Types Of Experimental Evidence Research Articles

PRODORIC: state-of-the-art database of prokaryotic gene regulation.

PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.

Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster

The regulation of gene expression is a key factor in the development and maintenance of life in all organisms. Even so, little is known at whole genome scale for most genes and contexts. We propose a method, Tool for Weighted Epigenomic Networks in Drosophila melanogaster (Fly T-WEoN), to generate context-specific gene regulatory networks starting from a reference network that contains all known gene regulations in the fly. Unlikely regulations are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from the literature. Experimental data files can be generated with several standard procedures and used solely when and if available. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster. Fly T-WEoN together with its step-by-step guide is available at https://weon.readthedocs.io.

Endocrine disruptors database selects by evidence

A new database identifies 686 potential endocrine-disrupting chemicals (EDCs) on the basis of published data from rodent and human studies. Endocrine-disrupting chemicals interfere with the body’s regulatory system. Such chemicals can cause adverse developmental, immune, metabolic, neurological, and reproductive effects. To create the Database of Endocrine Disrupting Chemicals and their Toxicity Profiles (DEDuCT), a team from India’s Institute of Mathematical Sciences (IMSc) computationally mined more than 16,000 published research articles to identify those with information on EDCs. The compounds included in DEDuCT are those that had in vivo rodent, in vitro human, or in vivo human experimental evidence for endocrine disruption (Sci. Total Environ. 2019, DOI: 10.1016/j.scitotenv.2019.07.225). DEDuCT classifies the chemicals based on the type of experimental evidence, exposure sources, chemical structures, and physiological systems they affect. The database also includes the compounds’ known and predicted...

YARG: A repository for arsenic-related genes in yeast.

Arsenic is a toxic metalloid. Moderate levels of arsenic exposure from drinking water can cause various human health problems such as skin lesions, circulatory disorders and cancers. Thus, arsenic toxicity is a key focus area for environmental and toxicological investigations. Many arsenic-related genes in yeast have been identified by experimental strategies such as phenotypic screening and transcriptional profiling. These identified arsenic-related genes are valuable information for studying arsenic toxicity. However, the literature about these identified arsenic-related genes is widely dispersed and cannot be easily acquired by researchers. This prompts us to develop YARG (Yeast Arsenic-Related Genes) database, which comprehensively collects 3396 arsenic-related genes in the literature. For each arsenic-related gene, the number and types of experimental evidence (phenotypic screening and/or transcriptional profiling) are provided. Users can use both search and browse modes to query arsenic-related genes in YARG. We used two case studies to show that YARG can return biologically meaningful arsenic-related information for the query gene(s). We believe that YARG is a useful resource for arsenic toxicity research. YARG is available at http://cosbi4.ee.ncku.edu.tw/YARG/.

ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data.

Transcription factors (TFs) play a fundamental role in coordinating biological processes in response to stimuli. Consequently, we often seek to determine the key TFs and their regulated target genes (TGs) amidst gene expression data. This requires a knowledge-base of TF-TG interactions, which would enable us to determine the topology of the transcriptional network and predict novel regulatory interactions. To address this, we generated an Open-access Repository of Transcriptional Interactions, ORTI, by integrating available TF-TG interaction databases. These databases rely on different types of experimental evidence, including low-throughput assays, high-throughput screens, and bioinformatics predictions. We have subsequently categorised TF-TG interactions in ORTI according to the quality of this evidence. To demonstrate its capabilities, we applied ORTI to gene expression data and identified modulated TFs using an enrichment analysis. Combining this with pairwise TF-TG interactions enabled us to visualise temporal regulation of a transcriptional network. Additionally, ORTI enables the prediction of novel TF-TG interactions, based on how well candidate genes co-express with known TGs of the target TF. By filtering out known TF-TG interactions that are unlikely to occur within the experimental context, this analysis predicts context-specific TF-TG interactions. We show that this can be applied to experimental designs of varying complexities. In conclusion, ORTI is a rich and publicly available database of experimentally validated mammalian transcriptional interactions which is accompanied with tools that can identify and predict transcriptional interactions, serving as a useful resource for unravelling the topology of transcriptional networks.

Increasing density of rare species of intertidal gastropods: tests of competitive ability compared with common species

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 453:107-116 (2012) - DOI: https://doi.org/10.3354/meps09639 Increasing density of rare species of intertidal gastropods: tests of competitive ability compared with common species Miguel G. Matias1,3,*, M. G. Chapman1, A. J. Underwood1, Nessa E. O’Connor2 1Centre for Research on Ecological Impacts of Coastal Cities, Marine Ecology Laboratories A11, The University of Sydney, New South Wales 2006, Australia 2School of Biological Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK 3Present address: Institut des Sciences de l’Evolution, UMR CNRS-UM2 5554, Université Montpellier 2, CC 065, Place Eugene Bataillon, 34095 Montpellier cedex 05, France *Email: miguel.matias@univ-montp2.fr ABSTRACT: Many assemblages contain numerous rare species, which can show large increases in abundances. Common species can become rare. Recent calls for experimental tests of the causes and consequences of rarity prompted us to investigate competition between co-existing rare and common species of intertidal gastropods. In various combinations, we increased densities of rare gastropod species to match those of common species to evaluate effects of intra- and interspecific competition on growth and survival of naturally rare or naturally common species at small and large densities. Rarity per se did not cause responses of rare species to differ from those of common species. Rare species did not respond to the abundances of other rare species, nor show consistently different responses from those of common species. Instead, individual species responded differently to different densities, regardless of whether they are naturally rare or abundant. This type of experimental evidence is important to be able to predict the effects of increased environmental variability on rare as opposed to abundant species and therefore, ultimately, on the structure of diverse assemblages. KEY WORDS: Additive-design · Competition · Gastropods · Species-abundance · Rarity Full text in pdf format PreviousNextCite this article as: Matias MG, Chapman MG, Underwood AJ, O’Connor NE (2012) Increasing density of rare species of intertidal gastropods: tests of competitive ability compared with common species. Mar Ecol Prog Ser 453:107-116. https://doi.org/10.3354/meps09639 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 453. Online publication date: May 07, 2012 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2012 Inter-Research.

Effect on Kinetics by Deuterium in the 1,5-Hydrogen Shift of a Cisoid-Locked 1,3(Z)-Pentadiene, 2-Methyl-10-methylenebicyclo[4.4.0]dec-1-ene: Evidence for Tunneling?

Prompted by extensive theoretical interest in the role of tunneling in the intramolecular 1,5-hydrogen shift in 1,3(Z)-pentadienes and the large uncertainty in the published values of the theoretically relevant kinetic deuterium-isotope effect and its dependence on temperature, we have examined a degenerate bicyclic version, 2-methyl-10-methylenebicyclo[4.4.0]dec-1-ene, which is locked into the rearrangement-competent cisoid conformation, in the hope of obtaining more precise and accurate values. From rate constants determined over a range of 33 degrees C from 167.7 to 201.6 degrees C, Arrhenius parameters, Ea = 32.8 +/- 0.4 kcal mol(-1) and log A = 11.1 +/- 0.2, were obtained. An average kinetic isotope effect of 4.2 +/- 0.5 obtained from all values for kH/kD and k-H/k-D may be compared with a value of 5.0 +/- 0.3, recalculated from data in the pioneering publication of Roth and König. From a highly problematic extrapolation of the temperature dependence, a value of kH/kD of 16.6 (standard error between 6.5 and 43) is calculated for the kinetic isotope effect at 25 degrees C (Roth and König: 12.2). With curvature in Arrhenius plots being one of the three types of experimental evidence considered indicative of tunneling, the kinetic study of the previously published rearrangement of 1-phenyl-5-p-tolyl-1,3(Z)-pentadiene has been extended over a period of 339 days to a range of 108 degrees C (77-185 degrees C) without discerning any deviation from a straight-line Arrhenius plot: Ea = 28.7 +/- 0.5 (kcal mol(-1)) and log A = 9.41 +/- 0.30.

Nitrate assimilation in Lotus japonicus

This paper summarizes some recent advances in the understanding of nitrate assimilation in the model legume Lotus japonicus. First, different types of experimental evidence are presented that emphasize the importance of the root in the nitrate-reducing assimilatory processes in this plant. Secondly, the main results from an ethyl methanesulphonate mutagenesis programme are presented. In this programme, chlorate-resistant and photorespiratory mutants were produced and characterized. The phenotype of one particular chlorate-resistant mutant suggested the importance of a low-affinity nitrate transport system for growth of L. japonicus plants under nitrate nutrition. The phenotype of photorespiratory mutants, affected in all forms of plastid glutamine synthetase in leaves, roots, and nodules, indicated that plastid glutamine synthetase was not required for primary nitrate assimilation nor for the symbiotic associations of the plant (nodulation, mycorrhization), provided photorespiration was suppressed. However, the phenotype of these mutants confirmed that plastid glutamine synthetase was required for the reassimilation of ammonium released by photorespiration. Finally, different aspects of the relationship between nitrate assimilation and osmotic stress in L. japonicus are also discussed, with specific reference to the biosynthesis of proline as an osmolyte.

Alternative stable states in ecology

The idea that alternative stable states may exist in communities has been a recurring theme in ecology since the late 1960s, and is now experiencing a resurgence of interest. Since the first papers on the subject appeared, two perspectives have developed to describe how communities shift from one stable state to another. One assumes a constant environment with shifts in variables such as population density, and the other anticipates changes to underlying parameters or environmental “drivers”. We review the theory behind alternative stable states and examine to what extent these perspectives are the same, and in what ways they differ. We discuss the concepts of resilience and hysteresis, and the role of stochasticity within the two formulations. In spite of differences in the two perspectives, the same type of experimental evidence is required to demonstrate the existence of alternative stable states.

Stimulation of human natural interferon-alpha response via paramyxovirus hemagglutinin lectin-cell interaction.

A lectin-carbohydrate recognition event without enzymatic function is proposed as molecular basis for an important innate immune response to enveloped viruses. It involves the hemagglutinin-neuraminidase (HN) glycoprotein of Newcastle disease virus (NDV) and sialic acid expressing cellular receptors on human natural interferon (IFN) alpha producing cells. This conclusion is based on two types of experimental evidence: (a) strong UV irradiation of NDV, which destroyed the cell binding and hemadsorption (HAd) but not the neuraminidase (NA) activity of HN, also destroyed its IFN-alpha inducing activity; (b) DNA transfectants expressing HN mutant molecules with greatly reduced NA but not HAd activity induced IFN-alpha while transfectants expressing HN mutant molecules with greatly reduced NA and HAd activity were incapabable of inducing IFN-alpha in human peripheral blood mononuclear cells. The results clarify molecular mechanisms involved in pattern recognition during innate immune responses.

Threshold-mediated mechanisms in mutagenesis: implications in the classification and regulation of chemical mutagens

Chemical mutagens are currently regulated and labelled on the basis of their hazardous properties defined in hazard classification schemes. The strength and type of experimental evidence is used as the only criterion for classification in categories which express different levels of concern for the possibility of adverse effects — notably transmissible genetic alterations — in humans. Differently from the classification of carcinogens, no consideration is given to potency, nor to the mechanism of action. The rationale of such hazard based classification is that the hazardous property of a chemical is an intrinsic feature, which is expressed independently of dosing. Changing of dose level results in a mere change in the probability to observe an adverse effect, but not in its potential occurrence. The lack of theoretical threshold underlying this approach can be envisaged, in principle, for stochastic processes such as DNA damage, which can be triggered by single molecular interactions. On the other hand, indirect mechanisms of genotoxicity, involving multiple interactions with non-DNA targets, are expected to show a threshold. At variance to DNA reactive agents, chemicals acting with threshold-mediated mechanism do change also qualitatively their toxic properties depending on the dose level. Possible problems arising in the application of hazard based schemes for the evaluation of chemicals with threshold-mediated mechanism of action are discussed, using the spindle poisons benzimidazole fungicides as an example.

Size Exclusion Chromatography of Substituted Acetylene Polymers: Effect of Autooxidative Degradation of the Polymer During the Analysis

The degradation of poly(phenylacetylene), a typical autoxidatively degradable polymer of substituted acetylene, is shown to take place inside the SEC (size exclusion chromatography) columns during the polymer analysis carried out with eluent (THF) not protected from air. Three types of experimental evidence are given based on the comparison of results of SEC analyses carried out: (i) with the eluent kept under air or argon atmosphere; (ii) with different flow rates of the eluent; and (iii) with and without the interruption of the analysis for a few hours. Other degradable polymers of substituted acetylene are mentioned and recommendations for their SEC analyses are given.

Contribution to the understanding of the reduction mechanism of nitrobenzene

Electrochemical reduction of nitrobenzenes has been studied extensively [1,2]. For the processes involved Haber [3] proposed a scheme which is generally accepted in a modified form [4,5]. Nitrobenzene was the first organic compound for which a current-voltage curve obtained with the dropping mercury electrode was reported [6]. At this electrode, where, because of the continuous surface renewal the short contact period excludes accumulation and side-reaction of products [7], the reduction occurs in a single four-electron step. In acidic media the monoand di-protonated forms of arylhydroxylamine [8-lo] formed in the first step are reduced at more negative potentials in a second, two-electron step. The overall four-electron process involves also a transfer of four protons (reaction 1): ArNO,+4e-+4H++ArNHOH+H,O (1) The sequence of transfer of protons and electrons cannot be deduced in aqueous media from the variation in the limiting current of the first step, as this is pH-independent. Mechanistic studies in non-aqueous media [11,12] do not offer information about the process in aqueous solutions because of the difference in solvation of all the species involved and in their acid-base properties. Similarly for mechanistic studies in the presence of surfactants [13-151 the role of micelles and other specific effects of adsorbed surfactants cannot be excluded. The first type of experimental evidence that can be used in the elucidation of the sequence of electron and proton transfer is the fact that the sequential reduction of the nitro group to a nitroso and a hydroxylamino group has never been reported to occur in two two-electron steps. The presence of a single four-electron wave

The mechanism of inactivation of lipoxygenases by acetylenic fatty acids.

The inactivation of soybean lipoxygenase by 5,8,11,14-eicosatetraynoic acid was studied in detail. The inactivation was found to be time-dependent and irreversible. A kinetic scheme, based on the assumption of a rapid inactivation of the enzyme-product complex, yielded a Km value for 5,8,11,14-eicosatetraynoic acid of 1.3 microM, which is about a tenth of that described for arachidonic acid, and a reaction constant k+2 of 0.006s-1, which is four orders of magnitude lower. The reasons for these differences are discussed. Several types of experimental evidence indicate that the first step of the enzyme inactivation is the conversion of 5,8,11,14-eicosatetraynoic acid via a lipoxygenase reaction: (a) the conversion of radioactively labelled methyl ester of 5,8,11,14-eicosatetraynoic acid to other products; (b) the oxygen requirement of the inactivation; (c) the competitive protective effect of linoleic acid; (d) the similarity of the activation energy for both the dioxygenation of linoleic acid and the enzyme inactivation by 5,8,11,14-eicosatetraynoic acid; (e) the formation of one mole methionine sulfoxide/mole enzyme during the reaction with 5,8,11,14-eicosatetraynoic acid, similar to the suicidal reaction of reticulocyte lipoxygenase with 13LS-hydroperoxy-linoleic acid. These results, as well as the lack of covalent binding of 14C-labelled 5,8,11,14-eicosatetraynoic acid methyl ester, contradict the allene mechanism postulated by others [D.T. Downing, D.G. Ahern, and M. Bachta (1970) Biochem. Biophys. Res. Commun. 40, 218-223; K.H. Gibson (1977) Chem. Soc. Rev. 6, 489-510]. It is assumed that the susceptible methionine is located at the active centre of the enzyme.

T lymphocyte-mediated cytolysis. II. Role of target cell histocompatibility antigens in recognition and lysis.

Although compelling genetic and serologic evidence implicate target cell (TC) MHC antigens in specific cytotoxic T lymphocyte (CTL)-TC interaction leading to lysis, it is not entirely clear whether TC recognition through an MHC determinant(s) is a prerequisite for lysis to occur. In fact the finding that both specific and nonspecific TC are lysed equally well in lectin-dependent cell-mediated cytotoxicity (LDCC) challenges the necessity for TC MHC involvement in the cytolytic process beyond providing the basis for specificity in direct (nonlectin-dependent) CTL-mediated lysis. In the present paper we present evidence suggesting that even in nonspecific LDCC, as well as in nonspecific lymphocyte-mediated lysis of TC oxidized by periodate treatment or by galactose oxidase (ODCC), TC MHC components are required for lytic interactions with cytotoxic effector cells. This conclusion is based on 3 types of experimental evidence: 1) cells displaying reduced amounts of MHC proteins are poor targets in LDCC; 2) removal of H-2 by papain renders murine target cells refractory to lysis in LDCC, even though Con A binding is only slightly reduced; 3) antisera to target cell H-2-coded products block lysis in both LDCC and ODCC, whereas antisera to other cell surface antigens do not. A theory explaining nonspecific effector target interaction leading to lysis based on involvement of CTL receptor(s) and TC MHC components is presented.

Simultaneous expression of H-2-restricted and alloreactive recognition by a cloned line of influenza virus-specific cytotoxic T lymphocytes.

Based on theoretical considerations and several types of experimental evidence with heterogeneous cell populations it has been proposed that alloreactive T cells and major histocompatibility complex (MHC)-restricted T cells directed to foreign non-NHC antigens represent overlapping subsets. In this report we provide direct evidence for this hypothesis at the clonal level. We have isolated a cloned continuous influenza virus-specific cytotoxic T cell (CTL) line derived from a single (H-2b X H-2d)F1 CTL precursor which simultaneously exhibits H-2-restricted cytotoxicity of influenza A/Japan/305/57 virus in association with H-2Kd and alloreactive cytotoxicity for H-2Kk alloantigen. Cold target inhibition data demonstrate that both MHC-restricted and alloreactive recognition is mediated by the same cell population. In addition to cross-reactivity at the target cell level, we shown that this cloned CTL line can be specifically stimulated to proliferate either by A/Japan/305/57 virus-infected cells expressing H-2Kd or by uninfected cells of the H-2Kk haplotype.

Evidence for a direct action of X-537 A on the cardiac plasma membrane as an ionophore.

In some cardiac muscles made inexcitable by inactivating the fast sodium channels with elevated potassium, it has been shown that several agents, including catecholamines, induce slow electrical responses with concomitant contractions. The response is considered to be carried through the slow Ca2+ or Ca2+-Na+ channels on the basis of several types of experimental evidence. X-537A produced this type of electrical and mechanical responses in papillary muscles from both normal and reserpinized guinea pigs. A beta-adrenergic blocking agent, sotalol, did not modify this X-537A-induced responses. Tyramine, an agent known to release endogenous catecholamines, produced the same mechanical responses in normal papillary muscles, but it did not in those from the reserpinized animals. Therefore, it can be concluded that X-537A does act, at least at relatively high concentrations, on the cardiac plasma membrane to increase the Ca2+ permeability, which can be visualized with the aid of the specially designed experiments as described above.

Control of induction of tubulin synthesis in Chlamydomonas reinhardi.

REMOVAL of the flagella from the biflagellate alga Chlamydomonas reinhardi results in the rapid production of new flagella1–3. Flagellar regeneration is 80–85% complete within 60 min (Fig. 1). Indirect evidence obtained from in vitro translation of polyribosomes and mRNA from deflagellated gametes1 has indicated that flagellar regeneration is accompanied by a strong but transient induction of tubulin synthesis. Kinetic analysis showed that tubulin mRNA could be detected in polyribosomes in as little as 15 min after deflagellation. Since the cytoplasm contains a reserve of tubulin of sufficient size to supply at least one-third to one-half of the tubulin subunits required for flagellar reassembly1,3, the rapid initiation of tubulin synthesis following deflagellation suggested the existence of a highly sensitive system for detecting and responding to the cell's anticipated need for additional tubulin. As an approach to seeking such a mechanism, we have carried out studies to determine if the depletion of tubulin reserves during flagellar outgrowth might provide the signal for the induction of tubulin synthesis. We present here two types of experimental evidence which clearly demonstrate that the induction of tubulin synthesis is independent of the utilisation of tubulin reserves during flagellar regeneration.

Control of Aggression by Singing in Crickets

Ethologists developed the idea that many animal species evolved mechanisms to control aggression among their members. This control is by the use of signals to reduce the probability of attacks by the opponent before injurious or lethal combats occur. Although there are observations that are best explained by the theory, no direct experimental evidence has been presented. We report here one type of experimental evidence that seems to fit the theory.

Conformational properties of isolated macromolecules

AbstractThe properties of many kinds of solid material (e.g., ionic crystals, quartz, etc.) appear to have only a tenuous correlation with those of the isolated individual atoms or molecules of which they are made. In macromolecular substances, however, thanks primarily to the great strength of covalent bonds, such correlations are strong and indeed essential to fundamental understanding of structure‐property relationships. With certain exceptions, such as polypeptides and polynucleotides with their remarkable helix‐coil transformations, the conformational properties of macromolecules in liquid or amorphous environment are only secondarily dependent on the nature or concentration of diluents; and in many cases the molecular conformation observed in the crystalline state is also the most stable conformation of the isolated chain. There are also strong correlations between the rates of conformational change for isolated macromolecules in dilute solution and various non‐equilibrium properties of polymeric substances in bulk.During the past decade, great progress has been made in the analysis and prediction of macromolecular conformations. Detailed accounts may be found in the books by VOLKENSTEIN, by BIRSTEIN and PTITSYN, and by FLORY. By combination of several types of experimental evidence with semi‐empirical and theoretical considerations, it has been possible to construct fairly reliable potential energies governing the conformations of a wide variety of chain molecules. An important simplifying feature of the results is that for many purposes it is sufficient to focus attention on the various minima of the potential energy, corresponding to the so‐called rotational‐isomeric states. Another essential feature is that as a rule one finds strong interdependence of the rotational states of adjoining bonds in the chain backbone; a simple example is found in the “pentane effect” for paraffin chains, which renders highly improbable the occurence of two successive gauche rotations of opposite sense. An important exception is seen in polyamides, where the essentially rigid planarity of the amide link allows independence of the rotations of the immediately adjacent bonds. Inclusion of other rigid or semi‐rigid elements in the chain backbone, such as the rings in cellulose and in terephthalate polyesters, leads to similar effects, but in detail each chain is sui generis. The conformations of chains bearing asymmetric centers (e.g., PVC, polypropylene) depends strongly on tacticity and stereoregularity.For the discussion of non‐equilibrium properties at a fundamental level, the maxima (barriers between minima) of the conformational potential energy also play an essential role, but at present most theories of viscoelasticity, for example, are based on less realistic models, such as beads‐and‐springs, random‐flight chain, KRATKY‐POROD wormlike chain, etc. The elaboration of these models and their relation to the detailed molecular structure is currently an active field of study.