Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes

MOTIVATION: Genome-wide experiments only rarely show resounding success in yielding genes associated with complex polygenic disorders. We evaluate 49 obesity-related genome-wide experiments with publicly available findings including microarray, genetics, proteomics and gene knock-down from human, mouse, rat and worm, in terms of their ability to rediscover a comprehensive set of genes previously found to be causally associated or having variants associated with obesity. RESULTS: Individual experiments show poor predictive ability for rediscovering known obesity-associated genes. We show that intersecting the results of experiments significantly improves the sensitivity, specificity and precision of the prediction of obesity-associated genes. We create an integrative model that statistically significantly outperforms all 49 individual genome-wide experiments. We find that genes known to be associated with obesity are significantly implicated in more obesity-related experiments and use this to provide a list of genes that we predict to have the highest likelihood of association for obesity. The approach described here can include any number and type of genome-wide experiments and might be useful for other complex polygenic disorders as well.     

Taking the Peppered Moth with a Grain of Salt

H. B. D. Kettlewell's (1955, 1956) classic field experiments on industrial melanism in polluted and unpolluted settings using the peppered moth, Biston betularia, are routinely cited as establishing that the melanic (dark) form of the moth rose in frequency downwind of industrial centers because of the cryptic advantage dark coloration provides against visual predators in soot-darkened environments. This paper critiques three common myths surrounding these investigations: (1) that Kettlewell used a model that identified crypsis as the only selective force responsible for the spread of the melanic gene, (2) that Kettlewell's field experiments alone established that selection for crypsis was the most important factor in the spread of melanic forms, and (3) that Kettlewell's investigations in an unpolluted wood near Dorset constituted a control for his earlier Birmingham studies (contra Hagen 1993, 1996). This analysis further identifies two features that distinguish manipulative experiments in evolutionary biology from experiments in other contexts. First, experiments in evolutionary biology rest on a wealth of information provided by strictly observational ecological studies; in the absence of such information experiments in evolutionary biology make no sense. Second, there is a trade-off between how much control investigators have over the conditions being studied and how informative the results of the experiment will be with regard to natural populations.     

Computational approaches toward the design of pools for the in vitro selection of complex aptamers

It is well known that using random RNA/DNA sequences for SELEX experiments will generally yield low-complexity structures. Early experimental results suggest that having a structurally diverse library, which, for instance, includes high-order junctions, may prove useful in finding new functional motifs. Here, we develop two computational methods to generate sequences that exhibit higher structural complexity and can be used to increase the overall structural diversity of initial pools for in vitro selection experiments. Random Filtering selectively increases the number of five-way junctions in RNA/DNA pools, and Genetic Filtering designs RNA/DNA pools to a specified structure distribution, whether uniform or otherwise. We show that using our computationally designed DNA pool greatly improves access to highly complex sequence structures for SELEX experiments (without losing our ability to select for common one-way and two-way junction sequences).     

Changes in the microflora of the intestine after administration of antibiotics to animals maintained conventionally

A series of experiments were performed on mice and rats subjected to total decontamination by oral administration of 3 antibiotics: gentamicin, ristomycin and nystatin. The results of experiments are summarized. It was shown that under the conventional conditions the decontamination was effective, when the intervals between the experiments were 3-5 months. When the intervals were less or the experiments were performed in the same room without intervals, the efficacy of the decontamination markedly decreased or it was ineffective. The results are discussed from the standpoints of the necessity of observing definite requirements for performance of such procedures in hospitals and laboratories.     

Response surfaces for overdispersion in the study of the conditions for fish eggs hatching

Response surface methodology, originally developed for determining optimal conditions in industrial experiments, was early adapted to experiments in marine ecology. However, these involved studying the shape of the complete response surface, not only detecting the optimum, and often had counts or durations as the response variable. Thus, nonlinear, nonnormal response models were required. For counts, binomial and beta-binomial models have been used, the latter because of substantial overdispersion. In closely controlled experiments, overdispersion among units held under the same conditions might indicate that some mishap has occurred in conducting the study. One possible check is to model the dispersion as a second response surface. This procedure is used to show that overdispersion in fish egg hatching experiments has a biological explanation in that it occurs only under suboptimal hatching conditions.     

Biodiversity–ecosystem function experiments reveal the mechanisms underlying the consequences of biodiversity change in real world ecosystems

In a recent Forum paper, Wardle (Journal of Vegetation Science, 2016) questions the value of biodiversity–ecosystem function (BEF) experiments with respect to their implications for biodiversity changes in real world communities. The main criticism is that the previous focus of BEF experiments on random species assemblages within each level of diversity has ‘limited the understanding of how natural communities respond to biodiversity loss.’ He concludes that a broader spectrum of approaches considering both non‐random gains and losses of diversity is essential to advance this field of research. Wardle's paper is timely because of recent observations of frequent local and regional biodiversity changes across ecosystems. While we appreciate that new and complementary experimental approaches are required for advancing the field, we question criticisms regarding the validity of BEF experiments. Therefore, we respond by briefly reiterating previous arguments emphasizing the reasoning behind random species composition in BEF experiments. We describe how BEF experiments have identified important mechanisms that play a role in real world ecosystems, advancing our understanding of ecosystem responses to species gains and losses. We discuss recent examples where theory derived from BEF experiments enriched our understanding of the consequences of biodiversity changes in real world ecosystems and where comprehensive analyses and integrative modelling approaches confirmed patterns found in BEF experiments. Finally, we provide some promising directions in BEF research.     

The Use of the Zebra fish,Brachydanio rerio,for the Study of Embryological Development in Schools

Courtship behaviour and mating patterns are easily observed in millipedes and experiments can be performed to demonstrate the functional significance of behaviours that have evolved through male-male competition or female choice. We describe simple methodologies and give examples of likely results together with a brief theoretical interpretation for two series of laboratory experiments. These experiments provide a useful framework for tackling the abstract concepts of sexual selection in practical classes at undergraduate level.     

Role of Bruch's membrane in the process of metaplasia of the ocular pigmented epithelium of Xenopus laevis]

The metaplasia of pigmented epithelium into retina with the formation of nuclear and reticular layers took place in the experiments with wrapping a sheet of pigmented epithelium from tadpoles up in the Bruch's membrane of adult frogs X. laevis. The implant with de novo formed retina resembled the inverted eye. In those experiments where the Bruch's membrane of tadpoles came into contact with that of adults only depigmentation of the pigmented epithelium cells was observed. The pigmented epithelium metaplasia suggests that the Bruch's membrane is permeable not only for low molecular weight substances, but also for inducing agents. The adult Bruch's membrane serves in the process of metaplasia in the experiments described as a new and limiting system which ensures more orderly formation of new retina.     

Analysis of the oligomeric structure of the motor protein prestin

Prestin, a member of the solute carrier family 26, is expressed in the basolateral membrane of outer hair cells. This protein provides the molecular basis for outer hair cell somatic electromotility, which is crucial for the frequency selectivity and sensitivity of mammalian hearing. It has long been known that there are abundantly expressed approximately 11-nM protein particles present in the basolateral membrane. These particles were hypothesized to be the motor proteins that drive electromotility. Because the calculated size of a prestin monomer is too small to form an approximately 11-nM particle, the possibility of prestin oligomerization was examined. We investigated possible quaternary structures of prestin by lithium dodecyl sulfate-PAGE, perfluoro-octanoate-PAGE, a membrane-based yeast two-hybrid system, and chemical cross-linking experiments. Prestin, obtained from different host or native cells, is resistant to dissociation by lithium dodecyl sulfate and behaves as a stable oligomer on lithium dodecyl sulfate-PAGE. In the membrane-based yeast two-hybrid system, homo-oligomeric interactions between prestin-bait/prestin-prey suggest that prestin molecules can associate with each other. Chemical cross-linking experiments, perfluoro-octanoate-PAGE/Western blot, and affinity purification experiments all indicate that prestin exists as a higher order oligomer, such as a tetramer, in prestin-expressing yeast, mammalian cell lines and native outer hair cells. Our data from experiments using hydrophobic and hydrophilic reducing reagents suggest that the prestin dimer is connected by a disulfide bond embedded in the prestin hydrophobic core. This stable dimer may act as the building block for producing the higher order oligomers that form the approximately 11-nM particles in the outer hair cell's basolateral membrane.     

Accumulation of the capacity of initiation of deoxyribonucleic acid replication in Escherichia coli.

Several temperature-sensitive initiation mutants of Escherichia coli were examined for the ability to initiate more than one round of replication after being held at nonpermissive temperature for approximately 1.5 generation equivalents. The capacity for initiation was measured by residual synthesis experiments and rate experiments under conditions where protein synthesis and ribonucleic acid synthesis were inhibited. Results of the rate and density transfer experiments suggest that the cells may initiate more than one round of replication in the absence of protein or ribonucleic acid synthesis. This contrasts with the results of the residual synthesis experiments which suggest that, under these conditions, only one round of synthesis is achieved. These findings suggest that the total amount of residual synthesis achieved in the presence of an inhibitor may be both a function of the number of initiation events which occur and the effect of the inhibitor of protein or ribonucleic acid synthesis on chain elongation.     

Population of on-pathway intermediates in the folding of ubiquitin

The role that intermediate states play in protein folding is the subject of intense investigation and in the case of ubiquitin has been controversial. We present fluorescence-detected kinetic data derived from single and double mixing stopped-flow experiments to show that the F45W mutant of ubiquitin (WT*), a well-studied single-domain protein and most recently regarded as a simple two-state system, folds via on-pathway intermediates. To account for the discrepancy we observe between equilibrium and kinetic stabilities and m-values, we show that the polypeptide chain undergoes rapid collapse to an intermediate whose presence we infer from a fast lag phase in interrupted refolding experiments. Double-jump kinetic experiments identify two direct folding phases that are not associated with slow isomerisation reactions in the unfolded state. These two phases are explained by kinetic partitioning which allows molecules to reach the native state from the collapsed state via two possible competing routes, which we further examine using two destabilised ubiquitin mutants. Interrupted refolding experiments allow us to observe the formation and decay of an intermediate along one of these pathways. A plausible model for the folding pathway of ubiquitin is presented that demonstrates that obligatory intermediates and/or chain collapse are important events in restricting the conformational search for the native state of ubiquitin.     

Identification of the composite parameters of the BBH-B model specifying the effects of biohydrologic processes on the water balance of crop fields

A model of soil hydrology incorporating rainfall interception and macropore flow, which are representative biohydorologic processes, (BBH-B model) has two composite parameters, Π and Φ. These parameters express the ratios of rainfall interception and macropore flow to gross rainfall, respectively. Their values, however, change widely with the vegetation, soil texture and wetness. The results of experiments that have been carried out for various objectives under various conditions by the present authors were reanalyzed to evaluate these two parameters. Further, two supplemental experiments were designed to identify the two parameters. In the experiments, the monthly mean of Π for a cornfield ranged from 0.18 to 0.64 in the summer months, while Φ for a weed-grown field reached a maximum of 0.8 when daily rainfall was more than 40 mm day⁻¹. From these analyses and experiments, we concluded that the effects of biohydrologic processes on the water balance of crop fields are rather large and not negligible.     

The state of the art in the analysis of two-dimensional gel electrophoresis images

Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field. An erratum to this article can be found at     

The nutrition of the carrot

In sand-culture experiments with carrots, it was shown that a moderate quantity only of nitrogen was necessary for optimum growth compared with, for example, the turnip root. A moderate amount of (available) phosphorus was also sufficient for this purpose, as with the turnip, but contrary to experience with lettuce roots and tops. The greatest concentration of potassium applied, however, was probably the best for root development. Deficiency of phosphorus caused bronzing of the leaves, and absence of potassium, serious scorch; absence of boron resulted in a small, immature plant. Initial field trials on an old river gravel during experiments throughout the last 7 years indicated that dung gave no advantage over artificials, that artificials were possibly not needed on dunged land or land in good heart, and that land out of good heart, undunged and unfertilized throughout the 7 years, responded well to artificials, particularly phosphate and potash. The incidence of carrot fly, according to preliminary experiments, seemed to depend greatly on the nutrition of the carrots.     

Interaction of telomestatin with the telomeric single-strand overhang

The extremities of chromosomes end in a G-rich single-stranded overhang that has been implicated in the onset of the replicative senescence. The repeated sequence forming a G-overhang is able to adopt a peculiar four-stranded DNA structure in vitro called a G-quadruplex, which is a poor substrate for telomerase. Small molecule ligands that selectively stabilize the telomeric G-quadruplex induce telomere shortening and a delayed growth arrest. Here we show that the G-quadruplex ligand telomestatin has a dramatic effect on the conformation of intracellular G-overhangs. Competition experiments indicate that telomestatin strongly binds in vitro and in vivo to the telomeric overhang and impairs its single-stranded conformation. Long-term treatment of cells with telomestatin greatly reduces the G-overhang size, as evidenced by specific hybridization or telomeric oligonucleotide ligation assay experiments, with a concomitant delayed loss of cell viability. In vivo protection experiments using dimethyl sulfate also indicate that telomestatin treatment alters the dimethyl sulfate effect on G-overhangs, a result compatible with the formation of a local quadruplex structure at telomeric overhang. Altogether these experiments strongly support the hypothesis that the telomeric G-overhang is an intracellular target for the action of telomestatin.     

Simple experiments to understand the ionic origins and characteristics of the ventricular cardiac action potential

Electrophysiological experiments are helpful for students to understand the role of electrical activity in heart function. Papillary muscle, which belongs to the ventricle, offers the advantage of being easily studied using glass microelectrodes. In addition, there is commercially available software that simulates ventricular electrical activity and can help overcome some difficulties, such as voltage clamp experiments, which need expensive apparatus when used for studies on living preparations. Here, we present a class practical session that is taken by undergraduate students at our University. In the first part of this class, students record action potentials from papillary muscles with the use of glass microelectrodes, and they change extracellular conditions to study the ionic basis of the action potential. In the second part of the class, students simulate action potentials using the Oxsoft Heart model (v. 4.0) and model their previous experiments on papillary muscle to quantify the effects. In particular, the model is very helpful in promoting understanding of the effect that extracellular potassium has on cardiac action potential by simulating voltage clamp experiments. This twin approach of papillary muscle experiments and computer modeling leads to a good understanding of the functioning of the action potential and can help introduce discussion of some abnormal cardiac functioning.     

Inadequacy of the Eucaryote Inhibitor Cycloheximide in Studies of Protozoan Grazing on Bacteria at the Freshwater-Sediment Interface

Four guilds from a lake sediment-water interface microbial community were isolated and tested for sensitivity to cycloheximide (0.1 to 200 mg liter⁻¹). Field experiments were conducted to compare the inhibition, dilution, and filtration methods for determining grazing rates. Cycloheximide inhibited anaerobic bacteria at 50 mg liter⁻¹, and inhibition of bacterial growth was observed in the grazing experiments. The results show that the assumption of selective inhibition of heterotrophic eucaryotes was violated and preclude the use of cycloheximide in grazing experiments.     

Characterization of the arginine repressor from Salmonella typhimurium and its interactions with the carAB operator.

Primer extension experiments showed that the argR gene, encoding the arginine repressor in Salmonella typhimurium, is transcribed from a single promoter that is negatively regulated by arginine. A repressor overproducing strain was constructed and the repressor was purified to homogeneity. Gel filtration, sedimentation and cross-linking studies established that the native repressor is a hexamer of identical 17,000 Mr subunits. Gel retardation experiments indicate that the apparent dissociation constant for repressor/carAB operator is 6 x 10(-12) M. These experiments showed that arginine is essential for binding of the repressor to the DNA and that pyrimidine nucleotides have no significant effect on this binding. These results indicate that the effect of pyrimidines on expression of the arginine sensitive "downstream" carAB promoter is not directly mediated by the arginine repressor. These experiments also suggest that a single hexamer binds to the carAB operator, which carries two previously defined "ARG box" sequences that characterize operators for arg genes. Gel retardation experiments with DNA fragments carrying the individual ARG boxes showed that both boxes are required for effective binding of the hexameric repressor to the operator, indicating that the ARG boxes comprise a single binding site for the repressor. Analysis of the potential secondary structure of the arginine repressor does not reveal any of the recognizable structural motifs common to a number of DNA-binding proteins. A combination of DNase I, premethylation interference, depurination and hydroxyl radical footprinting techniques were employed to characterize the interactions of the repressor with the carAB operator, with the results suggesting that the repressor predominantly interacts with A.T residues in this region. Comparative DNA sequence analysis of the known arginine operators of enteric bacteria further indicates that the specificity of interaction may be based more on the precise distance between two defined A.T-rich regions rather than on the specific nucleotide sequence.     

Characterization of the structure and properties of the His 62-->Ala and Arg 38-->Ala mutants of yeast phosphoglycerate kinase: an investigation of the catalytic and activatory sites by site-directed mutagenesis and NMR.

The role of two "basic patch" residues, Arg-38 and His-62, in the catalytic function and anion-dependent activation of yeast 3-phosphoglycerate kinase (PGK) was investigated by site-directed mutagenesis. Steady-state kinetics and NMR experiments were conducted to characterize the functional properties and structural integrity of the R38A and H62A mutants. The results of these studies, in combination with earlier mutagenesis experiments, suggest that Arg-38 is the only catalytically essential residue among the conserved histidines and arginines of the basic patch. It appears that, similar to the remaining basic patch residues, His-62 is important for anion-dependent activation but not for enzyme activity. Cumulative evidence from this study and from previous mutagenesis experiments suggests that the basic patch region is in effect an extended anion binding site that encompasses both the catalytic and the general anion-binding site. It is proposed that substitution of any one of the basic patch residues results in an increased localization of the catalytic site. Substrate and product may still bind to this site, but a simultaneous binding of activatory anions, required for activation, has been impaired. NMR experiments suggest that the conformational changes observed upon binding of 3-PG to wild-type PGK are necessary for anion- and substrate-dependent activation.