry Forest.

    Directory of Open Access Journals (Sweden)

    Holly Sitters

    Full Text Available Disturbance regimes are changing worldwide, and the consequences for ecosystem function and resilience are largely unknown. Functional diversity (FD provides a surrogate measure of ecosystem function by capturing the range, abundance and distribution of trait values in a community. Enhanced understanding of the responses of FD to measures of vegetation structure at landscape scales is needed to guide conservation management. To address this knowledge gap, we used a whole-of-landscape sampling approach to examine relationships between bird FD, vegetation diversity and time since fire. We surveyed birds and measured vegetation at 36 landscape sampling units in dry and wet forest in southeast Australia during 2010 and 2011. Four uncorrelated indices of bird FD (richness, evenness, divergence and dispersion were derived from six bird traits, and we investigated responses of these indices and species richness to both vertical and horizontal vegetation diversity using linear mixed models. We also considered the extent to which the mean and diversity of time since fire were related to vegetation diversity. Results showed opposing responses of FD to vegetation diversity in dry and wet forest. In dry forest, where fire is frequent, species richness and two FD indices (richness and dispersion were positively related to vertical vegetation diversity, consistent with theory relating to environmental variation and coexistence. However, in wet forest subject to infrequent fire, the same three response variables were negatively associated with vertical diversity. We suggest that competitive dominance by species results in lower FD as vegetation diversity increases in wet forest. The responses of functional evenness were opposite to those of species richness, functional richness and dispersion in both forest types, highlighting the value of examining multiple FD metrics at management-relevant scales. The mean and diversity of time since fire were uncorrelated

  20. Role of microProteins in controlling diverse biological pathways

    DEFF Research Database (Denmark)

    Dolde, Ulla Margrit

    a synthetic microProtein approach, we demonstrate that microProteins are able to regulate multi-domain proteins belonging to different protein classes. Furthermore, these results revealed that microProteins may provide a useful tool for post-translational regulation due to their role in protein regulation....... orthologous microProteins, miP1a and miP1b were identified using a computational analysis. MiP1a and miP1b are small B-Box containing proteins that interact with and negatively regulate CONSTANS (CO), a major regulator of flowering in Arabidopsis thaliana. They are known to be the first micro...... T (FT) expression. In agreement with the late flowering of overexpression plants, loss-of-function mutants of both miP1a and miP1b, generated using CRISPR/Cas9 genome engineering, showed also a slightly early flowering phenotype. In a forward genetic screen using transgenic plants overexpressing mi...

  1. Specialized functional diversity and interactions of the Na,K-ATPase

    Directory of Open Access Journals (Sweden)

    Igor I. Krivoi

    2016-05-01

    Full Text Available Na,K-ATPase is a protein ubiquitously expressed in the plasma membrane of all animal cells and vitally essential for their functions. A specialized functional diversity of the Na,K-ATPase isozymes is provided by molecular heterogeneity, distinct subcellular localizations and functional interactions with molecular environment. Studies over the last decades clearly demonstrated complex and isoform-specific reciprocal functional interactions between the Na,K-ATPase and neighboring proteins and lipids. These interactions are enabled by a spatially restricted ion homeostasis, direct protein-protein/lipid interactions and protein kinase signaling pathways. In addition to its ‘classical’ function in ion translocation, the Na,K-ATPase is now considered as one of the most important signaling molecules in neuronal, epithelial, skeletal, cardiac and vascular tissues. Accordingly, the Na,K-ATPase forms specialized sub-cellular multimolecular microdomains which act as receptors to circulating endogenous cardiotonic steroids triggering a number of signaling pathways. Changes in these endogenous cardiotonic steroid levels and initiated signaling responses have significant adaptive values for tissues and whole organisms under numerous physiological and pathophysiological conditions. This review discusses recent progress in the studies of functional interactions between the Na,K-ATPase and molecular microenvironment, the Na,K-ATPase-dependent signaling pathways and their significance for diversity of cell function.

  2. Functional diversity of CTCFs is encoded in their binding motifs.

    Science.gov (United States)

    Fang, Rongxin; Wang, Chengqi; Skogerbo, Geir; Zhang, Zhihua

    2015-08-28

    The CCCTC-binding factor (CTCF) has diverse regulatory functions. However, the definitive characteristics of the CTCF binding motif required for its functional diversity still remains elusive. Here, we describe a new motif discovery workflow by which we have identified three CTCF binding motif variations with highly divergent functionalities. Supported by transcriptomic, epigenomic and chromatin-interactomic data, we show that the functional diversity of the CTCF binding motifs is strongly associated with their GC content, CpG dinucleotide coverage and relative DNA methylation level at the 12th position of the motifs. Further analysis suggested that the co-localization of cohesin, the key factor in cohesion of sister chromatids, is negatively correlated with the CpG coverage and the relative DNA methylation level at the 12th position. Finally, we present evidences for a hypothetical model in which chromatin interactions between promoters and distal regulatory regions are likely mediated by CTCFs binding to sequences with high CpG. These results demonstrate the existence of definitive CTCF binding motifs corresponding to CTCF's diverse functions, and that the functional diversity of the motifs is strongly associated with genetic and epigenetic features at the 12th position of the motifs.

  3. Incorporating plant functional diversity effects in ecosystem service assessments.

    Science.gov (United States)

    Díaz, Sandra; Lavorel, Sandra; de Bello, Francesco; Quétier, Fabien; Grigulis, Karl; Robson, T Matthew

    2007-12-26

    Global environmental change affects the sustained provision of a wide set of ecosystem services. Although the delivery of ecosystem services is strongly affected by abiotic drivers and direct land use effects, it is also modulated by the functional diversity of biological communities (the value, range, and relative abundance of functional traits in a given ecosystem). The focus of this article is on integrating the different possible mechanisms by which functional diversity affects ecosystem properties that are directly relevant to ecosystem services. We propose a systematic way for progressing in understanding how land cover change affects these ecosystem properties through functional diversity modifications. Models on links between ecosystem properties and the local mean, range, and distribution of plant trait values are numerous, but they have been scattered in the literature, with varying degrees of empirical support and varying functional diversity components analyzed. Here we articulate these different components in a single conceptual and methodological framework that allows testing them in combination. We illustrate our approach with examples from the literature and apply the proposed framework to a grassland system in the central French Alps in which functional diversity, by responding to land use change, alters the provision of ecosystem services important to local stakeholders. We claim that our framework contributes to opening a new area of research at the interface of land change science and fundamental ecology.

  4. Incorporating plant functional diversity effects in ecosystem service assessments

    Science.gov (United States)

    Díaz, Sandra; Lavorel, Sandra; de Bello, Francesco; Quétier, Fabien; Grigulis, Karl; Robson, T. Matthew

    2007-01-01

    Global environmental change affects the sustained provision of a wide set of ecosystem services. Although the delivery of ecosystem services is strongly affected by abiotic drivers and direct land use effects, it is also modulated by the functional diversity of biological communities (the value, range, and relative abundance of functional traits in a given ecosystem). The focus of this article is on integrating the different possible mechanisms by which functional diversity affects ecosystem properties that are directly relevant to ecosystem services. We propose a systematic way for progressing in understanding how land cover change affects these ecosystem properties through functional diversity modifications. Models on links between ecosystem properties and the local mean, range, and distribution of plant trait values are numerous, but they have been scattered in the literature, with varying degrees of empirical support and varying functional diversity components analyzed. Here we articulate these different components in a single conceptual and methodological framework that allows testing them in combination. We illustrate our approach with examples from the literature and apply the proposed framework to a grassland system in the central French Alps in which functional diversity, by responding to land use change, alters the provision of ecosystem services important to local stakeholders. We claim that our framework contributes to opening a new area of research at the interface of land change science and fundamental ecology. PMID:18093933

  5. Structural and Function Prediction of Musa acuminata subsp. Malaccensis Protein

    Directory of Open Access Journals (Sweden)

    Anum Munir

    2016-03-01

    Full Text Available Hypothetical proteins (HPs are the proteins whose presence has been anticipated, yet in vivo function has not been built up. Illustrating the structural and functional privileged insights of these HPs might likewise prompt a superior comprehension of the protein-protein associations or networks in diverse types of life. Bananas (Musa acuminata spp., including sweet and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister grouped to the all-around considered Poales, which incorporate oats. Bananas are crucial for nourishment security in numerous tropical and subtropical nations and the most prominent organic product in industrialized nations. In the present study, the hypothetical protein of M. acuminata (Banana was chosen for analysis and modeling by distinctive bioinformatics apparatuses and databases. As indicated by primary and secondary structure analysis, XP_009393594.1 is a stable hydrophobic protein containing a noteworthy extent of α-helices; Homology modeling was done utilizing SWISS-MODEL server where the templates identity with XP_009393594.1 protein was less which demonstrated novelty of our protein. Ab initio strategy was conducted to produce its 3D structure. A few evaluations of quality assessment and validation parameters determined the generated protein model as stable with genuinely great quality. Functional analysis was completed by ProtFun 2.2, and KEGG (KAAS, recommended that the hypothetical protein is a transcription factor with cytoplasmic domain as zinc finger. The protein was observed to be vital for translation process, involved in metabolism, signaling and cellular processes, genetic information processing and Zinc ion binding. It is suggested that further test approval would help to anticipate the structures and functions of other uncharacterized proteins of different plants and living being.

  6. Bird functional diversity decreases with time since disturbance: Does patchy prescribed fire enhance ecosystem function?.

    Science.gov (United States)

    Sitters, Holly; Di Stefano, Julian; Christie, Fiona; Swan, Matthew; York, Alan

    2016-01-01

    Animal species diversity is often associated with time since disturbance, but the effects of disturbances such as fire on functional diversity are unknown. Functional diversity measures the range, abundance, and distribution of trait values in a community, and links changes in species composition with the consequences for ecosystem function. Improved understanding of the relationship between time since fire (TSF) and functional diversity is critical given that the frequency of both prescribed fire and wildfire is expected to increase. To address this knowledge gap, we examined responses of avian functional diversity to TSF and two direct measures of environmental heterogeneity, plant diversity, and structural heterogeneity. We surveyed birds across a 70-year chronosequence spanning four vegetation types in southeast Australia. Six bird functional traits were used to derive four functional diversity indices (richness, evenness, divergence, and dispersion) and the effects of TSF, plant diversity and structural heterogeneity on species richness and the functional diversity indices were examined using mixed models. We used a regression tree method to identify traits associated with species more common in young vegetation. Functional richness and dispersion were negatively associated with TSF in all vegetation types, suggesting that recent prescribed fire generates heterogeneous vegetation and provides greater opportunities for resource partitioning. Species richness was not significantly associated with TSF, and is probably an unreliable surrogate for functional diversity in fire-prone systems. A positive, relationship between functional evenness and structural heterogeneity was comnon to all vegetation types, suggesting that fine-scale (tens of meters) structural variation can enhance ecosystem function. Species more common in young vegetation were primarily linked by their specialist diets, indicating that ecosystem services such as seed dispersal and insect control

  7. Sensitivity of functional diversity metrics to sampling intensity

    NARCIS (Netherlands)

    van der Plas, Fons; van Klink, Roel; Manning, Pete; Olff, Han; Fischer, Andmarkus

    1. Functional diversity (FD) metrics are increasingly used in ecological research, particularly in the studies of community assembly and ecosystem functioning. However, studies using the FD metrics vary greatly in the intensity by which ecological communities were sampled and it is largely unknown

  8. Vaccinia complement control protein: Multi-functional protein and a ...

    Indian Academy of Sciences (India)

    Unknown

    molecule and potential drug. [Jha P and Kotwal G J 2003 Vaccinia complement control protein: Multi-functional protein and a potential wonder drug; J. Biosci. 28 265–271]. 1. Introduction. The pathogen-host interaction is a dynamic phenomenon which involves generation of defense mechanism by host and its evasion by ...

  9. Contrasting species and functional beta diversity in montane ant assemblages.

    Science.gov (United States)

    Bishop, Tom R; Robertson, Mark P; van Rensburg, Berndt J; Parr, Catherine L

    2015-09-01

    Beta diversity describes the variation in species composition between sites and can be used to infer why different species occupy different parts of the globe. It can be viewed in a number of ways. First, it can be partitioned into two distinct patterns: turnover and nestedness. Second, it can be investigated from either a species identity or a functional-trait point of view. We aim to document for the first time how these two aspects of beta diversity vary in response to a large environmental gradient. Maloti-Drakensberg Mountains, southern Africa. We sampled ant assemblages along an extensive elevational gradient (900-3000 m a.s.l.) twice yearly for 7 years, and collected functional-trait information related to the species' dietary and habitat-structure preferences. We used recently developed methods to partition species and functional beta diversity into their turnover and nestedness components. A series of null models were used to test whether the observed beta diversity patterns differed from random expectations. Species beta diversity was driven by turnover, but functional beta diversity was composed of both turnover and nestedness patterns at different parts of the gradient. Null models revealed that deterministic processes were likely to be responsible for the species patterns but that the functional changes were indistinguishable from stochasticity. Different ant species are found with increasing elevation, but they tend to represent an increasingly nested subset of the available functional strategies. This finding is unique and narrows down the list of possible factors that control ant existence across elevation. We conclude that diet and habitat preferences have little role in structuring ant assemblages in montane environments and that some other factor must be driving the non-random patterns of species turnover. This finding also highlights the importance of distinguishing between different kinds of beta diversity.

  10. Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes

    Science.gov (United States)

    García-Morales, Rodrigo; Badano, Ernesto I.; Zuria, Iriana; Galindo-González, Jorge; Rojas-Martínez, Alberto E.; Ávila-Gómez, Eva S.

    2016-01-01

    Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the state of Hidalgo, Mexico. We captured bats in each landscape using mist nets, and calculated functional diversity indices (functional richness and functional evenness) along with species richness and abundance. We analyzed these measures in terms of percent forest cover. We captured 906 bats (Phyllostomidae and Mormoopidae), including 10 genera and 12 species. Species richness, abundance and functional richness per night are positively related with forest cover. Generalized linear models show that species richness, abundance and functional richness per night are significantly related with forest cover, while seasonality had an effect on abundance and functional richness. Neither forest cover nor season had a significant effect on functional evenness. All these findings were consistent across three spatial scales (1, 3 and 5 km radius around sampling sites). The decrease in species, abundance and functional richness of bats with forest loss may have implications for the ecological processes they carry out such as seed dispersal, pollination and insect predation, among others. PMID:27926923

  11. Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes.

    Science.gov (United States)

    García-Morales, Rodrigo; Moreno, Claudia E; Badano, Ernesto I; Zuria, Iriana; Galindo-González, Jorge; Rojas-Martínez, Alberto E; Ávila-Gómez, Eva S

    2016-01-01

    Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the state of Hidalgo, Mexico. We captured bats in each landscape using mist nets, and calculated functional diversity indices (functional richness and functional evenness) along with species richness and abundance. We analyzed these measures in terms of percent forest cover. We captured 906 bats (Phyllostomidae and Mormoopidae), including 10 genera and 12 species. Species richness, abundance and functional richness per night are positively related with forest cover. Generalized linear models show that species richness, abundance and functional richness per night are significantly related with forest cover, while seasonality had an effect on abundance and functional richness. Neither forest cover nor season had a significant effect on functional evenness. All these findings were consistent across three spatial scales (1, 3 and 5 km radius around sampling sites). The decrease in species, abundance and functional richness of bats with forest loss may have implications for the ecological processes they carry out such as seed dispersal, pollination and insect predation, among others.

  12. Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes.

    Directory of Open Access Journals (Sweden)

    Rodrigo García-Morales

    Full Text Available Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the state of Hidalgo, Mexico. We captured bats in each landscape using mist nets, and calculated functional diversity indices (functional richness and functional evenness along with species richness and abundance. We analyzed these measures in terms of percent forest cover. We captured 906 bats (Phyllostomidae and Mormoopidae, including 10 genera and 12 species. Species richness, abundance and functional richness per night are positively related with forest cover. Generalized linear models show that species richness, abundance and functional richness per night are significantly related with forest cover, while seasonality had an effect on abundance and functional richness. Neither forest cover nor season had a significant effect on functional evenness. All these findings were consistent across three spatial scales (1, 3 and 5 km radius around sampling sites. The decrease in species, abundance and functional richness of bats with forest loss may have implications for the ecological processes they carry out such as seed dispersal, pollination and insect predation, among others.

  13. Functionally diverse reef-fish communities ameliorate coral disease.

    Science.gov (United States)

    Raymundo, Laurie J; Halford, Andrew R; Maypa, Aileen P; Kerr, Alexander M

    2009-10-06

    Coral reefs, the most diverse of marine ecosystems, currently experience unprecedented levels of degradation. Diseases are now recognized as a major cause of mortality in reef-forming corals and are complicit in phase shifts of reef ecosystems to algal-dominated states worldwide. Even so, factors contributing to disease occurrence, spread, and impact remain poorly understood. Ecosystem resilience has been linked to the conservation of functional diversity, whereas overfishing reduces functional diversity through cascading, top-down effects. Hence, we tested the hypothesis that reefs with trophically diverse reef fish communities have less coral disease than overfished reefs. We surveyed reefs across the central Philippines, including well-managed marine protected areas (MPAs), and found that disease prevalence was significantly negatively correlated with fish taxonomic diversity. Further, MPAs had significantly higher fish diversity and less disease than unprotected areas. We subsequently investigated potential links between coral disease and the trophic components of fish diversity, finding that only the density of coral-feeding chaetodontid butterflyfishes, seldom targeted by fishers, was positively associated with disease prevalence. These previously uncharacterized results are supported by a second large-scale dataset from the Great Barrier Reef. We hypothesize that members of the charismatic reef-fish family Chaetodontidae are major vectors of coral disease by virtue of their trophic specialization on hard corals and their ecological release in overfished areas, particularly outside MPAs.

  14. Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Jaiswal Dinesh Kumar

    2012-10-01

    Full Text Available Abstract Background Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. Results To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the identified proteins are putative integral membrane proteins, possessing transmembrane domains. Conclusions The proteomic analysis revealed many resident integral membrane proteins as well as membrane-associated proteins including those not reported earlier. To our knowledge, this is the first report of membrane proteome from aerial tissues of a crop plant. The findings may provide a better understanding of the biochemical machinery of the plant membranes at the molecular level that might help in functional genomics studies of different developmental pathways and stress-responses.

  15. Constructive Functional Diversity: a new paradigm beyond disability and impairment.

    Science.gov (United States)

    Patston, Philip

    This article presents a more dynamic and constructive paradigm than the current dominant ones (for example medical or social models), to describe and change the impact of impairment and disability. The reflections contained are inspired by personal and professional frustration with the existing polarized ideology of human function, which fails to adequately describe the diversity of physiological and psychosocial function amongst people. It aims to provoke and inspire dialogue about our current paradigm of human function in relation to value and capacity. Within this paper: I critique society's biases regarding of functional deficit relative to the subconscious fear of losing function; I question the polarity of the negatively framed language of impairment and disability; I offer constructive, creative 'solutions' to describe the experience of atypical function. In so doing, an entirely new language of diverse human function and a concept of Constructive Functional Diversity (CFD) is proposed, which includes a complex yet logical array of modes and outcomes of function. Finally I suggest the benefits of a more dynamic paradigm of functional change in enhancing rehabilitative outcomes, including client-directed practice.

  16. Opposing Responses of Bird Functional Diversity to Vegetation Structural Diversity in Wet and Dry Forest

    OpenAIRE

    Sitters, Holly; York, Alan; Swan, Matthew; Christie, Fiona; Di Stefano, Julian

    2016-01-01

    Disturbance regimes are changing worldwide, and the consequences for ecosystem function and resilience are largely unknown. Functional diversity (FD) provides a surrogate measure of ecosystem function by capturing the range, abundance and distribution of trait values in a community. Enhanced understanding of the responses of FD to measures of vegetation structure at landscape scales is needed to guide conservation management. To address this knowledge gap, we used a whole-of-landscape samplin...

  17. Influence of persistent monodominance on functional diversity and functional community assembly in African tropical forests.

    Science.gov (United States)

    Kearsley, Elizabeth; Verbeeck, Hans; Hufkens, Koen; Beeckman, Hans; Steppe, Kathy; Boeckx, Pascal; Huygens, Dries

    2015-04-01

    Lowland tropical rainforest are taxonomically diverse and complex systems, although not all tropical communities are equally diverse. Naturally occuring monodominant patches of Gilbertiodendron dewevrei are commonly found across Central Africa alongside higher diversity forests. Nevertheless, a low taxonomical diversity does not necessarily indicate an equivalently low functional diverse system. We investigate the functional diversity and functional community assembly of mixed and monodominant tropical forests in a central region of the Congo Basin in D. R. Congo using 15 leaf and wood traits covering 95% of all species within each community. This unique dataset allows us to investigate differences in functional diversity and ecosystem functioning between mixed and monodominant forest types. Functional richness, functional divergence and functional evenness are three functional diversity measures providing different aspects of functional diversity. The largest difference between the two forest types was found for functional richness, with a lower functional richness in the monodominant forest indicating a higher amount of niche space filled in the mixed forest. The mixed forest also had a higher species richness and Simpson diversity index, indicating that the higher species richness increases the functional niche space. Subsequently, we identified whole community trait shifts within the monodominant forest compared to the mixed forest. The dominance of Gilbertiodendron dewevrei, for which a distinct niche is found for most traits, presented a significant influence on the entire (trait) community expressing fundamental differences in ecosystem functioning. More detailed investigation of species unique within the monodominant forest and species occurring in both forest types provide more insight into the influence of Gilbertiodendron dewevrei. Both the unique and the shared species showed significant shifts in leaf nutrients, specific leaf area and water use

  18. Pull-down combined with proteomic strategy reveals functional diversity of synaptotagmin I.

    Science.gov (United States)

    Guo, Tianyao; Duan, Zhigui; Chen, Jia; Xie, Chunliang; Wang, Ying; Chen, Ping; Wang, Xianchun

    2017-01-01

    Synaptotagmin I (Syt I) is most abundant in the brain and is involved in multiple cellular processes. Its two C2 domains, C2A and C2B, are the main functional regions. Our present study employed a pull-down combined with proteomic strategy to identify the C2 domain-interacting proteins to comprehensively understand the biological roles of the C2 domains and thus the functional diversity of Syt I. A total of 135 non-redundant proteins interacting with the C2 domains of Syt I were identified. Out of them, 32 and 64 proteins only bound to C2A or C2B domains, respectively, and 39 proteins bound to both of them. Compared with C2A, C2B could bind to many more proteins particularly those involved in synaptic transmission and metabolic regulation. Functional analysis indicated that Syt I may exert impacts by interacting with other proteins on multiple cellular processes, including vesicular membrane trafficking, synaptic transmission, metabolic regulation, catalysis, transmembrane transport and structure formation, etc. These results demonstrate that the functional diversity of Syt I is higher than previously expected, that its two domains may mediate the same and different cellular processes cooperatively or independently, and that C2B domain may play even more important roles than C2A in the functioning of Syt I. This work not only further deepened our understanding of the functional diversity of Syt I and the functional differences between its two C2 domains, but also provided important clues for the further related researches.

  19. Specific protein homeostatic functions of small heat-shock proteins increase lifespan.

    Science.gov (United States)

    Vos, Michel J; Carra, Serena; Kanon, Bart; Bosveld, Floris; Klauke, Karin; Sibon, Ody C M; Kampinga, Harm H

    2016-04-01

    During aging, oxidized, misfolded, and aggregated proteins accumulate in cells, while the capacity to deal with protein damage declines severely. To cope with the toxicity of damaged proteins, cells rely on protein quality control networks, in particular proteins belonging to the family of heat-shock proteins (HSPs). As safeguards of the cellular proteome, HSPs assist in protein folding and prevent accumulation of damaged, misfolded proteins. Here, we compared the capacity of all Drosophila melanogaster small HSP family members for their ability to assist in refolding stress-denatured substrates and/or to prevent aggregation of disease-associated misfolded proteins. We identified CG14207 as a novel and potent small HSP member that exclusively assisted in HSP70-dependent refolding of stress-denatured proteins. Furthermore, we report that HSP67BC, which has no role in protein refolding, was the most effective small HSP preventing toxic protein aggregation in an HSP70-independent manner. Importantly, overexpression of both CG14207 and HSP67BC in Drosophila leads to a mild increase in lifespan, demonstrating that increased levels of functionally diverse small HSPs can promote longevity in vivo. © 2015 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

  20. Symbiotic Dinoflagellate Functional Diversity Mediates Coral Survival under Ecological Crisis.

    Science.gov (United States)

    Suggett, David J; Warner, Mark E; Leggat, William

    2017-10-01

    Coral reefs have entered an era of 'ecological crisis' as climate change drives catastrophic reef loss worldwide. Coral growth and stress susceptibility are regulated by their endosymbiotic dinoflagellates (genus Symbiodinium). The phylogenetic diversity of Symbiodinium frequently corresponds to patterns of coral health and survival, but knowledge of functional diversity is ultimately necessary to reconcile broader ecological success over space and time. We explore here functional traits underpinning the complex biology of Symbiodinium that spans free-living algae to coral endosymbionts. In doing so we propose a mechanistic framework integrating the primary traits of resource acquisition and utilisation as a means to explain Symbiodinium functional diversity and to resolve the role of Symbiodinium in driving the stability of coral reefs under an uncertain future. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Diversity of the Superfamily of Phloem Lectins (Phloem Protein 2) in Angiosperms1

    Science.gov (United States)

    Dinant, Sylvie; Clark, Anna M.; Zhu, Yanmin; Vilaine, Françoise; Palauqui, Jean-Christophe; Kusiak, Chantal; Thompson, Gary A.

    2003-01-01

    Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in the phloem sap. Although thought to be associated with structural P-protein, PP2 is translocated in the assimilate stream where its lectin activity or RNA-binding properties can exert effects over long distances. Analyzing the diversity of these proteins in vascular plants led to the identification of PP2-like genes in species from 17 angiosperm and gymnosperm genera. This wide distribution of PP2 genes in the plant kingdom indicates that they are ancient and common in vascular plants. Their presence in cereals and gymnosperms, both of which lack structural P-protein, also supports a wider role for these proteins. Within this superfamily, PP2 proteins have considerable size polymorphism. This is attributable to variability in the length of the amino terminus that extends from a highly conserved domain. The conserved PP2 domain was identified in the proteins encoded by six genes from several cucurbits, celery (Apium graveolens), and Arabidopsis that are specifically expressed in the sieve element-companion cell complex. The acquisition of additional modular domains in the amino-terminal extensions of other PP2-like proteins could reflect divergence from its phloem function. PMID:12529520

  2. Inferring protein function by domain context similarities in protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Sun Zhirong

    2009-12-01

    Full Text Available Abstract Background Genome sequencing projects generate massive amounts of sequence data but there are still many proteins whose functions remain unknown. The availability of large scale protein-protein interaction data sets makes it possible to develop new function prediction methods based on protein-protein interaction (PPI networks. Although several existing methods combine multiple information resources, there is no study that integrates protein domain information and PPI networks to predict protein functions. Results The domain context similarity can be a useful index to predict protein function similarity. The prediction accuracy of our method in yeast is between 63%-67%, which outperforms the other methods in terms of ROC curves. Conclusion This paper presents a novel protein function prediction method that combines protein domain composition information and PPI networks. Performance evaluations show that this method outperforms existing methods.

  3. Global patterns of guild composition and functional diversity of spiders.

    Directory of Open Access Journals (Sweden)

    Pedro Cardoso

    Full Text Available The objectives of this work are: (1 to define spider guilds for all extant families worldwide; (2 test if guilds defined at family level are good surrogates of species guilds; (3 compare the taxonomic and guild composition of spider assemblages from different parts of the world; (4 compare the taxonomic and functional diversity of spider assemblages and; (5 relate functional diversity with habitat structure. Data on foraging strategy, prey range, vertical stratification and circadian activity was collected for 108 families. Spider guilds were defined by hierarchical clustering. We searched for inconsistencies between family guild placement and the known guild of each species. Richness and abundance per guild before and after correcting guild placement were compared, as were the proportions of each guild and family between all possible pairs of sites. Functional diversity per site was calculated based on hierarchical clustering. Eight guilds were discriminated: (1 sensing, (2 sheet, (3 space, and (4 orb web weavers; (5 specialists; (6 ambush, (7 ground, and (8 other hunters. Sixteen percent of the species richness corresponding to 11% of all captured individuals was incorrectly attributed to a guild by family surrogacy; however, the correlation of uncorrected vs. corrected guilds was invariably high. The correlation of guild richness or abundances was generally higher than the correlation of family richness or abundances. Functional diversity was not always higher in the tropics than in temperate regions. Families may potentially serve as ecological surrogates for species. Different families may present similar roles in the ecosystems, with replacement of some taxa by other within the same guild. Spiders in tropical regions seem to have higher redundancy of functional roles and/or finer resource partitioning than in temperate regions. Although species and family diversity were higher in the tropics, functional diversity seems to be also

  4. Global Patterns of Guild Composition and Functional Diversity of Spiders

    Science.gov (United States)

    Cardoso, Pedro; Pekár, Stano; Jocqué, Rudy; Coddington, Jonathan A.

    2011-01-01

    The objectives of this work are: (1) to define spider guilds for all extant families worldwide; (2) test if guilds defined at family level are good surrogates of species guilds; (3) compare the taxonomic and guild composition of spider assemblages from different parts of the world; (4) compare the taxonomic and functional diversity of spider assemblages and; (5) relate functional diversity with habitat structure. Data on foraging strategy, prey range, vertical stratification and circadian activity was collected for 108 families. Spider guilds were defined by hierarchical clustering. We searched for inconsistencies between family guild placement and the known guild of each species. Richness and abundance per guild before and after correcting guild placement were compared, as were the proportions of each guild and family between all possible pairs of sites. Functional diversity per site was calculated based on hierarchical clustering. Eight guilds were discriminated: (1) sensing, (2) sheet, (3) space, and (4) orb web weavers; (5) specialists; (6) ambush, (7) ground, and (8) other hunters. Sixteen percent of the species richness corresponding to 11% of all captured individuals was incorrectly attributed to a guild by family surrogacy; however, the correlation of uncorrected vs. corrected guilds was invariably high. The correlation of guild richness or abundances was generally higher than the correlation of family richness or abundances. Functional diversity was not always higher in the tropics than in temperate regions. Families may potentially serve as ecological surrogates for species. Different families may present similar roles in the ecosystems, with replacement of some taxa by other within the same guild. Spiders in tropical regions seem to have higher redundancy of functional roles and/or finer resource partitioning than in temperate regions. Although species and family diversity were higher in the tropics, functional diversity seems to be also influenced by

  5. Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses.

    Science.gov (United States)

    Faith, Daniel P

    2015-02-19

    The phylogenetic diversity measure, ('PD'), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the evolutionarily distinct and globally endangered (EDGE) methods. Expected PD methods also have limitations. An alternative notion of expected diversity, expected functional trait diversity, relies on an alternative non-phylogenetic model and allows inferences of diversity at the level of functional traits. Expected PD also faces challenges in helping to address phylogenetic tipping points and worst-case PD losses. Expected PD may not choose conservation options that best avoid worst-case losses of long branches from the tree of life. We can expand the range of useful calculations based on expected PD, including methods for identifying phylogenetic key biodiversity areas. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  6. Functions of intrinsic disorder in transmembrane proteins

    DEFF Research Database (Denmark)

    Kjaergaard, Magnus; Kragelund, Birthe B.

    2017-01-01

    mechanisms. (3) Trafficking of membrane proteins. (4) Transient membrane associations. (5) Post-translational modifications most notably phosphorylation and (6) disorder-linked isoform dependent function. We finish the review by discussing the future challenges facing the membrane protein community regarding......Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane...... proteins, and address why the flexibility afforded by disorder is mechanistically important. Intrinsically disordered regions are present in many common classes of membrane proteins including ion channels and transporters; G-protein coupled receptors (GPCRs), receptor tyrosine kinases and cytokine...

  7. Intricate knots in proteins: Function and evolution.

    Directory of Open Access Journals (Sweden)

    Peter Virnau

    2006-09-01

    Full Text Available Our investigation of knotted structures in the Protein Data Bank reveals the most complicated knot discovered to date. We suggest that the occurrence of this knot in a human ubiquitin hydrolase might be related to the role of the enzyme in protein degradation. While knots are usually preserved among homologues, we also identify an exception in a transcarbamylase. This allows us to exemplify the function of knots in proteins and to suggest how they may have been created.

  8. Functional group diversity of bee pollinators increases crop yield.

    Science.gov (United States)

    Hoehn, Patrick; Tscharntke, Teja; Tylianakis, Jason M; Steffan-Dewenter, Ingolf

    2008-10-07

    Niche complementarity is a commonly invoked mechanism underlying the positive relationship between biodiversity and ecosystem functioning, but little empirical evidence exists for complementarity among pollinator species. This study related differences in three functional traits of pollinating bees (flower height preference, daily time of flower visitation and within-flower behaviour) to the seed set of the obligate cross-pollinated pumpkin Cucurbita moschata Duch. ex Poir. across a land-use intensity gradient from tropical rainforest and agroforests to grassland in Indonesia. Bee richness and abundance changed with habitat variables and we used this natural variation to test whether complementary resource use by the diverse pollinator community enhanced final yield. We found that pollinator diversity, but not abundance, was positively related to seed set of pumpkins. Bees showed species-specific spatial and temporal variation in flower visitation traits and within-flower behaviour, allowing for classification into functional guilds. Diversity of functional groups explained even more of the variance in seed set (r2=45%) than did species richness (r2=32%) highlighting the role of functional complementarity. Even though we do not provide experimental, but rather correlative evidence, we can link spatial and temporal complementarity in highly diverse pollinator communities to pollination success in the field, leading to enhanced crop yield without any managed honeybees.

  9. Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers.

    Science.gov (United States)

    Lefcheck, Jonathan S; Duffy, J Emmett

    2015-11-01

    The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori altered functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within multiple levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on generalized linear mixed-effects models. Combining inferences from eight traits into a single multivariate index increased prediction accuracy of these models relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context.

  10. Diversity and evolution of ABC proteins in mycorrhiza-forming fungi.

    Science.gov (United States)

    Kovalchuk, Andriy; Kohler, Annegret; Martin, Francis; Asiegbu, Fred O

    2015-12-28

    Transporter proteins are predicted to have an important role in the mycorrhizal symbiosis, due to the fact that this type of an interaction between plants and fungi requires a continuous nutrient and signalling exchange. ABC transporters are one of the large groups of transporter proteins found both in plants and in fungi. The crucial role of plant ABC transporters in the formation of the mycorrhizal symbiosis has been demonstrated recently. Some of the fungal ABC transporter-encoding genes are also induced during the mycorrhiza formation. However, no experimental evidences of the direct involvement of fungal ABC transporters in this process are available so far. To facilitate the identification of fungal ABC proteins with a potential role in the establishment of the mycorrhizal symbiosis, we have performed an inventory of the ABC protein-encoding genes in the genomes of 25 species of mycorrhiza-forming fungi. We have identified, manually annotated and curated more than 1300 gene models of putative ABC protein-encoding genes. Out of those, more than 1000 models are predicted to encode functional proteins, whereas about 300 models represent gene fragments or putative pseudogenes. We have also performed the phylogenetic analysis of the identified sequences. The sets of ABC proteins in the mycorrhiza-forming species were compared to the related saprotrophic or plant-pathogenic fungal species. Our results demonstrate the high diversity of ABC genes in the genomes of mycorrhiza-forming fungi. Via comparison of transcriptomics data from different species, we have identified candidate groups of ABC transporters that might have a role in the process of the mycorrhiza formation. Results of our inventory will facilitate the identification of fungal transporters with a role in the mycorrhiza formation. We also provide the first data on ABC protein-coding genes for the phylum Glomeromycota and for orders Pezizales, Atheliales, Cantharellales and Sebacinales, contributing to

  11. Higher phylogenetic diversity prevents loss of functional diversity caused by successive drying and rewetting cycles.

    Science.gov (United States)

    Bononi, Laura; Taketani, Rodrigo Gouvêa; Souza, Danilo Tosta; Moitinho, Marta Alves; Kavamura, Vanessa Nessner; Melo, Itamar Soares

    2017-12-29

    Microbial communities regulate nutrient cycling in soil, thus the impact of climate change on the structure and function of these communities can cause an imbalance of nutrients in the environment. Structural and functional changes of soil bacterial communities in two contrasting biomes in Brazil, the Atlantic Forest and the Tropical Dry Forest (Caatinga), were studied by simulating, in microcosms, rainfall and drought events. Soil samples were collected in three Brazilian states: Bahia, Pernambuco and São Paulo, in a total of four sampling sites. Analysis of 16S rRNA amplicon libraries revealed changes in microbial communities after three drying-rewetting cycles (60-30% water holding capacity). Alpha diversity indexes were obtained for bacterial communities, as well as the functional diversity index (Shannon) based on the activity of the following enzymes: acid and alkaline phosphatase, arylsulfatase, dehydrogenase, cellulase, amylase, urease and phytase. In general, the soils of Caatinga showed a decrease in the diversity indexes studied, conversely, however, the soils of Atlantic Forest were found to be more resistant during the drying-rewetting cycles. Functional diversity was significantly different for the two biomes, with a decrease in Caatinga soils, while Atlantic Forest samples demonstrated a greater stability of enzymatic activity. Further, the Atlantic Forest samples showed more resistance when compared to samples from Caatinga. The results found in this study have confirmed the hypothesis that biomes, independent of climate, when subjected to successive events of drought and rewetting exhibit structural and metabolic changes.

  12. Changing MADS-Box Transcription Factor Protein-Protein Interactions as a Mechanism for Generating Floral Morphological Diversity.

    Science.gov (United States)

    Bartlett, Madelaine E

    2017-12-01

    Flowers display fantastic morphological diversity. Despite extreme variability in form, floral organ identity is specified by a core set of deeply conserved proteins-the floral MADS-box transcription factors. This indicates that while core gene function has been maintained, MADS-box transcription factors have evolved to regulate different downstream genes. Thus, the evolution of gene regulation downstream of the MADS-box transcription factors is likely central to the evolution of floral form. Gene regulation is determined by the combination of transcriptional regulators present at a particular cis-regulatory element at a particular time. Therefore, the interactions between transcription factors can be of profound importance in determining patterns of gene regulation. Here, after a short primer on flowers and floral morphology, I discuss the centrality of protein-protein interactions to MADS-box transcription factor function, and review the evidence that the evolution of MADS-box protein-protein interactions is a key driver in the evolution of gene regulation downstream of the MADS-box genes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  13. Protein networks as logic functions in development and cancer.

    Directory of Open Access Journals (Sweden)

    Janusz Dutkowski

    2011-09-01

    Full Text Available Many biological and clinical outcomes are based not on single proteins, but on modules of proteins embedded in protein networks. A fundamental question is how the proteins within each module contribute to the overall module activity. Here, we study the modules underlying three representative biological programs related to tissue development, breast cancer metastasis, or progression of brain cancer, respectively. For each case we apply a new method, called Network-Guided Forests, to identify predictive modules together with logic functions which tie the activity of each module to the activity of its component genes. The resulting modules implement a diverse repertoire of decision logic which cannot be captured using the simple approximations suggested in previous work such as gene summation or subtraction. We show that in cancer, certain combinations of oncogenes and tumor suppressors exert competing forces on the system, suggesting that medical genetics should move beyond cataloguing individual cancer genes to cataloguing their combinatorial logic.

  14. Functional roles affect diversity-succession relationships for boreal beetles.

    Directory of Open Access Journals (Sweden)

    Heloise Gibb

    Full Text Available Species diversity commonly increases with succession and this relationship is an important justification for conserving large areas of old-growth habitats. However, species with different ecological roles respond differently to succession. We examined the relationship between a range of diversity measures and time since disturbance for boreal forest beetles collected over a 285 year forest chronosequence. We compared responses of "functional" groups related to threat status, dependence on dead wood habitats, diet and the type of trap in which they were collected (indicative of the breadth of ecologies of species. We examined fits of commonly used rank-abundance models for each age class and traditional and derived diversity indices. Rank abundance distributions were closest to the Zipf-Mandelbrot distribution, suggesting little role for competition in structuring most assemblages. Diversity measures for most functional groups increased with succession, but differences in slopes were common. Evenness declined with succession; more so for red-listed species than common species. Saproxylic species increased in diversity with succession while non-saproxylic species did not. Slopes for fungivores were steeper than other diet groups, while detritivores were not strongly affected by succession. Species trapped using emergence traps (log specialists responded more weakly to succession than those trapped using flight intercept traps (representing a broader set of ecologies. Species associated with microhabitats that accumulate with succession (fungi and dead wood thus showed the strongest diversity responses to succession. These clear differences between functional group responses to forest succession should be considered in planning landscapes for optimum conservation value, particularly functional resilience.

  15. Intraspecific functional and genetic diversity ofPetriella setifera.

    Science.gov (United States)

    Pertile, Giorgia; Panek, Jacek; Oszust, Karolina; Siczek, Anna; Frąc, Magdalena

    2018-01-01

    The aim of the study was an analysis of the intraspecific genetic and functional diversity of the new isolated fungal strains of P. setifera . This is the first report concerning the genetic and metabolic diversity of Petriella setifera strains isolated from industrial compost and the first description of a protocol for AFLP fingerprinting analysis optimised for these fungal species. The results showed a significant degree of variability among the isolates, which was demonstrated by the clearly subdivision of all the isolates into two clusters with 51% and 62% similarity, respectively. For the metabolic diversity, the BIOLOG system was used and this analysis revealed clearly different patterns of carbon substrates utilization between the isolates resulting in a clear separation of the five isolates into three clusters with 0%, 42% and 54% of similarity, respectively. These results suggest that genetic diversity does not always match the level of functional diversity, which may be useful in discovering the importance of this fungus to ecosystem functioning. The results indicated that P. setifera strains were able to degrade substrates produced in the degradation of hemicellulose (D-Arabinose, L-Arabinose, D-Glucuronic Acid, Xylitol, γ-Amino-Butyric Acid, D-Mannose, D-Xylose and L-Rhamnose), cellulose (α-D-Glucose and D-Cellobiose) and the synthesis of lignin (Quinic Acid) at a high level, showing their importance in ecosystem services as a decomposer of carbon compounds and as organisms, which make a significant contribution to carbon cycling in the ecosystem.The results showed for the first time that the use of molecular biology techniques (such as AFLP and BIOLOG analyses) may allow for the identification of intraspecific diversity of as yet poorly investigated fungal species with favourable consequences for our understanding their ecosystem function.

  16. An easy protocol for the domino synthesis of diversely functionalized ...

    Indian Academy of Sciences (India)

    struction of diversely functionalized heterocycles.3. Development of efficient methods to construct spiro compounds has been a topic of great relevance in organic synthesis due to their pronounced biological importance as they are used as anticancer agents,4 antibacterial agents,5 anticonvulsant agents,6 anti- tuberculosis ...

  17. Ectomycorrhizal symbiosis affects functional diversity of rhizosphere fluorescent pseudomonads

    NARCIS (Netherlands)

    Frey-Klett, P.; Chavatte, M.; Clausse, M.L.; Courrier, S.; Roux, Le C.; Raaijmakers, J.M.; Giovanna Martinotti, M.; Pierrat, J.C.; Garbaye, J.

    2005-01-01

    Here we characterized the effect of the ectomycorrhizal symbiosis on the genotypic and functional diversity of soil Pseudomonas fluorescens populations and analysed its possible consequences in terms of plant nutrition, development and health. ¿ Sixty strains of P. fluorescens were isolated from the

  18. Stress, Social Support, and Psychosocial Functioning of Ethnically Diverse Students

    Science.gov (United States)

    Farrell, Michelle; Langrehr, Kimberly J.

    2017-01-01

    This study examined the stress-buffering role of social support on indicators of psychosocial functioning among a combined and split sample of ethnically diverse college students. Although high social support significantly moderated 2 relationships in the combined sample, high and low levels of social support significantly reduced the effect of…

  19. Enzyme structure, enzyme function and allozyme diversity in ...

    African Journals Online (AJOL)

    In estimates of population genetic diversity based on allozyme heterozygosity, some enzymes are regularly more variable than others. Evolutionary theory suggests that functionally less important molecules, or parts of molecules, evolve more rapidly than more important ones; the latter enzymes should then theoretically be ...

  20. Beyond diversity: functional microbiomics of the human colon

    NARCIS (Netherlands)

    Egert, M.G.G.; Graaf, de A.; Smidt, H.; Vos, de W.M.; Venema, K.

    2006-01-01

    Molecular tools have revealed wide microbial diversity in the human alimentary tract. Most intestinal microorganisms have not been cultured and the in situ functions of distinct groups of the intestinal microbiota are largely unknown but pivotal to understanding the role of these microorganisms in

  1. Functional diversity exhibits a diverse relationship with area, even a decreasing one

    Science.gov (United States)

    Karadimou, Elpida K.; Kallimanis, Athanasios S.; Tsiripidis, Ioannis; Dimopoulos, Panayotis

    2016-01-01

    The relationship between species richness and area is one of the few well-established laws in ecology, and one might expect a similar relationship with functional diversity (FD). However, only a few studies investigate the relationship between trait-based FD and area, the Functional Diversity - Area Relationship (FDAR). To examine FDAR, we constructed the species accumulation curve and the corresponding FD curve. We used plant diversity data from nested plots (1–128 m2), recorded on the Volcanic islands of Santorini Archipelagos, Greece. Six multidimensional FD indices were calculated using 26 traits. We identified a typology of FDARs depending on the facet of FD analyzed: (A) strongly positive for indices quantifying the range of functional traits in the community, (B) negative correlation for indices quantifying the evenness in the distribution of abundance in the trait space, (C) no clear pattern for indices reflecting the functional similarity of species and (D) idiosyncratic patterns with area for functional divergence. As area increases, the range of traits observed in the community increases, but the abundance of traits does not increase proportionally and some traits become dominant, implying a reliance on some functions that may be located in either the center or the periphery of the trait space. PMID:27752086

  2. Functional Importance of Mobile Ribosomal Proteins

    Directory of Open Access Journals (Sweden)

    Kai-Chun Chang

    2015-01-01

    Full Text Available Although the dynamic motions and peptidyl transferase activity seem to be embedded in the rRNAs, the ribosome contains more than 50 ribosomal proteins (r-proteins, whose functions remain largely elusive. Also, the precise forms of some of these r-proteins, as being part of the ribosome, are not structurally solved due to their high flexibility, which hinders the efforts in their functional elucidation. Owing to recent advances in cryo-electron microscopy, single-molecule techniques, and theoretical modeling, much has been learned about the dynamics of these r-proteins. Surprisingly, allosteric regulations have been found in between spatially separated components as distant as those in the opposite sides of the ribosome. Here, we focus on the functional roles and intricate regulations of the mobile L1 and L12 stalks and L9 and S1 proteins. Conformational flexibility also enables versatile functions for r-proteins beyond translation. The arrangement of r-proteins may be under evolutionary pressure that fine-tunes mass distributions for optimal structural dynamics and catalytic activity of the ribosome.

  3. Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Nagesh R Aragam

    Full Text Available Circumsporozoite protein (CS is a leading vaccine antigen for falciparum malaria, but is highly polymorphic in natural parasite populations. The factors driving this diversity are unclear, but non-random assortment of the T cell epitopes TH2 and TH3 has been observed in a Kenyan parasite population. The recent publication of the crystal structure of the variable C terminal region of the protein allows the assessment of the impact of diversity on protein structure and T cell epitope assortment. Using data from the Gambia (55 isolates and Malawi (235 isolates, we evaluated the patterns of diversity within and between epitopes in these two distantly-separated populations. Only non-synonymous mutations were observed with the vast majority in both populations at similar frequencies suggesting strong selection on this region. A non-random pattern of T cell epitope assortment was seen in Malawi and in the Gambia, but structural analysis indicates no intramolecular spatial interactions. Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches. In addition, free energy analysis suggests residues forming and behind the novel pocket within CS are tightly constrained and well conserved in all alleles. In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids. In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

  4. Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions.

    Science.gov (United States)

    Aragam, Nagesh R; Thayer, Kelly M; Nge, Nabi; Hoffman, Irving; Martinson, Francis; Kamwendo, Debbie; Lin, Feng-Chang; Sutherland, Colin; Bailey, Jeffrey A; Juliano, Jonathan J

    2013-01-01

    Circumsporozoite protein (CS) is a leading vaccine antigen for falciparum malaria, but is highly polymorphic in natural parasite populations. The factors driving this diversity are unclear, but non-random assortment of the T cell epitopes TH2 and TH3 has been observed in a Kenyan parasite population. The recent publication of the crystal structure of the variable C terminal region of the protein allows the assessment of the impact of diversity on protein structure and T cell epitope assortment. Using data from the Gambia (55 isolates) and Malawi (235 isolates), we evaluated the patterns of diversity within and between epitopes in these two distantly-separated populations. Only non-synonymous mutations were observed with the vast majority in both populations at similar frequencies suggesting strong selection on this region. A non-random pattern of T cell epitope assortment was seen in Malawi and in the Gambia, but structural analysis indicates no intramolecular spatial interactions. Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches. In addition, free energy analysis suggests residues forming and behind the novel pocket within CS are tightly constrained and well conserved in all alleles. In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids. In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

  5. PROTEIN MALNUTRITION INCIDENCE COMPARISON AFTER GASTRIC BYPASS VERSUS BILIOPANCREATIC DIVERSION.

    Science.gov (United States)

    Suárez Llanos, José Pablo; Fuentes Ferrer, Manuel; Alvarez-Sala-Walther, Luis; García Bray, Bruno; Medina González, Laura; Bretón Lesmes, Irene; Moreno Esteban, Basilio

    2015-07-01

    bariatric surgery is widely employed nowadays. Nutritional complications following malabsorptive bariatric surgery are common. to compare protein malnutrition incidence, the amount of protein intake and the influence of various risk factors in patients undergoing Roux-en-Y gastric bypass (RYGB) and biliopancreatic diversion (BPD). retrospective study comparing the development of hypoalbuminemia in 92 patients undergoing BPD and 121 RYGB, before surgery and 3, 6, 12, 18 and 24 months after it. Protein intake was estimated by serum prealbumin. The influence of prior body mass index (BMI), age and sex was analyzed. hypoprealbuminemia was found in around 40% of patients 3 months after both procedures, decreasing to about 10% after 2 years of surgery. Hypoalbuminemia incidence was close to 20% in the first post-surgery year in BPD, persisting in 10-15% of cases thereafter. After RYGB, hypoalbuminemia incidence was lower (5-9% in all postoperative follow-up measurements). During the first year after surgery, hypoalbuminemia was more frequent after BPD than after RYGB (at the 3rd month (OR:3.9; p=0.006; 95%CI:1.5-10.4), 6th (OR:5.0; p=0.002; 95% CI:1.8-13.8), and at the 12th month (OR:4.4;p=0.007;95%;CI:1.5-12.8)), but not after the first year. A higher preoperative BMI favored it (OR: 1.03; p=0.046; 95% CI:1-1.06), as well as greater age during the first 6 months. Patients with BPD had a higher risk for hypoproteinemia than those undergoing RYGB, especially during the first year post-surgery. Higher preoperative BMI, and age (in the short-term period) could have a significant inverse relation to hypoproteinemia. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

  6. Mung bean proteins and peptides: nutritional, functional and bioactive properties

    Directory of Open Access Journals (Sweden)

    Zhu Yi-Shen

    2018-02-01

    Full Text Available To date, no extensive literature review exists regarding potential uses of mung bean proteins and peptides. As mung bean has long been widely used as a food source, early studies evaluated mung bean nutritional value against the Food and Agriculture Organization of the United Nations (FAO/the World Health Organization (WHO amino acids dietary recommendations. The comparison demonstrated mung bean to be a good protein source, except for deficiencies in sulphur-containing amino acids, methionine and cysteine. Methionine and cysteine residues have been introduced into the 8S globulin through protein engineering technology. Subsequently, purified mung bean proteins and peptides have facilitated the study of their structural and functional properties. Two main types of extraction methods have been reported for isolation of proteins and peptides from mung bean flours, permitting sequencing of major proteins present in mung bean, including albumins and globulins (notably 8S globulin. However, the sequence for albumin deposited in the UniProt database differs from other sequences reported in the literature. Meanwhile, a limited number of reports have revealed other useful bioactivities for proteins and hydrolysed peptides, including angiotensin-converting enzyme inhibitory activity, anti-fungal activity and trypsin inhibitory activity. Consequently, several mung bean hydrolysed peptides have served as effective food additives to prevent proteolysis during storage. Ultimately, further research will reveal other nutritional, functional and bioactive properties of mung bean for uses in diverse applications.

  7. New multidimensional functional diversity indices for a multifaceted framework in functional ecology.

    Science.gov (United States)

    Villéger, Sébastien; Mason, Norman W H; Mouillot, David

    2008-08-01

    Functional diversity is increasingly identified as an important driver of ecosystem functioning. Various indices have been proposed to measure the functional diversity of a community, but there is still no consensus on which are most suitable. Indeed, none of the existing indices meets all the criteria required for general use. The main criteria are that they must be designed to deal with several traits, take into account abundances, and measure all the facets of functional diversity. Here we propose three indices to quantify each facet of functional diversity for a community with species distributed in a multidimensional functional space: functional richness (volume of the functional space occupied by the community), functional evenness (regularity of the distribution of abundance in this volume), and functional divergence (divergence in the distribution of abundance in this volume). Functional richness is estimated using the existing convex hull volume index. The new functional evenness index is based on the minimum spanning tree which links all the species in the multidimensional functional space. Then this new index quantifies the regularity with which species abundances are distributed along the spanning tree. Functional divergence is measured using a novel index which quantifies how species diverge in their distances (weighted by their abundance) from the center of gravity in the functional space. We show that none of the indices meets all the criteria required for a functional diversity index, but instead we show that the set of three complementary indices meets these criteria. Through simulations of artificial data sets, we demonstrate that functional divergence and functional evenness are independent of species richness and that the three functional diversity indices are independent of each other. Overall, our study suggests that decomposition of functional diversity into its three primary components provides a meaningful framework for its quantification

  8. Bacterial flagellar capping proteins adopt diverse oligomeric states

    Energy Technology Data Exchange (ETDEWEB)

    Postel, Sandra; Deredge, Daniel; Bonsor, Daniel A.; Yu, Xiong; Diederichs, Kay; Helmsing, Saskia; Vromen, Aviv; Friedler, Assaf; Hust, Michael; Egelman, Edward H.; Beckett, Dorothy; Wintrode, Patrick L.; Sundberg, Eric J. (UV); (Braunschweig); (Maryland-MED); (Konstanz); (Maryland); (Hebrew)

    2016-09-24

    Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD fromPseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find thatPseudomonasFliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.

  9. Insights into structural and functional diversity of Dof (DNA binding with one finger) transcription factor.

    Science.gov (United States)

    Gupta, S; Malviya, N; Kushwaha, H; Nasim, J; Bisht, N C; Singh, V K; Yadav, D

    2015-03-01

    The structural, functional and in-silico studies of Dof transcription factor attempted so far reveals immense opportunity to analyze the plant genomes in terms of number of Dof genes and discuss in light of the evolution. The multiple functions of Dof genes needs to explored for crop improvement. Transcription factors play a very vital role in gene regulation at transcriptional level and are being extensively studied across phylas. In recent years, sequencing of plant genomes has led to genome-wide identification and characterizations of diverse types of plant-specific transcription factor gene family providing key insights into their structural and functional diversity. The DNA binding with one finger (Dof), a class belonging to C2H2-type zinc finger family proteins, is a plant-specific transcription factor having multiple roles such as seed maturation and germination, phytohormone and light-mediated regulation and plant responses to biotic and abiotic stresses. Dof proteins are present across plant lineage, from green algae to higher angiosperm, and represent a unique class of transcription factor having bifunctional binding activities, with both DNA and proteins, to regulate the complex transcriptional machinery in plant cells. The structural and functional diversity of the Dof transcription factor family along with the bioinformatics analysis highlighting the phylogeny of Dof families is reviewed in light of its importance in plant biotechnology for crop improvement.

  10. Changes in bird functional diversity across multiple land uses: interpretations of functional redundancy depend on functional group identity.

    Directory of Open Access Journals (Sweden)

    Gary W Luck

    Full Text Available Examinations of the impact of land-use change on functional diversity link changes in ecological community structure driven by land modification with the consequences for ecosystem function. Yet, most studies have been small-scale, experimental analyses and primarily focussed on plants. There is a lack of research on fauna communities and at large-scales across multiple land uses. We assessed changes in the functional diversity of bird communities across 24 land uses aligned along an intensification gradient. We tested the hypothesis that functional diversity is higher in less intensively used landscapes, documented changes in diversity using four diversity metrics, and examined how functional diversity varied with species richness to identify levels of functional redundancy. Functional diversity, measured using a dendogram-based metric, increased from high to low intensity land uses, but observed values did not differ significantly from randomly-generated expected values. Values for functional evenness and functional divergence did not vary consistently with land-use intensification, although higher than expected values were mostly recorded in high intensity land uses. A total of 16 land uses had lower than expected values for functional dispersion and these were mostly low intensity native vegetation sites. Relations between functional diversity and bird species richness yielded strikingly different patterns for the entire bird community vs. particular functional groups. For all birds and insectivores, functional evenness, divergence and dispersion showed a linear decline with increasing species richness suggesting substantial functional redundancy across communities. However, for nectarivores, frugivores and carnivores, there was a significant hump-shaped or non-significant positive linear relationship between these functional measures and species richness indicating less redundancy. Hump-shaped relationships signify that the most

  11. Changes in bird functional diversity across multiple land uses: interpretations of functional redundancy depend on functional group identity.

    Science.gov (United States)

    Luck, Gary W; Carter, Andrew; Smallbone, Lisa

    2013-01-01

    Examinations of the impact of land-use change on functional diversity link changes in ecological community structure driven by land modification with the consequences for ecosystem function. Yet, most studies have been small-scale, experimental analyses and primarily focussed on plants. There is a lack of research on fauna communities and at large-scales across multiple land uses. We assessed changes in the functional diversity of bird communities across 24 land uses aligned along an intensification gradient. We tested the hypothesis that functional diversity is higher in less intensively used landscapes, documented changes in diversity using four diversity metrics, and examined how functional diversity varied with species richness to identify levels of functional redundancy. Functional diversity, measured using a dendogram-based metric, increased from high to low intensity land uses, but observed values did not differ significantly from randomly-generated expected values. Values for functional evenness and functional divergence did not vary consistently with land-use intensification, although higher than expected values were mostly recorded in high intensity land uses. A total of 16 land uses had lower than expected values for functional dispersion and these were mostly low intensity native vegetation sites. Relations between functional diversity and bird species richness yielded strikingly different patterns for the entire bird community vs. particular functional groups. For all birds and insectivores, functional evenness, divergence and dispersion showed a linear decline with increasing species richness suggesting substantial functional redundancy across communities. However, for nectarivores, frugivores and carnivores, there was a significant hump-shaped or non-significant positive linear relationship between these functional measures and species richness indicating less redundancy. Hump-shaped relationships signify that the most functionally diverse

  12. Function-specific response to depletion of microbial diversity.

    Science.gov (United States)

    Peter, Hannes; Beier, Sara; Bertilsson, Stefan; Lindström, Eva S; Langenheder, Silke; Tranvik, Lars J

    2011-02-01

    Recent meta-analyses suggest that ecosystem functioning increases with biodiversity, but contradictory results have been presented for some microbial functions. Moreover, observations of only one function underestimate the functional role of diversity because of species-specific trade-offs in the ability to carry out different functions. We examined multiple functions in batch cultures of natural freshwater bacterial communities with different richness, achieved by a dilution-to-extinction approach. Community composition was assessed by molecular fingerprinting of 16S rRNA and chitinase genes, representing the total community and a trait characteristic for a functional group, respectively. Richness was positively related to abundance and biomass, negatively correlated to cell volumes and unrelated to maximum intrinsic growth rate. The response of chitin and cellulose degradation rates depended on the presence of a single phylotype. We suggest that species identity and community composition rather than richness matters for specific microbial processes.

  13. Diverse Regulation of Temperature Sensation by Trimeric G-Protein Signaling in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Tomoyo Ujisawa

    Full Text Available Temperature sensation by the nervous system is essential for life and proliferation of animals. The molecular-physiological mechanisms underlying temperature signaling have not been fully elucidated. We show here that diverse regulatory machinery underlies temperature sensation through trimeric G-protein signaling in the nematode Caenorhabditis elegans. Molecular-genetic studies demonstrated that cold tolerance is regulated by additive functions of three Gα proteins in a temperature-sensing neuron, ASJ, which is also known to be a light-sensing neuron. Optical recording of calcium concentration in ASJ upon temperature-changes demonstrated that three Gα proteins act in different aspects of temperature signaling. Calcium concentration changes in ASJ upon temperature change were unexpectedly decreased in a mutant defective in phosphodiesterase, which is well known as a negative regulator of calcium increase. Together, these data demonstrate commonalities and differences in the molecular components concerned with light and temperature signaling in a single sensory neuron.

  14. Diverse Regulation of Temperature Sensation by Trimeric G-Protein Signaling in Caenorhabditis elegans

    Science.gov (United States)

    Ujisawa, Tomoyo; Ohta, Akane; Uda-Yagi, Misato

    2016-01-01

    Temperature sensation by the nervous system is essential for life and proliferation of animals. The molecular-physiological mechanisms underlying temperature signaling have not been fully elucidated. We show here that diverse regulatory machinery underlies temperature sensation through trimeric G-protein signaling in the nematode Caenorhabditis elegans. Molecular-genetic studies demonstrated that cold tolerance is regulated by additive functions of three Gα proteins in a temperature-sensing neuron, ASJ, which is also known to be a light-sensing neuron. Optical recording of calcium concentration in ASJ upon temperature-changes demonstrated that three Gα proteins act in different aspects of temperature signaling. Calcium concentration changes in ASJ upon temperature change were unexpectedly decreased in a mutant defective in phosphodiesterase, which is well known as a negative regulator of calcium increase. Together, these data demonstrate commonalities and differences in the molecular components concerned with light and temperature signaling in a single sensory neuron. PMID:27788246

  15. Small diverse antioxidant functionalities for oxidative stress disease drug discovery.

    Science.gov (United States)

    Sikazwe, D; Grillo, A; Ramsinghani, S; Davis, J; McQuiston, K; Ablordeppey, S Y

    2012-07-01

    There is an up-surge of interest in antioxidants because of their potential use in mitigating a wide array of oxidative stress mediated diseases. In the course of our literature search for diverse functional groups, with utility in the design of potential drugs for preventing oxidative stress related cell injury, we have collected a small literature library of core structures or moieties possessing antioxidant activities. These functional groups can be re-configured into robust antioxidants drug molecules, in their own right, or incorporated into drug structures where the antioxidant capability is required. The lack of single papers presenting a collection of diverse small molecule antioxidant moieties as potential design leads prompted us to write this short review of twenty five such functionalities.

  16. Consumer diversity interacts with prey defenses to drive ecosystem function.

    Science.gov (United States)

    Rasher, Douglas B; Hoey, Andrew S; Hay, Mark E

    2013-06-01

    Prey traits linking consumer diversity to ecosystem function remain poorly understood. On tropical coral reefs, herbivores promote coral dominance by suppressing competing macroalgae, but the roles of herbivore identity and diversity, macroalgal defenses, and their interactions in affecting reef resilience and function are unclear. We studied adjacent pairs of no-take marine reserves and fished areas on reefs in Fiji and found that protected reefs supported 7-17x greater biomass, 2-3x higher species richness of herbivorous fishes, and 3-11x more live coral cover than did fished reefs. In contrast, macroalgae were 27-61x more abundant and 3-4x more species-rich on fished reefs. When we transplanted seven common macroalgae from fished reefs into reserves they were rapidly consumed, suggesting that rates of herbivory (ecosystem functioning) differed inside vs. outside reserves. We then video-recorded feeding activity on the same seven macroalgae when transplanted into reserves, and assessed the functional redundancy vs. complementarity of herbivorous fishes consuming these macroalgae. Of 29 species of larger herbivorous fishes on these reefs, only four species accounted for 97% of macroalgal consumption. Two unicornfish consumed a range of brown macroalgae, a parrotfish consumed multiple red algae, and a rabbitfish consumed a green alga, with almost no diet overlap among these groups. The two most chemically rich, allelopathic algae were each consumed by a single, but different, fish species. This striking complementarity resulted from herbivore species differing in their tolerances to macroalgal chemical and structural defenses. A model of assemblage diet breadth based on our feeding observations predicted that high browser diversity would be required for effective control of macroalgae on Fijian reefs. In support of this model, we observed strong negative relationships between herbivore diversity and macroalgal abundance and diversity across the six study reefs. Our

  17. Relating phylogenetic and functional diversity among denitrifiers and quantifying their capacity to predict community functioning

    Directory of Open Access Journals (Sweden)

    Joana eFalcão Salles

    2012-06-01

    Full Text Available Genetic diversity of phylogenetic or functional markers is widely used as a proxy of microbial diversity. However, it remains unclear at what extent functional diversity, gene sequence diversity and community functioning are linked. We analysed, for a range of denitrifying bacteria, the relationships between (i the similarity of functional traits evaluated from metabolic profiles (BIOLOG plates or from N2O accumulation patterns on different C sources, and (ii the similarity of phylogenetic (16S rRNA gene or functional (nir gene markers. We also calculated different proxies for the diversity of denitrifier community based on taxa richness, phylogenetic or functional similarities, and evaluated their performance in inferring the functioning of assembled denitrifying communities. For individual strains, the variation in the 16S rRNA gene sequence explained only 10% of the variation in metabolic patterns and were not related to N2O accumulation. The latter was correlated with the similarity of nitrite reductase residues. When nir genes were analysed separately, the similarity in amino acids coded by the nirS genes accounted for 48% of the variance of the observed pattern of N2O accumulation, whereas nirK amino acid residues were unrelated to N2O accumulation. For bacterial assemblages, phylogenetic diversity and mean community dissimilarity, calculated using 16S rRNA gene sequences, and functional diversity measures associated with BIOLOG, predicted poorly the variation in the functioning of assembled communities (below 15%. In contrast, the proxies of functional diversity based on N2O accumulation patterns performed better and explained from 23 to 42% of the variation in community functioning. Amongst those, community niche was the best metric, indicating the importance of complementarity for carbon resources among taxa in the context of denitrification.

  18. Effects of land use on taxonomic and functional diversity

    DEFF Research Database (Denmark)

    Hevia, Violeta; Carmona, Carlos P.; Azcárate, Francisco M.

    2016-01-01

    Land-use change is the major driver of biodiversity loss. However, taxonomic diversity (TD) and functional diversity (FD) might respond differently to land-use change, and this response might also vary depending on the biotic group being analysed. In this study, we compare the TD and FD of four......: the sampling unit scale and the site scale. Land-use intensity effects on TD and FD were quite different and highly varied among the four biotic groups, with no single clear pattern emerging that could be considered general for all organisms. Additive partitioning of species diversity revealed clear...... contrasting patterns between TD and FD in the percentage of variability observed at each spatial scale. While most variability in TD was found at the larger scales, irregardless of organism group and land-use type, most variability in FD was found at the smallest scale, indicating that species turnover among...

  19. Minor snake venom proteins: Structure, function and potential applications.

    Science.gov (United States)

    Boldrini-França, Johara; Cologna, Camila Takeno; Pucca, Manuela Berto; Bordon, Karla de Castro Figueiredo; Amorim, Fernanda Gobbi; Anjolette, Fernando Antonio Pino; Cordeiro, Francielle Almeida; Wiezel, Gisele Adriano; Cerni, Felipe Augusto; Pinheiro-Junior, Ernesto Lopes; Shibao, Priscila Yumi Tanaka; Ferreira, Isabela Gobbo; de Oliveira, Isadora Sousa; Cardoso, Iara Aimê; Arantes, Eliane Candiani

    2017-04-01

    Snake venoms present a great diversity of pharmacologically active compounds that may be applied as research and biotechnological tools, as well as in drug development and diagnostic tests for certain diseases. The most abundant toxins have been extensively studied in the last decades and some of them have already been used for different purposes. Nevertheless, most of the minor snake venom protein classes remain poorly explored, even presenting potential application in diverse areas. The main difficulty in studying these proteins lies on the impossibility of obtaining sufficient amounts of them for a comprehensive investigation. The advent of more sensitive techniques in the last few years allowed the discovery of new venom components and the in-depth study of some already known minor proteins. This review summarizes information regarding some structural and functional aspects of low abundant snake venom proteins classes, such as growth factors, hyaluronidases, cysteine-rich secretory proteins, nucleases and nucleotidases, cobra venom factors, vespryns, protease inhibitors, antimicrobial peptides, among others. Some potential applications of these molecules are discussed herein in order to encourage researchers to explore the full venom repertoire and to discover new molecules or applications for the already known venom components. Copyright © 2016. Published by Elsevier B.V.

  20. Rare species support vulnerable functions in high-diversity ecosystems.

    Directory of Open Access Journals (Sweden)

    David Mouillot

    Full Text Available Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees, we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by

  1. Rare species support vulnerable functions in high-diversity ecosystems.

    Science.gov (United States)

    Mouillot, David; Bellwood, David R; Baraloto, Christopher; Chave, Jerome; Galzin, Rene; Harmelin-Vivien, Mireille; Kulbicki, Michel; Lavergne, Sebastien; Lavorel, Sandra; Mouquet, Nicolas; Paine, C E Timothy; Renaud, Julien; Thuiller, Wilfried

    2013-01-01

    Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across

  2. Vaccinia complement control protein: Multi-functional protein and a ...

    Indian Academy of Sciences (India)

    Unknown

    cytokine receptors is a common immune evasion strategy adopted by large DNA viruses like poxviruses. Poxviruses encode soluble proteins that are secreted from infected cells and function as soluble IFNγ receptor (IFNγR) which blocks IFN-γ activity. Poxviruses express four vTNFRs, which have different properties.

  3. Protein-protein interaction network-based detection of functionally similar proteins within species.

    Science.gov (United States)

    Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

    2012-07-01

    Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

  4. Protein function prediction using neighbor relativity in protein-protein interaction network.

    Science.gov (United States)

    Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

    2013-04-01

    There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Plant functional diversity enhances associations of soil fungal diversity with vegetation and soil in the restoration of semiarid sandy grassland.

    Science.gov (United States)

    Zuo, Xiaoan; Wang, Shaokun; Lv, Peng; Zhou, Xin; Zhao, Xueyong; Zhang, Tonghui; Zhang, Jing

    2016-01-01

    The trait-based approach shows that plant functional diversity strongly affects ecosystem properties. However, few empirical studies show the relationship between soil fungal diversity and plant functional diversity in natural ecosystems. We investigated soil fungal diversity along a restoration gradient of sandy grassland (mobile dune, semifixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China, using the denaturing gradient gel electrophoresis of 18S rRNA and gene sequencing. We also examined associations of soil fungal diversity with plant functional diversity reflected by the dominant species' traits in community (community-weighted mean, CWM) and the dispersion of functional trait values (FD is). We further used the structure equation model (SEM) to evaluate how plant richness, biomass, functional diversity, and soil properties affect soil fungal diversity in sandy grassland restoration. Soil fungal richness in mobile dune and semifixed dune was markedly lower than those of fixed dune and grassland (P functional diversity explained nearly 70% variances of soil fungal richness. Strong association of soil fungal richness with the dominant species in the community supported the mass ratio hypothesis. Our results clearly highlight the role of plant functional diversity in enhancing associations of soil fungal diversity with community structure and soil properties in sandy grassland ecosystems.

  6. Predicting protein structure classes from function predictions

    DEFF Research Database (Denmark)

    Sommer, I.; Rahnenfuhrer, J.; de Lichtenberg, Ulrik

    2004-01-01

    membership. Even for structural families of small size, family members receive significantly higher scores. For some examples, we show that the relevant functional features identified by this method are biologically meaningful. The proposed approach can be used to improve existing sequence......We introduce a new approach to using the information contained in sequence-to-function prediction data in order to recognize protein template classes, a critical step in predicting protein structure. The data on which our method is based comprise probabilities of functional categories; for given...... query sequences these probabilities are obtained by a neural net that has previously been trained on a variety of functionally important features. On a training set of sequences we assess the relevance of individual functional categories for identifying a given structural family. Using a combination...

  7. Scoring protein relationships in functional interaction networks predicted from sequence data.

    Directory of Open Access Journals (Sweden)

    Gaston K Mazandu

    Full Text Available UNLABELLED: The abundance of diverse biological data from various sources constitutes a rich source of knowledge, which has the power to advance our understanding of organisms. This requires computational methods in order to integrate and exploit these data effectively and elucidate local and genome wide functional connections between protein pairs, thus enabling functional inferences for uncharacterized proteins. These biological data are primarily in the form of sequences, which determine functions, although functional properties of a protein can often be predicted from just the domains it contains. Thus, protein sequences and domains can be used to predict protein pair-wise functional relationships, and thus contribute to the function prediction process of uncharacterized proteins in order to ensure that knowledge is gained from sequencing efforts. In this work, we introduce information-theoretic based approaches to score protein-protein functional interaction pairs predicted from protein sequence similarity and conserved protein signature matches. The proposed schemes are effective for data-driven scoring of connections between protein pairs. We applied these schemes to the Mycobacterium tuberculosis proteome to produce a homology-based functional network of the organism with a high confidence and coverage. We use the network for predicting functions of uncharacterised proteins. AVAILABILITY: Protein pair-wise functional relationship scores for Mycobacterium tuberculosis strain CDC1551 sequence data and python scripts to compute these scores are available at http://web.cbio.uct.ac.za/~gmazandu/scoringschemes.

  8. Incorporating functional inter-relationships into protein function prediction algorithms

    Directory of Open Access Journals (Sweden)

    Kumar Vipin

    2009-05-01

    Full Text Available Abstract Background Functional classification schemes (e.g. the Gene Ontology that serve as the basis for annotation efforts in several organisms are often the source of gold standard information for computational efforts at supervised protein function prediction. While successful function prediction algorithms have been developed, few previous efforts have utilized more than the protein-to-functional class label information provided by such knowledge bases. For instance, the Gene Ontology not only captures protein annotations to a set of functional classes, but it also arranges these classes in a DAG-based hierarchy that captures rich inter-relationships between different classes. These inter-relationships present both opportunities, such as the potential for additional training examples for small classes from larger related classes, and challenges, such as a harder to learn distinction between similar GO terms, for standard classification-based approaches. Results We propose a method to enhance the performance of classification-based protein function prediction algorithms by addressing the issue of using these interrelationships between functional classes constituting functional classification schemes. Using a standard measure for evaluating the semantic similarity between nodes in an ontology, we quantify and incorporate these inter-relationships into the k-nearest neighbor classifier. We present experiments on several large genomic data sets, each of which is used for the modeling and prediction of over hundred classes from the GO Biological Process ontology. The results show that this incorporation produces more accurate predictions for a large number of the functional classes considered, and also that the classes benefitted most by this approach are those containing the fewest members. In addition, we show how our proposed framework can be used for integrating information from the entire GO hierarchy for improving the accuracy of

  9. Microbial diversity and functional capacity in polar soils.

    Science.gov (United States)

    Makhalanyane, Thulani Peter; Van Goethem, Marc Warwick; Cowan, Don Arthur

    2016-04-01

    Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. The structure and function of endophilin proteins

    DEFF Research Database (Denmark)

    Kjaerulff, Ole; Brodin, Lennart; Jung, Anita

    2011-01-01

    Members of the BAR domain protein superfamily are essential elements of cellular traffic. Endophilins are among the best studied BAR domain proteins. They have a prominent function in synaptic vesicle endocytosis (SVE), receptor trafficking and apoptosis, and in other processes that require remod...... remodeling of the membrane structure. Here, we discuss the role of endophilins in these processes and summarize novel insights into the molecular aspects of endophilin function. Also, we discuss phosphorylation of endophilins and how this and other mechanisms may contribute to disease....

  11. Functionality of system components: Conservation of protein function in protein feature space

    DEFF Research Database (Denmark)

    Jensen, Lars Juhl; Ussery, David; Brunak, Søren

    2003-01-01

    Many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties. We show here that such protein features are more conserved among orthologs than paralogs, indicating...... they are crucial for protein function and thus subject to selective pressure. This means that a function prediction method based on sequence-derived features may be able to discriminate between proteins with different function even when they have highly similar structure. Also, such a method is likely to perform...... well on organisms other than the one on which it was trained. We evaluate the performance of such a method, ProtFun, which relies on protein features as its sole input, and show that the method gives similar performance for most eukaryotes and performs much better than anticipated on archaea...

  12. Functionality of system components: Conservation of protein function in protein feature space

    DEFF Research Database (Denmark)

    Jensen, Lars Juhl; Ussery, David; Brunak, Søren

    2003-01-01

    well on organisms other than the one on which it was trained. We evaluate the performance of such a method, ProtFun, which relies on protein features as its sole input, and show that the method gives similar performance for most eukaryotes and performs much better than anticipated on archaea......Many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties. We show here that such protein features are more conserved among orthologs than paralogs, indicating...... they are crucial for protein function and thus subject to selective pressure. This means that a function prediction method based on sequence-derived features may be able to discriminate between proteins with different function even when they have highly similar structure. Also, such a method is likely to perform...

  13. Biogeographical disparity in the functional diversity and redundancy of corals.

    Science.gov (United States)

    McWilliam, Mike; Hoogenboom, Mia O; Baird, Andrew H; Kuo, Chao-Yang; Madin, Joshua S; Hughes, Terry P

    2018-03-05

    Corals are major contributors to a range of key ecosystem functions on tropical reefs, including calcification, photosynthesis, nutrient cycling, and the provision of habitat structure. The abundance of corals is declining at multiple scales, and the species composition of assemblages is responding to escalating human pressures, including anthropogenic global warming. An urgent challenge is to understand the functional consequences of these shifts in abundance and composition in different biogeographical contexts. While global patterns of coral species richness are well known, the biogeography of coral functions in provinces and domains with high and low redundancy is poorly understood. Here, we quantify the functional traits of all currently recognized zooxanthellate coral species ( n = 821) in both the Indo-Pacific and Atlantic domains to examine the relationships between species richness and the diversity and redundancy of functional trait space. We find that trait diversity is remarkably conserved (>75% of the global total) along latitudinal and longitudinal gradients in species richness, falling away only in species-poor provinces ( n functions and highlight the vulnerability of relatively depauperate, peripheral locations, which are often a low priority for targeted conservation efforts.

  14. A surprising role for conformational entropy in protein function

    Science.gov (United States)

    Wand, A. Joshua; Moorman, Veronica R.; Harpole, Kyle W.

    2014-01-01

    Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a grand challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to experimentally access is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned and what the future may hold for this emerging view of protein function. PMID:23478875

  15. Structural and Functional Diversity of Estrogen Receptor Ligands

    OpenAIRE

    Farooq, Amjad

    2015-01-01

    Estrogen receptors, comprised of ERα and ERβ isoforms in mammals, act as ligand-modulated transcription factors and orchestrate a plethora of cellular functions from sexual development and reproduction to metabolic homeostasis. Herein, I revisit the structural basis of the binding of ERα to DNA and estradiol in light of the recent discoveries and emerging trends in the field of nuclear receptors. A particular emphasis of this review is on the chemical and structural diversity of an ever-incre...

  16. Structural and regulatory diversity shape HLA-C protein expression levels

    DEFF Research Database (Denmark)

    Kaur, Gurman; Gras, Stephanie; Mobbs, Jesse I

    2017-01-01

    Expression of HLA-C varies widely across individuals in an allele-specific manner. This variation in expression can influence efficacy of the immune response, as shown for infectious and autoimmune diseases. MicroRNA binding partially influences differential HLA-C expression, but the additional...... contributing factors have remained undetermined. Here we use functional and structural analyses to demonstrate that HLA-C expression is modulated not just at the RNA level, but also at the protein level. Specifically, we show that variation in exons 2 and 3, which encode the α1/α2 domains, drives differential...... expression of HLA-C allomorphs at the cell surface by influencing the structure of the peptide-binding cleft and the diversity of peptides bound by the HLA-C molecules. Together with a phylogenetic analysis, these results highlight the diversity and long-term balancing selection of regulatory factors...

  17. Plant functional diversity affects climate-vegetation interaction

    Science.gov (United States)

    Groner, Vivienne P.; Raddatz, Thomas; Reick, Christian H.; Claussen, Martin

    2018-04-01

    We present how variations in plant functional diversity affect climate-vegetation interaction towards the end of the African Humid Period (AHP) in coupled land-atmosphere simulations using the Max Planck Institute Earth system model (MPI-ESM). In experiments with AHP boundary conditions, the extent of the green Sahara varies considerably with changes in plant functional diversity. Differences in vegetation cover extent and plant functional type (PFT) composition translate into significantly different land surface parameters, water cycling, and surface energy budgets. These changes have not only regional consequences but considerably alter large-scale atmospheric circulation patterns and the position of the tropical rain belt. Towards the end of the AHP, simulations with the standard PFT set in MPI-ESM depict a gradual decrease of precipitation and vegetation cover over time, while simulations with modified PFT composition show either a sharp decline of both variables or an even slower retreat. Thus, not the quantitative but the qualitative PFT composition determines climate-vegetation interaction and the climate-vegetation system response to external forcing. The sensitivity of simulated system states to changes in PFT composition raises the question how realistically Earth system models can actually represent climate-vegetation interaction, considering the poor representation of plant diversity in the current generation of land surface models.

  18. Amazonian functional diversity from forest canopy chemical assembly.

    Science.gov (United States)

    Asner, Gregory P; Martin, Roberta E; Tupayachi, Raul; Anderson, Christopher B; Sinca, Felipe; Carranza-Jiménez, Loreli; Martinez, Paola

    2014-04-15

    Patterns of tropical forest functional diversity express processes of ecological assembly at multiple geographic scales and aid in predicting ecological responses to environmental change. Tree canopy chemistry underpins forest functional diversity, but the interactive role of phylogeny and environment in determining the chemical traits of tropical trees is poorly known. Collecting and analyzing foliage in 2,420 canopy tree species across 19 forests in the western Amazon, we discovered (i) systematic, community-scale shifts in average canopy chemical traits along gradients of elevation and soil fertility; (ii) strong phylogenetic partitioning of structural and defense chemicals within communities independent of variation in environmental conditions; and (iii) strong environmental control on foliar phosphorus and calcium, the two rock-derived elements limiting CO2 uptake in tropical forests. These findings indicate that the chemical diversity of western Amazonian forests occurs in a regionally nested mosaic driven by long-term chemical trait adjustment of communities to large-scale environmental filters, particularly soils and climate, and is supported by phylogenetic divergence of traits essential to foliar survival under varying environmental conditions. Geographically nested patterns of forest canopy chemical traits will play a role in determining the response and functional rearrangement of western Amazonian ecosystems to changing land use and climate.

  19. Testing the link between functional diversity and ecosystem functioning in a Minnesota grassland experiment.

    Science.gov (United States)

    Clark, Christopher M; Flynn, Dan F B; Butterfield, Bradley J; Reich, Peter B

    2012-01-01

    The functional diversity of a community can influence ecosystem functioning and reflects assembly processes. The large number of disparate metrics used to quantify functional diversity reflects the range of attributes underlying this concept, generally summarized as functional richness, functional evenness, and functional divergence. However, in practice, we know very little about which attributes drive which ecosystem functions, due to a lack of field-based tests. Here we test the association between eight leading functional diversity metrics (Rao's Q, FD, FDis, FEve, FDiv, convex hull volume, and species and functional group richness) that emphasize different attributes of functional diversity, plus 11 extensions of these existing metrics that incorporate heterogeneous species abundances and trait variation. We assess the relationships among these metrics and compare their performances for predicting three key ecosystem functions (above- and belowground biomass and light capture) within a long-term grassland biodiversity experiment. Many metrics were highly correlated, although unique information was captured in FEve, FDiv, and dendrogram-based measures (FD) that were adjusted by abundance. FD adjusted by abundance outperformed all other metrics in predicting both above- and belowground biomass, although several others also performed well (e.g. Rao's Q, FDis, FDiv). More generally, trait-based richness metrics and hybrid metrics incorporating multiple diversity attributes outperformed evenness metrics and single-attribute metrics, results that were not changed when combinations of metrics were explored. For light capture, species richness alone was the best predictor, suggesting that traits for canopy architecture would be necessary to improve predictions. Our study provides a comprehensive test linking different attributes of functional diversity with ecosystem function for a grassland system.

  20. Testing the Link between Functional Diversity and Ecosystem Functioning in a Minnesota Grassland Experiment

    Science.gov (United States)

    Butterfield, Bradley J.; Reich, Peter B.

    2012-01-01

    The functional diversity of a community can influence ecosystem functioning and reflects assembly processes. The large number of disparate metrics used to quantify functional diversity reflects the range of attributes underlying this concept, generally summarized as functional richness, functional evenness, and functional divergence. However, in practice, we know very little about which attributes drive which ecosystem functions, due to a lack of field-based tests. Here we test the association between eight leading functional diversity metrics (Rao’s Q, FD, FDis, FEve, FDiv, convex hull volume, and species and functional group richness) that emphasize different attributes of functional diversity, plus 11 extensions of these existing metrics that incorporate heterogeneous species abundances and trait variation. We assess the relationships among these metrics and compare their performances for predicting three key ecosystem functions (above- and belowground biomass and light capture) within a long-term grassland biodiversity experiment. Many metrics were highly correlated, although unique information was captured in FEve, FDiv, and dendrogram-based measures (FD) that were adjusted by abundance. FD adjusted by abundance outperformed all other metrics in predicting both above- and belowground biomass, although several others also performed well (e.g. Rao’s Q, FDis, FDiv). More generally, trait-based richness metrics and hybrid metrics incorporating multiple diversity attributes outperformed evenness metrics and single-attribute metrics, results that were not changed when combinations of metrics were explored. For light capture, species richness alone was the best predictor, suggesting that traits for canopy architecture would be necessary to improve predictions. Our study provides a comprehensive test linking different attributes of functional diversity with ecosystem function for a grassland system. PMID:23300787

  1. Testing the link between functional diversity and ecosystem functioning in a Minnesota grassland experiment.

    Directory of Open Access Journals (Sweden)

    Christopher M Clark

    Full Text Available The functional diversity of a community can influence ecosystem functioning and reflects assembly processes. The large number of disparate metrics used to quantify functional diversity reflects the range of attributes underlying this concept, generally summarized as functional richness, functional evenness, and functional divergence. However, in practice, we know very little about which attributes drive which ecosystem functions, due to a lack of field-based tests. Here we test the association between eight leading functional diversity metrics (Rao's Q, FD, FDis, FEve, FDiv, convex hull volume, and species and functional group richness that emphasize different attributes of functional diversity, plus 11 extensions of these existing metrics that incorporate heterogeneous species abundances and trait variation. We assess the relationships among these metrics and compare their performances for predicting three key ecosystem functions (above- and belowground biomass and light capture within a long-term grassland biodiversity experiment. Many metrics were highly correlated, although unique information was captured in FEve, FDiv, and dendrogram-based measures (FD that were adjusted by abundance. FD adjusted by abundance outperformed all other metrics in predicting both above- and belowground biomass, although several others also performed well (e.g. Rao's Q, FDis, FDiv. More generally, trait-based richness metrics and hybrid metrics incorporating multiple diversity attributes outperformed evenness metrics and single-attribute metrics, results that were not changed when combinations of metrics were explored. For light capture, species richness alone was the best predictor, suggesting that traits for canopy architecture would be necessary to improve predictions. Our study provides a comprehensive test linking different attributes of functional diversity with ecosystem function for a grassland system.

  2. Proteins with Novel Structure, Function and Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  3. Intracellular transport proteins: classification, structure and function of kinesins

    Directory of Open Access Journals (Sweden)

    Agnieszka Chudy

    2011-09-01

    Full Text Available Correct cell functioning, division and morphogenesis rely on efficient intracellular transport. Apart from dyneins and myosins, kinesins are the main proteins responsible for intracellular movement. Kinesins are a large, diverse group of motor proteins, which based on phylogenetic similarity were classified into fourteen families. Among these families, due to the location of their motor domains, three groups have been characterized: N-, C- and M-kinesin. As molecular motors, kinesins transport various molecules and vesicles mainly towards the microtubule plus end (from the cell body participating in anterograde transport, although there are also kinesins involved in retrograde transport (C-kinesins. Kinesins are also involved in spindle formation, chromosome segregation, and spermatogenesis. Because of their great importance for the correct functioning of cells, mutations in kinesin coding genes may lead to such neurodegenerative diseases as dominant hereditary spastic paraplegia or Charcot-Marie-Tooth disease.

  4. Functional Classification of Immune Regulatory Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Rubinstein, Rotem [Albert Einstein College of Medicine, Bronx, NY (United States); Ramagopal, Udupi A. [Albert Einstein College of Medicine, Bronx, NY (United States); Nathenson, Stanley G. [Albert Einstein College of Medicine, Bronx, NY (United States); Almo, Steven C. [Albert Einstein College of Medicine, Bronx, NY (United States); Fiser, Andras [Albert Einstein College of Medicine, Bronx, NY (United States)

    2013-05-01

    Members of the immunoglobulin superfamily (IgSF) control innate and adaptive immunity and are prime targets for the treatment of autoimmune diseases, infectious diseases, and malignancies. We describe a computational method, termed the Brotherhood algorithm, which utilizes intermediate sequence information to classify proteins into functionally related families. This approach identifies functional relationships within the IgSF and predicts additional receptor-ligand interactions. As a specific example, we examine the nectin/nectin-like family of cell adhesion and signaling proteins and propose receptor-ligand interactions within this family. We were guided by the Brotherhood approach and present the high-resolution structural characterization of a homophilic interaction involving the class-I MHC-restricted T-cell-associated molecule, which we now classify as a nectin-like family member. The Brotherhood algorithm is likely to have a significant impact on structural immunology by identifying those proteins and complexes for which structural characterization will be particularly informative.

  5. Functional diversity and mutational analysis of Agrobacterium 6B oncoproteins.

    Science.gov (United States)

    Helfer, A; Pien, S; Otten, L

    2002-07-01

    Many Agrobacterium T-DNA genes belong to a diverse family of T-DNA genes, the rolB family. These genes cause various growth abnormalities but their modes of action remain largely unknown. So far, none of the RolB-like proteins has been subjected to mutational analysis. The RolB-like oncoprotein 6B, which induces tumours on species such as Nicotiana glauca and Kalanchoe tubiflora, was chosen to investigate the role of the most conserved amino acid residues within the RolB family. We first determined which of the natural 6B variants had the strongest oncogenic activity; to this end, six 6b coding sequences (A- 6b, AB- 6b, C- 6b, CG- 6b, S- 6b and T- 6b) were placed under the control of the strong constitutive 2x35S promoter and compared for tumour induction on N. glauca, N. tabacum and K. daigremontiana. Oncogenicity increased in the order C- 6b/CG- 6b, A- 6b/AB- 6b, and S- 6b/T- 6b. The most conserved amino acid residues in the strongly oncogenic T-6B protein were mutated and shown to be required for oncogenicity and accumulation of the T-6B protein in planta but not in bacteria. Hybrids between T-6B and the weakly oncogenic A-6B protein revealed an additional oncogenic determinant required for the formation of large tumours.

  6. Leucocyte Function in Protein Deficiency States

    African Journals Online (AJOL)

    Total proteins and serum albumin levels were correlated in each group, according to the following: (i) the total leucocyte count; (ii) the number of cells containing NBT; and (Ui) the number of cells ... show no increase in leucocyte count; however. their leucocytes ... could find no deficiency in intracellular leucocyte function ...

  7. Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

    Science.gov (United States)

    Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feedin...

  8. Morphological and functional diversity of primary producers group in savannas

    International Nuclear Information System (INIS)

    Medina, E.

    1996-01-01

    The meaning of biological diversity for the operation and stability of natural ecosystems is matter of great theoretical and practical interest. The appearance and permanency of species in a given atmosphere indicates its capacity to compete with other species with similar habit and requirements, and to accumulate the resources that allow its reproduction. On the other hand, the coexistence of similar species in the same ecosystem allows to wonder if ever biological redundancy exists, that is to say, if several species coexist with the same function inside the ecosystem, so that the disappearance of one of them would not have biological significant consequences. A strategy to simplify the analysis of relationships between biodiversity and ecosystems operation is by grouping species with similar function, called functional groups. In this work the the primary producers functional group is analyzed, essentially superiors plants, in a savannas ecosystems. The analysis establishes that the gives the primary producers group is heterogeneous and complex, so much morphological as functionally: 1) the structural complexity and diversity forms of life in an savannas ecosystem are associated with the stratified exploitation of resources over (light) and under the floor (nourishment and water). Changes in diversity that affect the system structure will probably also affect its operations. 2 )Very similar morphological species can differ physiologically up to constitute production units with contrasting nutritional requirements. The echo-physiologic analysis of this differentiation can explain the habitat preferences that are naturally observed. 3) The long-time permanency of rare species, of low frequency, show the inability of dominant species to capture all the available resources. 4) The primary producers and the floor microorganisms have strong interactions. Changes in the community composition can generate significant changes in other community. These biotic interactions

  9. Tet protein function during Drosophila development.

    Directory of Open Access Journals (Sweden)

    Fei Wang

    Full Text Available The TET (Ten-eleven translocation 1, 2 and 3 proteins have been shown to function as DNA hydroxymethylases in vertebrates and their requirements have been documented extensively. Recently, the Tet proteins have been shown to also hydroxylate 5-methylcytosine in RNA. 5-hydroxymethylcytosine (5hmrC is enriched in messenger RNA but the function of this modification has yet to be elucidated. Because Cytosine methylation in DNA is barely detectable in Drosophila, it serves as an ideal model to study the biological function of 5hmrC. Here, we characterized the temporal and spatial expression and requirement of Tet throughout Drosophila development. We show that Tet is essential for viability as Tet complete loss-of-function animals die at the late pupal stage. Tet is highly expressed in neuronal tissues and at more moderate levels in somatic muscle precursors in embryos and larvae. Depletion of Tet in muscle precursors at early embryonic stages leads to defects in larval locomotion and late pupal lethality. Although Tet knock-down in neuronal tissue does not cause lethality, it is essential for neuronal function during development through its affects upon locomotion in larvae and the circadian rhythm of adult flies. Further, we report the function of Tet in ovarian morphogenesis. Together, our findings provide basic insights into the biological function of Tet in Drosophila, and may illuminate observed neuronal and muscle phenotypes observed in vertebrates.

  10. Trade-off between taxon diversity and functional diversity in European lake ecosystems.

    Science.gov (United States)

    Grossmann, Lars; Beisser, Daniela; Bock, Christina; Chatzinotas, Antonis; Jensen, Manfred; Preisfeld, Angelika; Psenner, Roland; Rahmann, Sven; Wodniok, Sabina; Boenigk, Jens

    2016-12-01

    Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater data set which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a.s.l) to 3110 m a.s.l. The dominant taxa were Chlorophyta and streptophytic algae, Ciliophora, Bacillariophyta and Chrysophyta. Metatranscriptomics provided insights into differences in community composition and into functional diversity via the relative share of taxa to the overall read abundance of distinct functional genes on the ecosystem level. The dominant metabolic pathways in terms of the fraction of expressed sequences in the cDNA libraries were affiliated with primary metabolism, specifically oxidative phosphorylation, photosynthesis and the TCA cycle. Our analyses indicate that community composition is a good first proxy for the analysis of ecosystem functions. However, differential gene regulation modifies the relative importance of taxa in distinct pathways. Whereas taxon composition varies considerably between lakes, the relative importance of distinct metabolic pathways is much more stable, indicating that ecosystem functioning is buffered against shifts in community composition through a functional redundancy of taxa. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  11. Kinesin-2: a family of heterotrimeric and homodimeric motors with diverse intracellular transport functions.

    Science.gov (United States)

    Scholey, Jonathan M

    2013-01-01

    Kinesin-2 was first purified as a heterotrimeric, anterograde, microtubule-based motor consisting of two distinct kinesin-related subunits and a novel associated protein (KAP) that is currently best known for its role in intraflagellar transport and ciliogenesis. Subsequent work, however, has revealed diversity in the oligomeric state of different kinesin-2 motors owing to the combinatorial heterodimerization of its subunits and the coexistence of both heterotrimeric and homodimeric kinesin-2 motors in some cells. Although the functional significance of the homo- versus heteromeric organization of kinesin-2 motor subunits and the role of KAP remain uncertain, functional studies suggest that cooperation between different types of kinesin-2 motors or between kinesin-2 and a member of a different motor family can generate diverse patterns of anterograde intracellular transport. Moreover, despite being restricted to ciliated eukaryotes, kinesin-2 motors are now known to drive diverse transport events outside cilia. Here, I review the organization, assembly, phylogeny, biological functions, and motility mechanism of this diverse family of intracellular transport motors.

  12. Functional annotation of chemical libraries across diverse biological processes.

    Science.gov (United States)

    Piotrowski, Jeff S; Li, Sheena C; Deshpande, Raamesh; Simpkins, Scott W; Nelson, Justin; Yashiroda, Yoko; Barber, Jacqueline M; Safizadeh, Hamid; Wilson, Erin; Okada, Hiroki; Gebre, Abraham A; Kubo, Karen; Torres, Nikko P; LeBlanc, Marissa A; Andrusiak, Kerry; Okamoto, Reika; Yoshimura, Mami; DeRango-Adem, Eva; van Leeuwen, Jolanda; Shirahige, Katsuhiko; Baryshnikova, Anastasia; Brown, Grant W; Hirano, Hiroyuki; Costanzo, Michael; Andrews, Brenda; Ohya, Yoshikazu; Osada, Hiroyuki; Yoshida, Minoru; Myers, Chad L; Boone, Charles

    2017-09-01

    Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound's mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.

  13. Conserving Phylogenetic Diversity Can Be a Poor Strategy for Conserving Functional Diversity.

    Science.gov (United States)

    Mazel, Florent; Mooers, Arne O; Riva, Giulio Valentino Dalla; Pennell, Matthew W

    2017-11-01

    For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policy makers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and features (functional diversity [FD]), which may be valuable for a number of reasons. The claim that PD-maximized ("maxPD") sets of taxa will also have high FD is often taken at face value and in cases where researchers have actually tested it, they have done so by measuring the phylogenetic signal in ecologically important functional traits. The rationale is that if traits closely mirror phylogeny, then saving the maxPD set of taxa will tend to maximize FD and if traits do not have phylogenetic structure, then saving the maxPD set of taxa will be no better at capturing FD than criteria that ignore PD. Here, we suggest that measuring the phylogenetic signal in traits is uninformative for evaluating the effectiveness of using PD in conservation. We evolve traits under several different models and, for the first time, directly compare the FD of a set of taxa that maximize PD to the FD of a random set of the same size. Under many common models of trait evolution and tree shapes, conserving the maxPD set of taxa will conserve more FD than conserving a random set of the same size. However, this result cannot be generalized to other classes of models. We find that under biologically plausible scenarios, using PD to select species can actually lead to less FD compared with a random set. Critically, this can occur even when there is phylogenetic signal in the traits. Predicting exactly when we expect using PD to be a good strategy for conserving FD is challenging, as it depends on complex interactions between tree shape and the assumptions of the evolutionary model. Nonetheless, if our goal is to maintain trait diversity, the fact

  14. Functional Dynamics and Proton Transfer in Proteins

    Science.gov (United States)

    Boxer, Steven

    2014-03-01

    Internal proton transfer between an enzyme and substrate is a common feature of many enzyme mechanisms. Likewise, internal proton transfer between the chromophore of green fluorescent protein (GFP) and amino acids on the inside of the beta barrel are important both in the ground and excited state. I will discuss an interesting connection between the proton transfer dynamics in GFP and those in an enzyme, ketosteroid isomerase (KSI), bound to substrate analogs. In both cases there is a tug of war between the protein and bound substrate analog or chromophore that depends on their affinities for a proton and which can be tuned either by changing the substrate/chromophore or the protein. This can be observed in the ground state by optical methods (absorption and IR) as well as by nmr, or in the excited state by time-resolved fluorescence or visible pump-IR probe measurements. In both cases the proton dynamics have important functional consequences.

  15. Extracellular Enzyme Activity assay as indicator of soil microbial functional diversity and activity

    DEFF Research Database (Denmark)

    Hendriksen, Niels Bohse; Winding, Anne

    2012-01-01

    and soil ecosystem services. The soil enzyme activity has been measured by the use of fluorogenic model substrates e.g. methylumbelliferyl (MUF) substrates for a number of enzymes involved in the degradation of polysaccharides as cellulose, hemicellulose and chitin, while degradation of proteins has been......Extracellular Enzyme Activity assay as indicator of soil microbial functional diversity and activity Niels Bohse Hendriksen, Anne Winding. Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark Soil enzymes originate from a variety of organisms, notably fungi and bacteria......, experimental conditions of extraction of enzymes from soils, buffer and pH, substrate concentration, temperature and the necessary controls were optimized and standardized. This has resulted in an optimized standard operating procedure of EEA, which are being tested as an indicator of soil functional diversity...

  16. Diversity in protein profiles of individual calcium oxalate kidney stones.

    Science.gov (United States)

    Okumura, Nobuaki; Tsujihata, Masao; Momohara, Chikahiro; Yoshioka, Iwao; Suto, Kouzou; Nonomura, Norio; Okuyama, Akihiko; Takao, Toshifumi

    2013-01-01

    Calcium oxalate kidney stones contain low amounts of proteins, some of which have been implicated in progression or prevention of kidney stone formation. To gain insights into the pathophysiology of urolithiasis, we have characterized protein components of calcium oxalate kidney stones by proteomic approaches. Proteins extracted from kidney stones showed highly heterogeneous migration patterns in gel electrophoresis as reported. This was likely to be mainly due to proteolytic degradation and protein-protein crosslinking of Tamm-Horsfall protein and prothrombin. Protein profiles of calcium oxalate kidney stones were obtained by in-solution protease digestion followed by nanoLC-MALDI-tandem mass spectrometry, which resulted in identification of a total of 92 proteins in stones from 9 urolithiasis patients. Further analysis showed that protein species and their relative amounts were highly variable among individual stones. Although proteins such as prothrombin, osteopontin, calgranulin A and calgranulin B were found in most stones tested, some samples had high contents of prothrombin and osteopontin, while others had high contents of calgranulins. In addition, calgranulin-rich stones had various neutrophil-enriched proteins such as myeloperoxidase and lactotransferrin. These proteomic profiles of individual kidney stones suggest that multiple systems composed of different groups of proteins including leucocyte-derived ones are differently involved in pathogenesis of individual kidney stones depending on situations.

  17. Reducing the impacts of Neotropical oil palm development on functional diversity

    OpenAIRE

    Prescott, Graham W.; Gilroy, James J.; Haugaasen, Torbjørn; Medina Uribe, Claudia A.; Foster, William A.; Edwards, David P.

    2016-01-01

    Large-scale conversion of natural habitats to agriculture reduces species richness and functional diversity, with important implications for the provision of many ecosystem services. We investigated possible solutions to minimise loss of functional diversity: retaining forest fragments to enhance functional diversity within agricultural lands, and restricting future expansion of tropical crops to degraded lands or low-productivity farmlands to conserve functional diversity at a landscape leve...

  18. Multiple metrics of diversity have different effects on temperate forest functioning over succession.

    OpenAIRE

    Yuan, Zuoqiang; Wang, Shaopeng; Gazol, Antonio; Mellard, Jarad Pope; Lin, Fei; Ye, Ji; Hao, Zhanqing; Wang, Xugao; Loreau, Michel

    2016-01-01

    Biodiversity can be measured by taxonomic, phylogenetic, and functional diversity. How ecosystem functioning depends on these measures of diversity can vary from site to site and depends on successional stage. Here, we measured taxonomic, phylogenetic, and functional diversity, and examined their relationship with biomass in two successional stages of the broad-leaved Korean pine forest in northeastern China. Functional diversity was calculated from six plant traits, and aboveground biomass (...

  19. Evaluation of nine distance-based measures of functional diversity applied to forest communities

    OpenAIRE

    Jin-Tun Zhang; Naiqi Song; Lihong Fan

    2013-01-01

    Several methods for the estimation of functional diversity are employed in plant communities. However, it is hard to select the most suitable measures in practice. This work presents comparisons of nine distance-based measures applied to functional diversity analysis in forest communities (36 plots) along an elevational gradient in the Pangquangou Reserve, China. The employed indices and methods were: functional attribute diversity (FAD), Raos functional diversity (Raos index), single linkage...

  20. Consumers control diversity and functioning of a natural marine ecosystem.

    Directory of Open Access Journals (Sweden)

    Andrew H Altieri

    Full Text Available BACKGROUND: Our understanding of the functional consequences of changes in biodiversity has been hampered by several limitations of previous work, including limited attention to trophic interactions, a focus on species richness rather than evenness, and the use of artificially assembled communities. METHODOLOGY AND PRINCIPAL FINDINGS: In this study, we manipulated the density of an herbivorous snail in natural tide pools and allowed seaweed communities to assemble in an ecologically relevant and non-random manner. Seaweed species evenness and biomass-specific primary productivity (mg O(2 h(-1 g(-1 were higher in tide pools with snails because snails preferentially consumed an otherwise dominant seaweed species that can reduce biomass-specific productivity rates of algal assemblages. Although snails reduced overall seaweed biomass in tide pools, they did not affect gross primary productivity at the scale of tide pools (mg O(2 h(-1 pool(-1 or mg O(2 h(-1 m(-2 because of the enhanced biomass-specific productivity associated with grazer-mediated increases in algal evenness. SIGNIFICANCE: Our results suggest that increased attention to trophic interactions, diversity measures other than richness, and particularly the effects of consumers on evenness and primary productivity, will improve our understanding of the relationship between diversity and ecosystem functioning and allow more effective links between experimental results and real-world changes in biodiversity.

  1. Functional biogeography of oceanic islands and the scaling of functional diversity in the Azores.

    Science.gov (United States)

    Whittaker, Robert J; Rigal, François; Borges, Paulo A V; Cardoso, Pedro; Terzopoulou, Sofia; Casanoves, Fernando; Pla, Laura; Guilhaumon, François; Ladle, Richard J; Triantis, Kostas A

    2014-09-23

    Analyses of species-diversity patterns of remote islands have been crucial to the development of biogeographic theory, yet little is known about corresponding patterns in functional traits on islands and how, for example, they may be affected by the introduction of exotic species. We collated trait data for spiders and beetles and used a functional diversity index (FRic) to test for nonrandomness in the contribution of endemic, other native (also combined as indigenous), and exotic species to functional-trait space across the nine islands of the Azores. In general, for both taxa and for each distributional category, functional diversity increases with species richness, which, in turn scales with island area. Null simulations support the hypothesis that each distributional group contributes to functional diversity in proportion to their species richness. Exotic spiders have added novel trait space to a greater degree than have exotic beetles, likely indicating greater impact of the reduction of immigration filters and/or differential historical losses of indigenous species. Analyses of species occurring in native-forest remnants provide limited indications of the operation of habitat filtering of exotics for three islands, but only for beetles. Although the general linear (not saturating) pattern of trait-space increase with richness of exotics suggests an ongoing process of functional enrichment and accommodation, further work is urgently needed to determine how estimates of extinction debt of indigenous species should be adjusted in the light of these findings.

  2. Genetic diversity and evolution of human metapneumovirus fusion protein over twenty years

    Directory of Open Access Journals (Sweden)

    Liem Alexis

    2009-09-01

    Full Text Available Abstract Background Human metapneumovirus (HMPV is an important cause of acute respiratory illness in children. We examined the diversity and molecular evolution of HMPV using 85 full-length F (fusion gene sequences collected over a 20-year period. Results The F gene sequences fell into two major groups, each with two subgroups, which exhibited a mean of 96% identity by predicted amino acid sequences. Amino acid identity within and between subgroups was higher than nucleotide identity, suggesting structural or functional constraints on F protein diversity. There was minimal progressive drift over time, and the genetic lineages were stable over the 20-year period. Several canonical amino acid differences discriminated between major subgroups, and polymorphic variations tended to cluster in discrete regions. The estimated rate of mutation was 7.12 × 10-4 substitutions/site/year and the estimated time to most recent common HMPV ancestor was 97 years (95% likelihood range 66-194 years. Analysis suggested that HMPV diverged from avian metapneumovirus type C (AMPV-C 269 years ago (95% likelihood range 106-382 years. Conclusion HMPV F protein remains conserved over decades. HMPV appears to have diverged from AMPV-C fairly recently.

  3. Genetic diversity and evolution of human metapneumovirus fusion protein over twenty years

    Science.gov (United States)

    Yang, Chin-Fen; Wang, Chiaoyin K; Tollefson, Sharon J; Piyaratna, Rohith; Lintao, Linda D; Chu, Marla; Liem, Alexis; Mark, Mary; Spaete, Richard R; Crowe, James E; Williams, John V

    2009-01-01

    Background Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in children. We examined the diversity and molecular evolution of HMPV using 85 full-length F (fusion) gene sequences collected over a 20-year period. Results The F gene sequences fell into two major groups, each with two subgroups, which exhibited a mean of 96% identity by predicted amino acid sequences. Amino acid identity within and between subgroups was higher than nucleotide identity, suggesting structural or functional constraints on F protein diversity. There was minimal progressive drift over time, and the genetic lineages were stable over the 20-year period. Several canonical amino acid differences discriminated between major subgroups, and polymorphic variations tended to cluster in discrete regions. The estimated rate of mutation was 7.12 × 10-4 substitutions/site/year and the estimated time to most recent common HMPV ancestor was 97 years (95% likelihood range 66-194 years). Analysis suggested that HMPV diverged from avian metapneumovirus type C (AMPV-C) 269 years ago (95% likelihood range 106-382 years). Conclusion HMPV F protein remains conserved over decades. HMPV appears to have diverged from AMPV-C fairly recently. PMID:19740442

  4. Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield.

    Science.gov (United States)

    Bhadra, Pratiti; Pal, Debnath

    2017-04-01

    Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for Function) to query protein function from ≥1 µs long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Functional Diversity of Plant–Pollinator Interaction Webs Enhances the Persistence of Plant Communities

    Science.gov (United States)

    Dajoz, Isabelle; Meriguet, Jacques; Loreau, Michel

    2006-01-01

    Pollination is exclusively or mainly animal mediated for 70% to 90% of angiosperm species. Thus, pollinators provide an essential ecosystem service to humankind. However, the impact of human-induced biodiversity loss on the functioning of plant–pollinator interactions has not been tested experimentally. To understand how plant communities respond to diversity changes in their pollinating fauna, we manipulated the functional diversity of both plants and pollinators under natural conditions. Increasing the functional diversity of both plants and pollinators led to the recruitment of more diverse plant communities. After two years the plant communities pollinated by the most functionally diverse pollinator assemblage contained about 50% more plant species than did plant communities pollinated by less-diverse pollinator assemblages. Moreover, the positive effect of functional diversity was explained by a complementarity between functional groups of pollinators and plants. Thus, the functional diversity of pollination networks may be critical to ecosystem sustainability. PMID:16332160

  6. Functional diversity of plant-pollinator interaction webs enhances the persistence of plant communities.

    Science.gov (United States)

    Fontaine, Colin; Dajoz, Isabelle; Meriguet, Jacques; Loreau, Michel

    2006-01-01

    Pollination is exclusively or mainly animal mediated for 70% to 90% of angiosperm species. Thus, pollinators provide an essential ecosystem service to humankind. However, the impact of human-induced biodiversity loss on the functioning of plant-pollinator interactions has not been tested experimentally. To understand how plant communities respond to diversity changes in their pollinating fauna, we manipulated the functional diversity of both plants and pollinators under natural conditions. Increasing the functional diversity of both plants and pollinators led to the recruitment of more diverse plant communities. After two years the plant communities pollinated by the most functionally diverse pollinator assemblage contained about 50% more plant species than did plant communities pollinated by less-diverse pollinator assemblages. Moreover, the positive effect of functional diversity was explained by a complementarity between functional groups of pollinators and plants. Thus, the functional diversity of pollination networks may be critical to ecosystem sustainability.

  7. Functional Diversity of Plant-Pollinator Interaction Webs Enhances the Persistence of Plant Communities.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available Pollination is exclusively or mainly animal mediated for 70% to 90% of angiosperm species. Thus, pollinators provide an essential ecosystem service to humankind. However, the impact of human-induced biodiversity loss on the functioning of plant-pollinator interactions has not been tested experimentally. To understand how plant communities respond to diversity changes in their pollinating fauna, we manipulated the functional diversity of both plants and pollinators under natural conditions. Increasing the functional diversity of both plants and pollinators led to the recruitment of more diverse plant communities. After two years the plant communities pollinated by the most functionally diverse pollinator assemblage contained about 50% more plant species than did plant communities pollinated by less-diverse pollinator assemblages. Moreover, the positive effect of functional diversity was explained by a complementarity between functional groups of pollinators and plants. Thus, the functional diversity of pollination networks may be critical to ecosystem sustainability.

  8. Functional diversity of plant-pollinator interaction webs enhances the persistence of plant communities.

    Directory of Open Access Journals (Sweden)

    Colin Fontaine

    2006-01-01

    Full Text Available Pollination is exclusively or mainly animal mediated for 70% to 90% of angiosperm species. Thus, pollinators provide an essential ecosystem service to humankind. However, the impact of human-induced biodiversity loss on the functioning of plant-pollinator interactions has not been tested experimentally. To understand how plant communities respond to diversity changes in their pollinating fauna, we manipulated the functional diversity of both plants and pollinators under natural conditions. Increasing the functional diversity of both plants and pollinators led to the recruitment of more diverse plant communities. After two years the plant communities pollinated by the most functionally diverse pollinator assemblage contained about 50% more plant species than did plant communities pollinated by less-diverse pollinator assemblages. Moreover, the positive effect of functional diversity was explained by a complementarity between functional groups of pollinators and plants. Thus, the functional diversity of pollination networks may be critical to ecosystem sustainability.

  9. Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

    Directory of Open Access Journals (Sweden)

    Mariana Gomes Germano

    2012-05-01

    Full Text Available The objective of this work was to evaluate the catabolic gene diversity for the bacterial degradation of aromatic hydrocarbons in anthropogenic dark earth of Amazonia (ADE and their biochar (BC. Functional diversity analyses in ADE soils can provide information on how adaptive microorganisms may influence the fertility of soils and what is their involvement in biogeochemical cycles. For this, clone libraries containing the gene encoding for the alpha subunit of aromatic ring-hydroxylating dioxygenases (α-ARHD bacterial gene were constructed, totaling 800 clones. These libraries were prepared from samples of an ADE soil under two different land uses, located at the Caldeirão Experimental Station - secondary forest (SF and agriculture (AG -, and the biochar (SF_BC and AG_BC, respectively. Heterogeneity estimates indicated greater diversity in BC libraries; and Venn diagrams showed more unique operational protein clusters (OPC in the SF_BC library than the ADE soil, which indicates that specific metabolic processes may occur in biochar. Phylogenetic analysis showed unidentified dioxygenases in ADE soils. Libraries containing functional gene encoding for the alpha subunit of the aromatic ring-hydroxylating dioxygenases (ARHD gene from biochar show higher diversity indices than those of ADE under secondary forest and agriculture.

  10. Diversity Indices as Measures of Functional Annotation Methods in Metagenomics Studies

    KAUST Repository

    Jankovic, Boris R.

    2016-01-26

    Applications of high-throughput techniques in metagenomics studies produce massive amounts of data. Fragments of genomic, transcriptomic and proteomic molecules are all found in metagenomics samples. Laborious and meticulous effort in sequencing and functional annotation are then required to, amongst other objectives, reconstruct a taxonomic map of the environment that metagenomics samples were taken from. In addition to computational challenges faced by metagenomics studies, the analysis is further complicated by the presence of contaminants in the samples, potentially resulting in skewed taxonomic analysis. The functional annotation in metagenomics can utilize all available omics data and therefore different methods that are associated with a particular type of data. For example, protein-coding DNA, non-coding RNA or ribosomal RNA data can be used in such an analysis. These methods would have their advantages and disadvantages and the question of comparison among them naturally arises. There are several criteria that can be used when performing such a comparison. Loosely speaking, methods can be evaluated in terms of computational complexity or in terms of the expected biological accuracy. We propose that the concept of diversity that is used in the ecosystems and species diversity studies can be successfully used in evaluating certain aspects of the methods employed in metagenomics studies. We show that when applying the concept of Hill’s diversity, the analysis of variations in the diversity order provides valuable clues into the robustness of methods used in the taxonomical analysis.

  11. The functional properties, modification and utilization of whey proteins

    Directory of Open Access Journals (Sweden)

    B. G. Venter

    1986-03-01

    Full Text Available Whey protein has an excellent nutritional value and exhibits a functional potential. In comparison with certain other food proteins, the whey protein content of essential amino acids is extremely favourable for human consumption. Depending on the heat-treatment history thereof, soluble whey proteins with utilizable functional properties, apart from high biological value, true digestibility, protein efficiency ratio and nett protein utilization, can be recovered. Various technological and chemical recovery processes have been designed. Chemically and enzymatically modified whey protein is manufactured to obtain technological and functional advantages. The important functional properties of whey proteins, namely hydration, gelation, emulsifying and foaming properties, are reviewed.

  12. Functional trait diversity across trophic levels determines herbivore impact on plant community biomass.

    Science.gov (United States)

    Deraison, Hélène; Badenhausser, Isabelle; Loeuille, Nicolas; Scherber, Christoph; Gross, Nicolas

    2015-12-01

    Understanding the consequences of trophic interactions for ecosystem functioning is challenging, as contrasting effects of species and functional diversity can be expected across trophic levels. We experimentally manipulated functional identity and diversity of grassland insect herbivores and tested their impact on plant community biomass. Herbivore resource acquisition traits, i.e. mandible strength and the diversity of mandibular traits, had more important effects on plant biomass than body size. Higher herbivore functional diversity increased overall impact on plant biomass due to feeding niche complementarity. Higher plant functional diversity limited biomass pre-emption by herbivores. The functional diversity within and across trophic levels therefore regulates the impact of functionally contrasting consumers on primary producers. By experimentally manipulating the functional diversity across trophic levels, our study illustrates how trait-based approaches constitute a promising way to tackle existing links between trophic interactions and ecosystem functioning. © 2015 John Wiley & Sons Ltd/CNRS.

  13. Ontogenetic functional diversity: size structure of a keystone predator drives functioning of a complex ecosystem.

    Science.gov (United States)

    Rudolf, Volker H W; Rasmussen, Nick L

    2013-05-01

    A central challenge in community ecology is to understand the connection between biodiversity and the functioning of ecosystems. While traditional approaches have largely focused on species-level diversity, increasing evidence indicates that there exists substantial ecological diversity among individuals within species. By far, the largest source of this intraspecific diversity stems from variation among individuals in ontogenetic stage and size. Although such ontogenetic shifts are ubiquitous in natural communities, whether and how they scale up to influence the structure and functioning of complex ecosystems is largely unknown. Here we take an experimental approach to examine the consequences of ontogenetic niche shifts for the structure of communities and ecosystem processes. In particular we experimentally manipulated the stage structure in a keystone predator, larvae of the dragonfly Anax junius, in complex experimental pond communities to test whether changes in the population stage or size structure of a keystone species scale up to alter community structure and ecosystem processes, and how functional differences scale with relative differences in size among stages. We found that the functional role of A. junius was stage-specific. Altering what stages were present in a pond led to concurrent changes in community structure, primary producer biomass (periphyton and phytoplankton), and ultimately altered ecosystem processes (respiration and net primary productivity), indicating a strong, but stage-specific, trophic cascade. Interestingly, the stage-specific effects did not simply scale with size or biomass of the predator, but instead indicated clear ontogenetic niche shifts in ecological interactions. Thus, functional differences among stages within a keystone species scaled up to alter the functioning of entire ecosystems. Therefore, our results indicate that the classical approach of assuming an average functional role of a species can be misleading because

  14. Platyhelminth Venom Allergen-Like (VAL) proteins: revealing structural diversity, class-specific features and biological associations across the phylum

    Science.gov (United States)

    CHALMERS, IAIN W.; HOFFMANN, KARL F.

    2012-01-01

    SUMMARY During platyhelminth infection, a cocktail of proteins is released by the parasite to aid invasion, initiate feeding, facilitate adaptation and mediate modulation of the host immune response. Included amongst these proteins is the Venom Allergen-Like (VAL) family, part of the larger sperm coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) superfamily. To explore the significance of this protein family during Platyhelminthes development and host interactions, we systematically summarize all published proteomic, genomic and immunological investigations of the VAL protein family to date. By conducting new genomic and transcriptomic interrogations to identify over 200 VAL proteins (228) from species in all 4 traditional taxonomic classes (Trematoda, Cestoda, Monogenea and Turbellaria), we further expand our knowledge related to platyhelminth VAL diversity across the phylum. Subsequent phylogenetic and tertiary structural analyses reveal several class-specific VAL features, which likely indicate a range of roles mediated by this protein family. Our comprehensive analysis of platyhelminth VALs represents a unifying synopsis for understanding diversity within this protein family and a firm context in which to initiate future functional characterization of these enigmatic members. PMID:22717097

  15. The E4 protein; structure, function and patterns of expression

    Energy Technology Data Exchange (ETDEWEB)

    Doorbar, John, E-mail: jdoorba@nimr.mrc.ac.uk

    2013-10-15

    The papillomavirus E4 open reading frame (ORF) is contained within the E2 ORF, with the primary E4 gene-product (E1{sup ∧}E4) being translated from a spliced mRNA that includes the E1 initiation codon and adjacent sequences. E4 is located centrally within the E2 gene, in a region that encodes the E2 protein′s flexible hinge domain. Although a number of minor E4 transcripts have been reported, it is the product of the abundant E1{sup ∧}E4 mRNA that has been most extensively analysed. During the papillomavirus life cycle, the E1{sup ∧}E4 gene products generally become detectable at the onset of vegetative viral genome amplification as the late stages of infection begin. E4 contributes to genome amplification success and virus synthesis, with its high level of expression suggesting additional roles in virus release and/or transmission. In general, E4 is easily visualised in biopsy material by immunostaining, and can be detected in lesions caused by diverse papillomavirus types, including those of dogs, rabbits and cattle as well as humans. The E4 protein can serve as a biomarker of active virus infection, and in the case of high-risk human types also disease severity. In some cutaneous lesions, E4 can be expressed at higher levels than the virion coat proteins, and can account for as much as 30% of total lesional protein content. The E4 proteins of the Beta, Gamma and Mu HPV types assemble into distinctive cytoplasmic, and sometimes nuclear, inclusion granules. In general, the E4 proteins are expressed before L2 and L1, with their structure and function being modified, first by kinases as the infected cell progresses through the S and G2 cell cycle phases, but also by proteases as the cell exits the cell cycle and undergoes true terminal differentiation. The kinases that regulate E4 also affect other viral proteins simultaneously, and include protein kinase A, Cyclin-dependent kinase, members of the MAP Kinase family and protein kinase C. For HPV16 E1{sup

  16. Functional Diversity of Fibroblast Growth Factors in Bone Formation

    Directory of Open Access Journals (Sweden)

    Yuichiro Takei

    2015-01-01

    Full Text Available The functional significance of fibroblast growth factor (FGF signaling in bone formation has been demonstrated through genetic loss-of-function and gain-of-function approaches. FGFs, comprising 22 family members, are classified into three subfamilies: canonical, hormone-like, and intracellular. The former two subfamilies activate their signaling pathways through FGF receptors (FGFRs. Currently, intracellular FGFs appear to be primarily involved in the nervous system. Canonical FGFs such as FGF2 play significant roles in bone formation, and precise spatiotemporal control of FGFs and FGFRs at the transcriptional and posttranscriptional levels may allow for the functional diversity of FGFs during bone formation. Recently, several research groups, including ours, have shown that FGF23, a member of the hormone-like FGF subfamily, is primarily expressed in osteocytes/osteoblasts. This polypeptide decreases serum phosphate levels by inhibiting renal phosphate reabsorption and vitamin D3 activation, resulting in mineralization defects in the bone. Thus, FGFs are involved in the positive and negative regulation of bone formation. In this review, we focus on the reciprocal roles of FGFs in bone formation in relation to their local versus systemic effects.

  17. Genetic and functional diversity of Pseudomonas aeruginosa lipopolysaccharide

    Directory of Open Access Journals (Sweden)

    Joseph S. Lam

    2011-06-01

    Full Text Available Lipopolysccharide (LPS is an integral component of the Pseudomonas aeruginosa cell envelope, occupying the outer leaflet of the outer membrane in this Gram-negative opportunistic pathogen. It is important for bacteria-host interactions and has been shown to be a major virulence factor for this organism. Structurally, P. aeruginosa LPS is composed of three domains, namely, lipid A, core oligosaccharide, and the distal O antigen (O-Ag. Most P. aeruginosa strains produce two distinct forms of O-Ag, one a homopolymer of D-rhamnose that is a common polysaccharide antigen (CPA, formerly termed A band, and the other a heteropolymer of three to five distinct (and often unique dideoxy sugars in its repeat units, known as O-specific antigen (OSA, formerly termed B band. Compositional differences in the O units among the OSA from different strains form the basis of the International Antigenic Typing Scheme for classification via serotyping of different strains of P. aeruginosa. The focus of this review is to provide state-of-the-art knowledge on the genetic and resultant functional diversity of LPS produced by P. aeruginosa. The underlying factors contributing to this diversity will be thoroughly discussed and presented in the context of its contributions to host-pathogen interactions and the control/prevention of infection.

  18. Structure, function and diversity of the healthy human microbiome.

    Science.gov (United States)

    2012-06-13

    Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

  19. Limiting similarity and functional diversity along environmental gradients

    Science.gov (United States)

    Schwilk, D.W.; Ackerly, D.D.

    2005-01-01

    Recent developments in community models emphasize the importance of incorporating stochastic processes (e.g. ecological drift) in models of niche-structured community assembly. We constructed a finite, spatially explicit, lottery model to simulate the distribution of species in a one-dimensional landscape with an underlying gradient in environmental conditions. Our framework combines the potential for ecological drift with environmentally-mediated competition for space in a heterogeneous environment. We examined the influence of niche breadth, dispersal distances, community size (total number of individuals) and the breadth of the environmental gradient on levels of species and functional trait diversity (i.e. differences in niche optima). Three novel results emerge from this model: (1) niche differences between adjacent species (e.g. limiting similarity) increase in smaller communities, because of the interaction of competitive effects and finite population sizes; (2) immigration from a regional species pool, stochasticity and niche-assembly generate a bimodal distribution of species residence times ('transient' and 'resident') under a heterogeneous environment; and (3) the magnitude of environmental heterogeneity has a U-shaped effect on diversity, because of shifts in species richness of resident vs. transient species. These predictions illustrate the potential importance of stochastic (although not necessarily neutral) processes in community assembly. ??2005 Blackwell Publishing Ltd/CNRS.

  20. Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide.

    Science.gov (United States)

    Lam, Joseph S; Taylor, Véronique L; Islam, Salim T; Hao, Youai; Kocíncová, Dana

    2011-01-01

    Lipopolysccharide (LPS) is an integral component of the Pseudomonas aeruginosa cell envelope, occupying the outer leaflet of the outer membrane in this Gram-negative opportunistic pathogen. It is important for bacterium-host interactions and has been shown to be a major virulence factor for this organism. Structurally, P. aeruginosa LPS is composed of three domains, namely, lipid A, core oligosaccharide, and the distal O antigen (O-Ag). Most P. aeruginosa strains produce two distinct forms of O-Ag, one a homopolymer of D-rhamnose that is a common polysaccharide antigen (CPA, formerly termed A band), and the other a heteropolymer of three to five distinct (and often unique dideoxy) sugars in its repeat units, known as O-specific antigen (OSA, formerly termed B band). Compositional differences in the O units among the OSA from different strains form the basis of the International Antigenic Typing Scheme for classification via serotyping of different strains of P. aeruginosa. The focus of this review is to provide state-of-the-art knowledge on the genetic and resultant functional diversity of LPS produced by P. aeruginosa. The underlying factors contributing to this diversity will be thoroughly discussed and presented in the context of its contributions to host-pathogen interactions and the control/prevention of infection.

  1. Growth hormone receptor/binding protein: physiology and function.

    Science.gov (United States)

    Herington, A C; Ymer, S I; Stevenson, J L; Roupas, P

    1994-07-01

    Soluble truncated forms of the growth hormone receptor (GHR) are present in the circulation of many species and are also produced by many tissues/cell types. The major high-affinity forms of these GH-binding proteins (GHBP) are derived by alternative splicing of GHR mRNA in rodents, but probably by proteolytic cleavage in other species. Questions still remain with respect to the origins, native molecular form(s), physiology, and function of the GHBPs, however. The observation that GH induces dimerization of the soluble GHBP and membrane GHR, and that dimerization of GHR appears to be critical for GH bioactivity suggests that the presentation of GH to target cells, in an unbound form or as a monomeric or dimeric complex with GHBP, may have significant implications for the ability of GH to activate specific postreceptor signaling pathways (tyrosine kinase, protein kinase C, G-protein pathways) known to be utilized by GH for its diverse biological effects. This minireview addresses some of these aspects and highlights several new questions which have arisen as a result of recent advances in our understanding of the structure, function, and signaling mechanisms of the membrane bound GHR.

  2. Growth hormone receptor/binding protein: Physiology and function

    Energy Technology Data Exchange (ETDEWEB)

    Herington, A.C.; Ymer, S.I.; Stevenson, J.L.; Roupas, P. [Royal Children`s Hospital, Melbourne (Australia)

    1994-12-31

    Soluble truncated forms of the growth hormone receptor (GHR) are present in the circulation of many species and are also produced by many tissues/cell types. The major high-affinity forms of these GH-binding proteins (GHBP) are derived by alternative splicing of GHR mRNA in rodents, but probably by proteolytic cleavage in other species. Questions still remain with respect to the origins, native molecular forms(s), physiology, and function of the GHBPs, however. The observation that GH induces dimerization of the soluble GHBP and a membrane GHR, and that dimerization of GHR appears to be critical for GH bioactivity suggests that the presentation of GH to target cells, in an unbound form or as a monomeric or dimeric complex with GHBP, may have significant implications for the ability of GH to activate specific postreceptor signaling pathways (tyrosine kinase, protein kinase C, G-protein pathways) known to be utilized by GH for its diverse biological effects. This minireview addresses some of these aspects and highlights several new questions which have arisen as a result of recent advances in our understanding of the structure, function, and signaling mechanisms of the membrane bound GHR. 43 refs.

  3. The functions of biological diversity in an age of extinction.

    Science.gov (United States)

    Naeem, Shahid; Duffy, J Emmett; Zavaleta, Erika

    2012-06-15

    Ecosystems worldwide are rapidly losing taxonomic, phylogenetic, genetic, and functional diversity as a result of human appropriation of natural resources, modification of habitats and climate, and the spread of pathogenic, exotic, and domestic plants and animals. Twenty years of intense theoretical and empirical research have shown that such biotic impoverishment can markedly alter the biogeochemical and dynamic properties of ecosystems, but frontiers remain in linking this research to the complexity of wild nature, and in applying it to pressing environmental issues such as food, water, energy, and biosecurity. The question before us is whether these advances can take us beyond merely invoking the precautionary principle of conserving biodiversity to a predictive science that informs practical and specific solutions to mitigate and adapt to its loss.

  4. Taxonomic and functional diversity of Streptomyces in a forest soil.

    Science.gov (United States)

    Bontemps, Cyril; Toussaint, Maxime; Revol, Pierre-Vincent; Hotel, Laurence; Jeanbille, Mathilde; Uroz, Stéphane; Turpault, Marie-Pierre; Blaudez, Damien; Leblond, Pierre

    2013-05-01

    In this work we report the isolation and the characterization of 79 Streptomyces isolates from a French forest soil. The 16S rRNA gene phylogeny indicated that a great diversity of Streptomyces was present in this soil, with at least nine different and potentially new species. Growth plate assays showed that most Streptomyces lineages exhibit cellulolytic and hemicellulolytic capacities and potentially participate in wood decomposition. Molecular screening for a specific hydrogenase also indicated a widespread potential for atmospheric H2 uptake. Co-culture experiments with representative strains showed antagonistic effects between Streptomyces of the same population and between Streptomyces and various fungi. Interestingly, in certain conditions, growth promotion of some fungi also occurred. We conclude that in forest soil, Streptomyces populations exhibit many important functions involved in different biogeochemical cycles and also influence the structure of soil microbial communities. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  5. Unrecognized coral species diversity masks differences in functional ecology.

    Science.gov (United States)

    Boulay, Jennifer N; Hellberg, Michael E; Cortés, Jorge; Baums, Iliana B

    2014-02-07

    Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating asexual coral fragments. These fragments proliferate in marginal habitat not colonized by P. lobata. The two Porites species also show a differential bleaching response despite hosting the same dominant symbiont subclade. Thus, hidden diversity within these reef-builders has until now obscured differences in trophic interactions, reproductive dynamics and bleaching susceptibility, indicative of differential responses when confronted with future climate change.

  6. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.

    2017-01-17

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  7. Using Gel Electrophoresis To Illustrate Protein Diversity and Isoelectric Point.

    Science.gov (United States)

    Browning, Mark; Vanable, Joseph

    2002-01-01

    Demonstrates the differences in protein structures by focusing on isoelectric point with an experiment that is observable under certain pH levels in gel electrophoresis. Explains the electrophoresis procedure and reports results of the experiments. (YDS)

  8. Diverse Functional Properties of Wilson Disease ATP7B Variants

    Science.gov (United States)

    Huster, Dominik; Kühne, Angelika; Bhattacharjee, Ashima; Raines, Lily; Jantsch, Vanessa; Noe, Johannes; Schirrmeister, Wiebke; Sommerer, Ines; Sabri, Osama; Berr, Frieder; Mössner, Joachim; Stieger, Bruno; Caca, Karel; Lutsenko, Svetlana

    2012-01-01

    BACKGROUND & AIMS Wilson disease is a severe disorder of copper metabolism caused by mutations in ATP7B, which encodes a copper-transporting adenosine triphosphatase. The disease presents with a variable phenotype that complicates the diagnostic process and treatment. Little is known about the mechanisms that contribute to the different phenotypes of the disease. METHODS We analyzed 28 variants of ATP7B from patients with Wilson disease that affected different functional domains; the gene products were expressed using the baculovirus expression system in Sf9 cells. Protein function was analyzed by measuring catalytic activity and copper (64Cu) transport into vesicles. We studied intracellular localization of variants of ATP7B that had measurable transport activities and were tagged with green fluorescent protein in mammalian cells using confocal laser scanning microscopy. RESULTS Properties of ATP7B variants with pathogenic amino-acid substitution varied greatly even if substitutions were in the same functional domain. Some variants had complete loss of catalytic and transport activity, whereas others lost transport activity but retained phosphor-intermediate formation or had partial losses of activity. In mammalian cells, transport-competent variants differed in stability and subcellular localization. CONCLUSIONS Variants in ATP7B associated with Wilson disease disrupt the protein’s transport activity, result in its mislocalization, and reduce its stability. Single assays are insufficient to accurately predict the effects of ATP7B variants the function of its product and development of Wilson disease. These findings will contribute to our understanding of genotype–phenotype correlation and mechanisms of disease pathogenesis. PMID:22240481

  9. UTILIZATION OF PLANT PROTEINS IN FUNCTIONAL NUTRITION

    Directory of Open Access Journals (Sweden)

    V. G. Kulakov

    2017-01-01

    Full Text Available Development of functional food products technology is considered to be a prospect way for creating new food products. Such products are known to be popular among consumers. Utilization of plant proteins allows to widen and improve food assortment and quality. The article represents a review of plant proteins utilization in production of functional food. For optimization of flour confectionery chemical composition the authors utilized a method of receipts modeling. Simulation of combined products is based on the principles of food combinatorics and aims to create recipes of new types of food products on basis of methods of mathematical optimization by reasonable selection of the basic raw materials, ingredients, food additives and dietary supplements, totality of which ensures formation desired organoleptic, physical and chemical properties product as well as a predetermined level of food, biological and energy value. Modeling process of combined products recipes includes the following three stages: preparation of input data for the design, formalization requirements for the composition and properties of raw ingredients and quality final product, process modeling; product design with desired structural properties.

  10. Butterflies show different functional and species diversity in relationship to vegetation structure and land use

    NARCIS (Netherlands)

    Aguirre-Gutiérrez, Jesús; Wallis de Vries, Michiel; Marshall, Leon; Zelfde, van 't Maarten; Villalobos-Arámbula, Alma R.; Boekelo, Bastiaen; Bartholomeus, Harm; Franzén, Markus; Biesmeijer, Jacobus C.

    2017-01-01


    Aim

    Biodiversity is rapidly disappearing at local and global scales also affecting the functional diversity of ecosystems. We aimed to assess whether functional diversity was correlated with species diversity and whether both were affected by similar land use and vegetation structure

  11. Regulation of Protein Function and Signaling by Reversible Cysteine S-Nitrosylation*

    Science.gov (United States)

    Gould, Neal; Doulias, Paschalis-Thomas; Tenopoulou, Margarita; Raju, Karthik; Ischiropoulos, Harry

    2013-01-01

    NO is a versatile free radical that mediates numerous biological functions within every major organ system. A molecular pathway by which NO accomplishes functional diversity is the selective modification of protein cysteine residues to form S-nitrosocysteine. This post-translational modification, S-nitrosylation, impacts protein function, stability, and location. Despite considerable advances with individual proteins, the in vivo biological chemistry, the structural elements that govern the selective S-nitrosylation of cysteine residues, and the potential overlap with other redox modifications are unknown. In this minireview, we explore the functional features of S-nitrosylation at the proteome level and the structural diversity of endogenously modified residues, and we discuss the potential overlap and complementation that may exist with other cysteine modifications. PMID:23861393

  12. Regulation of protein function and signaling by reversible cysteine S-nitrosylation.

    Science.gov (United States)

    Gould, Neal; Doulias, Paschalis-Thomas; Tenopoulou, Margarita; Raju, Karthik; Ischiropoulos, Harry

    2013-09-13

    NO is a versatile free radical that mediates numerous biological functions within every major organ system. A molecular pathway by which NO accomplishes functional diversity is the selective modification of protein cysteine residues to form S-nitrosocysteine. This post-translational modification, S-nitrosylation, impacts protein function, stability, and location. Despite considerable advances with individual proteins, the in vivo biological chemistry, the structural elements that govern the selective S-nitrosylation of cysteine residues, and the potential overlap with other redox modifications are unknown. In this minireview, we explore the functional features of S-nitrosylation at the proteome level and the structural diversity of endogenously modified residues, and we discuss the potential overlap and complementation that may exist with other cysteine modifications.

  13. Structure, diversity and evolution of protein toxins from spore-forming entomopathogenic bacteria

    NARCIS (Netherlands)

    Maagd, de R.A.; Bravo, A.; Berry, C.; Crickmore, N.; Schnepf, H.E.

    2003-01-01

    Gram-positive spore-forming entomopathogenic bacteria can utilize a large variety of protein toxins to help them invade, infect, and finally kill their hosts, through their action on the insect midgut. These toxins belong to a number of homology groups containing a diversity of protein structures

  14. Engineering Escherichia coli for Functional Expression of Membrane Proteins

    NARCIS (Netherlands)

    Ho, Franz Y; Poolman, Bert

    2015-01-01

    A major bottleneck in the characterization of membrane proteins is low yield of functional protein in recombinant expression. Microorganisms are widely used for recombinant protein production, because of ease of cultivation and high protein yield. However, the target proteins do not always obtain

  15. Glycosphingolipid Modification: Structural Diversity, Functional and Mechanistic Integration of Diabetes

    Directory of Open Access Journals (Sweden)

    Tadashi Yamashita

    2011-08-01

    Full Text Available Glycosphingolipids (GSLs are present in all mammalian cell plasma membranes and intracellular membrane structures. They are especially concentrated in plasma membrane lipid domains that are specialized for cell signaling. Plasma membranes have typical structures called rafts and caveola domain structures, with large amounts of sphingolipids, cholesterol, and sphingomyelin. GSLs are usually observed in many organs ubiquitously. However, GSLs, including over 400 derivatives, participate in diverse cellular functions. Several studies indicate that GSLs might have an effect on signal transduction related to insulin receptors and epidermal growth factor receptors. GSLs may modulate immune responses by transmitting signals from the exterior to the interior of the cell. Guillain-Barré syndrome is one of the autoimmune disorders characterized by symmetrical weakness in the muscles of the legs. The targets of the immune response are thought to be gangliosides, which are one group of GSLs. Other GSLs may serve as second messengers in several signaling pathways that are important to cell survival or programmed cell death. In the search for clear evidence that GSLs may play critical roles in various biological functions, many researchers have made genetically engineered mice. Before the era of gene manipulation, spontaneous animal models or chemical-induced disease models were used.

  16. Protein landmarks for diversity assessment in wheat genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2009-05-04

    May 4, 2009 ... Millsp. (Pigeon pea and its wild relatives based on seed protein profiles. Genet. Resour. Crop Evol. 43: 275-281. Khan MF, Schumann E, Weber WE (2002). Characterization of. Pakistani Wheat Varieties for General Cultivation in the Mountainous. Regions of Azad Kashmir. Asian J. Plant Sci. 1(6): 699-702.

  17. Assessment of Genetic Diversity in Quality Protein Maize (QPM ...

    African Journals Online (AJOL)

    sriram

    were successful in releasing several quality protein maize. (QPM) hybrids both in Africa and Latin America. India has imported the Mexican QPM lines and developed several. QPM hybrids in recent past. However, it is very much essential to develop the QPM hybrids which can yield on par with normal hybrids. SSR markers ...

  18. Phylogenetic and Functional Diversity of Fleshy-Fruited Plants Are Positively Associated with Seedling Diversity in a Tropical Montane Forest

    Directory of Open Access Journals (Sweden)

    Marcia C. Muñoz

    2017-08-01

    Full Text Available Mutualistic interactions between plants and animals can affect both plant and animal communities, and potentially leave imprints on plant demography. Yet, no study has simultaneously tested how trait variation in plant resources shapes the diversity of animal consumers, and how these interactions influence seedling recruitment. Here, we analyzed whether (i phylogenetic diversity and functional diversity of fruiting plants were correlated with the corresponding diversity of frugivorous birds, and (ii whether phylogenetic diversity and functional identity of plant and bird communities influenced the corresponding diversity and identity of seedling communities. We recorded mutualistic interactions between fleshy-fruited plants and frugivorous birds and seedling communities in 10 plots along an elevational gradient in the Colombian Andes. We built a phylogeny for plants/seedlings and birds and measured relevant morphological plant and bird traits that influence plant-bird interactions and seedling recruitment. We found that phylogenetic diversity and functional diversity of frugivorous birds were positively associated with the corresponding diversities of fruiting plants, consistent with a bottom-up effect of plants on birds. Moreover, the phylogenetic diversity of seedlings was related to the phylogenetic diversity of plants, but was unrelated to the phylogenetic diversity of frugivorous birds, suggesting that top-down effects of animals on seedlings were weak. Mean seed mass of seedling communities was positively associated with the mean fruit mass of plants, but was not associated with the mean avian body mass in the frugivore communities. Our study shows that variation in the traits of fleshy-fruited plants was associated with the diversity of frugivorous birds and affected the future trajectory of seedling recruitment, whereas the morphological traits of animal seed dispersers were unrelated to the phylogenetic and functional structure of

  19. Exotic species enhance response diversity to land-use change but modify functional composition.

    Science.gov (United States)

    Stavert, Jamie R; Pattemore, David E; Gaskett, Anne C; Beggs, Jacqueline R; Bartomeus, Ignasi

    2017-08-16

    Two main mechanisms may buffer ecosystem functions despite biodiversity loss. First, multiple species could share similar ecological roles, thus providing functional redundancy. Second, species may respond differently to environmental change (response diversity). However, ecosystem function would be best protected when functionally redundant species also show response diversity. This linkage has not been studied directly, so we investigated whether native and exotic pollinator species with similar traits (functional redundancy) differed in abundance (response diversity) across an agricultural intensification gradient. Exotic pollinator species contributed most positive responses, which partially stabilized overall abundance of the pollinator community. However, although some functionally redundant species exhibited response diversity, this was not consistent across functional groups and aggregate abundances within each functional group were rarely stabilized. This shows functional redundancy and response diversity do not always operate in concert. Hence, despite exotic species becoming increasingly dominant in human-modified systems, they cannot replace the functional composition of native species. © 2017 The Author(s).

  20. Intraspecific functional diversity of common species enhances community stability.

    Science.gov (United States)

    Wood, Connor M; McKinney, Shawn T; Loftin, Cynthia S

    2017-03-01

    Common species are fundamental to the structure and function of their communities and may enhance community stability through intraspecific functional diversity (iFD). We measured among-habitat and within-habitat iFD (i.e., among- and within-plant community types) of two common small mammal species using stable isotopes and functional trait dendrograms, determined whether iFD was related to short-term population stability and small mammal community stability, and tested whether spatially explicit trait filters helped explain observed patterns of iFD. Southern red-backed voles ( Myodes gapperi ) had greater iFD than deer mice ( Peromyscus maniculatus ), both among habitats, and within the plant community in which they were most abundant (their "primary habitat"). Peromyscus maniculatus populations across habitats differed significantly between years and declined 78% in deciduous forests, their primary habitat, as did the overall deciduous forest small mammal community. Myodes gapperi populations were stable across habitats and within coniferous forest, their primary habitat, as was the coniferous forest small mammal community. Generalized linear models representing internal trait filters (e.g., competition), which increase within-habitat type iFD, best explained variation in M. gapperi diet, while models representing internal filters and external filters (e.g., climate), which suppress within-habitat iFD, best explained P. maniculatus diet. This supports the finding that M. gapperi had higher iFD than P. maniculatus and is consistent with the theory that internal trait filters are associated with higher iFD than external filters. Common species with high iFD can impart a stabilizing influence on their communities, information that can be important for conserving biodiversity under environmental change.

  1. Intraspecific functional diversity of common species enhances community stability

    Science.gov (United States)

    Wood, Connor M.; McKinney, Shawn T.; Loftin, Cynthia S.

    2017-01-01

    Common species are fundamental to the structure and function of their communities and may enhance community stability through intraspecific functional diversity (iFD). We measured among-habitat and within-habitat iFD (i.e., among- and within-plant community types) of two common small mammal species using stable isotopes and functional trait dendrograms, determined whether iFD was related to short-term population stability and small mammal community stability, and tested whether spatially explicit trait filters helped explain observed patterns of iFD. Southern red-backed voles (Myodes gapperi) had greater iFD than deer mice (Peromyscus maniculatus), both among habitats, and within the plant community in which they were most abundant (their “primary habitat”). Peromyscus maniculatus populations across habitats differed significantly between years and declined 78% in deciduous forests, their primary habitat, as did the overall deciduous forest small mammal community. Myodes gapperi populations were stable across habitats and within coniferous forest, their primary habitat, as was the coniferous forest small mammal community. Generalized linear models representing internal trait filters (e.g., competition), which increase within-habitat type iFD, best explained variation in M. gapperidiet, while models representing internal filters and external filters (e.g., climate), which suppress within-habitat iFD, best explained P. maniculatus diet. This supports the finding that M. gapperi had higher iFD than P. maniculatus and is consistent with the theory that internal trait filters are associated with higher iFD than external filters. Common species with high iFD can impart a stabilizing influence on their communities, information that can be important for conserving biodiversity under environmental change.

  2. The Diverse Roles of Arrestin Scaffolds in G Protein-Coupled Receptor Signaling.

    Science.gov (United States)

    Peterson, Yuri K; Luttrell, Louis M

    2017-07-01

    The visual/ β -arrestins, a small family of proteins originally described for their role in the desensitization and intracellular trafficking of G protein-coupled receptors (GPCRs), have emerged as key regulators of multiple signaling pathways. Evolutionarily related to a larger group of regulatory scaffolds that share a common arrestin fold, the visual/ β -arrestins acquired the capacity to detect and bind activated GPCRs on the plasma membrane, which enables them to control GPCR desensitization, internalization, and intracellular trafficking. By acting as scaffolds that bind key pathway intermediates, visual/ β -arrestins both influence the tonic level of pathway activity in cells and, in some cases, serve as ligand-regulated scaffolds for GPCR-mediated signaling. Growing evidence supports the physiologic and pathophysiologic roles of arrestins and underscores their potential as therapeutic targets. Circumventing arrestin-dependent GPCR desensitization may alleviate the problem of tachyphylaxis to drugs that target GPCRs, and find application in the management of chronic pain, asthma, and psychiatric illness. As signaling scaffolds, arrestins are also central regulators of pathways controlling cell growth, migration, and survival, suggesting that manipulating their scaffolding functions may be beneficial in inflammatory diseases, fibrosis, and cancer. In this review we examine the structure-function relationships that enable arrestins to perform their diverse roles, addressing arrestin structure at the molecular level, the relationship between arrestin conformation and function, and sites of interaction between arrestins, GPCRs, and nonreceptor-binding partners. We conclude with a discussion of arrestins as therapeutic targets and the settings in which manipulating arrestin function might be of clinical benefit. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

  3. Improving understanding of the functional diversity of fisheries by exploring the influence of global catch reconstruction.

    Science.gov (United States)

    Nash, Kirsty L; Watson, Reg A; Halpern, Benjamin S; Fulton, Elizabeth A; Blanchard, Julia L

    2017-09-06

    Functional diversity is thought to enhance ecosystem resilience, driving research focused on trends in the functional composition of fisheries, most recently with new reconstructions of global catch data. However, there is currently little understanding of how accounting for unreported catches (e.g. small-scale and illegal fisheries, bycatch and discards) influences functional diversity trends in global fisheries. We explored how diversity estimates varied among reported and unreported components of catch in 2010, and found these components had distinct functional fingerprints. Incorporating unreported catches had little impact on global-scale functional diversity patterns. However, at smaller, management-relevant scales, the effects of incorporating unreported catches were large (changes in functional diversity of up to 46%). Our results suggest there is greater uncertainty about the risks to ecosystem integrity and resilience from current fishing patterns than previously recognized. We provide recommendations and suggest a research agenda to improve future assessments of functional diversity of global fisheries.

  4. Molecular Characteristics and Biological Functions of Surface-Active and Surfactant Proteins.

    Science.gov (United States)

    Sunde, Margaret; Pham, Chi L L; Kwan, Ann H

    2017-06-20

    Many critical biological processes take place at hydrophobic:hydrophilic interfaces, and a wide range of organisms produce surface-active proteins and peptides that reduce surface and interfacial tension and mediate growth and development at these boundaries. Microorganisms produce both small lipid-associated peptides and amphipathic proteins that allow growth across water:air boundaries, attachment to surfaces, predation, and improved bioavailability of hydrophobic substrates. Higher-order organisms produce surface-active proteins with a wide variety of functions, including the provision of protective foam environments for vulnerable reproductive stages, evaporative cooling, and gas exchange across airway membranes. In general, the biological functions supported by these diverse polypeptides require them to have an amphipathic nature, and this is achieved by a diverse range of molecular structures, with some proteins undergoing significant conformational change or intermolecular association to generate the structures that are surface active.

  5. Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein-Protein Interaction Analysis, and Protein Function Exploration.

    Science.gov (United States)

    Beghein, Els; Gettemans, Jan

    2017-01-01

    Over the last two decades, nanobodies or single-domain antibodies have found their way in research, diagnostics, and therapy. These antigen-binding fragments, derived from Camelid heavy chain only antibodies, possess remarkable characteristics that favor their use over conventional antibodies or fragments thereof, in selected areas of research. In this review, we assess the current status of nanobodies as research tools in diverse aspects of fundamental research. We discuss the use of nanobodies as detection reagents in fluorescence microscopy and focus on recent advances in super-resolution microscopy. Second, application of nanobody technology in investigating protein-protein interactions is reviewed, with emphasis on possible uses in mass spectrometry. Finally, we discuss the potential value of nanobodies in studying protein function, and we focus on their recently reported application in targeted protein degradation. Throughout the review, we highlight state-of-the-art engineering strategies that could expand nanobody versatility and we suggest future applications of the technology in the selected areas of fundamental research.

  6. Combined thermal and herbicide stress in functionally diverse coral symbionts.

    Science.gov (United States)

    van Dam, J W; Uthicke, S; Beltran, V H; Mueller, J F; Negri, A P

    2015-09-01

    Most reef building corals rely on symbiotic microalgae (genus Symbiodinium) to supply a substantial proportion of their energy requirements. Functional diversity of different Symbiodinium genotypes, endorsing the host with physiological advantages, has been widely reported. Yet, the influence of genotypic specificity on the symbiont's susceptibility to contaminants or cumulative stressors is unknown. Cultured Symbiodinium of presumed thermal-tolerant clade D tested especially vulnerable to the widespread herbicide diuron, suggesting important free-living populations may be at risk in areas subjected to terrestrial runoff. Co-exposure experiments where cultured Symbiodinium were exposed to diuron over a thermal stress gradient demonstrated how fast-growing clade C1 better maintained photosynthetic capability than clade D. The mixture toxicity model of Independent Action, considering combined thermal stress and herbicide contamination, revealed response additivity for inhibition of photosynthetic yield in both tested cultures, emphasizing the need to account for cumulative stressor impacts in ecological risk assessment and resource management. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  7. Combined thermal and herbicide stress in functionally diverse coral symbionts

    International Nuclear Information System (INIS)

    Dam, J.W. van; Uthicke, S.; Beltran, V.H.; Mueller, J.F.; Negri, A.P.

    2015-01-01

    Most reef building corals rely on symbiotic microalgae (genus Symbiodinium) to supply a substantial proportion of their energy requirements. Functional diversity of different Symbiodinium genotypes, endorsing the host with physiological advantages, has been widely reported. Yet, the influence of genotypic specificity on the symbiont's susceptibility to contaminants or cumulative stressors is unknown. Cultured Symbiodinium of presumed thermal-tolerant clade D tested especially vulnerable to the widespread herbicide diuron, suggesting important free-living populations may be at risk in areas subjected to terrestrial runoff. Co-exposure experiments where cultured Symbiodinium were exposed to diuron over a thermal stress gradient demonstrated how fast-growing clade C1 better maintained photosynthetic capability than clade D. The mixture toxicity model of Independent Action, considering combined thermal stress and herbicide contamination, revealed response additivity for inhibition of photosynthetic yield in both tested cultures, emphasizing the need to account for cumulative stressor impacts in ecological risk assessment and resource management. - Highlights: • Water quality influences thermal stress thresholds in different Symbiodinium types. • Photosystem of clade D tested more sensitive than C1 to a common herbicide. • Increased thermal tolerance quickly countered in presence of herbicide. • Mixture toxicity approach demonstrated response additivity for combined stressors. • Symbiotic partnership may be compromised in areas subjected to terrestrial runoff. - Thermal-tolerant Symbiodinium type D tested especially vulnerable to a common herbicide, emphasizing the significance of cumulative stressors in ecological risk management

  8. Functional diversity of supragranular GABAergic neurons in the barrel cortex

    Directory of Open Access Journals (Sweden)

    Luc J Gentet

    2012-08-01

    Full Text Available Although the neocortex forms a distributed system comprised of several functional areas, its vertical columnar organization is largely conserved across areas and species, suggesting the existence of a canonical neocortical microcircuit. In order to elucidate the principles governing the organization of such a cortical diagram, a detailed understanding of the dynamics binding different types of cortical neurons into a coherent algorithm is essential. Within this complex circuitry, GABAergic interneurons, while forming approximately only 15-20% of all cortical neurons, appear critical in maintaining a dynamic balance between excitation and inhibition. Despite their importance, cortical GABAergic neurons have not been extensively studied in vivo and their precise role in shaping the local microcircuit sensory response still remains to be determined. Their paucity, combined with their molecular, anatomical and physiological diversity, has made it difficult to even establish a consensual nomenclature.However, recent technological advances in microscopy and mouse genetics have fostered a renewed interest in neocortical interneurons by putting them within visible reach of experimenters. The anatomically well-defined whisker-to-barrel pathway of the rodent is particularly amenable to studies attempting to link cortical circuit dynamics to behavior. To each whisker corresponds a discrete cortical unit equivalent to a single column, specialized in the encoding and processing of the sensory information it receives. In this review, we will focus on the functional role that each subtype of supragranular GABAergic neuron embedded within such a single neocortical unit may play in shaping the dynamics of the local circuit during somatosensory integration.

  9. Production of small cysteine-rich effector proteins in Escherichia coli for structural and functional studies.

    Science.gov (United States)

    Zhang, Xiaoxiao; Nguyen, Neal; Breen, Susan; Outram, Megan A; Dodds, Peter N; Kobe, Bostjan; Solomon, Peter S; Williams, Simon J

    2017-01-01

    Although the lifestyles and infection strategies of plant pathogens are diverse, a prevailing feature is the use of an arsenal of secreted proteins, known as effectors, which aid in microbial infection. In the case of eukaryotic filamentous pathogens, such as fungi and oomycetes, effector proteins are typically dissimilar, at the protein sequence level, to known protein families and functional domains. Consequently, we currently have a limited understanding of how fungal and oomycete effectors promote disease. Protein biochemistry and structural biology are two methods that can contribute greatly to the understanding of protein function. Both techniques are dependent on obtaining proteins that are pure and functional, and generally require the use of heterologous recombinant protein expression systems. Here, we present a general scheme and methodology for the production and characterization of small cysteine-rich (SCR) effectors utilizing Escherichia coli expression systems. Using this approach, we successfully produced cysteine-rich effectors derived from the biotrophic fungal pathogen Melampsora lini and the necrotrophic fungal pathogen Parastagonospora nodorum. Access to functional recombinant proteins facilitated crystallization and functional experiments. These results are discussed in the context of a general workflow that may serve as a template for others interested in understanding the function of SCR effector(s) from their plant pathogen(s) of interest. © 2016 BSPP and John Wiley & Sons Ltd.

  10. Syndecans as cell surface receptors: Unique structure equates with functional diversity

    DEFF Research Database (Denmark)

    Choi, Youngsil; Chung, Heesung; Jung, Heyjung

    2011-01-01

    An increasing number of functions for syndecan cell surface heparan sulfate proteoglycans have been proposed over the last decade. Moreover, aberrant syndecan regulation has been found to play a critical role in multiple pathologies, including cancers, as well as wound healing and inflammation....... As receptors, they have much in common with other molecules on the cell surface. Syndecans are type I transmembrane molecules with cytoplasmic domains that link to the actin cytoskeleton and can interact with a number of regulators. However, they are also highly complex by virtue of their external...... glycosaminoglycan chains, especially heparan sulfate. This heterodisperse polysaccharide has the potential to interact with many ligands from diverse protein families. Here, we relate the structural features of syndecans to some of their known functions....

  11. Distance-based functional diversity measures and their decomposition: a framework based on Hill numbers.

    Science.gov (United States)

    Chiu, Chun-Huo; Chao, Anne

    2014-01-01

    Hill numbers (or the "effective number of species") are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify "the effective number of equally abundant and (functionally) equally distinct species" in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the

  12. Functionalization of protein crystals with metal ions, complexes and nanoparticles.

    Science.gov (United States)

    Abe, Satoshi; Maity, Basudev; Ueno, Takafumi

    2018-04-01

    Self-assembled proteins have specific functions in biology. With inspiration provided by natural protein systems, several artificial protein assemblies have been constructed via site-specific mutations or metal coordination, which have important applications in catalysis, material and bio-supramolecular chemistry. Similar to natural protein assemblies, protein crystals have been recognized as protein assemblies formed of densely-packed monomeric proteins. Protein crystals can be functionalized with metal ions, metal complexes or nanoparticles via soaking, co-crystallization, creating new metal binding sites by site-specific mutations. The field of protein crystal engineering with metal coordination is relatively new and has gained considerable attention for developing solid biomaterials as well as structural investigations of enzymatic reactions, growth of nanoparticles and catalysis. This review highlights recent and significant research on functionalization of protein crystals with metal coordination and future prospects. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

    Science.gov (United States)

    Du, Yushen; Wu, Nicholas C; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting; Sun, Ren

    2016-11-01

    Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is

  14. Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems.

    Science.gov (United States)

    Leenay, Ryan T; Maksimchuk, Kenneth R; Slotkowski, Rebecca A; Agrawal, Roma N; Gomaa, Ahmed A; Briner, Alexandra E; Barrangou, Rodolphe; Beisel, Chase L

    2016-04-07

    CRISPR-Cas adaptive immune systems in prokaryotes boast a diversity of protein families and mechanisms of action, where most systems rely on protospacer-adjacent motifs (PAMs) for DNA target recognition. Here, we developed an in vivo, positive, and tunable screen termed PAM-SCANR (PAM screen achieved by NOT-gate repression) to elucidate functional PAMs as well as an interactive visualization scheme termed the PAM wheel to convey individual PAM sequences and their activities. PAM-SCANR and the PAM wheel identified known functional PAMs while revealing complex sequence-activity landscapes for the Bacillus halodurans I-C (Cascade), Escherichia coli I-E (Cascade), Streptococcus thermophilus II-A CRISPR1 (Cas9), and Francisella novicida V-A (Cpf1) systems. The PAM wheel was also readily applicable to existing high-throughput screens and garnered insights into SpyCas9 and SauCas9 PAM diversity. These tools offer powerful means of elucidating and visualizing functional PAMs toward accelerating our ability to understand and exploit the multitude of CRISPR-Cas systems in nature. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Loss of functional diversity of ant assemblages in secondary tropical forests.

    Science.gov (United States)

    Bihn, Jochen H; Gebauer, Gerhard; Brandl, Roland

    2010-03-01

    Secondary forests and plantations increasingly dominate the tropical wooded landscape in place of primary forests. The expected reduction of biodiversity and its impact on ecological functions provided by these secondary forests are of major concern to society and ecologists. The potential effect of biodiversity loss on ecosystem functioning depends largely on the associated loss in the functional diversity of animal and plant assemblages, i.e., the degree of functional redundancy among species. However, the relationship between species and functional diversity is still poorly documented for most ecosystems. Here, we analyze how changes in the species diversity of ground-foraging ant assemblages translate into changes of functional diversity along a successional gradient of secondary forests in the Atlantic Forest of Brazil. Our analysis uses continuous measures of functional diversity and is based on four functional traits related to resource use of ants: body size, relative eye size, relative leg length, and trophic position. We find a strong relationship between species and functional diversity, independent of the functional traits used, with no evidence for saturation in this relationship. Recovery of species richness and diversity of ant assemblages in tropical secondary forests was accompanied by a proportional increase of functional richness and diversity of assemblages. Moreover, our results indicate that the increase in functional diversity along the successional gradient of secondary forests is primarily driven by rare species, which are functionally unique. The observed loss of both species and functional diversity in secondary forests offers no reason to believe that the ecological functions provided by secondary forests are buffered against species loss through functional redundancy.

  16. An overview of the applicability of functional diversity in Biological Conservation.

    Science.gov (United States)

    Freitas, J R; Mantovani, W

    2017-10-23

    Functional diversity is increasingly pointed as a useful approach to reach Biological Conservation goals. Here, we provide an overview of the functional diversity approach status in the Biological Conservation field. We sought for peer-reviewed papers published over a period of twenty years (from 1994 to 2014). First we used the general topic "functional diversity" and then refined our search using the key-word "conservation". We have identified the conservation strategies addressed, the organism studied, and the continent of study site in each paper. Thirteen classes of conservation strategies were identified. Plants were the most commonly studied organism group and most study-sites were located in Europe. The functional diversity approach was introduced in the Biological Conservation field in the early 2000's and its inclusion in conservation strategies is broadly advised. However, the number of papers that operationalise such inclusion by developing models and systems is still low. Functional diversity responds differently and eventually better than other measures to changes in land use and management, which suggests that this approach can potentially better predict the impacts. More studies are needed to corroborate this hypothesis. We pointed out knowledge gaps regarding identification of the responses for functional diversity about urban impacts and in research on the level of management intensity of land needed to maintain functional diversity. We recommend the use of functional diversity measures to find ecological indicators. Future studies should focus on the development of functional diversity measures of other taxa beyond plants as well as test hypothesis in tropical ecosystems.

  17. Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

    Science.gov (United States)

    Lee, Myung-Bok; Martin, James A

    2017-01-01

    While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010-2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon's landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non

  18. Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity.

    Science.gov (United States)

    Zhang, Ximei; Johnston, Eric R; Barberán, Albert; Ren, Yi; Lü, Xiaotao; Han, Xingguo

    2017-10-01

    Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity. © 2017 John Wiley & Sons Ltd.

  19. Determining and comparing protein function in Bacterial genome sequences

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla

    annotation of genes – the descriptions assigned to genes that describe the likely function of the encoded proteins. This process is limited by several factors, including the definition of a function which can be more or less specific as well as how many genes can actually be assigned a function based...... of proteins were clustered based on sequence domains so that each group represented a protein function. Each function was then modeled using Arti- ficial Neural Networks (ANN) and the model was evaluated based on its ability to identify true positives and negatives, that is proteins with or without...... the function of the model. The models were used to annotate a number of proteins without functional annotations and predicted functions for 98% of the genes. Evaluation of the precision of the method was performed, using data from the Critical Assessment of Functional Annotation (CAFA) project, and correct...

  20. Decomposing changes in phylogenetic and functional diversity over space and time

    Science.gov (United States)

    Chalmandrier, Loïc; Münkemüller, Tamara; Devictor, Vincent; Lavergne, Sébastien; Thuiller, Wilfried

    2015-01-01

    Summary The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity. Using the properties of Chao’s index, we adapted Rao’s framework of diversity decomposition between orthogonal dimensions to a multiplicative α, β, γ decomposition of functional or phylogenetic diversity over space and time, thereby combining their respective properties. We also developed guidelines for interpreting both temporal and spatial β-diversities and their interaction. We characterised the range of β-diversity estimates and their relationship to the nested decomposition of diversity. Using simulations, we empirically demonstrated that temporal and spatial β-diversities are independent from each other and from α and γ-diversities when the study design is balanced, but not otherwise. Furthermore, we showed that the interaction term between the temporal and the spatial β-diversities lacked such properties. We illustrated our methodology with a case study of the spatio-temporal dynamics of functional diversity in bird assemblages in four regions of France. Based on these data, our method makes it possible to discriminate between regions experiencing different diversity changes in time. Our methodology may therefore be valuable for comparing diversity changes over space and time using large-scale datasets of repeated surveys. PMID:25685310

  1. Leaf and stem economics spectra drive diversity of functional plant traits in a dynamic global vegetation model

    NARCIS (Netherlands)

    Sakschewski, B.; Bloh, von W.; Boit, A.; Rammig, A.; Kattge, J.; Poorter, L.; Peñualeas, J.; Thonicke, K.

    2015-01-01

    Functional diversity is critical for ecosystem dynamics, stability and productivity. However, dynamic global vegetation models (DGVMs) which are increasingly used to simulate ecosystem functions under global change, condense functional diversity to plant functional types (PFTs) with constant

  2. Bam35 tectivirus intraviral interaction map unveils new function and localization of phage ORFan proteins.

    Science.gov (United States)

    Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter; Salas, Margarita; Redrejo-Rodríguez, Modesto

    2017-07-26

    Tectiviridae comprises a group of tail-less, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria.In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing the knowledge of the viral proteome, we carried out a comprehensive yeast two-hybrid analysis among all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprises 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggested that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, being the latter also supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving non-structural proteins, such as the DNA binding protein P1 and the genome terminal protein (P4), which was confirmed by co-immunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tail-less viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown

  3. Mapping functional diversity from remotely sensed morphological and physiological forest traits.

    Science.gov (United States)

    Schneider, Fabian D; Morsdorf, Felix; Schmid, Bernhard; Petchey, Owen L; Hueni, Andreas; Schimel, David S; Schaepman, Michael E

    2017-11-13

    Assessing functional diversity from space can help predict productivity and stability of forest ecosystems at global scale using biodiversity-ecosystem functioning relationships. We present a new spatially continuous method to map regional patterns of tree functional diversity using combined laser scanning and imaging spectroscopy. The method does not require prior taxonomic information and integrates variation in plant functional traits between and within plant species. We compare our method with leaf-level field measurements and species-level plot inventory data and find reasonable agreement. Morphological and physiological diversity show consistent change with topography and soil, with low functional richness at a mountain ridge under specific environmental conditions. Overall, functional richness follows a logarithmic increase with area, whereas divergence and evenness are scale invariant. By mapping diversity at scales of individual trees to whole communities we demonstrate the potential of assessing functional diversity from space, providing a pathway only limited by technological advances and not by methodology.

  4. Plant and algal cell walls: diversity and functionality.

    Science.gov (United States)

    Popper, Zoë A; Ralet, Marie-Christine; Domozych, David S

    2014-10-01

    Although plants and many algae (e.g. the Phaeophyceae, brown, and Rhodophyceae, red) are only very distantly related they are united in their possession of carbohydrate-rich cell walls, which are of integral importance being involved in many physiological processes. Furthermore,wall components have applications within food, fuel, pharmaceuticals, fibres (e.g. for textiles and paper) and building materials and have long been an active topic of research. As shown in the 27 papers in this Special Issue, as the major deposit of photosynthetically fixed carbon, and therefore energy investment, cell walls are of undisputed importance to the organisms that possess them, the photosynthetic eukaryotes ( plants and algae). The complexities of cell wall components along with their interactions with the biotic and abiotic environment are becoming increasingly revealed. The importance of plant and algal cell walls and their individual components to the function and survival of the organism, and for a number of industrial applications, are illustrated by the breadth of topics covered in this issue, which includes papers concentrating on various plants and algae, developmental stages, organs, cell wall components, and techniques. Although we acknowledge that there are many alternative ways in which the papers could be categorized (and many would fit within several topics), we have organized them as follows: (1) cell wall biosynthesis and remodelling, (2) cell wall diversity, and (3) application of new technologies to cell walls. Finally, we will consider future directions within plant cell wall research. Expansion of the industrial uses of cell walls and potentially novel uses of cell wall components are both avenues likely to direct future research activities. Fundamentally, it is the continued progression from characterization (structure, metabolism, properties and localization) of individual cell wall components through to defining their roles in almost every aspect of plant

  5. Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold

    Directory of Open Access Journals (Sweden)

    Iyer Lakshminarayan M

    2007-07-01

    Full Text Available Abstract Background The β-grasp fold (β-GF, prototyped by ubiquitin (UB, has been recruited for a strikingly diverse range of biochemical functions. These functions include providing a scaffold for different enzymatic active sites (e.g. NUDIX phosphohydrolases and iron-sulfur clusters, RNA-soluble-ligand and co-factor-binding, sulfur transfer, adaptor functions in signaling, assembly of macromolecular complexes and post-translational protein modification. To understand the basis for the functional versatility of this small fold we undertook a comprehensive sequence-structure analysis of the fold and developed a natural classification for its members. Results As a result we were able to define the core distinguishing features of the fold and numerous elaborations, including several previously unrecognized variants. Systematic analysis of all known interactions of the fold showed that its manifold functional abilities arise primarily from the prominent β-sheet, which provides an exposed surface for diverse interactions or additionally, by forming open barrel-like structures. We show that in the β-GF both enzymatic activities and the binding of diverse co-factors (e.g. molybdopterin have independently evolved on at least three occasions each, and iron-sulfur-cluster-binding on at least two independent occasions. Our analysis identified multiple previously unknown large monophyletic assemblages within the β-GF, including one which unifies versions found in the fasciclin-1 superfamily, the ribosomal protein L25, the phosphoribosyl AMP cyclohydrolase (HisI and glutamine synthetase. We also uncovered several new groups of β-GF domains including a domain found in bacterial flagellar and fimbrial assembly components, and 5 new UB-like domains in the eukaryotes. Conclusion Evolutionary reconstruction indicates that the β-GF had differentiated into at least 7 distinct lineages by the time of the last universal common ancestor of all extant organisms

  6. Evaluation of nine distance-based measures of functional diversity applied to forest communities

    Directory of Open Access Journals (Sweden)

    Jin-Tun Zhang

    2013-07-01

    Full Text Available Several methods for the estimation of functional diversity are employed in plant communities. However, it is hard to select the most suitable measures in practice. This work presents comparisons of nine distance-based measures applied to functional diversity analysis in forest communities (36 plots along an elevational gradient in the Pangquangou Reserve, China. The employed indices and methods were: functional attribute diversity (FAD, Rao’s functional diversity (Rao’s index, single linkage (SL, complete linkage (CL, Unweighted Pair Group Method with Arithmetic Mean (UPGMA, Unweighted Pair-Group Method using Centroids (UPGMC, Median linkage (Median, fuzzy equivalence diversity (Fuzzy index and minimum spanning tree index (MST. The results showed that all the nine measures successfully quantified the functional diversity in plant communities and described the changes along environmental gradient. It was concluded that all the employed indices and methods were equally effective and significantly correlated. Comparatively, fuzzy index, MST, UPGMC, UPGMA and Median were more suitable and should have priority over the other four measures in functional diversity analysis. A combination of a few measures of functional diversity within the same study was recommended. Functional diversity indices were significantly decreasing with elevation and correlated with species richness in the studied forest communities. 

  7. Evaluation of nine distance-based measures of functional diversity applied to forest communities

    Directory of Open Access Journals (Sweden)

    Jin-Tun Zhang

    2013-05-01

    Full Text Available Several methods for the estimation of functional diversity are employed in plant communities. However, it is hard to select the most suitable measures in practice. This work presents comparisons of nine distance-based measures applied to functional diversity analysis in forest communities (36m plots along an elevational gradient in the Pangquangou Reserve, China. The employed indices and methods were: functional attribute diversity (FAD, Rao’s functional diversity (Rao’s index, single linkage (SL, complete linkage (CL, Unweighted Pair Group Method with Arithmetic Mean (UPGMA, Unweighted Pair-Group Method using Centroids (UPGMC, Median linkage (Median, fuzzy equivalence diversity (Fuzzy index and minimum spanning tree index (MST. The results showed that all the nine measures successfully quantified the functional diversity in plant communities and described the changes along environmental gradient. It was concludedthat all the employed indices and methods were equally effectiveand significantly correlated. Comparatively, fuzzy index, MST, UPGMC,UPGMA and Median were more suitable and should have priority over theother four measures in functional diversity analysis. A combination of a few measures of functional diversity within the same study was recommended. Functional diversity indices were significantly decreasing with elevation and correlated with species richness in the studied forest communities.

  8. COMPUTATIONAL APPROACHES FOR RATIONAL DESIGN OF PROTEINS WITH NOVEL FUNCTIONALITIES

    Directory of Open Access Journals (Sweden)

    Manish Kumar Tiwari

    2012-09-01

    Full Text Available Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes.

  9. Functional analysis of thermostable proteins involved in carbohydrate metabolism

    NARCIS (Netherlands)

    Akerboom, A.P.

    2007-01-01

    Thermostable proteins can resist temperature stress whilst keeping their integrity and functionality. In many cases, thermostable proteins originate from hyperthermophilic microorganisms that thrive in extreme environments. These systems are generally located close to geothermal (volcanic) activity,

  10. Single proteins that serve linked functions in intracellular and extracellular microenvironments

    Energy Technology Data Exchange (ETDEWEB)

    Radisky, Derek C.; Stallings-Mann, Melody; Hirai, Yohei; Bissell, Mina J.

    2009-06-03

    Maintenance of organ homeostasis and control of appropriate response to environmental alterations requires intimate coordination of cellular function and tissue organization. An important component of this coordination may be provided by proteins that can serve distinct, but linked, functions on both sides of the plasma membrane. Here we present a novel hypothesis in which non-classical secretion can provide a mechanism through which single proteins can integrate complex tissue functions. Single genes can exert a complex, dynamic influence through a number of different processes that act to multiply the function of the gene product(s). Alternative splicing can create many different transcripts that encode proteins of diverse, even antagonistic, function from a single gene. Posttranslational modifications can alter the stability, activity, localization, and even basic function of proteins. A protein can exist in different subcellular localizations. More recently, it has become clear that single proteins can function both inside and outside the cell. These proteins often lack defined secretory signal sequences, and transit the plasma membrane by mechanisms separate from the classical ER/Golgi secretory process. When examples of such proteins are examined individually, the multifunctionality and lack of a signal sequence are puzzling - why should a protein with a well known function in one context function in such a distinct fashion in another? We propose that one reason for a single protein to perform intracellular and extracellular roles is to coordinate organization and maintenance of a global tissue function. Here, we describe in detail three specific examples of proteins that act in this fashion, outlining their specific functions in the extracellular space and in the intracellular space, and we discuss how these functions may be linked. We present epimorphin/syntaxin-2, which may coordinate morphogenesis of secretory organs (as epimorphin) with control of

  11. Genetic diversity of soybean accessions using seed storage proteins

    International Nuclear Information System (INIS)

    Iqbal, Z.; Naeem, R.

    2015-01-01

    Soybean, Glycine max (L) Merrill, is the most important grain legume in the world that has a fairly wide range of adaptations to different climatic conditions. The present study was conducted to assess genetic variations on 139 Soybean genotypes collected from different countries including Australia, Brazil, India, Japan, Pakistan, Tiwan, USA, Yugoslavia and China. A total of 17 bands have been identified for 139 Soybean genotypes which include 9 monomorphic bands and 8 polymorphic bands. Total number of bands was found highest for India (215) while these were lowest for Yugoslavia (33). Cluster analysis, clustered these accessions into 10 clusters without having any indication of grouping on the basis of their relationships to their regions. Pairwise comparisons based on Nei and Li similarities for inter-population genetic distances of soybean accessions ranged from 0.14 to 1.12. Genetic distances for soybean germplasm from different countries were found highest for Brazil (0.97+-0.03) while it was lowest for Taiwan (0.91+-0.02). Clustering for Soybean groups was clustered into three clusters including Korea, Taiwan in the first group while Yugoslavia and Japan were clustered in the second group. The third cluster was comprised of Soybean genotypes from China, Pakistan, USA, India Brazil and Australia. Total seed storage protein variation was partitioned by AMOVA on the basis of their origins into within-population and among-population components which revealed 10.00% of the total variation resided among countries and 90.0% within countries. Genetic patterns obtained from this study can help soybean breeders to make better plan for selecting germplasm from wide sources for a specific purposes. (author)

  12. Distinct profiles of functional discrimination among G proteins determine the actions of G protein-coupled receptors.

    Science.gov (United States)

    Masuho, Ikuo; Ostrovskaya, Olga; Kramer, Grant M; Jones, Christopher D; Xie, Keqiang; Martemyanov, Kirill A

    2015-12-01

    Members of the heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptor (GPCR) family play key roles in many physiological functions and are extensively exploited pharmacologically to treat diseases. Many of the diverse effects of individual GPCRs on cellular physiology are transduced by heterotrimeric G proteins, which are composed of α, β, and γ subunits. GPCRs interact with and stimulate the binding of guanosine triphosphate (GTP) to the α subunit to initiate signaling. Mammalian genomes encode 16 different G protein α subunits, each one of which has distinct properties. We developed a single-platform, optical strategy to monitor G protein activation in live cells. With this system, we profiled the coupling ability of individual GPCRs for different α subunits, simultaneously quantifying the magnitude of the signal and the rates at which the receptors activated the G proteins. We found that individual receptors engaged multiple G proteins with varying efficacy and kinetics, generating fingerprint-like profiles. Different classes of GPCR ligands, including full and partial agonists, allosteric modulators, and antagonists, distinctly affected these fingerprints to functionally bias GPCR signaling. Finally, we showed that intracellular signaling modulators further altered the G protein-coupling profiles of GPCRs, which suggests that their differential abundance may alter signaling outcomes in a cell-specific manner. These observations suggest that the diversity of the effects of GPCRs on cellular physiology may be determined by their differential engagement of multiple G proteins, coupling to which produces signals with varying signal magnitudes and activation kinetics, properties that may be exploited pharmacologically. Copyright © 2015, American Association for the Advancement of Science.

  13. Developing optimal non-linear scoring function for protein design.

    Science.gov (United States)

    Hu, Changyu; Li, Xiang; Liang, Jie

    2004-11-22

    Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process, a design scoring function is critically important. Such a scoring function should be able to characterize the global fitness landscape of many proteins simultaneously. To find optimal design scoring functions, we introduce two geometric views and propose a formulation using a mixture of non-linear Gaussian kernel functions. We aim to solve a simplified protein sequence design problem. Our goal is to distinguish each native sequence for a major portion of representative protein structures from a large number of alternative decoy sequences, each a fragment from proteins of different folds. Our scoring function discriminates perfectly a set of 440 native proteins from 14 million sequence decoys. We show that no linear scoring function can succeed in this task. In a blind test of unrelated proteins, our scoring function misclassfies only 13 native proteins out of 194. This compares favorably with about three-four times more misclassifications when optimal linear functions reported in the literature are used. We also discuss how to develop protein folding scoring function.

  14. Dung Beetles along a Tropical Altitudinal Gradient: Environmental Filtering on Taxonomic and Functional Diversity.

    Science.gov (United States)

    Nunes, Cássio Alencar; Braga, Rodrigo Fagundes; Figueira, José Eugênio Cortes; Neves, Frederico de Siqueira; Fernandes, G Wilson

    2016-01-01

    Mountains provide an interesting context in which to study the many facets of biodiversity in response to macroclimate, since environmental conditions change rapidly due to elevation. Although the decrease in biodiversity with increasing elevation is generally accepted, our understanding of the variation of functional diversity along altitudinal gradients is still poorly known. The partitioning of diversity into spatial components can help to understand the processes that influence the distribution of species, and these studies are urgently needed in face of the increasing threats to mountain environments throughout the world. We describe the distribution of dung beetle diversity along an altitudinal gradient on a tropical mountain in southeastern Brazil, including the spatial partitioning of taxonomic and functional diversities. The altitudinal gradient ranged from 800 up to 1400 m a.s.l. and we collected dung beetles at every 100 m of altitude. We used the Rao Index to calculate γ, α and β diversity for taxonomic and functional diversity of dung beetles. Climatic, soil and vegetation variables were used to explain variation in community attributes along the altitudinal gradient. Dung beetle richness declined with altitude and was related to climatic and vegetation variables, but functional diversity did not follow the same pattern. Over 50% of γ taxonomic diversity was caused by among altitudes diversity (β), while almost 100% of functional diversity was due to the α component. Contrasting β taxonomic with β functional diversity, we suggest that there is ecological redundancy among communities and that the environment is filtering species in terms of the Grinnellian niche, rather than the Eltonian niche. β taxonomic diversity is caused mainly by the turnover component, reinforcing the hypothesis of environmental filtering. Global warming may have strong effects on mountain communities due to upslope range shifts and extinctions, and these events will

  15. Probabilistic protein function prediction from heterogeneous genome-wide data.

    Directory of Open Access Journals (Sweden)

    Naoki Nariai

    2007-03-01

    Full Text Available Dramatic improvements in high throughput sequencing technologies have led to a staggering growth in the number of predicted genes. However, a large fraction of these newly discovered genes do not have a functional assignment. Fortunately, a variety of novel high-throughput genome-wide functional screening technologies provide important clues that shed light on gene function. The integration of heterogeneous data to predict protein function has been shown to improve the accuracy of automated gene annotation systems. In this paper, we propose and evaluate a probabilistic approach for protein function prediction that integrates protein-protein interaction (PPI data, gene expression data, protein motif information, mutant phenotype data, and protein localization data. First, functional linkage graphs are constructed from PPI data and gene expression data, in which an edge between nodes (proteins represents evidence for functional similarity. The assumption here is that graph neighbors are more likely to share protein function, compared to proteins that are not neighbors. The functional linkage graph model is then used in concert with protein domain, mutant phenotype and protein localization data to produce a functional prediction. Our method is applied to the functional prediction of Saccharomyces cerevisiae genes, using Gene Ontology (GO terms as the basis of our annotation. In a cross validation study we show that the integrated model increases recall by 18%, compared to using PPI data alone at the 50% precision. We also show that the integrated predictor is significantly better than each individual predictor. However, the observed improvement vs. PPI depends on both the new source of data and the functional category to be predicted. Surprisingly, in some contexts integration hurts overall prediction accuracy. Lastly, we provide a comprehensive assignment of putative GO terms to 463 proteins that currently have no assigned function.

  16. Functional Molecular Diversity of Marine Dissolved Organic Matter Is Reduced during Degradation

    Directory of Open Access Journals (Sweden)

    Andrea Mentges

    2017-06-01

    Full Text Available Dissolved organic matter (DOM is a highly diverse mixture of compounds, accounting for one of the world's largest active carbon pools. The surprising recalcitrance of some DOM compounds to bacterial degradation has recently been associated with its diversity. However, little is known about large-scale patterns of marine DOM diversity and its change through degradation, in particular considering the functional diversity of DOM. Here, we analyze the development of marine DOM diversity during degradation in two data sets comprising DOM of very different ages: a three-year mesocosm experiment and highly-resolved field samples from the Atlantic and Southern Ocean. The DOM molecular composition was determined using ultra-high resolution mass spectrometry. We quantify DOM diversity using three conceptually different diversity measures, namely richness of molecular formulas, abundance-based diversity, and functional molecular diversity. Using these measures we find stable molecular richness of DOM with age >1 year, systematic changes in the molecules' abundance distribution with degradation state, and increasing homogeneity with respect to chemical properties for more degraded DOM. Coinciding with differences in sea water density, the spatial field data separated clearly into regions of high and low diversity. The joint application of different diversity measures yields a comprehensive overview on temporal and spatial patterns of molecular diversity, valuable for general conclusions on drivers and consequences of marine DOM diversity.

  17. Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea.

    Science.gov (United States)

    Mindel, Beth L; Neat, Francis C; Trueman, Clive N; Webb, Thomas J; Blanchard, Julia L

    2016-01-01

    Biodiversity is well studied in ecology and the concept has been developed to include traits of species, rather than solely taxonomy, to better reflect the functional diversity of a system. The deep sea provides a natural environmental gradient within which to study changes in different diversity metrics, but traits of deep-sea fish are not widely known, hampering the application of functional diversity to this globally important system. We used morphological traits to determine the functional richness and functional divergence of demersal fish assemblages along the continental slope in the Northeast Atlantic, at depths of 300-2,000 m. We compared these metrics to size diversity based on individual body size and species richness. Functional richness and size diversity showed similar patterns, with the highest diversity at intermediate depths; functional divergence showed the opposite pattern, with the highest values at the shallowest and deepest parts of the study site. Species richness increased with depth. The functional implications of these patterns were deduced by examining depth-related changes in morphological traits and the dominance of feeding guilds as illustrated by stable isotope analyses. The patterns in diversity and the variation in certain morphological traits can potentially be explained by changes in the relative dominance of pelagic and benthic feeding guilds. All measures of diversity examined here suggest that the deep areas of the continental slope may be equally or more diverse than assemblages just beyond the continental shelf.

  18. Plant-pollinator coextinctions and the loss of plant functional and phylogenetic diversity.

    Science.gov (United States)

    Vieira, Marcos Costa; Cianciaruso, Marcus Vinicius; Almeida-Neto, Mário

    2013-01-01

    Plant-pollinator coextinctions are likely to become more frequent as habitat alteration and climate change continue to threaten pollinators. The consequences of the resulting collapse of plant communities will depend partly on how quickly plant functional and phylogenetic diversity decline following pollinator extinctions. We investigated the functional and phylogenetic consequences of pollinator extinctions by simulating coextinctions in seven plant-pollinator networks coupled with independent data on plant phylogeny and functional traits. Declines in plant functional diversity were slower than expected under a scenario of random extinctions, while phylogenetic diversity often decreased faster than expected by chance. Our results show that plant functional diversity was relatively robust to plant-pollinator coextinctions, despite the underlying rapid loss of evolutionary history. Thus, our study suggests the possibility of uncoupled responses of functional and phylogenetic diversity to species coextinctions, highlighting the importance of considering both dimensions of biodiversity explicitly in ecological studies and when planning for the conservation of species and interactions.

  19. Plant-Pollinator Coextinctions and the Loss of Plant Functional and Phylogenetic Diversity

    Science.gov (United States)

    Vieira, Marcos Costa; Cianciaruso, Marcus Vinicius; Almeida-Neto, Mário

    2013-01-01

    Plant-pollinator coextinctions are likely to become more frequent as habitat alteration and climate change continue to threaten pollinators. The consequences of the resulting collapse of plant communities will depend partly on how quickly plant functional and phylogenetic diversity decline following pollinator extinctions. We investigated the functional and phylogenetic consequences of pollinator extinctions by simulating coextinctions in seven plant-pollinator networks coupled with independent data on plant phylogeny and functional traits. Declines in plant functional diversity were slower than expected under a scenario of random extinctions, while phylogenetic diversity often decreased faster than expected by chance. Our results show that plant functional diversity was relatively robust to plant-pollinator coextinctions, despite the underlying rapid loss of evolutionary history. Thus, our study suggests the possibility of uncoupled responses of functional and phylogenetic diversity to species coextinctions, highlighting the importance of considering both dimensions of biodiversity explicitly in ecological studies and when planning for the conservation of species and interactions. PMID:24312281

  20. Functional identity and diversity of animals predict ecosystem functioning better than species-based indices.

    Science.gov (United States)

    Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo

    2015-02-22

    Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  1. Environmental Conditions Influence the Plant Functional Diversity Effect on Potential Denitrification

    Science.gov (United States)

    Sutton-Grier, Ariana E.; Wright, Justin P.; McGill, Bonnie M.; Richardson, Curtis

    2011-01-01

    Global biodiversity loss has prompted research on the relationship between species diversity and ecosystem functioning. Few studies have examined how plant diversity impacts belowground processes; even fewer have examined how varying resource levels can influence the effect of plant diversity on microbial activity. In a field experiment in a restored wetland, we examined the role of plant trait diversity (or functional diversity, (FD)) and its interactions with natural levels of variability of soil properties, on a microbial process, denitrification potential (DNP). We demonstrated that FD significantly affected microbial DNP through its interactions with soil conditions; increasing FD led to increased DNP but mainly at higher levels of soil resources. Our results suggest that the effect of species diversity on ecosystem functioning may depend on environmental factors such as resource availability. Future biodiversity experiments should examine how natural levels of environmental variability impact the importance of biodiversity to ecosystem functioning. PMID:21311768

  2. Environmental conditions influence the plant functional diversity effect on potential denitrification.

    Directory of Open Access Journals (Sweden)

    Ariana E Sutton-Grier

    2011-02-01

    Full Text Available Global biodiversity loss has prompted research on the relationship between species diversity and ecosystem functioning. Few studies have examined how plant diversity impacts belowground processes; even fewer have examined how varying resource levels can influence the effect of plant diversity on microbial activity. In a field experiment in a restored wetland, we examined the role of plant trait diversity (or functional diversity, (FD and its interactions with natural levels of variability of soil properties, on a microbial process, denitrification potential (DNP. We demonstrated that FD significantly affected microbial DNP through its interactions with soil conditions; increasing FD led to increased DNP but mainly at higher levels of soil resources. Our results suggest that the effect of species diversity on ecosystem functioning may depend on environmental factors such as resource availability. Future biodiversity experiments should examine how natural levels of environmental variability impact the importance of biodiversity to ecosystem functioning.

  3. Functional diversity in a fragmented landscape — Habitat alterations affect functional trait composition of frog assemblages in Madagascar

    Directory of Open Access Journals (Sweden)

    Jana C. Riemann

    2017-04-01

    Full Text Available Anthropogenic habitat alterations cause biodiversity loss, which in turn negatively affects ecosystem functioning and services, and thus human well-being. To be able to consider ecosystem functioning in conservation actions, analyzing the effects of habitat alteration on functional diversity is essential. Some altered habitats can maintain a significant part of regional biodiversity, however, functional diversity information in altered habitats is so far mostly lacking. We compared functional richness and functional β-diversity based on resource-use traits of frogs between three land-use categories in a rainforest ecosystem in Madagascar. Land-use categories represent a habitat alteration gradient ranging from continuous forest over forest fragments to matrix habitats including different agricultures. Our study revealed distinct changes in resource-use trait composition and complex patterns in the relationship between species richness and functional richness. Thus, the functional structure of frog assemblages changed due to habitat alterations. However, altered habitats likely provide different, rather than fewer functions compared to intact forest. Streams in all land-use categories were the functionally richest habitats, and thus important for ecosystem functioning. Species richness was one, but not the only driver of functional richness in our system. Functional clustering, potentially due to environmental filters depending on resource availability, was caused by anthropogenic and natural drivers. Our study shows that, even in systems where fragmented landscapes still maintain high species diversity, functional diversity can be altered in human altered habitats, which may affect ecosystem processes like productivity, nutrient cycling, and energy flows.

  4. FUNCTIONAL DIVERSITY AND ITS ATTRIBUTE FACTORS IN THE YUNMENG MOUNTAIN NATIONAL FOREST PARK IN BEIJING, CHINA

    OpenAIRE

    Zhang, Jin-Tun; Bai, Xiaohang; Shao, Dan

    2017-01-01

    ABSTRACT The interaction of diversity with environmental gradients is an important topic in ecology. This study investigated the pattern of change in functional diversity in forest communities along an altitudinal gradient in Yunmeng Mountain National Forest Park, China. Forty-two quadrats measuring 10 x 10 m in the forest communities were set up along this altitudinal gradient; plant species, traits and environmental variables were measured and recorded. Six functional diversity indices, nam...

  5. Human-Mediated Loss of Phylogenetic and Functional Diversity in Coral Reef Fishes

    OpenAIRE

    D’agata, Stéphanie; Mouillot, David; Kulbicki, Michel; Andréfouët, Serge; Bellwood, David R.; Cinner, Joshua E.; Cowman, Peter F.; Kronen, Mecki; Pinca, Silvia; Vigliola, Laurent

    2014-01-01

    Beyond the loss of species richness [1-3], human activities may also deplete the breadth of evolutionary history (phylogenetic diversity) and the diversity of roles (functional diversity) carried out by species within communities, two overlooked components of biodiversity. Both are, however, essential to sustain ecosystem functioning and the associated provision of ecosystem services, particularly under fluctuating environmental conditions [1-7]. We quantified the effect of human activities o...

  6. Functional diversity of macrobenthic assemblages decreases in response to sewage discharges

    NARCIS (Netherlands)

    Gusmao, Joao B.; Brauko, Kalina M.; Eriksson, Britas K.; Lana, Paulo C.

    We analyzed the effects of sewage discharge on a subtropical estuary by comparing the functional diversity of intertidal macroinvertebrate assemblages in contaminated with non-contaminated reference areas. Functional structure was assessed using biological traits analysis (BTA) and four multivariate

  7. Structural and functional diversity of acidic scorpion potassium channel toxins.

    Directory of Open Access Journals (Sweden)

    Zong-Yun Chen

    Full Text Available BACKGROUND: Although the basic scorpion K(+ channel toxins (KTxs are well-known pharmacological tools and potential drug candidates, characterization the acidic KTxs still has the great significance for their potential selectivity towards different K(+ channel subtypes. Unfortunately, research on the acidic KTxs has been ignored for several years and progressed slowly. PRINCIPAL FINDINGS: Here, we describe the identification of nine new acidic KTxs by cDNA cloning and bioinformatic analyses. Seven of these toxins belong to three new α-KTx subfamilies (α-KTx28, α-KTx29, and α-KTx30, and two are new members of the known κ-KTx2 subfamily. ImKTx104 containing three disulfide bridges, the first member of the α-KTx28 subfamily, has a low sequence homology with other known KTxs, and its NMR structure suggests ImKTx104 adopts a modified cystine-stabilized α-helix-loop-β-sheet (CS-α/β fold motif that has no apparent α-helixs and β-sheets, but still stabilized by three disulfide bridges. These newly described acidic KTxs exhibit differential pharmacological effects on potassium channels. Acidic scorpion toxin ImKTx104 was the first peptide inhibitor found to affect KCNQ1 channel, which is insensitive to the basic KTxs and is strongly associated with human cardiac abnormalities. ImKTx104 selectively inhibited KCNQ1 channel with a K(d of 11.69 µM, but was less effective against the basic KTxs-sensitive potassium channels. In addition to the ImKTx104 toxin, HeTx204 peptide, containing a cystine-stabilized α-helix-loop-helix (CS-α/α fold scaffold motif, blocked both Kv1.3 and KCNQ1 channels. StKTx23 toxin, with a cystine-stabilized α-helix-loop-β-sheet (CS-α/β fold motif, could inhibit Kv1.3 channel, but not the KCNQ1 channel. CONCLUSIONS/SIGNIFICANCE: These findings characterize the structural and functional diversity of acidic KTxs, and could accelerate the development and clinical use of acidic KTxs as pharmacological tools and

  8. Assessing Genetic Diversity Based on Gliadin Proteins in Aegilops cylindrica Populations from Northwest of Iran

    Directory of Open Access Journals (Sweden)

    Toraj KHABIRI

    2013-02-01

    Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ω type of geliadins. Conversely, the lowest number of bands were pertained to the β type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to β type while, the lowest one was belonged to ω type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

  9. Relationships between functional diversity and aboveground biomass production in the Northern Tibetan alpine grasslands.

    Science.gov (United States)

    Zhu, Juntao; Jiang, Lin; Zhang, Yangjian

    2016-09-26

    Functional diversity, the extent of functional differences among species in a community, drives biodiversity-ecosystem function (BEF) relationships. Here, four species traits and aboveground biomass production (ABP) were considered. We used two community-wide measures of plant functional composition, (1) community weighted means of trait values (CWM) and (2) functional trait diversity based on Rao's quadratic diversity (FD Q ) to evaluate the effects of functional diversity on the ABP in the Northern Tibetan alpine grasslands. Both species and functional diversity were positively related to the ABP. Functional trait composition had a larger predictive power for the ABP than species diversity and FD Q , indicating a primary dependence of ecosystem property on the identity of dominant species in our study system. Multivariate functional diversity was ineffective in predicting ecosystem function due to the trade-offs among different traits or traits selection criterions. Our study contributes to a better understanding of the mechanisms driving the BEF relationships in stressed ecosystems, and especially emphasizes that abiotic and biotic factors affect the BEF relationships in alpine grasslands.

  10. Mapping functional diversity from remotely sensed morphological and physiological forest traits

    OpenAIRE

    Schneider, Fabian D.; Morsdorf, Felix; Schmid, Bernhard; Petchey, Owen L.; Hueni, Andreas; Schimel, David S.; Schaepman, Michael E.

    2017-01-01

    Assessing functional diversity from space can help predict productivity and stability of forest ecosystems at global scale using biodiversity–ecosystem functioning relationships. We present a new spatially continuous method to map regional patterns of tree functional diversity using combined laser scanning and imaging spectroscopy. The method does not require prior taxonomic information and integrates variation in plant functional traits between and within plant species. We compare our method...

  11. Random heteropolymers preserve protein function in foreign environments

    Science.gov (United States)

    Panganiban, Brian; Qiao, Baofu; Jiang, Tao; DelRe, Christopher; Obadia, Mona M.; Nguyen, Trung Dac; Smith, Anton A. A.; Hall, Aaron; Sit, Izaac; Crosby, Marquise G.; Dennis, Patrick B.; Drockenmuller, Eric; Olvera de la Cruz, Monica; Xu, Ting

    2018-03-01

    The successful incorporation of active proteins into synthetic polymers could lead to a new class of materials with functions found only in living systems. However, proteins rarely function under the conditions suitable for polymer processing. On the basis of an analysis of trends in protein sequences and characteristic chemical patterns on protein surfaces, we designed four-monomer random heteropolymers to mimic intrinsically disordered proteins for protein solubilization and stabilization in non-native environments. The heteropolymers, with optimized composition and statistical monomer distribution, enable cell-free synthesis of membrane proteins with proper protein folding for transport and enzyme-containing plastics for toxin bioremediation. Controlling the statistical monomer distribution in a heteropolymer, rather than the specific monomer sequence, affords a new strategy to interface with biological systems for protein-based biomaterials.

  12. Cloning and characterization of functional keratinassociated protein ...

    African Journals Online (AJOL)

    Keratin-associated proteins (KAPs) 5-4 which belongs to keratin-associated protein (KRTAP) type 5 family has two major groups: high/ultrahigh cysteine (HS) and high glycine-tyrosine (HGT). Based on bioinformatic prediction, we experimentally cloned a fragment containingan open reading frame of 1849 bp from maize, ...

  13. Design and functionality of dense protein particles

    NARCIS (Netherlands)

    Saglam, D.

    2012-01-01

    Food products that contain high levels of protein can help to control food intake and to maintain a healthy body weight due to their strong satiating properties. They are also beneficial in the nutrition of elderly and commonly used in medical nutrition. Preparation of food products at high protein

  14. An Index for Measuring Functional Diversity in Plant Communities Based on Neural Network Theory

    Directory of Open Access Journals (Sweden)

    Naiqi Song

    2013-01-01

    Full Text Available Functional diversity in plant communities is a key driver of ecosystem processes. The effective methods for measuring functional diversity are important in ecological studies. A new method based on neural network, self-organizing feature map (SOFM index, was put forward and described. A case application to the study of functional diversity of Phellodendron amurense communities in Xiaolongmen Forest Park of Beijing was carried out in this paper. The results showed that SOFM index was an effective method in the evaluation of functional diversity and its change in plant communities. Significant nonlinear correlations of SOFM index with the common used methods, FAD, MFAD, FDp, FDc, FRic, and FDiv indices, also proved that SOFM index is useful in the studies of functional diversity.

  15. Multiple metrics of diversity have different effects on temperate forest functioning over succession.

    Science.gov (United States)

    Yuan, Zuoqiang; Wang, Shaopeng; Gazol, Antonio; Mellard, Jarad; Lin, Fei; Ye, Ji; Hao, Zhanqing; Wang, Xugao; Loreau, Michel

    2016-12-01

    Biodiversity can be measured by taxonomic, phylogenetic, and functional diversity. How ecosystem functioning depends on these measures of diversity can vary from site to site and depends on successional stage. Here, we measured taxonomic, phylogenetic, and functional diversity, and examined their relationship with biomass in two successional stages of the broad-leaved Korean pine forest in northeastern China. Functional diversity was calculated from six plant traits, and aboveground biomass (AGB) and coarse woody productivity (CWP) were estimated using data from three forest censuses (10 years) in two large fully mapped forest plots (25 and 5 ha). 11 of the 12 regressions between biomass variables (AGB and CWP) and indices of diversity showed significant positive relationships, especially those with phylogenetic diversity. The mean tree diversity-biomass regressions increased from 0.11 in secondary forest to 0.31 in old-growth forest, implying a stronger biodiversity effect in more mature forest. Multi-model selection results showed that models including species richness, phylogenetic diversity, and single functional traits explained more variation in forest biomass than other candidate models. The models with a single functional trait, i.e., leaf area in secondary forest and wood density in mature forest, provided better explanations for forest biomass than models that combined all six functional traits. This finding may reflect different strategies in growth and resource acquisition in secondary and old-growth forests.

  16. Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

    Science.gov (United States)

    Dey, Samrat; Tribedi, Prosun

    2018-03-01

    Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both

  17. Mechanisms underlying local functional and phylogenetic beta diversity in two temperate forests.

    Science.gov (United States)

    Wang, Xugao; Wiegand, Thorsten; Swenson, Nathan G; Wolf, Amy T; Howe, Robert W; Hao, Zhanqing; Lin, Fei; Ye, Ji; Yuan, Zuoqiang

    2015-04-01

    Although trait information has been widely used to explore underlying mechanisms of forest community structure, most studies have focused on local patterns of phylogenetic or functional alpha diversity. Investigations of functional beta diversity, on the other hand, have not been conducted at local scales in a spatially explicit way. In this study, we provide a powerful methodology based on recent advances in spatial point pattern analysis using fully mapped data of large and small trees in two large temperate forest plots. This approach allowed us to assess the relative importance of different ecological processes and mechanisms for explaining patterns of local phylogenetic and functional beta diversity. For both forests and size classes, we found a clear hierarchy of scales: habitat filtering accounted for patterns of phylogenetic and functional beta diversity at larger distances (150-250 m), dispersal limitation accounted for the observed decline in beta diversity at distances below 150 m, and species interactions explained small departures from functional and phylogenetic beta diversity at the immediate plant-neighborhood scale (below 20 m). Thus, both habitat filtering and dispersal limitation influenced the observed patterns in phylogenetic and functional beta diversity at local scales. This result contrasts with a previous study from the same forests, where dispersal limitation alone approximated the observed species beta diversity for distances up to 250 m. In addition, species interactions were relatively unimportant for predicting phylogenetic and functional beta diversity. Our analysis suggests that phylogenetic and functional beta diversity can provide insights into the mechanisms of local community assembly that are missed by studies focusing exclusively on species beta diversity.

  18. Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum

    Directory of Open Access Journals (Sweden)

    Daniela Kajihara

    2012-01-01

    Full Text Available Transposable elements (TEs account for a large portion of plant genomes, particularly in grasses, in which they correspond to 50%-80% of the genomic content. TEs have recently been shown to be a source of new genes and new regulatory networks. The most striking contribution of TEs is referred as “molecular domestication”, by which the element coding sequence loses its movement capacity and acquires cellular function. Recently, domesticated transposases known as mustang and derived from the Mutator element have been described in sugarcane. In order to improve our understanding of the function of these proteins, we identified mustang genes from Sorghum bicolor and Zea mays and performed a phenetic analysis to assess the diversity and evolutionary history of this gene family. This analysis identified orthologous groups and showed that mustang genes are highly conserved in grass genomes. We also explored the transcriptional activity of sugarcane mustang genes in heterologous and homologous systems. These genes were found to be ubiquitously transcribed, with shoot apical meristem having the highest expression levels, and were downregulated by phytohormones. Together, these findings suggest the possible involvement of mustang proteins in the maintenance of hormonal homeostasis.

  19. Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum.

    Science.gov (United States)

    Kajihara, Daniela; de Godoy, Fabiana; Hamaji, Thais Alves; Blanco, Silvia Regina; Van Sluys, Marie-Anne; Rossi, Magdalena

    2012-07-01

    Transposable elements (TEs) account for a large portion of plant genomes, particularly in grasses, in which they correspond to 50%-80% of the genomic content. TEs have recently been shown to be a source of new genes and new regulatory networks. The most striking contribution of TEs is referred as "molecular domestication", by which the element coding sequence loses its movement capacity and acquires cellular function. Recently, domesticated transposases known as mustang and derived from the Mutator element have been described in sugarcane. In order to improve our understanding of the function of these proteins, we identified mustang genes from Sorghum bicolor and Zea mays and performed a phenetic analysis to assess the diversity and evolutionary history of this gene family. This analysis identified orthologous groups and showed that mustang genes are highly conserved in grass genomes. We also explored the transcriptional activity of sugarcane mustang genes in heterologous and homologous systems. These genes were found to be ubiquitously transcribed, with shoot apical meristem having the highest expression levels, and were downregulated by phytohormones. Together, these findings suggest the possible involvement of mustang proteins in the maintenance of hormonal homeostasis.

  20. Diversity and Functional Analysis of the FeMo-Cofactor Maturase NifB

    Directory of Open Access Journals (Sweden)

    Simon Arragain

    2017-11-01

    Full Text Available One of the main hurdles to engineer nitrogenase in a non-diazotrophic host is achieving NifB activity. NifB is an extremely unstable and oxygen sensitive protein that catalyzes a low-potential SAM-radical dependent reaction. The product of NifB activity is called NifB-co, a complex [8Fe-9S-C] cluster that serves as obligate intermediate in the biosyntheses of the active-site cofactors of all known nitrogenases. Here we study the diversity and phylogeny of naturally occurring NifB proteins, their protein architecture and the functions of the distinct NifB domains in order to understand what defines a catalytically active NifB. Focus is on NifB from the thermophile Chlorobium tepidum (two-domain architecture, the hyperthermophile Methanocaldococcus infernus (single-domain architecture and the mesophile Klebsiella oxytoca (two-domain architecture, showing in silico characterization of their nitrogen fixation (nif gene clusters, conserved NifB motifs, and functionality. C. tepidum and M. infernus NifB were able to complement an Azotobacter vinelandii (ΔnifB mutant restoring the Nif+ phenotype and thus demonstrating their functionality in vivo. In addition, purified C. tepidum NifB exhibited activity in the in vitro NifB-dependent nitrogenase reconstitution assay. Intriguingly, changing the two-domain K. oxytoca NifB to single-domain by removal of the C-terminal NifX-like extension resulted in higher in vivo nitrogenase activity, demonstrating that this domain is not required for nitrogen fixation in mesophiles.

  1. Diversity and the Political Function of Religious Education

    Science.gov (United States)

    Skeie, Geir

    2006-01-01

    Questions about the relationship between religion and politics are discussed with particular focus on the consequences for religious education. Norway is taken as an example of a country where increasing cultural diversity challenges traditional politics of religion. In the present climate of conflicting views on the role of religion in politics,…

  2. Molecular and functional diversity in Capsicum landraces of ...

    African Journals Online (AJOL)

    The present study analyzed the diversity in 26 landraces of Capsicum from Andaman Islands using 20 morphological, 16 biochemical and 10 DNA markers. Significant differences were observed in tested landraces and 16 reference genotypes from mainland India. Biochemical markers grouped all the genotypes into eight ...

  3. Host Determinants of Prion Strain Diversity Independent of Prion Protein Genotype

    Science.gov (United States)

    Crowell, Jenna; Hughson, Andrew; Caughey, Byron

    2015-01-01

    ABSTRACT Phenotypic diversity in prion diseases can be specified by prion strains in which biological traits are propagated through an epigenetic mechanism mediated by distinct PrPSc conformations. We investigated the role of host-dependent factors on phenotypic diversity of chronic wasting disease (CWD) in different host species that express the same prion protein gene (Prnp). Two CWD strains that have distinct biological, biochemical, and pathological features were identified in transgenic mice that express the Syrian golden hamster (SGH) Prnp. The CKY strain of CWD had a shorter incubation period than the WST strain of CWD, but after transmission to SGH, the incubation period of CKY CWD was ∼150 days longer than WST CWD. Limited proteinase K digestion revealed strain-specific PrPSc polypeptide patterns that were maintained in both hosts, but the solubility and conformational stability of PrPSc differed for the CWD strains in a host-dependent manner. WST CWD produced PrPSc amyloid plaques in the brain of the SGH that were partially insoluble and stable at a high concentration of protein denaturant. However, in transgenic mice, PrPSc from WST CWD did not assemble into plaques, was highly soluble, and had low conformational stability. Similar studies using the HY and DY strains of transmissible mink encephalopathy resulted in minor differences in prion biological and PrPSc properties between transgenic mice and SGH. These findings indicate that host-specific pathways that are independent of Prnp can alter the PrPSc conformation of certain prion strains, leading to changes in the biophysical properties of PrPSc, neuropathology, and clinical prion disease. IMPORTANCE Prions are misfolded pathogenic proteins that cause neurodegeneration in humans and animals. Transmissible prion diseases exhibit a spectrum of disease phenotypes and the basis of this diversity is encoded in the structure of the pathogenic prion protein and propagated by an epigenetic mechanism. In

  4. Assessing Natural Resource Use by Forest-Reliant Communities in Madagascar Using Functional Diversity and Functional Redundancy Metrics

    OpenAIRE

    Brown, Kerry A.; Flynn, Dan F. B.; Abram, Nicola K.; Ingram, J. Carter; Johnson, Steig E.; Wright, Patricia

    2011-01-01

    Biodiversity plays an integral role in the livelihoods of subsistence-based forest-dwelling communities and as a consequence it is increasingly important to develop quantitative approaches that capture not only changes in taxonomic diversity, but also variation in natural resources and provisioning services. We apply a functional diversity metric originally developed for addressing questions in community ecology to assess utilitarian diversity of 56 forest plots in Madagascar. The use categor...

  5. High-throughput proteome dynamics for discovery of key proteins in sentinel species: Unsuspected vitellogenins diversity in the crustacean Gammarus fossarum.

    Science.gov (United States)

    Trapp, Judith; Armengaud, Jean; Gaillard, Jean-Charles; Pible, Olivier; Chaumot, Arnaud; Geffard, Olivier

    2016-09-02

    In environmental science, omics-based approaches are widely used for the identification of gene products related to stress response. However, when dealing with non-model species, functional prediction of genes is challenging. Indeed, functional predictions are often obtained by sequence similarity searches and functional data from phylogenetically distant organisms, which can lead to inaccurate predictions due to quite different evolutionary scenarios. In oviparous females, vitellogenin production is vital for embryonic development, ensuring population viability. Its abnormal presence in fish male organisms is commonly employed as a biomarker of exposure to xenoestrogens, named endocrine disruptors. Here, in the freshwater amphipod Gammarus fossarum, we identified vitellogenin proteins by means of a proteome temporal dynamics analysis during oogenesis and embryogenesis. This exhaustive approach allows several functional molecular hypotheses in the oogenesis process to be drawn. Moreover, we revealed an unsuspected diversity of molecular players involved in yolk formation as eight proteins originating from different families of the large lipid transfer protein superfamily were identified as "true vitellogenins". In non-model species, next generation sequencing technologies development enables quickly deciphering gene and protein sequences but accuracy of associated functional prediction remains to be established. Here, in the crustacean Gammarus fossarum, a key sentinel species in freshwater biomonitoring, we identified key molecular players involved in the female reproduction by studying the proteome dynamics of ovaries and embryos. An unsuspected diversity of vitellogenin proteins was evidenced. These proteins being vital for offspring development, their high diversity may be advantageous for the organism's reproduction. Phylogenetic analysis showed that some forms are true vitellogenin orthologs while others are included in the apolipoprotein family, a paralogous

  6. Production of functional protein hydrolysates from Egyptian breeds ...

    African Journals Online (AJOL)

    Production of functional protein hydrolysates from Egyptian breeds of soybean and lupin seeds. AA khalil, SS Mohamed, FS Taha, EN Karlsson. Abstract. Enzymatic hydrolysis is an agro-processing aid that can be utilized in order to improve nutritional quality of protein extracts from many sources. In this study, protein ...

  7. Protein mechanics: a route from structure to function

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    Why do proteins have such varied and complicated structures and how are these structures related to the functions that each protein must perform? Almost 50 years after the first protein structures were solved (Kendrew et al 1958; Perutz 1960), these questions are still very much part of molecular biology. While structures ...

  8. Functional roles of intrinsic disorder in CRISPR-associated protein Cas9.

    Science.gov (United States)

    Du, Zhihua; Uversky, Vladimir N

    2017-08-22

    Protein intrinsic disorder is an important characteristic commonly detected in multifunctional or RNA- and DNA-binding proteins. Due to their high conformational flexibility and solvent accessibility, intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) execute diverse functions including interaction with multiple partners, and are frequently subjected to various post-translational modifications. Recent studies on the components comprising the CRISPR (clustered regularly interspaced short palindromic repeats) system have elucidated the crystal structure of Cas9 proteins and the mechanism by which the Cas9-sgRNA complex recognizes and cleaves its target DNA. Yet the extent and functional implications of intrinsic disorder in the Cas9 protein have never been fully assessed. Here, we present a comprehensive computational analysis based on both sequence and structural data in an attempt to investigate the roles of IDPRs in the functioning of Cas9 proteins of different origin. We conclude that among the functional roles of IDPRs in Cas9 proteins are recognition of the target DNA and mediation of nucleic acid and protein binding.

  9. Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

    Science.gov (United States)

    Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

    2014-03-01

    Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein

  10. Alkylation damage by lipid electrophiles targets functional protein systems.

    Science.gov (United States)

    Codreanu, Simona G; Ullery, Jody C; Zhu, Jing; Tallman, Keri A; Beavers, William N; Porter, Ned A; Marnett, Lawrence J; Zhang, Bing; Liebler, Daniel C

    2014-03-01

    Protein alkylation by reactive electrophiles contributes to chemical toxicities and oxidative stress, but the functional impact of alkylation damage across proteomes is poorly understood. We used Click chemistry and shotgun proteomics to profile the accumulation of proteome damage in human cells treated with lipid electrophile probes. Protein target profiles revealed three damage susceptibility classes, as well as proteins that were highly resistant to alkylation. Damage occurred selectively across functional protein interaction networks, with the most highly alkylation-susceptible proteins mapping to networks involved in cytoskeletal regulation. Proteins with lower damage susceptibility mapped to networks involved in protein synthesis and turnover and were alkylated only at electrophile concentrations that caused significant toxicity. Hierarchical susceptibility of proteome systems to alkylation may allow cells to survive sublethal damage while protecting critical cell functions.

  11. Alkylation Damage by Lipid Electrophiles Targets Functional Protein Systems*

    Science.gov (United States)

    Codreanu, Simona G.; Ullery, Jody C.; Zhu, Jing; Tallman, Keri A.; Beavers, William N.; Porter, Ned A.; Marnett, Lawrence J.; Zhang, Bing; Liebler, Daniel C.

    2014-01-01

    Protein alkylation by reactive electrophiles contributes to chemical toxicities and oxidative stress, but the functional impact of alkylation damage across proteomes is poorly understood. We used Click chemistry and shotgun proteomics to profile the accumulation of proteome damage in human cells treated with lipid electrophile probes. Protein target profiles revealed three damage susceptibility classes, as well as proteins that were highly resistant to alkylation. Damage occurred selectively across functional protein interaction networks, with the most highly alkylation-susceptible proteins mapping to networks involved in cytoskeletal regulation. Proteins with lower damage susceptibility mapped to networks involved in protein synthesis and turnover and were alkylated only at electrophile concentrations that caused significant toxicity. Hierarchical susceptibility of proteome systems to alkylation may allow cells to survive sublethal damage while protecting critical cell functions. PMID:24429493

  12. Phylogenetic beta diversity metrics, trait evolution and inferring the functional beta diversity of communities.

    Directory of Open Access Journals (Sweden)

    Nathan G Swenson

    Full Text Available The beta diversity of communities along gradients has fascinated ecologists for decades. Traditionally such studies have focused on the species composition of communities, but researchers are becoming increasingly interested in analyzing the phylogenetic composition in the hope of achieving mechanistic insights into community structure. To date many metrics of phylogenetic beta diversity have been published, but few empirical studies have been published. Further inferences made from such phylogenetic studies critically rely on the pattern of trait evolution. The present work provides a study of the phylogenetic dissimilarity of 96 tree communities in India. The work compares and contrasts eight metrics of phylogenetic dissimilarity, considers the role of phylogenetic signal in trait data and shows that environmental distance rather than spatial distance is the best correlate of phylogenetic dissimilarity in the study system.

  13. A large-scale evaluation of computational protein function prediction.

    Science.gov (United States)

    Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kaßner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas A; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-03-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.

  14. Small-molecule control of protein function through Staudinger reduction

    Science.gov (United States)

    Luo, Ji; Liu, Qingyang; Morihiro, Kunihiko; Deiters, Alexander

    2016-11-01

    Using small molecules to control the function of proteins in live cells with complete specificity is highly desirable, but challenging. Here we report a small-molecule switch that can be used to control protein activity. The approach uses a phosphine-mediated Staudinger reduction to activate protein function. Genetic encoding of an ortho-azidobenzyloxycarbonyl amino acid using a pyrrolysyl transfer RNA synthetase/tRNACUA pair in mammalian cells enables the site-specific introduction of a small-molecule-removable protecting group into the protein of interest. Strategic placement of this group renders the protein inactive until deprotection through a bioorthogonal Staudinger reduction delivers the active wild-type protein. This developed methodology was applied to the conditional control of several cellular processes, including bioluminescence (luciferase), fluorescence (enhanced green fluorescent protein), protein translocation (nuclear localization sequence), DNA recombination (Cre) and gene editing (Cas9).

  15. Prediction of protein function and pathways in the genome era.

    NARCIS (Netherlands)

    Gabaldon, T.; Huynen, M.A.

    2004-01-01

    The growing number of completely sequenced genomes adds new dimensions to the use of sequence analysis to predict protein function. Compared with the classical knowledge transfer from one protein to a similar sequence (homology-based function prediction), knowledge about the corresponding genes in

  16. Liver Function Status in some Nigerian Children with Protein Energy ...

    African Journals Online (AJOL)

    Objective: To ascertain functional status of the liver in Nigeria Children with Protein energy malnutrition. Materials and Methods: Liver function tests were performed on a total of 88 children with protein energy malnutrition (PEM). These were compared with 22 apparently well-nourished children who served as controls.

  17. The contact activation proteins: a structure/function overview

    NARCIS (Netherlands)

    Meijers, J. C.; McMullen, B. A.; Bouma, B. N.

    1992-01-01

    In recent years, extensive knowledge has been obtained on the structure/function relationships of blood coagulation proteins. In this overview, we present recent developments on the structure/function relationships of the contact activation proteins: factor XII, high molecular weight kininogen,

  18. Large-scale identification of human cerebrovascular proteins: Inter-tissue and intracerebral vascular protein diversity.

    Directory of Open Access Journals (Sweden)

    Soo Jung Lee

    Full Text Available The human cerebrovascular system is responsible for regulating demand-dependent perfusion and maintaining the blood-brain barrier (BBB. In addition, defects in the human cerebrovasculature lead to stroke, intracerebral hemorrhage, vascular malformations, and vascular cognitive impairment. The objective of this study was to discover new proteins of the human cerebrovascular system using expression data from the Human Protein Atlas, a large-scale project which allows public access to immunohistochemical analysis of human tissues. We screened 20,158 proteins in the HPA and identified 346 expression patterns correlating to blood vessels in human brain. Independent experiments showed that 51/52 of these distributions could be experimentally replicated across different brain samples. Some proteins (40% demonstrated endothelial cell (EC-enriched expression, while others were expressed primarily in vascular smooth muscle cells (VSMC; 18%; 39% of these proteins were expressed in both cell types. Most brain EC markers were tissue oligospecific; that is, they were expressed in endothelia in an average of 4.8 out of 9 organs examined. Although most markers expressed in endothelial cells of the brain were present in all cerebral capillaries, a significant number (21% were expressed only in a fraction of brain capillaries within each brain sample. Among proteins found in cerebral VSMC, virtually all were also expressed in peripheral VSMC and in non-vascular smooth muscle cells (SMC. Only one was potentially brain specific: VHL (Von Hippel-Lindau tumor suppressor. HRC (histidine rich calcium binding protein and VHL were restricted to VSMC and not found in non-vascular tissues such as uterus or gut. In conclusion, we define a set of brain vascular proteins that could be relevant to understanding the unique physiology and pathophysiology of the human cerebrovasculature. This set of proteins defines inter-organ molecular differences in the vasculature and

  19. BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins

    Directory of Open Access Journals (Sweden)

    Kankainen Matti

    2012-02-01

    Full Text Available Abstract Background Automated function prediction has played a central role in determining the biological functions of bacterial proteins. Typically, protein function annotation relies on homology, and function is inferred from other proteins with similar sequences. This approach has become popular in bacterial genomics because it is one of the few methods that is practical for large datasets and because it does not require additional functional genomics experiments. However, the existing solutions produce erroneous predictions in many cases, especially when query sequences have low levels of identity with the annotated source protein. This problem has created a pressing need for improvements in homology-based annotation. Results We present an automated method for the functional annotation of bacterial protein sequences. Based on sequence similarity searches, BLANNOTATOR accurately annotates query sequences with one-line summary descriptions of protein function. It groups sequences identified by BLAST into subsets according to their annotation and bases its prediction on a set of sequences with consistent functional information. We show the results of BLANNOTATOR's performance in sets of bacterial proteins with known functions. We simulated the annotation process for 3090 SWISS-PROT proteins using a database in its state preceding the functional characterisation of the query protein. For this dataset, our method outperformed the five others that we tested, and the improved performance was maintained even in the absence of highly related sequence hits. We further demonstrate the value of our tool by analysing the putative proteome of Lactobacillus crispatus strain ST1. Conclusions BLANNOTATOR is an accurate method for bacterial protein function prediction. It is practical for genome-scale data and does not require pre-existing sequence clustering; thus, this method suits the needs of bacterial genome and metagenome researchers. The method and a

  20. Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning.

    Science.gov (United States)

    Davies, T Jonathan; Urban, Mark C; Rayfield, Bronwyn; Cadotte, Marc W; Peres-Neto, Pedro R

    2016-09-01

    Recent studies have supported a link between phylogenetic diversity and various ecological properties including ecosystem function. However, such studies typically assume that phylogenetic branches of equivalent length are more or less interchangeable. Here we suggest that there is a need to consider not only branch lengths but also their placement on the phylogeny. We demonstrate how two common indices of network centrality can be used to describe the evolutionary distinctiveness of network elements (nodes and branches) on a phylogeny. If phylogenetic diversity enhances ecosystem function via complementarity and the representation of functional diversity, we would predict a correlation between evolutionary distinctiveness of network elements and their contribution to ecosystem process. In contrast, if one or a few evolutionary innovations play key roles in ecosystem function, the relationship between evolutionary distinctiveness and functional contribution may be weak or absent. We illustrate how network elements associated with high functional contribution can be identified from regressions between phylogenetic diversity and productivity using a well-known empirical data set on plant productivity from the Cedar Creek Long-Term Ecological Research. We find no association between evolutionary distinctiveness and ecosystem functioning, but we are able to identify phylogenetic elements associated with species of known high functional contribution within the Fabaceae. Our perspective provides a useful guide in the search for ecological traits linking diversity and ecosystem function, and suggests a more nuanced consideration of phylogenetic diversity is required in the conservation and biodiversity-ecosystem-function literature. © 2016 by the Ecological Society of America.

  1. Membrane Protein Production in Lactococcus lactis for Functional Studies.

    Science.gov (United States)

    Seigneurin-Berny, Daphne; King, Martin S; Sautron, Emiline; Moyet, Lucas; Catty, Patrice; André, François; Rolland, Norbert; Kunji, Edmund R S; Frelet-Barrand, Annie

    2016-01-01

    Due to their unique properties, expression and study of membrane proteins in heterologous systems remains difficult. Among the bacterial systems available, the Gram-positive lactic bacterium, Lactococcus lactis, traditionally used in food fermentations, is nowadays widely used for large-scale production and functional characterization of bacterial and eukaryotic membrane proteins. The aim of this chapter is to describe the different possibilities for the functional characterization of peripheral or intrinsic membrane proteins expressed in Lactococcus lactis.

  2. Functional Resilience against Climate-Driven Extinctions – Comparing the Functional Diversity of European and North American Tree Floras

    Science.gov (United States)

    Liebergesell, Mario; Stahl, Ulrike; Freiberg, Martin; Welk, Erik; Kattge, Jens; Cornelissen, J. Hans C.; Peñuelas, Josep

    2016-01-01

    Future global change scenarios predict a dramatic loss of biodiversity for many regions in the world, potentially reducing the resistance and resilience of ecosystem functions. Once before, during Plio-Pleistocene glaciations, harsher climatic conditions in Europe as compared to North America led to a more depauperate tree flora. Here we hypothesize that this climate driven species loss has also reduced functional diversity in Europe as compared to North America. We used variation in 26 traits for 154 North American and 66 European tree species and grid-based co-occurrences derived from distribution maps to compare functional diversity patterns of the two continents. First, we identified similar regions with respect to contemporary climate in the temperate zone of North America and Europe. Second, we compared the functional diversity of both continents and for the climatically similar sub-regions using the functional dispersion-index (FDis) and the functional richness index (FRic). Third, we accounted in these comparisons for grid-scale differences in species richness, and, fourth, investigated the associated trait spaces using dimensionality reduction. For gymnosperms we find similar functional diversity on both continents, whereas for angiosperms functional diversity is significantly greater in Europe than in North America. These results are consistent across different scales, for climatically similar regions and considering species richness patterns. We decomposed these differences in trait space occupation into differences in functional diversity vs. differences in functional identity. We show that climate-driven species loss on a continental scale might be decoupled from or at least not linearly related to changes in functional diversity. This might be important when analyzing the effects of climate-driven biodiversity change on ecosystem functioning. PMID:26848836

  3. Functional Resilience against Climate-Driven Extinctions - Comparing the Functional Diversity of European and North American Tree Floras.

    Directory of Open Access Journals (Sweden)

    Mario Liebergesell

    Full Text Available Future global change scenarios predict a dramatic loss of biodiversity for many regions in the world, potentially reducing the resistance and resilience of ecosystem functions. Once before, during Plio-Pleistocene glaciations, harsher climatic conditions in Europe as compared to North America led to a more depauperate tree flora. Here we hypothesize that this climate driven species loss has also reduced functional diversity in Europe as compared to North America. We used variation in 26 traits for 154 North American and 66 European tree species and grid-based co-occurrences derived from distribution maps to compare functional diversity patterns of the two continents. First, we identified similar regions with respect to contemporary climate in the temperate zone of North America and Europe. Second, we compared the functional diversity of both continents and for the climatically similar sub-regions using the functional dispersion-index (FDis and the functional richness index (FRic. Third, we accounted in these comparisons for grid-scale differences in species richness, and, fourth, investigated the associated trait spaces using dimensionality reduction. For gymnosperms we find similar functional diversity on both continents, whereas for angiosperms functional diversity is significantly greater in Europe than in North America. These results are consistent across different scales, for climatically similar regions and considering species richness patterns. We decomposed these differences in trait space occupation into differences in functional diversity vs. differences in functional identity. We show that climate-driven species loss on a continental scale might be decoupled from or at least not linearly related to changes in functional diversity. This might be important when analyzing the effects of climate-driven biodiversity change on ecosystem functioning.

  4. Functional Resilience against Climate-Driven Extinctions - Comparing the Functional Diversity of European and North American Tree Floras.

    Science.gov (United States)

    Liebergesell, Mario; Reu, Björn; Stahl, Ulrike; Freiberg, Martin; Welk, Erik; Kattge, Jens; Cornelissen, J Hans C; Peñuelas, Josep; Wirth, Christian

    2016-01-01

    Future global change scenarios predict a dramatic loss of biodiversity for many regions in the world, potentially reducing the resistance and resilience of ecosystem functions. Once before, during Plio-Pleistocene glaciations, harsher climatic conditions in Europe as compared to North America led to a more depauperate tree flora. Here we hypothesize that this climate driven species loss has also reduced functional diversity in Europe as compared to North America. We used variation in 26 traits for 154 North American and 66 European tree species and grid-based co-occurrences derived from distribution maps to compare functional diversity patterns of the two continents. First, we identified similar regions with respect to contemporary climate in the temperate zone of North America and Europe. Second, we compared the functional diversity of both continents and for the climatically similar sub-regions using the functional dispersion-index (FDis) and the functional richness index (FRic). Third, we accounted in these comparisons for grid-scale differences in species richness, and, fourth, investigated the associated trait spaces using dimensionality reduction. For gymnosperms we find similar functional diversity on both continents, whereas for angiosperms functional diversity is significantly greater in Europe than in North America. These results are consistent across different scales, for climatically similar regions and considering species richness patterns. We decomposed these differences in trait space occupation into differences in functional diversity vs. differences in functional identity. We show that climate-driven species loss on a continental scale might be decoupled from or at least not linearly related to changes in functional diversity. This might be important when analyzing the effects of climate-driven biodiversity change on ecosystem functioning.

  5. Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application

    Directory of Open Access Journals (Sweden)

    Cristina M. Prieto-Barajas

    2018-01-01

    Full Text Available Microbial mats are horizontally stratified microbial communities, exhibiting a structure defined by physiochemical gradients, which models microbial diversity, physiological activities, and their dynamics as a whole system. These ecosystems are commonly associated with aquatic habitats, including hot springs, hypersaline ponds, and intertidal coastal zones and oligotrophic environments, all of them harbour phototrophic mats and other environments such as acidic hot springs or acid mine drainage harbour non-photosynthetic mats. This review analyses the complex structure, diversity, and interactions between the microorganisms that form the framework of different types of microbial mats located around the globe. Furthermore, the many tools that allow studying microbial mats in depth and their potential biotechnological applications are discussed.

  6. Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.

    Science.gov (United States)

    Zha, Yinghua; Berga, Mercè; Comte, Jérôme; Langenheder, Silke

    2016-01-01

    Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted.

  7. Functionalization of whey proteins by reactive supercritical fluid extrusion

    Directory of Open Access Journals (Sweden)

    Khanitta Ruttarattanamongkol

    2012-09-01

    Full Text Available Whey protein, a by-product from cheese-making, is often used in a variety of food formulations due to its unsurpassednutritional quality and inherent functional properties. However, the possibilities for the improvement and upgrading of wheyprotein utilization still need to be explored. Reactive supercritical fluid extrusion (SCFX is a novel technique that has beenrecently reported to successfully functionalize commercially available whey proteins into a product with enhanced functionalproperties. The specific goal of this review is to provide fundamental understanding of the reinforcement mechanism andprocessing of protein functionalization by reactive SCFX process. The superimposed extrusion variables and their interactionmechanism affect the physico-chemical properties of whey proteins. By understanding the structure, functional properties andprocessing relationships of such materials, the rational design criteria for novel functionalized proteins could be developedand effectively utilized in food systems.

  8. A survey of computational intelligence techniques in protein function prediction.

    Science.gov (United States)

    Tiwari, Arvind Kumar; Srivastava, Rajeev

    2014-01-01

    During the past, there was a massive growth of knowledge of unknown proteins with the advancement of high throughput microarray technologies. Protein function prediction is the most challenging problem in bioinformatics. In the past, the homology based approaches were used to predict the protein function, but they failed when a new protein was different from the previous one. Therefore, to alleviate the problems associated with homology based traditional approaches, numerous computational intelligence techniques have been proposed in the recent past. This paper presents a state-of-the-art comprehensive review of various computational intelligence techniques for protein function predictions using sequence, structure, protein-protein interaction network, and gene expression data used in wide areas of applications such as prediction of DNA and RNA binding sites, subcellular localization, enzyme functions, signal peptides, catalytic residues, nuclear/G-protein coupled receptors, membrane proteins, and pathway analysis from gene expression datasets. This paper also summarizes the result obtained by many researchers to solve these problems by using computational intelligence techniques with appropriate datasets to improve the prediction performance. The summary shows that ensemble classifiers and integration of multiple heterogeneous data are useful for protein function prediction.

  9. Effects of plant diversity, habitat and agricultural landscape structure on the functional diversity of carabid assemblages in the North China Plain

    OpenAIRE

    Liu, Y.; Duan, M.; Zhang, X.; Zhang, X.; Yu, Z.; Axmacher, J. C.

    2015-01-01

    1. This study investigated the effects of plant diversity, habitat type and landscape structure on the functional diversity of the carabid assemblages in the agro-landscape of the North China Plain. We hypothesize (i) small, herbivorous and omnivorous carabids are more strongly affected by local plant diversity, while large and predatory carabids are strongly affected by landscape structure, and (ii) habitat type influences the diversity across functional groups. 2. In 2010, carabid beetles w...

  10. GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking

    Science.gov (United States)

    Baek, Minkyung; Shin, Woong-Hee; Chung, Hwan Won; Seok, Chaok

    2017-07-01

    Protein-ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein-ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein-ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

  11. An overview of the applicability of functional diversity in Biological Conservation

    OpenAIRE

    Freitas, J. R.; Mantovani, W.

    2017-01-01

    Abstract Functional diversity is increasingly pointed as a useful approach to reach Biological Conservation goals. Here, we provide an overview of the functional diversity approach status in the Biological Conservation field. We sought for peer-reviewed papers published over a period of twenty years (from 1994 to 2014). First we used the general topic “functional diversity” and then refined our search using the key-word “conservation”. We have identified the conservation strategies addressed,...

  12. Negative Impacts of Human Land Use on Dung Beetle Functional Diversity

    OpenAIRE

    Barragán, Felipe; Moreno, Claudia E.; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario

    2011-01-01

    The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in ...

  13. Protein Carbonylation and Adipocyte Mitochondrial Function*

    Science.gov (United States)

    Curtis, Jessica M.; Hahn, Wendy S.; Stone, Matthew D.; Inda, Jacob J.; Droullard, David J.; Kuzmicic, Jovan P.; Donoghue, Margaret A.; Long, Eric K.; Armien, Anibal G.; Lavandero, Sergio; Arriaga, Edgar; Griffin, Timothy J.; Bernlohr, David A.

    2012-01-01

    Carbonylation is the covalent, non-reversible modification of the side chains of cysteine, histidine, and lysine residues by lipid peroxidation end products such as 4-hydroxy- and 4-oxononenal. In adipose tissue the effects of such modifications are associated with increased oxidative stress and metabolic dysregulation centered on mitochondrial energy metabolism. To address the role of protein carbonylation in the pathogenesis of mitochondrial dysfunction, quantitative proteomics was employed to identify specific targets of carbonylation in GSTA4-silenced or overexpressing 3T3-L1 adipocytes. GSTA4-silenced adipocytes displayed elevated carbonylation of several key mitochondrial proteins including the phosphate carrier protein, NADH dehydrogenase 1α subcomplexes 2 and 3, translocase of inner mitochondrial membrane 50, and valyl-tRNA synthetase. Elevated protein carbonylation is accompanied by diminished complex I activity, impaired respiration, increased superoxide production, and a reduction in membrane potential without changes in mitochondrial number, area, or density. Silencing of the phosphate carrier or NADH dehydrogenase 1α subcomplexes 2 or 3 in 3T3-L1 cells results in decreased basal and maximal respiration. These results suggest that protein carbonylation plays a major instigating role in cytokine-dependent mitochondrial dysfunction and may be linked to the development of insulin resistance in the adipocyte. PMID:22822087

  14. Protein carbonylation and adipocyte mitochondrial function.

    Science.gov (United States)

    Curtis, Jessica M; Hahn, Wendy S; Stone, Matthew D; Inda, Jacob J; Droullard, David J; Kuzmicic, Jovan P; Donoghue, Margaret A; Long, Eric K; Armien, Anibal G; Lavandero, Sergio; Arriaga, Edgar; Griffin, Timothy J; Bernlohr, David A

    2012-09-21

    Carbonylation is the covalent, non-reversible modification of the side chains of cysteine, histidine, and lysine residues by lipid peroxidation end products such as 4-hydroxy- and 4-oxononenal. In adipose tissue the effects of such modifications are associated with increased oxidative stress and metabolic dysregulation centered on mitochondrial energy metabolism. To address the role of protein carbonylation in the pathogenesis of mitochondrial dysfunction, quantitative proteomics was employed to identify specific targets of carbonylation in GSTA4-silenced or overexpressing 3T3-L1 adipocytes. GSTA4-silenced adipocytes displayed elevated carbonylation of several key mitochondrial proteins including the phosphate carrier protein, NADH dehydrogenase 1α subcomplexes 2 and 3, translocase of inner mitochondrial membrane 50, and valyl-tRNA synthetase. Elevated protein carbonylation is accompanied by diminished complex I activity, impaired respiration, increased superoxide production, and a reduction in membrane potential without changes in mitochondrial number, area, or density. Silencing of the phosphate carrier or NADH dehydrogenase 1α subcomplexes 2 or 3 in 3T3-L1 cells results in decreased basal and maximal respiration. These results suggest that protein carbonylation plays a major instigating role in cytokine-dependent mitochondrial dysfunction and may be linked to the development of insulin resistance in the adipocyte.

  15. Effects of fishing and regional species pool on the functional diversity of fish communities.

    Science.gov (United States)

    Martins, Gustavo M; Arenas, Francisco; Neto, Ana I; Jenkins, Stuart R

    2012-01-01

    The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities' functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities' functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning.

  16. Dynamical properties and functions of proteins

    International Nuclear Information System (INIS)

    Inagaki, Fuyuhiko; Miyazawa, Tatsuo

    1982-01-01

    The advantages of nuclear magnetic resonance analyses for studying conformations and dynamical properties of protein molecules in aqueous solution are reviewed. For erabutoxin b, a short neurotoxin, and for α-cobratoxin, a long neurotoxin, th e local environments and proximity relations of amino acid residues have been elucidated. The conformations of these molecules in neutral aqueous solution are different, in part, from those in crystal. From the analyses of the deuterium exchange rates of amide protons, the long neurotoxins are found to be less flexible than short neurotoxins, corresponding to the lower dissociation/association rates of long toxins for acetylcholin receptor proteins. (author)

  17. A comprehensive software suite for protein family construction and functional site prediction.

    Directory of Open Access Journals (Sweden)

    David Renfrew Haft

    Full Text Available In functionally diverse protein families, conservation in short signature regions may outperform full-length sequence comparisons for identifying proteins that belong to a subgroup within which one specific aspect of their function is conserved. The SIMBAL workflow (Sites Inferred by Metabolic Background Assertion Labeling is a data-mining procedure for finding such signature regions. It begins by using clues from genomic context, such as co-occurrence or conserved gene neighborhoods, to build a useful training set from a large number of uncharacterized but mutually homologous proteins. When training set construction is successful, the YES partition is enriched in proteins that share function with the user's query sequence, while the NO partition is depleted. A selected query sequence is then mined for short signature regions whose closest matches overwhelmingly favor proteins from the YES partition. High-scoring signature regions typically contain key residues critical to functional specificity, so proteins with the highest sequence similarity across these regions tend to share the same function. The SIMBAL algorithm was described previously, but significant manual effort, expertise, and a supporting software infrastructure were required to prepare the requisite training sets. Here, we describe a new, distributable software suite that speeds up and simplifies the process for using SIMBAL, most notably by providing tools that automate training set construction. These tools have broad utility for comparative genomics, allowing for flexible collection of proteins or protein domains based on genomic context as well as homology, a capability that can greatly assist in protein family construction. Armed with this new software suite, SIMBAL can serve as a fast and powerful in silico alternative to direct experimentation for characterizing proteins and their functional interactions.

  18. Vaccinia complement control protein: Multi-functional protein and a ...

    Indian Academy of Sciences (India)

    In addition to binding complement, VCP also binds to heparin. These two binding abilities can take place simultaneously and contribute to its many function and to its potential use in several inflammatory diseases, e.g. Alzheimer's disease (AD), CNS injury, xenotransplantation, etc. making it a truly fascinating molecule and ...

  19. Automated functional classification of experimental and predicted protein structures

    Directory of Open Access Journals (Sweden)

    Samudrala Ram

    2006-06-01

    Full Text Available Abstract Background Proteins that are similar in sequence or structure may perform different functions in nature. In such cases, function cannot be inferred from sequence or structural similarity. Results We analyzed experimental structures belonging to the Structural Classification of Proteins (SCOP database and showed that about half of them belong to multi-functional fold families for which protein similarity alone is not adequate to assign function. We also analyzed predicted structures from the LiveBench and the PDB-CAFASP experiments and showed that accurate homology-based functional assignments cannot be achieved approximately one third of the time, when the protein is a member of a multi-functional fold family. We then conducted extended performance evaluation and comparisons on both experimental and predicted structures using our Functional Signatures from Structural Alignments (FSSA algorithm that we previously developed to handle the problem of classifying proteins belonging to multi-functional fold families. Conclusion The results indicate that the FSSA algorithm has better accuracy when compared to homology-based approaches for functional classification of both experimental and predicted protein structures, in part due to its use of local, as opposed to global, information for classifying function. The FSSA algorithm has also been implemented as a webserver and is available at http://protinfo.compbio.washington.edu/fssa.

  20. Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity.

    Directory of Open Access Journals (Sweden)

    Remco Stam

    Full Text Available Phytophthora species secrete a large array of effectors during infection of their host plants. The Crinkler (CRN gene family encodes a ubiquitous but understudied class of effectors with possible but as of yet unknown roles in infection. To appreciate CRN effector function in Phytophthora, we devised a simple Crn gene identification and annotation pipeline to improve effector prediction rates. We predicted 84 full-length CRN coding genes and assessed CRN effector domain diversity in sequenced Oomycete genomes. These analyses revealed evidence of CRN domain innovation in Phytophthora and expansion in the Peronosporales. We performed gene expression analyses to validate and define two classes of CRN effectors, each possibly contributing to infection at different stages. CRN localisation studies revealed that P. capsici CRN effector domains target the nucleus and accumulate in specific sub-nuclear compartments. Phenotypic analyses showed that few CRN domains induce necrosis when expressed in planta and that one cell death inducing effector, enhances P. capsici virulence on Nicotiana benthamiana. These results suggest that the CRN protein family form an important class of intracellular effectors that target the host nucleus during infection. These results combined with domain expansion in hemi-biotrophic and necrotrophic pathogens, suggests specific contributions to pathogen lifestyles. This work will bolster CRN identification efforts in other sequenced oomycete species and set the stage for future functional studies towards understanding CRN effector functions.

  1. Functional characterization of Angptl4 protein

    NARCIS (Netherlands)

    Lichtenstein, L.L.

    2009-01-01

    Background: Elevated plasma triglycerides (TG) are increasingly recognized as a risk factor for atherosclerosis. A new adipocytokine was discovered by several groups which is referred to as Angptl4 (Angiopoietin-like protein 4). Angptl4 was recently identified as a major determinant of plasma TG

  2. Molecular and functional characterization of MICAL proteins

    NARCIS (Netherlands)

    Zhou, Y.

    2011-01-01

    Since their original identification in 2002, MICAL proteins have been implicated in various physiological and pathological processes including axon guidance, tight junction formation, spinal cord injury and cancer. MICALs mediate cell signaling via their unusual N-terminal monooxygenase (MO) domain

  3. Functional differences in yeast protein disulfide isomerases

    DEFF Research Database (Denmark)

    Nørgaard, P; Westphal, V; Tachibana, C

    2001-01-01

    PDI1 is the essential gene encoding protein disulfide isomerase in yeast. The Saccharomyces cerevisiae genome, however, contains four other nonessential genes with homology to PDI1: MPD1, MPD2, EUG1, and EPS1. We have investigated the effects of simultaneous deletions of these genes. In several...

  4. Design and functionality of dense protein particles

    NARCIS (Netherlands)

    Saglam, D.

    2012-01-01

    Food products that contain high levels of protein can help to control food intake and to maintain a healthy body weight due to their strong satiating properties. They are also beneficial in the nutrition of elderly and commonly used in medical nutrition. Preparation of food products at high

  5. Diversity-interaction modeling: estimating contributions of species identities and interactions to ecosystem function

    DEFF Research Database (Denmark)

    Kirwan, L; Connolly, J; Finn, J A

    2009-01-01

    We develop a modeling framework that estimates the effects of species identity and diversity on ecosystem function and permits prediction of the diversity-function relationship across different types of community composition. Rather than just measure an overall effect of diversity, we separately...... estimate the contributions of different species interactions. This is especially important when both positive and negative interactions occur or where there are patterns in the interactions. Based on different biological assumptions, we can test for different patterns of interaction that correspond...... to the roles of evenness, functional groups, and functional redundancy. These more parsimonious descriptions can be especially useful in identifying general diversity-function relationships in communities with large numbers of species. We provide an example of the application of the modeling framework...

  6. Studying Membrane Protein Structure and Function Using Nanodiscs

    DEFF Research Database (Denmark)

    Huda, Pie

    The structure and dynamic of membrane proteins can provide valuable information about general functions, diseases and effects of various drugs. Studying membrane proteins are a challenge as an amphiphilic environment is necessary to stabilise the protein in a functionally and structurally relevant...... form. This is most typically achieved through the use of detergent based reconstitution systems. However, time and again such systems fail to provide a suitable environment causing aggregation and inactivation. Nanodiscs are self-assembled lipoproteins containing two membrane scaffold proteins...... and a lipid bilayer in defined nanometer size, which can act as a stabiliser for membrane proteins. This enables both functional and structural investigation of membrane proteins in a detergent free environment which is closer to the native situation. Understanding the self-assembly of nanodiscs is important...

  7. Impacts of Urban Areas and Their Characteristics on Avian Functional Diversity

    Directory of Open Access Journals (Sweden)

    Emily Oliveira Hagen

    2017-07-01

    Full Text Available Urban development is rapidly expanding across the globe and is a major driver of environmental change. Despite considerable improvements in our understanding of how species richness responds to urbanization, there is still insufficient knowledge of how other measures of assemblage composition and structure respond to urban development. Functional diversity metrics provide a useful approach for quantifying ecological function. We compare avian functional diversity in 25 urban areas, located across the globe, with paired non-urban assemblages using a database of 27 functional traits that capture variation in resource use (amount and type of resources and how they are acquired across the 529 species occurring across these assemblages. Using three standard functional diversity metrics (FD, MNTD, and convex hull we quantify observed functional diversity and, using standardized effect sizes, how this diverges from that expected under random community assembly null models. We use regression trees to investigate whether human population density, amount of vegetation and city size (spatial extent of urban land, bio-region and use of semi-natural or agricultural assemblages as a baseline modulate the effect of urbanization on functional diversity. Our analyses suggest that observed functional diversity of urban avian assemblages is not consistently different from that of non-urban assemblages. After accounting for species richness avian functional diversity is higher in cities than areas of semi-natural habitat. This creates a paradox as species responses to urban development are determined by their ecological traits, which should generate assemblages clustered within a narrow range of trait space. Greater habitat diversity within cities compared to semi-natural areas dominated by a single habitat may enhance functional diversity in cities and explain this paradox. Regression trees further suggest that smaller urban areas, lower human population densities

  8. Origination and immigration drive latitudinal gradients in marine functional diversity.

    Directory of Open Access Journals (Sweden)

    Sarah K Berke

    Full Text Available Global patterns in the functional attributes of organisms are critical to understanding biodiversity trends and predicting biotic responses to environmental change. In the first global marine analysis, we find a strong decrease in functional richness, but a strong increase in functional evenness, with increasing latitude using intertidal-to-outer-shelf bivalves as a model system (N = 5571 species. These patterns appear to be driven by the interplay between variation in origination rates among functional groups, and latitudinal patterns in origination and range expansion, as documented by the rich fossil record of the group. The data suggest that (i accumulation of taxa in spatial bins and functional categories has not impeded continued diversification in the tropics, and (ii extinctions will influence ecosystem function differentially across latitudes.

  9. The Structure and Function of Non-Collagenous Bone Proteins

    Science.gov (United States)

    Hook, Magnus; McQuillan, David J.

    1997-01-01

    The research done under the cooperative research agreement for the project titled 'The structure and function of non-collagenous bone proteins' represented the first phase of an ongoing program to define the structural and functional relationships of the principal noncollagenous proteins in bone. An ultimate goal of this research is to enable design and execution of useful pharmacological compounds that will have a beneficial effect in treatment of osteoporosis, both land-based and induced by long-duration space travel. The goals of the now complete first phase were as follows: 1. Establish and/or develop powerful recombinant protein expression systems; 2. Develop and refine isolation and purification of recombinant proteins; 3. Express wild-type non-collagenous bone proteins; 4. Express site-specific mutant proteins and domains of wild-type proteins to enhance likelihood of crystal formation for subsequent solution of structure.

  10. Tree aboveground carbon storage correlates with environmental gradients and functional diversity in a tropical forest

    Science.gov (United States)

    Shen, Yong; Yu, Shixiao; Lian, Juyu; Shen, Hao; Cao, Honglin; Lu, Huanping; Ye, Wanhui

    2016-01-01

    Tropical forests play a disproportionately important role in the global carbon (C) cycle, but it remains unclear how local environments and functional diversity regulate tree aboveground C storage. We examined how three components (environments, functional dominance and diversity) affected C storage in Dinghushan 20-ha plot in China. There was large fine-scale variation in C storage. The three components significantly contributed to regulate C storage, but dominance and diversity of traits were associated with C storage in different directions. Structural equation models (SEMs) of dominance and diversity explained 34% and 32% of variation in C storage. Environments explained 26–44% of variation in dominance and diversity. Similar proportions of variation in C storage were explained by dominance and diversity in regression models, they were improved after adding environments. Diversity of maximum diameter was the best predictor of C storage. Complementarity and selection effects contributed to C storage simultaneously, and had similar importance. The SEMs disengaged the complex relationships among the three components and C storage, and established a framework to show the direct and indirect effects (via dominance and diversity) of local environments on C storage. We concluded that local environments are important for regulating functional diversity and C storage. PMID:27278688

  11. Tree aboveground carbon storage correlates with environmental gradients and functional diversity in a tropical forest.

    Science.gov (United States)

    Shen, Yong; Yu, Shixiao; Lian, Juyu; Shen, Hao; Cao, Honglin; Lu, Huanping; Ye, Wanhui

    2016-06-09

    Tropical forests play a disproportionately important role in the global carbon (C) cycle, but it remains unclear how local environments and functional diversity regulate tree aboveground C storage. We examined how three components (environments, functional dominance and diversity) affected C storage in Dinghushan 20-ha plot in China. There was large fine-scale variation in C storage. The three components significantly contributed to regulate C storage, but dominance and diversity of traits were associated with C storage in different directions. Structural equation models (SEMs) of dominance and diversity explained 34% and 32% of variation in C storage. Environments explained 26-44% of variation in dominance and diversity. Similar proportions of variation in C storage were explained by dominance and diversity in regression models, they were improved after adding environments. Diversity of maximum diameter was the best predictor of C storage. Complementarity and selection effects contributed to C storage simultaneously, and had similar importance. The SEMs disengaged the complex relationships among the three components and C storage, and established a framework to show the direct and indirect effects (via dominance and diversity) of local environments on C storage. We concluded that local environments are important for regulating functional diversity and C storage.

  12. Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.

    Science.gov (United States)

    Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Chu, Haiyan

    2016-01-01

    The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500-2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.

  13. AVID: An integrative framework for discovering functional relationships among proteins

    Directory of Open Access Journals (Sweden)

    Keating Amy E

    2005-06-01

    Full Text Available Abstract Background Determining the functions of uncharacterized proteins is one of the most pressing problems in the post-genomic era. Large scale protein-protein interaction assays, global mRNA expression analyses and systematic protein localization studies provide experimental information that can be used for this purpose. The data from such experiments contain many false positives and false negatives, but can be processed using computational methods to provide reliable information about protein-protein relationships and protein function. An outstanding and important goal is to predict detailed functional annotation for all uncharacterized proteins that is reliable enough to effectively guide experiments. Results We present AVID, a computational method that uses a multi-stage learning framework to integrate experimental results with sequence information, generating networks reflecting functional similarities among proteins. We illustrate use of the networks by making predictions of detailed Gene Ontology (GO annotations in three categories: molecular function, biological process, and cellular component. Applied to the yeast Saccharomyces cerevisiae, AVID provides 37,451 pair-wise functional linkages between 4,191 proteins. These relationships are ~65–78% accurate, as assessed by cross-validation testing. Assignments of highly detailed functional descriptors to proteins, based on the networks, are estimated to be ~67% accurate for GO categories describing molecular function and cellular component and ~52% accurate for terms describing biological process. The predictions cover 1,490 proteins with no previous annotation in GO and also assign more detailed functions to many proteins annotated only with less descriptive terms. Predictions made by AVID are largely distinct from those made by other methods. Out of 37,451 predicted pair-wise relationships, the greatest number shared in common with another method is 3,413. Conclusion AVID provides

  14. ESG: extended similarity group method for automated protein function prediction.

    Science.gov (United States)

    Chitale, Meghana; Hawkins, Troy; Park, Changsoon; Kihara, Daisuke

    2009-07-15

    Importance of accurate automatic protein function prediction is ever increasing in the face of a large number of newly sequenced genomes and proteomics data that are awaiting biological interpretation. Conventional methods have focused on high sequence similarity-based annotation transfer which relies on the concept of homology. However, many cases have been reported that simple transfer of function from top hits of a homology search causes erroneous annotation. New methods are required to handle the sequence similarity in a more robust way to combine together signals from strongly and weakly similar proteins for effectively predicting function for unknown proteins with high reliability. We present the extended similarity group (ESG) method, which performs iterative sequence database searches and annotates a query sequence with Gene Ontology terms. Each annotation is assigned with probability based on its relative similarity score with the multiple-level neighbors in the protein similarity graph. We will depict how the statistical framework of ESG improves the prediction accuracy by iteratively taking into account the neighborhood of query protein in the sequence similarity space. ESG outperforms conventional PSI-BLAST and the protein function prediction (PFP) algorithm. It is found that the iterative search is effective in capturing multiple-domains in a query protein, enabling accurately predicting several functions which originate from different domains. ESG web server is available for automated protein function prediction at http://dragon.bio.purdue.edu/ESG/.

  15. Functional diversity and functional traits of periphytic algae during a short-term successional process in a Neotropical floodplain lake.

    Science.gov (United States)

    Dunck, B; Rodrigues, L; Bicudo, D C

    2015-08-01

    Due to the lack of knowledge in periphytic algae functional diversity patterns during successional processes in floodplains, the present study aimed to analyze the dynamics of the functional traits and functional diversity of periphytic species during a short-term successional process in a floodplain lake. The functional traits analyzed were size class, growth form, strength of attachment to the substratum, and functional strategies. We evaluated the dynamics of these traits, considering richness, density and biovolume during an 18-day colonization in two hydrological periods. The functional diversity was assessed using the mean pairwise distance index (MPD). Dominant functional traits during the colonization changed in association with the flood pulse. Under the pulse effect, higher development of C-S strategist, loosely attached, filamentous and nanoperiphytic species occurred. The highest values of functional diversity were associated with the algal biomass peak during the colonization and the high water hydrological period, possibly indicating greater efficiency in the ecosystem functioning. These findings show the importance of the functional traits approach in periphyton studies and that the selection of functional traits must be performed taking into account traits that represent the species niche.

  16. Functional diversity and functional traits of periphytic algae during a short-term successional process in a Neotropical floodplain lake

    Directory of Open Access Journals (Sweden)

    B Dunck

    Full Text Available AbstractDue to the lack of knowledge in periphytic algae functional diversity patterns during successional processes in floodplains, the present study aimed to analyze the dynamics of the functional traits and functional diversity of periphytic species during a short-term successional process in a floodplain lake. The functional traits analyzed were size class, growth form, strength of attachment to the substratum, and functional strategies. We evaluated the dynamics of these traits, considering richness, density and biovolume during an 18-day colonization in two hydrological periods. The functional diversity was assessed using the mean pairwise distance index (MPD. Dominant functional traits during the colonization changed in association with the flood pulse. Under the pulse effect, higher development of C-S strategist, loosely attached, filamentous and nanoperiphytic species occurred. The highest values of functional diversity were associated with the algal biomass peak during the colonization and the high water hydrological period, possibly indicating greater efficiency in the ecosystem functioning. These findings show the importance of the functional traits approach in periphyton studies and that the selection of functional traits must be performed taking into account traits that represent the species niche.

  17. Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere

    NARCIS (Netherlands)

    Yan, Y.; Kuramae, E.E.; De Hollander, M.; Klinkhamer, P.G.L.; van Veen, J.A.

    2017-01-01

    We studied the impact of community diversity on the selection of bacterial communities in the rhizosphere by comparing the composition and the functional traits of these communities in soil and rhizosphere. Differences in diversity were established by inoculating into sterilized soils diluted

  18. Function and structure of GFP-like proteins in the protein data bank.

    Science.gov (United States)

    Ong, Wayne J-H; Alvarez, Samuel; Leroux, Ivan E; Shahid, Ramza S; Samma, Alex A; Peshkepija, Paola; Morgan, Alicia L; Mulcahy, Shawn; Zimmer, Marc

    2011-04-01

    The RCSB protein databank contains 266 crystal structures of green fluorescent proteins (GFP) and GFP-like proteins. This is the first systematic analysis of all the GFP-like structures in the pdb. We have used the pdb to examine the function of fluorescent proteins (FP) in nature, aspects of excited state proton transfer (ESPT) in FPs, deformation from planarity of the chromophore and chromophore maturation. The conclusions reached in this review are that (1) The lid residues are highly conserved, particularly those on the "top" of the β-barrel. They are important to the function of GFP-like proteins, perhaps in protecting the chromophore or in β-barrel formation. (2) The primary/ancestral function of GFP-like proteins may well be to aid in light induced electron transfer. (3) The structural prerequisites for light activated proton pumps exist in many structures and it's possible that like bioluminescence, proton pumps are secondary functions of GFP-like proteins. (4) In most GFP-like proteins the protein matrix exerts a significant strain on planar chromophores forcing most GFP-like proteins to adopt non-planar chromophores. These chromophoric deviations from planarity play an important role in determining the fluorescence quantum yield. (5) The chemospatial characteristics of the chromophore cavity determine the isomerization state of the chromophore. The cavities of highlighter proteins that can undergo cis/trans isomerization have chemospatial properties that are common to both cis and trans GFP-like proteins.

  19. Effects of protein separation conditions on the functional and thermal properties of canola protein isolates.

    Science.gov (United States)

    Manamperi, Wajira A R; Wiesenborn, Dennis P; Chang, Sam K C; Pryor, Scott W

    2011-04-01

    Canola meal protein isolates were prepared from defatted canola meal flour using alkaline solubilization and acid precipitation. A central composite design was used to model 2nd-order response surfaces for the protein yield and the functional properties of protein isolates. The solubilization pH and precipitation pH were used as design factors. The models showed that the protein yield and functional properties of isolates, such as water absorption and fat absorption, were sensitive to both solubilization pH and precipitation pH, whereas the emulsification was sensitive to only solubilization pH. Gel electrophoresis analysis of protein fractions gave evidence to the compositional changes between proteins isolated under different conditions. Differences in glass transition temperatures suggest that proteins tend to be more denatured when solubilized at highly alkaline conditions. These conformational and compositional changes due to different protein separation conditions have contributed to the changes in functional properties of protein isolates.   Protein isolation conditions may be determined primarily through optimization of total protein yield. Improvements in protein functional properties may be achieved with a relatively small sacrifice in yield by altering isolation conditions.

  20. Improving protein function prediction methods with integrated literature data

    Directory of Open Access Journals (Sweden)

    Gabow Aaron P

    2008-04-01

    Full Text Available Abstract Background Determining the function of uncharacterized proteins is a major challenge in the post-genomic era due to the problem's complexity and scale. Identifying a protein's function contributes to an understanding of its role in the involved pathways, its suitability as a drug target, and its potential for protein modifications. Several graph-theoretic approaches predict unidentified functions of proteins by using the functional annotations of better-characterized proteins in protein-protein interaction networks. We systematically consider the use of literature co-occurrence data, introduce a new method for quantifying the reliability of co-occurrence and test how performance differs across species. We also quantify changes in performance as the prediction algorithms annotate with increased specificity. Results We find that including information on the co-occurrence of proteins within an abstract greatly boosts performance in the Functional Flow graph-theoretic function prediction algorithm in yeast, fly and worm. This increase in performance is not simply due to the presence of additional edges since supplementing protein-protein interactions with co-occurrence data outperforms supplementing with a comparably-sized genetic interaction dataset. Through the combination of protein-protein interactions and co-occurrence data, the neighborhood around unknown proteins is quickly connected to well-characterized nodes which global prediction algorithms can exploit. Our method for quantifying co-occurrence reliability shows superior performance to the other methods, particularly at threshold values around 10% which yield the best trade off between coverage and accuracy. In contrast, the traditional way of asserting co-occurrence when at least one abstract mentions both proteins proves to be the worst method for generating co-occurrence data, introducing too many false positives. Annotating the functions with greater specificity is harder

  1. Diversity of sainfoin (Onobrychis Mill. collection samples according to the spectra of storage proteins

    Directory of Open Access Journals (Sweden)

    Bulatova Kulpash

    2015-01-01

    Full Text Available Sainfoin (Onobrychis Mill. is a valuable forage plant of the legume family (Fabaceae. In Kazakhstan the sainfoin introduced as field fodder in the 50s of the XX century and because of its biological features widely spread as a promising crop for forage resources increasing. The electrophoresis of seed storage proteins of Onobrychis viciifolia, Onobrychis arenaria and Onobrychis transcaucasica species was carried out. Considerable diversity of the number, mobility and intensity of components was determined.

  2. Phenotypic Diversity Using Bimodal and Unimodal Expression of Stress Response Proteins

    OpenAIRE

    Garcia-Bernardo, Javier; Dunlop, Mary J.

    2016-01-01

    Populations of cells need to express proteins to survive the sudden appearance of stressors. However, these mechanisms may be taxing. Populations can introduce diversity, allowing individual cells to stochastically switch between fast-growing and stress-tolerant states. One way to achieve this is to use genetic networks coupled with noise to generate bimodal distributions with two distinct subpopulations, each adapted to a stress condition. Another survival strategy is to rely on random fluct...

  3. Plant Functional Diversity Can Be Independent of Species Diversity: Observations Based on the Impact of 4-Yrs of Nitrogen and Phosphorus Additions in an Alpine Meadow.

    Science.gov (United States)

    Li, Wei; Cheng, Ji-Min; Yu, Kai-Liang; Epstein, Howard E; Guo, Liang; Jing, Guang-Hua; Zhao, Jie; Du, Guo-Zhen

    2015-01-01

    Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH4)2 HPO4) at 0, 15, 30 and 60 g m-2 yr-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao's index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production.

  4. Evolutionary Algorithms for Boolean Functions in Diverse Domains of Cryptography.

    Science.gov (United States)

    Picek, Stjepan; Carlet, Claude; Guilley, Sylvain; Miller, Julian F; Jakobovic, Domagoj

    2016-01-01

    The role of Boolean functions is prominent in several areas including cryptography, sequences, and coding theory. Therefore, various methods for the construction of Boolean functions with desired properties are of direct interest. New motivations on the role of Boolean functions in cryptography with attendant new properties have emerged over the years. There are still many combinations of design criteria left unexplored and in this matter evolutionary computation can play a distinct role. This article concentrates on two scenarios for the use of Boolean functions in cryptography. The first uses Boolean functions as the source of the nonlinearity in filter and combiner generators. Although relatively well explored using evolutionary algorithms, it still presents an interesting goal in terms of the practical sizes of Boolean functions. The second scenario appeared rather recently where the objective is to find Boolean functions that have various orders of the correlation immunity and minimal Hamming weight. In both these scenarios we see that evolutionary algorithms are able to find high-quality solutions where genetic programming performs the best.

  5. Does logging and forest conversion to oil palm agriculture alter functional diversity in a biodiversity hotspot?

    Science.gov (United States)

    Edwards, F A; Edwards, D P; Larsen, T H; Hsu, W W; Benedick, S; Chung, A; Vun Khen, C; Wilcove, D S; Hamer, K C

    2014-04-01

    Forests in Southeast Asia are rapidly being logged and converted to oil palm. These changes in land-use are known to affect species diversity but consequences for the functional diversity of species assemblages are poorly understood. Environmental filtering of species with similar traits could lead to disproportionate reductions in trait diversity in degraded habitats. Here, we focus on dung beetles, which play a key role in ecosystem processes such as nutrient recycling and seed dispersal. We use morphological and behavioural traits to calculate a variety of functional diversity measures across a gradient of disturbance from primary forest through intensively logged forest to oil palm. Logging caused significant shifts in community composition but had very little effect on functional diversity, even after a repeated timber harvest. These data provide evidence for functional redundancy of dung beetles within primary forest and emphasize the high value of logged forests as refugia for biodiversity. In contrast, conversion of forest to oil palm greatly reduced taxonomic and functional diversity, with a marked decrease in the abundance of nocturnal foragers, a higher proportion of species with small body sizes and the complete loss of telecoprid species (dung-rollers), all indicating a decrease in the functional capacity of dung beetles within plantations. These changes also highlight the vulnerability of community functioning within logged forests in the event of further environmental degradation.

  6. Human-mediated loss of phylogenetic and functional diversity in coral reef fishes.

    Science.gov (United States)

    D'agata, Stéphanie; Mouillot, David; Kulbicki, Michel; Andréfouët, Serge; Bellwood, David R; Cinner, Joshua E; Cowman, Peter F; Kronen, Mecki; Pinca, Silvia; Vigliola, Laurent

    2014-03-03

    Beyond the loss of species richness, human activities may also deplete the breadth of evolutionary history (phylogenetic diversity) and the diversity of roles (functional diversity) carried out by species within communities, two overlooked components of biodiversity. Both are, however, essential to sustain ecosystem functioning and the associated provision of ecosystem services, particularly under fluctuating environmental conditions. We quantified the effect of human activities on the taxonomic, phylogenetic, and functional diversity of fish communities in coral reefs, while teasing apart the influence of biogeography and habitat along a gradient of human pressure across the Pacific Ocean. We detected nonlinear relationships with significant breaking points in the impact of human population density on phylogenetic and functional diversity of parrotfishes, at 25 and 15 inhabitants/km(2), respectively, while parrotfish species richness decreased linearly along the same population gradient. Over the whole range, species richness decreased by 11.7%, while phylogenetic and functional diversity dropped by 35.8% and 46.6%, respectively. Our results call for caution when using species richness as a benchmark for measuring the status of ecosystems since it appears to be less responsive to variation in human population densities than its phylogenetic and functional counterparts, potentially imperiling the functioning of coral reef ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Text mining improves prediction of protein functional sites.

    Directory of Open Access Journals (Sweden)

    Karin M Verspoor

    Full Text Available We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites. The structure analysis was carried out using Dynamics Perturbation Analysis (DPA, which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

  8. Text mining improves prediction of protein functional sites.

    Science.gov (United States)

    Verspoor, Karin M; Cohn, Judith D; Ravikumar, Komandur E; Wall, Michael E

    2012-01-01

    We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

  9. Text Mining Improves Prediction of Protein Functional Sites

    Science.gov (United States)

    Cohn, Judith D.; Ravikumar, Komandur E.

    2012-01-01

    We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions. PMID:22393388

  10. Functional diversity supports the physiological tolerance hypothesis for plant species richness along climatic gradients

    Science.gov (United States)

    Spasojevic, Marko J.; Grace, James B.; Harrison, Susan; Damschen, Ellen Ingman

    2013-01-01

    1. The physiological tolerance hypothesis proposes that plant species richness is highest in warm and/or wet climates because a wider range of functional strategies can persist under such conditions. Functional diversity metrics, combined with statistical modeling, offer new ways to test whether diversity-environment relationships are consistent with this hypothesis. 2. In a classic study by R. H. Whittaker (1960), herb species richness declined from mesic (cool, moist, northerly) slopes to xeric (hot, dry, southerly) slopes. Building on this dataset, we measured four plant functional traits (plant height, specific leaf area, leaf water content and foliar C:N) and used them to calculate three functional diversity metrics (functional richness, evenness, and dispersion). We then used a structural equation model to ask if ‘functional diversity’ (modeled as the joint responses of richness, evenness, and dispersion) could explain the observed relationship of topographic climate gradients to species richness. We then repeated our model examining the functional diversity of each of the four traits individually. 3. Consistent with the physiological tolerance hypothesis, we found that functional diversity was higher in more favorable climatic conditions (mesic slopes), and that multivariate functional diversity mediated the relationship of the topographic climate gradient to plant species richness. We found similar patterns for models focusing on individual trait functional diversity of leaf water content and foliar C:N. 4. Synthesis. Our results provide trait-based support for the physiological tolerance hypothesis, suggesting that benign climates support more species because they allow for a wider range of functional strategies.

  11. Functional trait space and the latitudinal diversity gradient

    DEFF Research Database (Denmark)

    Lamanna, Christine; Blonder, Benjamin; Violle, Cyrille

    2014-01-01

    spanning the temperate and tropical New World. Alpha-scale trait volume decreases with absolute latitude and is often lower than sampling expectation, consistent with environmental filtering theory. Beta-scale overlap decays with geographic distance fastest in the temperate zone, again consistent...... with environmental filtering theory. In contrast, gamma-scale trait space shows a hump-shaped relationship with absolute latitude, consistent with no theory. Furthermore, the overall temperate trait hypervolume was larger than the overall tropical hypervolume, indicating that the temperate zone permits a wider range...... of trait combinations or that niche packing is stronger in the tropical zone. Although there are limitations in the data, our analyses suggest that multiple processes have shaped trait diversity in trees, reflecting no consistent support for any one theory....

  12. Plant litter functional diversity effects on litter mass loss depend on the macro-detritivore community.

    Science.gov (United States)

    Patoine, Guillaume; Thakur, Madhav P; Friese, Julia; Nock, Charles; Hönig, Lydia; Haase, Josephine; Scherer-Lorenzen, Michael; Eisenhauer, Nico

    2017-11-01

    A better understanding of the mechanisms driving litter diversity effects on decomposition is needed to predict how biodiversity losses affect this crucial ecosystem process. In a microcosm study, we investigated the effects of litter functional diversity and two major groups of soil macro-detritivores on the mass loss of tree leaf litter mixtures. Furthermore, we tested the effects of litter trait community means and dissimilarity on litter mass loss for seven traits relevant to decomposition. We expected macro-detritivore effects on litter mass loss to be most pronounced in litter mixtures of high functional diversity. We used 24 leaf mixtures differing in functional diversity, which were composed of litter from four species from a pool of 16 common European tree species. Earthworms, isopods, or a combination of both were added to each litter combination for two months. Litter mass loss was significantly higher in the presence of earthworms than in that of isopods, whereas no synergistic effects of macro-detritivore mixtures were found. The effect of functional diversity of the litter material was highest in the presence of both macro-detritivore groups, supporting the notion that litter diversity effects are most pronounced in the presence of different detritivore species. Species-specific litter mass loss was explained by nutrient content, secondary compound concentration, and structural components. Moreover, dissimilarity in N concentrations increased litter mass loss, probably because detritivores having access to nutritionally diverse food sources. Furthermore, strong competition between the two macro-detritivores for soil surface litter resulted in a decrease of survival of both macro-detritivores. These results show that the effects of litter functional diversity on decomposition are contingent upon the macro-detritivore community and composition. We conclude that the temporal dynamics of litter trait diversity effects and their interaction with

  13. Functional diversity of supragranular GABAergic neurons in the barrel cortex.

    NARCIS (Netherlands)

    Gentet, L.J.

    2012-01-01

    Although the neocortex forms a distributed system comprised of several functional areas, its vertical columnar organization is largely conserved across areas and species, suggesting the existence of a canonical neocortical microcircuit. In order to elucidate the principles governing the organization

  14. Wide diversity in structure and expression profiles among members of the Caenorhabditis elegans globin protein family

    Directory of Open Access Journals (Sweden)

    Vinogradov Serge

    2007-10-01

    Full Text Available Abstract Background The emergence of high throughput genome sequencing facilities and powerful high performance bioinformatic tools has highlighted hitherto unexpected wide occurrence of globins in the three kingdoms of life. In silico analysis of the genome of C. elegans identified 33 putative globin genes. It remains a mystery why this tiny animal might need so many globins. As an inroad to understanding this complexity we initiated a structural and functional analysis of the globin family in C. elegans. Results All 33 C. elegans putative globin genes are transcribed. The translated sequences have the essential signatures of single domain bona fide globins, or they contain a distinct globin domain that is part of a larger protein. All globin domains can be aligned so as to fit the globin fold, but internal interhelical and N- and C-terminal extensions and a variety of amino acid substitutions generate much structural diversity among the globins of C. elegans. Likewise, the encoding genes lack a conserved pattern of intron insertion positioning. We analyze the expression profiles of the globins during the progression of the life cycle, and we find that distinct subsets of globins are induced, or repressed, in wild-type dauers and in daf-2(e1370/insulin-receptor mutant adults, although these animals share several physiological features including resistance to elevated temperature, oxidative stress and hypoxic death. Several globin genes are upregulated following oxygen deprivation and we find that HIF-1 and DAF-2 each are required for this response. Our data indicate that the DAF-2 regulated transcription factor DAF-16/FOXO positively modulates hif-1 transcription under anoxia but opposes expression of the HIF-1 responsive globin genes itself. In contrast, the canonical globin of C. elegans, ZK637.13, is not responsive to anoxia. Reduced DAF-2 signaling leads to enhanced transcription of this globin and DAF-16 is required for this effect

  15. ProFET: Feature engineering captures high-level protein functions.

    Science.gov (United States)

    Ofer, Dan; Linial, Michal

    2015-11-01

    The amount of sequenced genomes and proteins is growing at an unprecedented pace. Unfortunately, manual curation and functional knowledge lag behind. Homologous inference often fails at labeling proteins with diverse functions and broad classes. Thus, identifying high-level protein functionality remains challenging. We hypothesize that a universal feature engineering approach can yield classification of high-level functions and unified properties when combined with machine learning approaches, without requiring external databases or alignment. In this study, we present a novel bioinformatics toolkit called ProFET (Protein Feature Engineering Toolkit). ProFET extracts hundreds of features covering the elementary biophysical and sequence derived attributes. Most features capture statistically informative patterns. In addition, different representations of sequences and the amino acids alphabet provide a compact, compressed set of features. The results from ProFET were incorporated in data analysis pipelines, implemented in python and adapted for multi-genome scale analysis. ProFET was applied on 17 established and novel protein benchmark datasets involving classification for a variety of binary and multi-class tasks. The results show state of the art performance. The extracted features' show excellent biological interpretability. The success of ProFET applies to a wide range of high-level functions such as subcellular localization, structural classes and proteins with unique functional properties (e.g. neuropeptide precursors, thermophilic and nucleic acid binding). ProFET allows easy, universal discovery of new target proteins, as well as understanding the features underlying different high-level protein functions. ProFET source code and the datasets used are freely available at https://github.com/ddofer/ProFET. michall@cc.huji.ac.il Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights

  16. Application of the Nutrition Functional Diversity indicator to assess food system contributions to dietary diversity and sustainable diets of Malawian households.

    Science.gov (United States)

    Luckett, Brian G; DeClerck, Fabrice A J; Fanzo, Jessica; Mundorf, Adrienne R; Rose, Donald

    2015-09-01

    Dietary diversity is associated with nutrient adequacy and positive health outcomes but indicators to measure diversity have focused primarily on consumption, rather than sustainable provisioning of food. The Nutritional Functional Diversity score was developed by ecologists to describe the contribution of biodiversity to sustainable diets. We have employed this tool to estimate the relative contribution of home production and market purchases in providing nutritional diversity to agricultural households in Malawi and examine how food system provisioning varies by time, space and socio-economic conditions. A secondary analysis of nationally representative household consumption data to test the applicability of the Nutritional Functional Diversity score. The data were collected between 2010 and 2011 across the country of Malawi. Households (n 11 814) from predominantly rural areas of Malawi. Nutritional Functional Diversity varied demographically, geographically and temporally. Nationally, purchased foods contributed more to household nutritional diversity than home produced foods (mean score=17·5 and 7·8, respectively). Households further from roads and population centres had lower overall diversity (PNutritional diversity was lowest during the growing season when farmers plant and tend crops (PNutritional Functional Diversity score is an effective indicator for identifying populations with low nutritional diversity and the relative roles that markets, agricultural extension and home production play in achieving nutritional diversity. This information may be used by policy makers to plan agricultural and market-based interventions that support sustainable diets and local food systems.

  17. Functional diversity response to hardwood forest management varies across taxa and spatial scales.

    Science.gov (United States)

    Murray, Bryan D; Holland, Jeffrey D; Summerville, Keith S; Dunning, John B; Saunders, Michael R; Jenkins, Michael A

    2017-06-01

    Contemporary forest management offers a trade-off between the potential positive effects of habitat heterogeneity on biodiversity, and the potential harm to mature forest communities caused by habitat loss and perforation of the forest canopy. While the response of taxonomic diversity to forest management has received a great deal of scrutiny, the response of functional diversity is largely unexplored. However, functional diversity may represent a more direct link between biodiversity and ecosystem function. To examine how forest management affects diversity at multiple spatial scales, we analyzed a long-term data set that captured changes in taxonomic and functional diversity of moths (Lepidoptera), longhorned beetles (Coleoptera: Cerambycidae), and breeding birds in response to contemporary silvicultural systems in oak-hickory hardwood forests. We used these data sets to address the following questions: how do even- and uneven-aged silvicultural systems affect taxonomic and functional diversity at the scale of managed landscapes compared to the individual harvested and unharvested forest patches that comprise the landscapes, and how do these silvicultural systems affect the functional similarity of assemblages at the scale of managed landscapes and patches? Due to increased heterogeneity within landscapes, we expected even-aged silviculture to increase and uneven-aged silviculture to decrease functional diversity at the landscape level regardless of impacts at the patch level. Functional diversity responses were taxon-specific with respect to the direction of change and time since harvest. Responses were also consistent across patch and landscape levels within each taxon. Moth assemblage species richness, functional richness, and functional divergence were negatively affected by harvesting, with stronger effects resulting from uneven-aged than even-aged management. Longhorned beetle assemblages exhibited a peak in species richness two years after harvesting

  18. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  19. Diversity-dependent temporal divergence of ecosystem functioning in experimental ecosystems

    Science.gov (United States)

    Nathaly R. Guerrero-Ramírez; Dylan Craven; Peter B. Reich; John J. Ewel; Forest Isbell; Julia Koricheva; John A. Parrotta; Harald Auge; Heather E. Erickson; David I. Forrester; Andy Hector; Jasmin Joshi; Florencia Montagnini; Cecilia Palmborg; Daniel Piotto; Catherine Potvin; Christiane Roscher; Jasper van Ruijven; David Tilman; Brian Wilsey; Nico Eisenhauer

    2017-01-01

    The effects of biodiversity on ecosystem functioning generally increase over time, but the underlying processes remain unclear. Using 26 long-term grassland and forest experimental ecosystems, we demonstrate that biodiversity–ecosystem functioning relationships strengthen mainly by greater increases in functioning in high-diversity communities in grasslands and forests...

  20. Targeting functional motifs of a protein family

    Science.gov (United States)

    Bhadola, Pradeep; Deo, Nivedita

    2016-10-01

    The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.

  1. GPCR-interacting proteins (GIPs): nature and functions.

    Science.gov (United States)

    Bockaert, J; Roussignol, G; Bécamel, C; Gavarini, S; Joubert, L; Dumuis, A; Fagni, L; Marin, P

    2004-11-01

    The simplistic idea that seven transmembrane receptors are single monomeric proteins that interact with heterotrimeric G-proteins after agonist binding is definitively out of date. Indeed, GPCRs (G-protein-coupled receptors) are part of multiprotein networks organized around scaffolding proteins. These GIPs (GPCR-interacting proteins) are either transmembrane or cytosolic proteins. Proteomic approaches can be used to get global pictures of these 'receptosomes'. This approach allowed us to identify direct but also indirect binding partners of serotonin receptors. GIPs are involved in a wide range of functions including control of the targeting, trafficking and signalling of GPCRs. One of them, Shank, which is a secondary and tertiary partner of metabotropic and ionotropic glutamate receptors, respectively, can induce the formation of a whole functional glutamate 'receptosome' and the structure to which it is associated, the dendritic spine.

  2. Is the A-Chain the Engine That Drives the Diversity of C1q Functions? Revisiting Its Unique Structure

    Directory of Open Access Journals (Sweden)

    Berhane Ghebrehiwet

    2018-02-01

    Full Text Available The immunopathological functions associated with human C1q are still growing in terms of novelty, diversity, and pathologic relevance. It is, therefore, not surprising that C1q is being recognized as an important molecular bridge between innate and adaptive immunity. The secret of this functional diversity, in turn, resides in the elegant but complex structure of the C1q molecule, which is assembled from three distinct gene products: A, B, and C, each of which has evolved from a separate and unique ancestral gene template. The C1q molecule is made up of 6A, 6B, and 6C polypeptide chains, which are held together through strong covalent and non-covalent bonds to form the 18-chain, bouquet-of-flower-like protein that we know today. The assembled C1q protein displays at least two distinct structural and functional regions: the collagen-like region (cC1q and the globular head region (gC1q, each being capable of driving a diverse range of ligand- or receptor-mediated biological functions. What is most intriguing, however, is the observation that most of the functions appear to be predominantly driven by the A-chain of the molecule, which begs the question: what are the evolutionary modifications or rearrangements that singularly shaped the primordial A-chain gene to become a pluripotent and versatile component of the intact C1q molecule? Here, we revisit and discuss some of the known unique structural and functional features of the A-chain, which may have contributed to its versatility.

  3. A functional protein retention and release multilayer with high stability

    Science.gov (United States)

    Nie, Kun; An, Qi; Zhang, Yihe

    2016-04-01

    Effective and robust interfacial protein retention lies at the heart of the fabrication of protein-based functional interfaces, which is potentially applicable in catalysis, medical therapy, antifouling, and smart devices, but remains challenging due to the sensitive nature of proteins. This study reports a general protein retention strategy to spatial-temporally confine various types of proteins at interfacial regions. The proteins were preserved in mesoporous silica nanoparticles embedded in covalently woven multilayers. It is worth noting that the protein retention strategy effectively preserves the catalytic capabilities of the proteins, and the multilayer structure is robust enough to withstand the bubbling catalytic reactions and could be repeatedly used due to conservation of proteins. The spatiotemporal retention of proteins could be adjusted by varying the number of capping layers. Furthermore, we demonstrate that the protein-loaded interfacial layers could not only be used to construct catalytic-active interfaces, but also be integrated as the power-generating unit to propel a macroscopic floating device.Effective and robust interfacial protein retention lies at the heart of the fabrication of protein-based functional interfaces, which is potentially applicable in catalysis, medical therapy, antifouling, and smart devices, but remains challenging due to the sensitive nature of proteins. This study reports a general protein retention strategy to spatial-temporally confine various types of proteins at interfacial regions. The proteins were preserved in mesoporous silica nanoparticles embedded in covalently woven multilayers. It is worth noting that the protein retention strategy effectively preserves the catalytic capabilities of the proteins, and the multilayer structure is robust enough to withstand the bubbling catalytic reactions and could be repeatedly used due to conservation of proteins. The spatiotemporal retention of proteins could be adjusted by

  4. Diverse functions of uterine proteoglycans in human reproduction (review).

    Science.gov (United States)

    Kitaya, Kotaro; Tada, Yoshihiro; Hayashi, Terumi; Taguchi, Sagiri; Funabiki, Miyako; Nakamura, Yoshitaka; Yasuo, Tadahiro

    2012-06-01

    Proteoglycans (PGs) are a group of heavily glycosylated proteins that are present throughout the mammalian body and are involved in a wide variety of biological phenomena, including structural maintenance, tissue remodeling, molecular presentation, cell adhesion and signal transmission. Previous studies have revealed an increasing number of roles for PGs in human reproduction. Several PGs are currently utilized or regarded as biomarkers for the diagnosis of certain pathological uterine conditions associated with infertility and obstetrical complications. The aim of this review was to discuss the involvement of PGs in the human uterus in reproductive biology and pathophysiology.

  5. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

    KAUST Repository

    Neave, Matthew J.

    2016-08-24

    Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.

  6. Do the morphological and functional traits of free-living marine nematodes mirror taxonomical diversity?

    Science.gov (United States)

    Semprucci, F; Cesaroni, L; Guidi, L; Balsamo, M

    2018-04-01

    The taxonomical structure and diversity of nematode assemblages are the main attributes analyzed in ecology, but nematode adaptations to their habitats are still understudied. Accordingly, a survey on some known and other newly proposed morpho-functional traits was carried out in order to: determine if the morpho-functional diversity of nematodes mirrors their taxonomical diversity; and assess potential nematode adaptations to sediment type and hydrodynamic stress. Morpho-functional traits were investigated both singularly and together and showed significant differences related to these environmental factors. The greatest taxonomical and morpho-functional diversity was found in medium-coarse sand (M-CS) and at an intermedium energy level (IEL). The M-CS and IEL were probably richer in micro-habitats and subject to a low selective pressure, hosting nematodes with a wide range of adaptations. The mirroring of morpho-functional diversity with taxonomical diversity is crucial for the future growth of the use of nematodes in biomonitoring. This is because the study of their morpho-functional traits could reduce the level of work involved and the costs of any analyses. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Diverse Effects, Complex Causes: Children Use Information about Machines' Functional Diversity to Infer Internal Complexity

    Science.gov (United States)

    Ahl, Richard E.; Keil, Frank C.

    2017-01-01

    Four studies explored the abilities of 80 adults and 180 children (4-9 years), from predominantly middle-class families in the Northeastern United States, to use information about machines' observable functional capacities to infer their internal, "hidden" mechanistic complexity. Children as young as 4 and 5 years old used machines'…

  8. Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities.

    Science.gov (United States)

    Carrara, Francesco; Giometto, Andrea; Seymour, Mathew; Rinaldo, Andrea; Altermatt, Florian

    2015-05-01

    Unveiling the mechanisms that promote coexistence in biological communities is a fundamental problem in ecology. Stable coexistence of many species is commonly observed in natural communities. Most of these natural communities, however, are composed of species from multiple trophic and functional groups, while theory and experiments on coexistence have been focusing on functionally similar species. Here, we investigated how functional diversity affects the stability of species coexistence and productivity in multispecies communities by characterizing experimentally all pairwise species interactions in a pool of 11 species of eukaryotes (10 protists and one rotifer) belonging to three different functional groups. Species within the same functional group showed stronger competitive interactions compared to among-functional group interactions. This often led to competitive exclusion between species that had higher functional relatedness, but only at low levels of species richness. Communities with higher functional diversity resulted in increased species coexistence and community biomass production. Our experimental findings and the results of a stochastic model tailored to the experimental interaction matrix suggest the emergence of strong stabilizing forces when species from different functional groups interact in a homogeneous environment. By combining theoretical analysis with experiments we could also disentangle the relationship between species richness and functional diversity, showing that functional diversity per se is a crucial driver of productivity and stability in multispecies community.

  9. Homogenization and impoverishment of taxonomic and functional diversity of ants in Eucalyptus plantations.

    Science.gov (United States)

    Martello, Felipe; de Bello, Francesco; Morini, Maria Santina de Castro; Silva, Rogério R; Souza-Campana, Débora Rodriges de; Ribeiro, Milton Cezar; Carmona, Carlos P

    2018-02-19

    Despite its negative impacts on the environment and biodiversity, tree plantations can contribute to biodiversity conservation in fragmented landscapes, as they harbor many native species. In this study, we investigated the impact of Eucalyptus plantations on the taxonomic and functional diversity of ant communities, comparing ant communities sampled in managed and unmanaged (abandoned for 28 years) Eucalyptus plantations, and native Atlantic rain forests. Eucalyptus plantations, both managed and unmanaged, reduced the functional diversity and increased the similarity between ant communities leading to functional homogenization. While communities in managed plantations had the lowest values of both taxonomic and functional ant diversities, ant communities from unmanaged plantations had similar values of species richness, functional redundancy and Rao's Q compared to ant communities from forest patches (although functional richness was lower). In addition, communities in unmanaged Eucalyptus plantations were taxonomically and functionally more similar to communities located in managed plantations, indicating that Eucalyptus plantations have a severe long-term impact on ant communities. These results indicate that natural regeneration may mitigate the impact of Eucalyptus management, particularly regarding the functional structure of the community (α diversity), although it does not attenuate the effects of long term homogenization in community composition (β diversity).

  10. Using a Multi-Trait Approach to Manipulate Plant Functional Diversity in a Biodiversity-Ecosystem Function Experiment

    Science.gov (United States)

    Schittko, Conrad; Hawa, Mahmoud; Wurst, Susanne

    2014-01-01

    A frequent pattern emerging from biodiversity-ecosystem function studies is that functional group richness enhances ecosystem functions such as primary productivity. However, the manipulation of functional group richness goes along with major disadvantages like the transformation of functional trait data into categories or the exclusion of functional differences between organisms in the same group. In a mesocosm study we manipulated plant functional diversity based on the multi-trait Functional Diversity (FD)-approach of Petchey and Gaston by using database data of seven functional traits and information on the origin of the species in terms of being native or exotic. Along a gradient ranging from low to high FD we planted 40 randomly selected eight-species mixtures under controlled conditions. We found a significant positive linear correlation of FD with aboveground productivity and a negative correlation with invasibility of the plant communities. Based on community-weighted mean calculations for each functional trait, we figured out that the traits N-fixation and species origin, i.e. being native or exotic, played the most important role for community productivity. Our results suggest that the identification of the impact of functional trait diversity and the relative contributions of relevant traits is essential for a mechanistic understanding of the role of biodiversity for ecosystem functions such as aboveground biomass production and resistance against invasion. PMID:24897501

  11. Prediction of human protein function according to Gene Ontology categories

    DEFF Research Database (Denmark)

    Jensen, Lars Juhl; Gupta, Ramneek; Stærfeldt, Hans Henrik

    2003-01-01

    developed a method for prediction of protein function for a subset of classes from the Gene Ontology classification scheme. This subset includes several pharmaceutically interesting categories-transcription factors, receptors, ion channels, stress and immune response proteins, hormones and growth factors...

  12. Preparation of functional lupine protein fractions by dry separation

    NARCIS (Netherlands)

    Pelgrom, P.J.M.; Berghout, J.A.M.; Goot, van der A.J.; Boom, R.M.; Schutyser, M.A.I.

    2014-01-01

    Lupine protein concentrate is a promising ingredient that can be obtained by a combination of milling and air classification, generally called dry fractionation. This is a more sustainable route than conventional wet extraction and delivers a protein concentrate with native functional properties.

  13. Jatropha seed protein functional properties for technical applications

    NARCIS (Netherlands)

    Lestari, D.; Mulder, W.J.; Sanders, J.P.M.

    2011-01-01

    Jatropha press cake, by-product after oil expression from Jatropha seeds, contains 24–28% protein on dry basis. Objectives of this research were to investigate functional properties, such as solubility, emulsifying, foaming, film forming, and adhesive properties, of Jatropha press cake proteins and

  14. Dry fractionation for production of functional pea protein concentrates

    NARCIS (Netherlands)

    Pelgrom, P.J.M.; Vissers, A.M.; Boom, R.M.; Schutyser, M.A.I.

    2013-01-01

    Dry milling in combination with air classification was evaluated as an alternative to conventional wet extraction of protein from yellow field peas (Pisum sativum). Major advantages of dry fractionation are retention of native functionality of proteins and its lower energy and water use. Peas were

  15. Regulation of Cellular and Molecular Functions by Protein ...

    Indian Academy of Sciences (India)

    critical role in the regulation of many cellular functions. Phosphorylation of proteins is carried out by a group of enzymes known as protein kinases which transfer terminal phosphate of. ATP (sometimes GTP) to the hydroxyl group of amino acids - serine, threonine and tyrosine. Phosphate group on these three hydroxy amino ...

  16. Epigenetic variation predicts regional and local intraspecific functional diversity in a perennial herb.

    Science.gov (United States)

    Medrano, Mónica; Herrera, Carlos M; Bazaga, Pilar

    2014-10-01

    The ecological significance of epigenetic variation has been generally inferred from studies on model plants under artificial conditions, but the importance of epigenetic differences between individuals as a source of intraspecific diversity in natural plant populations remains essentially unknown. This study investigates the relationship between epigenetic variation and functional plant diversity by conducting epigenetic (methylation-sensitive amplified fragment length polymorphisms, MSAP) and genetic (amplified fragment length polymorphisms, AFLP) marker-trait association analyses for 20 whole-plant, leaf and regenerative functional traits in a large sample of wild-growing plants of the perennial herb Helleborus foetidus from ten sampling sites in south-eastern Spain. Plants differed widely in functional characteristics, and exhibited greater epigenetic than genetic diversity, as shown by per cent polymorphism of MSAP fragments (92%) or markers (69%) greatly exceeding that for AFLP ones (41%). After controlling for genetic structuring and possible cryptic relatedness, every functional trait considered exhibited a significant association with at least one AFLP or MSAP marker. A total of 27 MSAP (13.0% of total) and 12 AFLP (4.4%) markers were involved in significant associations, which explained on average 8.2% and 8.0% of trait variance, respectively. Individual MSAP markers were more likely to be associated with functional traits than AFLP markers. Between-site differences in multivariate functional diversity were directly related to variation in multilocus epigenetic diversity after multilocus genetic diversity was statistically accounted for. Results suggest that epigenetic variation can be an important source of intraspecific functional diversity in H. foetidus, possibly endowing this species with the capacity to exploit a broad range of ecological conditions despite its modest genetic diversity. © 2014 John Wiley & Sons Ltd.

  17. Diversity of structure and function of DNA polymerase (gp43) of T4-related bacteriophages.

    Science.gov (United States)

    Petrov, V M; Karam, J D

    2004-11-01

    The replication DNA polymerase (gp43) of the bacteriophage T4 is a member of the pol B family of DNA polymerases, which are found in all divisions of life in the biosphere. The enzyme is a modularly organized protein that has several activities in one polypeptide chain (approximately 900 amino acid residues). These include two catalytic functions, POL (polymerase) and EXO (3 -exonuclease), and specific binding activities to DNA, the mRNA for gp43, deoxyribonucleotides (dNTPs), and other T4 replication proteins. The gene for this multifunctional enzyme (gene 43) has been preserved in evolution of the diverse group of T4-like phages in nature, but has diverged in sequence, organization, and specificity of the binding functions of the gene product. We describe here examples of T4-like phages where DNA rearrangements have created split forms of gene 43 consisting of two cistrons instead of one. These gene 43 variants specify separate gp43A (N-terminal) and gp43B (C-terminal) subunits of a split form of gp43. Compared to the monocistronic form, the interruption in contiguity of the gene 43 reading frame maps in a highly diverged sequence separating the code for essential components of two major modules of this pol B enzyme, the FINGERS and PALM domains, which contain the dNTP binding pocket and POL catalytic residues of the enzyme. We discuss the biological implications of these gp43 splits and compare them to other types of pol B splits in nature. Our studies suggest that DNA mobile elements may allow genetic information for pol B modules to be exchanged between organisms.

  18. Mining prokaryotes for antimicrobial compounds : From diversity to function

    NARCIS (Netherlands)

    Tracanna, Vittorio; de Jong, Anne; Medema, Marnix H; Kuipers, Oscar P

    The bacterial kingdom provides a major source of antimicrobials that can either be directly applied or used as scaffolds to further improve their functionality in the host. The rapidly increasing amount of bacterial genomic, metabolomic and transcriptomic data offers unique opportunities to apply a

  19. Mycorrhizal symbioses of Salix repens : diversity and functional significance

    NARCIS (Netherlands)

    Heijden, van der E.W.

    2000-01-01

    This thesis investigates the significance of different mycorrhizal fungi, belonging to different functional types (arbuscular mycorrhiza-AM and ectomycorrhiza-EcM), in Salix repens . A comparison between above-ground and below-ground observations on ectomycorrhizal

  20. Selective ligand recognition by a diversity-generating retroelement variable protein.

    Directory of Open Access Journals (Sweden)

    Jason L Miller

    2008-06-01

    Full Text Available Diversity-generating retroelements (DGRs recognize novel ligands through massive protein sequence variation, a property shared uniquely with the adaptive immune response. Little is known about how recognition is achieved by DGR variable proteins. Here, we present the structure of the Bordetella bacteriophage DGR variable protein major tropism determinant (Mtd bound to the receptor pertactin, revealing remarkable adaptability in the static binding sites of Mtd. Despite large dissimilarities in ligand binding mode, principles underlying selective recognition were strikingly conserved between Mtd and immunoreceptors. Central to this was the differential amplification of binding strengths by avidity (i.e., multivalency, which not only relaxed the demand for optimal complementarity between Mtd and pertactin but also enhanced distinctions among binding events to provide selectivity. A quantitatively similar balance between complementarity and avidity was observed for Bordetella bacteriophage DGR as occurs in the immune system, suggesting that variable repertoires operate under a narrow set of conditions to recognize novel ligands.

  1. Seasonal cycles, phylogenetic assembly, and functional diversity of orchid bee communities.

    Science.gov (United States)

    Ramírez, Santiago R; Hernández, Carlos; Link, Andres; López-Uribe, Margarita M

    2015-05-01

    Neotropical rainforests sustain some of the most diverse terrestrial communities on Earth. Euglossine (or orchid) bees are a diverse lineage of insect pollinators distributed throughout the American tropics, where they provide pollination services to a staggering diversity of flowering plant taxa. Elucidating the seasonal patterns of phylogenetic assembly and functional trait diversity of bee communities can shed new light into the mechanisms that govern the assembly of bee pollinator communities and the potential effects of declining bee populations. Male euglossine bees collect, store, and accumulate odoriferous compounds (perfumes) to subsequently use during courtship display. Thus, synthetic chemical baits can be used to attract and monitor euglossine bee populations. We conducted monthly censuses of orchid bees in three sites in the Magdalena valley of Colombia - a region where Central and South American biotas converge - to investigate the structure, diversity, and assembly of euglossine bee communities through time in relation to seasonal climatic cycles. In particular, we tested the hypothesis that phylogenetic community structure and functional trait diversity changed in response to seasonal rainfall fluctuations. All communities exhibited strong to moderate phylogenetic clustering throughout the year, with few pronounced bursts of phylogenetic overdispersion that coincided with the transition from wet-to-dry seasons. Despite the heterogeneous distribution of functional traits (e.g., body size, body mass, and proboscis length) and the observed seasonal fluctuations in phylogenetic diversity, we found that functional trait diversity, evenness, and divergence remained constant during all seasons in all communities. However, similar to the pattern observed with phylogenetic diversity, functional trait richness fluctuated markedly with rainfall in all sites. These results emphasize the importance of considering seasonal fluctuations in community assembly and

  2. Assessment of protein set coherence using functional annotations

    Directory of Open Access Journals (Sweden)

    Carazo Jose M

    2008-10-01

    Full Text Available Abstract Background Analysis of large-scale experimental datasets frequently produces one or more sets of proteins that are subsequently mined for functional interpretation and validation. To this end, a number of computational methods have been devised that rely on the analysis of functional annotations. Although current methods provide valuable information (e.g. significantly enriched annotations, pairwise functional similarities, they do not specifically measure the degree of homogeneity of a protein set. Results In this work we present a method that scores the degree of functional homogeneity, or coherence, of a set of proteins on the basis of the global similarity of their functional annotations. The method uses statistical hypothesis testing to assess the significance of the set in the context of the functional space of a reference set. As such, it can be used as a first step in the validation of sets expected to be homogeneous prior to further functional interpretation. Conclusion We evaluate our method by analysing known biologically relevant sets as well as random ones. The known relevant sets comprise macromolecular complexes, cellular components and pathways described for Saccharomyces cerevisiae, which are mostly significantly coherent. Finally, we illustrate the usefulness of our approach for validating 'functional modules' obtained from computational analysis of protein-protein interaction networks. Matlab code and supplementary data are available at http://www.cnb.csic.es/~monica/coherence/

  3. Structural and Functional Annotation of Hypothetical Proteins of O139

    Directory of Open Access Journals (Sweden)

    Md. Saiful Islam

    2015-06-01

    Full Text Available In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

  4. Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

    Energy Technology Data Exchange (ETDEWEB)

    Galat, Andrzej, E-mail: galat@dsvidf.cea.fr; Thai, Robert

    2014-08-08

    Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome.

  5. Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

    International Nuclear Information System (INIS)

    Galat, Andrzej; Thai, Robert

    2014-01-01

    Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome

  6. Evolutionary relationships and functional diversity of plant sulfate transporters

    Directory of Open Access Journals (Sweden)

    Hideki eTakahashi

    2012-01-01

    Full Text Available Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal sulfate transporters (SUL and animal anion exchangers (SLC26. The lineage of plant SULTR family is expanded into four subfamilies (SULTR1 to SULTR4 in land plant species. By contrast, the putative SULTR homologues from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4, and the other diverged before the appearance of lineages for SUL, SULTR and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13 and plant tonoplast-localized dicarboxylate transporters (TDT. The putative sulfur-sensing protein (SAC1 and SAC1-like transporters (SLT of Chlorophyte green algae, bryophyte and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is completely absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.

  7. Using PFP and ESG Protein Function Prediction Web Servers.

    Science.gov (United States)

    Wei, Qing; McGraw, Joshua; Khan, Ishita; Kihara, Daisuke

    2017-01-01

    Elucidating biological function of proteins is a fundamental problem in molecular biology and bioinformatics. Conventionally, protein function is annotated based on homology using sequence similarity search tools such as BLAST and FASTA. These methods perform well when obvious homologs exist for a query sequence; however, they will not provide any functional information otherwise. As a result, the functions of many genes in newly sequenced genomes are left unknown, which await functional interpretation. Here, we introduce two webservers for function prediction methods, which effectively use distantly related sequences to improve function annotation coverage and accuracy: Protein Function Prediction (PFP) and Extended Similarity Group (ESG). These two methods have been tested extensively in various benchmark studies and ranked among the top in community-based assessments for computational function annotation, including Critical Assessment of Function Annotation (CAFA) in 2010-2011 (CAFA1) and 2013-2014 (CAFA2). Both servers are equipped with user-friendly visualizations of predicted GO terms, which provide intuitive illustrations of relationships of predicted GO terms. In addition to PFP and ESG, we also introduce NaviGO, a server for the interactive analysis of GO annotations of proteins. All the servers are available at http://kiharalab.org/software.php .

  8. Negative impacts of human land use on dung beetle functional diversity.

    Science.gov (United States)

    Barragán, Felipe; Moreno, Claudia E; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario

    2011-03-23

    The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed.

  9. Negative impacts of human land use on dung beetle functional diversity.

    Directory of Open Access Journals (Sweden)

    Felipe Barragán

    Full Text Available The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (20 ha. Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed.

  10. Bee diversity effects on pollination depend on functional complementarity and niche shifts.

    Science.gov (United States)

    Fründ, Jochen; Dormann, Carsten F; Holzschuh, Andrea; Tscharntke, Teja

    2013-09-01

    Biodiversity is important for many ecosystem processes. Global declines in pollinator diversity and abundance have been recognized, raising concerns about a pollination crisis of crops and wild plants. However, experimental evidence for effects of pollinator species diversity on plant reproduction is extremely scarce. We established communities with 1-5 bee species to test how seed production of a plant community is determined by bee diversity. Higher bee diversity resulted in higher seed production, but the strongest difference was observed for one compared to more than one bee species. Functional complementarity among bee species had a far higher explanatory power than bee diversity, suggesting that additional bee species only benefit pollination when they increase coverage of functional niches. In our experiment, complementarity was driven by differences in flower and temperature preferences. Interspecific interactions among bee species contributed to realized functional complementarity, as bees reduced interspecific overlap by shifting to alternative flowers in the presence of other species. This increased the number of plant species visited by a bee community and demonstrates a new mechanism for a biodiversity-function relationship ("interactive complementarity"). In conclusion, our results highlight both the importance of bee functional diversity for the reproduction of plant communities and the need to identify complementarity traits for accurately predicting pollination services by different bee communities.

  11. Protein domain recurrence and order can enhance prediction of protein functions

    KAUST Repository

    Abdel Messih, Mario A.

    2012-09-07

    Motivation: Burgeoning sequencing technologies have generated massive amounts of genomic and proteomic data. Annotating the functions of proteins identified in this data has become a big and crucial problem. Various computational methods have been developed to infer the protein functions based on either the sequences or domains of proteins. The existing methods, however, ignore the recurrence and the order of the protein domains in this function inference. Results: We developed two new methods to infer protein functions based on protein domain recurrence and domain order. Our first method, DRDO, calculates the posterior probability of the Gene Ontology terms based on domain recurrence and domain order information, whereas our second method, DRDO-NB, relies on the nave Bayes methodology using the same domain architecture information. Our large-scale benchmark comparisons show strong improvements in the accuracy of the protein function inference achieved by our new methods, demonstrating that domain recurrence and order can provide important information for inference of protein functions. The Author(s) 2012. Published by Oxford University Press.

  12. Polymeric Biomaterials: Diverse Functions Enabled by Advances in Macromolecular Chemistry.

    Science.gov (United States)

    Liang, Yingkai; Li, Linqing; Scott, Rebecca A; Kiick, Kristi L

    2017-01-24

    Biomaterials have been extensively used to leverage beneficial outcomes in various therapeutic applications, such as providing spatial and temporal control over the release of therapeutic agents in drug delivery as well as engineering functional tissues and promoting the healing process in tissue engineering and regenerative medicine. This perspective presents important milestones in the development of polymeric biomaterials with defined structures and properties. Contemporary studies of biomaterial design have been reviewed with focus on constructing materials with controlled structure, dynamic functionality, and biological complexity. Examples of these polymeric biomaterials enabled by advanced synthetic methodologies, dynamic chemistry/assembly strategies, and modulated cell-material interactions have been highlighted. As the field of polymeric biomaterials continues to evolve with increased sophistication, current challenges and future directions for the design and translation of these materials are also summarized.

  13. Redundancy and response diversity of functional groups: implications for the resilience of coral reefs.

    Science.gov (United States)

    Nyström, Magnus

    2006-02-01

    To improve coral reef management, a deeper understanding of biodiversity across scales in the context of functional groups is required. The focus of this paper is on the role of diversity within functional groups in securing important ecosystem processes that contribute to the resilience of coral-dominated reef states. Two important components of species biodiversity that confer ecosystem resilience are analyzed: redundancy and the diversity of responses within functional groups to change. Three critical functional groups are used to illustrate the interaction between these two components and their role in coral reef resilience: zooxanthellae (symbiotic micro algae in reef-building corals), reef-building corals, and herbivores. The paper further examines the consequences of undermining fu