Testosterone, and winning and losing in human competition

Testosterone and cortisol were measured in six university tennis players across six matches during their varsity season. Testosterone rose just before most matches, and players with the highest prematch testosterone had the most positive improvement in mood before their matches. After matches, mean testosterone rose for winners relative to losers, especially for winners with very positive moods after their victories and who evaluated their own performance highly. Winners with rising testosterone had higher testosterone before their next match, in contrast to losers with falling testosterone, who had lower testosterone before their next match. Cortisol was not related to winning or losing, but it was related to seed (top players having low cortisol), and cortisol generally declined as the season progressed. These results are consistent with a biosocial theory of status.     

Domestication, comparative biology and interactions of wild and cultured fish: convenor's synthesis

Aquaculture is expanding rapidly and many fish species are brought into cultivation, entering a process of domestication with consequences for their morphology, physiology, ecology and evolution. In some species the abundance of cultured populations matches or exceeds that of wild stocks, and interactions between cultured and wild fish can pose significant conservation challenges. At the same time, captive breeding and re‐introduction play an important role in the conservation of some of the world's most endangered fishes. Drawing on contributions from the FSBI Symposium and the wider literature, we synthesize current knowledge of the process and extend of fish domestication, interactions between cultured and wild fish, and the use of cultured fish in fisheries enhancement and restoration. We provide a perspective on the role of biological issues within the wider context of aquaculture development and aquatic conservation biology, and conclude with a discussion of promising avenues for further research.     

Songbird cheaters pay a retaliation cost: evidence for auditory conventional signals

Conventional signals impose costs on senders through receiver retaliation rather than through investment in signal production. While several visual conventional signals have been described (mainly 'badges of status'), acoustic examples are rare; however, several aspects of repertoire use in songbirds are potential candidates. We performed interactive playback experiments to determine whether song-type matches (responding to a song with the same song type), repertoire matches (responding to a song with a different song type, but one in the repertoires of both singers) and unshared song types serve as conventional signals during male-male territorial interactions in banded wrens, Thryothorus pleurostictus. Our results demonstrate that these three signals incite varying levels of receiver aggression: song-type matches induce faster approach than do repertoire matches, and repertoire matches induce faster approach than do unshared song types. Production costs do not differ, while the receiver response does. Because territorial banded wrens approach opponents who signal aggressively, such opponents risk attack. This system will punish and prevent cheaters, as weak males signalling aggression will be subject to escalation by stronger or more-motivated opponents.     

Tests of hypotheses on predation as a factor maintaining polymorphic melanism in coastalplain fox squirrels (Sciurus niger L.)

Fox squirrels ( Sciurus niger ) in the south-eastern U.S. coastal plain differ from those in the rest of the species' range by having black heads with white nose and ears. Postcranially on the dorsum, they also show interindividual colour variation, ranging from all-light agouti to all-black non-agouti. I present results of experiments undertaken to test whether the evolution of these pigmentary features can be attributed to interactions with predators. Comparative static crypsis (when the squirrels are still) was tested by determining how well specimens of the squirrel morphs matched their backgrounds in terms of intensity (brightness) distributions and patch size. Comparative dynamic effects (when the squirrels are moving) were tested using captive red-tailed hawks ( Buteo jamaicensis ) and models of the fox squirrel morphs. Results indicated that morphs of coastal-plain fox squirrels with all-light backs are better static matches to unburned backgrounds than are the darker morphs with which they coexist. Against fire-blackened backgrounds, fox squirrel morphs with intermediate and all-black backs are better intensity matches than those with all-light backs, but the dark morphs are not better patch-length matches than light morphs. The superiority of dark morphs in intensity matching for a short time after a fire does not seem sufficient to account for their long-term maintenance. Hawks responded more slowly to moving fox squirrel models with intermediate amounts of black on the back than to all-light or all-dark morphs; this result suggests a possible factor that would favour retention of genes for dorsal blackness in the coastal-plain population. Patchy black and white heads appear to promote static crypsis of south-eastern fox squirrels, and hawks reacted more slowly to moving squirrel models with such colouration than to those with plain heads.     

Modeling the cuckoo’s brood parasitic behavior in the presence of egg polymorphism

The common cuckoo Cuculus canorus is a brood parasite that utilizes many host species. These have evolved defense against parasitism to reject cuckoo eggs that look unlike their own and some cuckoos have evolved egg mimicry to counter this defense. Egg phenotype indeed plays a key role for both the cuckoo and its hosts to successfully reproduce. It has been argued that cuckoos should parasitize host nests where egg phenotype matches because this makes parasitism more successful. Details of the cuckoo’s parasitic behavior, however, largely remains unknown if they really parasitize hosts depending on “egg matching”. In this paper, we model a time sequence of parasitic events in which a cuckoo finds host nests and decides to parasitize them or not in the presence of egg polymorphism. We evaluate which strategy is optimal: (1) opportunistic parasitism where cuckoos parasitize hosts irrespective of the phenotype, or (2) non-opportunistic parasitism where cuckoos parasitize hosts where egg phenotype matches. The analysis showed that either of the two strategies can be optimal. Factors not considered in the model, e.g., ecological and evolutionary changes both in the cuckoo and the host side, are discussed to explain apparent contrasts observed in some cuckoo–host interactions.     

Does age matter in song bird vocal interactions? Results from interactive playback experiments

The song of oscines provides an extensively studied model of age-dependent behaviour changes. Male and female receivers might use song characteristics to obtain information about the age of a signaller, which is often related to its quality. Whereas most of the age-dependent song changes have been studied in solo singing, the role of age in vocal interactions is less well understood. We addressed this issue in a playback study with common nightingales (Luscinia megarhynchos). Previous studies showed that male nightingales had smaller repertoires in their first year than older males and males adjusted their repertoire towards the most common songs in the breeding population. We now compared vocal interaction patterns in a playback study in 12 one year old and 12 older nightingales (cross-sectional approach). Five of these males were tested both in their first and second breeding season (longitudinal approach). Song duration and latency to respond did not differ between males of different ages in either approach. In the cross-sectional approach, one year old nightingales matched song types twice as often as did older birds. Similarly, in the longitudinal approach all except one bird reduced the number of song type matches in their second season. Individuals tended to overlap songs at higher rates in their second breeding season than in their first. The higher levels of song type matches in the first year and song overlapping by birds in their second year suggest that these are communicative strategies to establish relationships with competing males and/or choosy females.     

Assembling global maps of cellular function through integrative analysis of physical and genetic networks

To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies 'modules' as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules. This protocol begins with importing interaction networks into Cytoscape, followed by filtering and basic network visualization. Next, PanGIA is used to infer a set of modules and their functional inter-relationships. This module map is visualized in a number of intuitive ways, and modules are tested for functional enrichment and overlap with known complexes. The full protocol can be completed between 10 and 30 min, depending on the size of the data set being analyzed.     

Winner and loser effects in human competitions. Evidence from equally matched tennis players

Animals winning an agonistic encounter are more likely to win their next encounter while losers are less likely, even when controlling for motivation and physical size. Do these winner and loser effects exist in human competitions? Drawing on a large database of professional tennis matches, we were able to control for players' ability and thereby test for winner and loser effects. We narrowed the database to matches between players who on average did not differ significantly in rank, and further to matches in which the first set was fought to a long tie-break. These closely fought matches present a natural experiment because players are assigned to treatment conditions – winning or losing a set – despite similar ability and performance. We found that among men, the winner of a closely fought tie-break had an approximate 60% chance of winning the second set, the loser a 40% chance. These effects did not exist among women, a finding consistent with the hypothesis that androgens mediate winner and loser effects. Our results may help in the design of competitions in sport as well as in work environments, where it may prove useful to either encourage winner effects or to attenuate their occasional adverse consequences.     

The size of the intermolecular energy funnel in protein-protein interactions

Revealing the fundamental principles of protein interactions is essential for the basic knowledge of molecular processes and designing better predictive tools. Protein docking procedures allow systematic sampling of intermolecular energy landscapes, revealing the distribution of energy basins and their characteristics. A systematic search docking procedure GRAMM-X was applied to a comprehensive nonredundant database of nonobligate protein-protein complexes to determine the size of the intermolecular energy funnel. The unbound structures were simulated using rotamer library. The procedure generated grid-based matches, based on a smoothed Lennard-Jones potential, and minimized them off the grid with the same potential. The minimization generated a distribution of distances, based on a variety of metrics, between the grid-based and the minimized matches. The metric selected for the analysis, ligand interface RMSD, provided three independent estimates of the funnel size: based on the distribution amplitude for the near-native matches, deviation from random, and correlation with the energy values. The three methods converge to similar estimates of approximately 6-8 A ligand interface RMSD. The results indicated dependence of the funnel size on the type of the complex (smaller for antigen-antibody, medium for enzyme-inhibitor, and larger for the rest of the complexes) and the funnel size correlation with the size of the interface. Guidelines for the optimal sampling of docking coordinates, based on the funnel size estimates, were explored.     

Discharge properties of motoneurones: how are they matched to the properties and use of their muscle units?

A general survey is given of old as well as more recent findings concerning matches between electrophysiological properties of motoneurones and contractile properties of their muscle fibres. Mechanisms for creating and maintaining such matches are discussed. It is pointed out that it is not sufficient to describe the variation of functional motoneurone characteristics simply in terms of 'fast' or 'slow': all properties seem continuously graded and there is cytochemical evidence for several, seemingly independent parameters of functional specialisation.     

How common is the funnel‐like energy landscape in protein‐protein interactions?

The goal of this study is to verify the concept of the funnel-like intermolecular energy landscape in protein-protein interactions by use of a series of computational experiments. Our preliminary analysis revealed the existence of the funnel in many protein-protein interactions. However, because of the uncertainties in the modeling of these interactions and the ambiguity of the analysis procedures, the detection of the funnels requires detailed quantitative approaches to the energy landscape analysis. A number of such approaches are presented in this study. We show that the funnel detection problem is equivalent to a problem of distinguishing between distributions of low-energy intermolecular matches in the funnel and in the low-frequency landscape fluctuations. If the fluctuations are random, the decision about whether the minimum is the funnel is equivalent to determining whether this minimum is significantly different from a would-be random one. A database of 475 nonredundant cocrystallized protein-protein complexes was used to re-dock the proteins by use of smoothed potentials. To detect the funnel, we developed a set of sophisticated models of random matches. The funnel was considered detected if the binding area was more populated by the low-energy docking predictions than by the matches generated in the random models. The number of funnels detected by use of different random models varied significantly. However, the results confirmed that the funnel may be the general feature in protein-protein association.     

Finding anchors for genomic sequence comparison.

Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them, to identify and characterize their commonalities and differences. Programs that align whole genomes generally use a seed-and-extend technique, starting from exact or near-exact matches and selecting a reliable subset of these, called anchors, and then filling in the remaining portions between the anchors using a combination of local and global alignment algorithms, but their choices for the parameters so far have been primarily heuristic.We present a statistical framework and practical methods for selecting a set of matches that is both sensitive and specific and can constitute a reliable set of anchors for a one-to-one mapping of two genomes from which a whole-genome alignment can be built. Starting from exact matches, we introduce a novel per-base repeat annotation, the Z-score, from which noise and repeat filtering conditions are explored. Dynamic programming-based chaining algorithms are also evaluated as context-based filters. We apply the methods described here to the comparison of two progressive assemblies of the human genome, NCBI build 28 and build 34 (www.genome.ucsc.edu), and show that a significant portion of the two genomes can be found in selected exact matches, with very limited amount of sequence duplication.     

Separating significant matches from spurious matches in DNA sequences

Word matches are widely used to compare genomic sequences. Complete genome alignment methods often rely on the use of matches as anchors for building their alignments, and various alignment-free approaches that characterize similarities between large sequences are based on word matches. Among matches that are retrieved from the comparison of two genomic sequences, a part of them may correspond to spurious matches (SMs), which are matches obtained by chance rather than by homologous relationships. The number of SMs depends on the minimal match length (?) that has to be set in the algorithm used to retrieve them. Indeed, if ? is too small, a lot of matches are recovered but most of them are SMs. Conversely, if ? is too large, fewer matches are retrieved but many smaller significant matches are certainly ignored. To date, the choice of ? mostly depends on empirical threshold values rather than robust statistical methods. To overcome this problem, we propose a statistical approach based on the use of a mixture model of geometric distributions to characterize the distribution of the length of matches obtained from the comparison of two genomic sequences.     

miRNA与其靶mRNA的相互作用：绑定位点的质量与数量特征的整合计算分析

miRNAs通过完全或不完全的碱基互补绑定到信使RNA(mRNA)上,通过抑制翻译或者直接导致mRNA降解的方式来调节靶基因的表达．为了研究miRNAs在转录水平上面的调控作用,两种人类基因组中组织特异的miRNAs(miR-1和miR-124)被转染到HeLa细胞中,微阵列(microarray)分析转染前后细胞中各基因mRNA表达水平变化情况的结果表明：动物基因组中靶基因与miRNAs不完全的碱基互补也会导致mRNA的直接降解．通过分析实验得到的mRNA表达水平变化数据,发现这相同miRNA的不同靶基因mRNA表达水平的下调倍数有着明显的差别,推测这些靶基因mRNA序列本身存在某些影响其受调节程度的因素．为此,提取和分析这些靶基因mRNA的序列特征,通过对这些序列特征与mRNA表达水平下调数据进行统计相关分析,最终发现,miRNA靶基因受调节的程度与以下几个因素相关联：mRNA序列中miRNA靶位点的个数,靶位点与miRNA序列碱基互补的程度,以及绑定后形成二级结构的稳定程度(即最低自由能的大小)．在此基础上,初步建立起一个多因子作用下的miRNA 靶基因mRNA表达水平下调程度模型,分析表明：该模型在一定程度上可以反映了部分序列特征对于miRNA靶基因mRNA表达水平下调程度的影响．     

MultiProtIdent: identifying proteins using database search and protein-protein interactions

Protein identification is important in proteomics. Proteomic analyses based on mass spectra (MS) constitute innovative ways to identify the components of protein complexes. Instruments can obtain the mass spectrum to an accuracy of 0.01 Da or better, but identification errors are inevitable. This study shows a novel tool, MultiProtIdent, which can identify proteins using additional information about protein-protein interactions and protein functional associations. Both single and multiple Peptide Mass Fingerprints (PMFs) are input to MultiProtIdent, which matches the PMFs to a theoretical peptide mass database. The relationships or interactions among proteins are considered to reduce false positives in PMF matching. Experiments to identify protein complexes reveal that MultiProtIdent is highly promising. The website associated with this study is http://dbms104.csie.ncu.edu.tw/.     

MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains

Background  

Many protein interactions, especially those involved in signaling, involve short linear motifs consisting of 5-10 amino acid residues that interact with modular protein domains such as the SH3 binding domains and the kinase catalytic domains. One straightforward way of identifying these interactions is by scanning for matches to the motif against all the sequences in a target proteome. However, predicting domain targets by motif sequence alone without considering other genomic and structural information has been shown to be lacking in accuracy.     

Mode matches in hydrophobic free energy eigenfunctions predict peptide–protein interactions

The dominant statistical hydrophobic free energy inverse frequencies, amino acid wavelengths as hydrophobic modes, of neurotensin (NT), cholescystokinin (CCK), the human dopamine D₂ receptor [(DA)D₂], and the human dopamine transporter (DAT) were determined using orthogonal decomposition of the autocovariance matrices of their amino acid sequences as hydrophobic free energy equivalents in kcal/mol. The leading eigenvalues-associated eigenvectors were convolved with the original series to construct eigenfunctions. Eigenfunctions were further analyzed using discrete trigonometric wavelet and all poles, maximum entropy power spectral transformations. This yielded clean representations of the dominant hydrophobic free energy modes, most of which are otherwise lost in the smoothing of hydropathy plots or contaminated by end effects and multimodality in conventional Fourier transformations. Mode matches were found between NT and (DA)D₂ and between CCK and DAT, but not the converse. These mode matches successfully predicted the nonlinear kinetic interactions of NT-(DA)D₂ in contrast with CCK-(DA)D₂ on ³H-spiperone binding to (DA)D₂, and by CCK-DAT but not NT-DAT on [N-methyl-³H]-WIN 35,428 binding to DAT in (DA)D₂ and DAT cDNA stably transfected cell lines without known NT or CCK receptors. Computation of the dominant modes of hydrophobic free energy eigenfunctions may help predict functionally relevant peptide–membrane protein interactions, even across neurotransmitter families. © 1998 John Wiley & Sons, Inc. Biopoly 46: 89–101, 1998     

Database-derived potentials dependent on protein size for in silico folding and design

Knowledge-based potentials are widely used in simulations of protein folding, structure prediction, and protein design. Their advantages include limited computational requirements and the ability to deal with low-resolution protein models compatible with long-scale simulations. Their drawbacks comprehend their dependence on specific features of the dataset from which they are derived, such as the size of the proteins it contains, and their physical meaning is still a subject of debate. We address these issues by probing the theoretical validity of these potentials as mean-force potentials that take the solvent implicitly into account and involve entropic contributions due to atomic degrees of freedom and solvation. The dependence on the size of the system is checked on distance-dependent amino acid pair potentials, derived from six protein structure sets containing proteins of increasing length N. For large inter-residue distances, they are found to display the theoretically predicted 1/N behavior weighted by a factor depending on the boundaries and the compressibility of the system. For short distances, different trends are observed according to the nature of the residue pairs and their ability to form, for example, electrostatic, cation-pi or pi-pi interactions, or hydrophobic packing. The results of this analysis are used to devise a novel protein size-dependent distance potential, which displays an improved performance in discriminating native sequence-structure matches among decoy models.     

PvuII endonuclease contains two calcium ions in active sites

Restriction endonucleases differ in their use of metal cofactors despite having remarkably similar folds for their catalytic regions. To explore this, we have characterized the interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex, determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all structurally examined endonucleases, while the second position is similar to that of EcoRV but is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen leaving group. However, the interactions between the DNA scissile phosphate and the metals, the first metal and the attacking water, and the attacking water and DNA are the same in PvuII as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed three-metal or the two-metal models of EcoRV.     

The mixed xylem sap proteome of Fusarium oxysporum-infected tomato plants

Secreted proteins are known to play decisive roles in plant–fungus interactions. To study the molecular details of the interaction between the xylem-colonizing, plant-pathogenic fungus Fusarium oxysporum and tomato, the composition of the xylem sap proteome of infected tomato plants was investigated and compared with that of healthy plants. Two-dimensional gel separation and mass spectrometry yielded peptide masses and peptide sequences of 33 different proteins. Despite the absence of complete genome sequences of either tomato or F. oxysporum , 21 proteins were identified as tomato proteins and seven as fungal proteins. Thirteen of the tomato proteins were specific for infected plants. Sixteen tomato proteins were found in xylem sap for the first time, four of which were identified based on matches to expressed sequences only. Coding sequences for new proteins from F. oxysporum were identified through either direct matching to a database sequence, matching of peptide sequences to genome or expressed sequence tag databases of other Fusarium species, or PCR with degenerate primers on cDNA derived from infected plants followed by screening of a F. oxysporum BAC library. Together, these findings provide an excellent basis for further exploration of the interaction between xylem-colonizing pathogens and their hosts.