The mechanism of the Einstellung (set) effect: A pervasive source of cognitive bias

Copyright @ The Authors 2010The eye movements of expert players trying to solve a chess problem show that the first idea that comes to mind directs attention towards sources of information consistent with itself and away from inconsistent information. This bias continues unconsciously even when the player believes he is looking for alternatives. The result is that alternatives to the first idea are ignored. This mechanism for biasing attention ensures a speedy response in familiar situations but it can lead to errors when the first thought that comes to mind is not appropriate. We propose that this mechanism is the source of many cognitive biases from phenomena in problem solving and reasoning, to perceptual errors and failures in memory

A comparison of high-throughput techniques for assaying circadian rhythms in plants

Over the last two decades, the development of high-throughput techniques has enabled us to probe the plant circadian clock, a key coordinator of vital biological processes, in ways previously impossible. With the circadian clock increasingly implicated in key fitness and signalling pathways, this has opened up new avenues for understanding plant development and signalling. Our tool-kit has been constantly improving through continual development and novel techniques that increase throughput, reduce costs and allow higher resolution on the cellular and subcellular levels. With circadian assays becoming more accessible and relevant than ever to researchers, in this paper we offer a review of the techniques currently available before considering the horizons in circadian investigation at ever higher throughputs and resolutions

A Novel Genome-Wide Association Study Approach Using Genotyping by Exome Sequencing Leads to the Identification of a Primary Open Angle Glaucoma Associated Inversion Disrupting ADAMTS17

Closed breeding populations in the dog in conjunction with advances in gene mapping and sequencing techniques facilitate mapping of autosomal recessive diseases and identification of novel disease-causing variants, often using unorthodox experimental designs. In our investigation we demonstrate successful mapping of the locus for primary open angle glaucoma in the Petit Basset Griffon Vendéen dog breed with 12 cases and 12 controls, using a novel genotyping by exome sequencing approach. The resulting genome-wide association signal was followed up by genome sequencing of an individual case, leading to the identification of an inversion with a breakpoint disrupting the ADAMTS17 gene. Genotyping of additional controls and expression analysis provide strong evidence that the inversion is disease causing. Evidence of cryptic splicing resulting in novel exon transcription as a consequence of the inversion in ADAMTS17 is identified through RNAseq experiments. This investigation demonstrates how a novel genotyping by exome sequencing approach can be used to map an autosomal recessive disorder in the dog, with the use of genome sequencing to facilitate identification of a disease-associated variant

Effect of Sun and Planet-Bound Dark Matter on Planet and Satellite Dynamics in the Solar System

We apply our recent results on orbital dynamics around a mass-varying central body to the phenomenon of accretion of Dark Matter-assumed not self-annihilating-on the Sun and the major bodies of the solar system due to its motion throughout the Milky Way halo. We inspect its consequences on the orbits of the planets and their satellites over timescales of the order of the age of the solar system. It turns out that a solar Dark Matter accretion rate of \approx 10^-12 yr^-1, inferred from the upper limit \Delta M/M= 0.02-0.05 on the Sun's Dark Matter content, assumed somehow accumulated during last 4.5 Gyr, would have displaced the planets faraway by about 10^-2-10^1 au 4.5 Gyr ago. Another consequence is that the semimajor axis of the Earth's orbit, approximately equal to the Astronomical Unit, would undergo a secular increase of 0.02-0.05 m yr^-1, in agreement with the latest observational determinations of the Astronomical Unit secular increase of 0.07 +/- 0.02 m yr^-1 and 0.05 m yr^-1. By assuming that the Sun will continue to accrete Dark Matter in the next billions year at the same rate as in the past, the orbits of its planets will shrink by about 10^-1-10^1 au (\approx 0.2-0.5 au for the Earth), with consequences for their fate, especially of the inner planets. On the other hand, lunar and planetary ephemerides set upper bounds on the secular variation of the Sun's gravitational parameter GM which are one one order of magnitude smaller than 10^-12 yr^-1. Dark Matter accretion on planets has, instead, less relevant consequences for their satellites. Indeed, 4.5 Gyr ago their orbits would have been just 10^-2-10^1 km wider than now. (Abridged)Comment: LaTex2e, 17 pages, no figures, 7 tables, 61 references. Small problem with a reference fixed. To appear in Journal of Cosmology and Astroparticle Physics (JCAP

Aquaporins in Saccharomyces: Genetic and functional distinctions between laboratory and wild-type strains

Aquaporin water channel proteins mediate the transport of water across cell membranes in numerous species. The Saccharomyces genome data base contains an open reading frame (here designated AQY1) that encodes a protein with strong homology to aquaporins. AQY1 from laboratory and wild-type strains of Saccharomyces were expressed in Xenopus oocytes to determine the coefficients of osmotic water permeability (Pf). Oocytes injected with wild-type AQY1 cRNAs exhibit high Pf values, whereas oocytes injected with AQY1 cRNAs from laboratory strains exhibit low Pf values and have reduced levels of Aqy1p due to two amino acid substitutions. When the AQY1 gene was deleted from a wild-type yeast and cells were cultured in vitro with cycled hypo-osmolar or hyper-osmolar stresses, the AQY1 null yeast showed significantly improved viability when compared with the parental wild-type strain. We conclude that Saccharomyces cerevisiae contains at least one aquaporin gene, but it is not functional in laboratory strains due to apparent negative selection pressures resulting from in vitro methods

Finding Needles in Haystacks: The Use of Quantitative Proteomics for the Early Detection of Colorectal Cancer

Colorectal cancer (CRC) is a common and treatable disease if diagnosed early. Current population screening programs are suboptimal, and consequently, there is a need for the development of new methodologies for early diagnosis of CRC. In the past 10 years, unprecedented technological advancements in the field of mass spectrometry (MS)-based proteomics have progressively increased the sophistication and utility of these investigations, leading to the draft mapping of the human proteome. These exciting studies have shaped our mechanistic understanding of the human genome and begun to provide us with a suite of novel biomarkers to predict the onset, progression and severity of many debilitating diseases. Thus, sophisticated MS workflows coupled with revolutionary protein quantification techniques hold promise for the field of MS-based plasma proteomics, particularly valuable in the context of early stage identification of curable CRC. However, within the last 40 years, no new plasma protein biomarkers of CRC have been translated into clinical practice. Here. we discuss the application of proteomic technologies within the field of CRC, highlighting contemporary MS-based plasma proteomic strategies that could be exploited to deliver on the promise of a panel of sensitive and specific plasma-based biomarkers with which to non-invasively detect early stage CRC

HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 Is Required for Circadian Periodicity through the Promotion of Nucleo-Cytoplasmic mRNA Export in Arabidopsis.

notes: PMCID: PMC3875725This is an open access article that is freely available in ORE or from the publisher's web site. Please cite the published version. © 2013 American Society of Plant Biologists. All rights reserved.Cold acclimation has been shown to be attenuated by the degradation of the INDUCER OF CBF EXPRESSION1 protein by the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1). However, recent work has suggested that HOS1 may have a wider range of roles in plants than previously appreciated. Here, we show that hos1 mutants are affected in circadian clock function, exhibiting a long-period phenotype in a wide range of temperature and light environments. We demonstrate that hos1 mutants accumulate polyadenylated mRNA in the nucleus and that the circadian defect in hos1 is shared by multiple mutants with aberrant mRNA export, but not in a mutant attenuated in nucleo-cytoplasmic transport of microRNAs. As revealed by RNA sequencing, hos1 exhibits gross changes to the transcriptome with genes in multiple functional categories being affected. In addition, we show that hos1 and other previously described mutants with altered mRNA export affect cold signaling in a similar manner. Our data support a model in which altered mRNA export is important for the manifestation of hos1 circadian clock defects and suggest that HOS1 may indirectly affect cold signaling through disruption of the circadian clock.Biotechnology and Biological Science Research Counci

Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis

Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of sequencing a backcrossed line in limiting the number of SNPs considered. We identify a SNP in the gene AtNFXL-2 as the likely cause of the ebi-1 phenotype