Multilevel Deconstruction of the In Vivo Behavior of Looped DNA-Protein Complexes

Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and their integration into the cellular function still remain largely unexplored. Here, we present a multilevel approach that efficiently connects in both directions molecular properties with cell physiology and use it to characterize the molecular properties of the looped DNA-lac repressor complex while functioning in vivo. The properties we uncover include the presence of two representative conformations of the complex, the stabilization of one conformation by DNA architectural proteins, and precise values of the underlying twisting elastic constants and bending free energies. Incorporation of all this molecular information into gene-regulation models reveals an unprecedented versatility of looped DNA-protein complexes at shaping the properties of gene expression.Comment: Open Access article available at http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.000035

Effect of the dog positioning on X-ray table on hip dysplasia parameter evaluation

Research Areas: Veterinary Sciences; ZoologyABSTRACT - Objective The aim of this study was to evaluate the effect of pelvic tilting along the long axis and femoral rotation on Norberg angle (NA), subluxation index (SI) and subluxation category (SC) in the standard ventrodorsal hip extended (VDHE) radiographical view on live animals. Study Type This was a retrospective clinical study. Materials and Methods Pairs of VDHE views, one adequately positioned and the other with pelvic tilting or femoral internal or external rotation, were compared for the NA, SI and SC. Results On the malpositioned pelvis set, on the underside the mean +/- SD NA was 98.7 +/- 6.1 degrees, the SI was 0.27 +/- 0.12 and the SC was 2.8 +/- 0.8 versus, on the acceptable set, the NA was 99.2 +/- 6.4 degrees ( p > 0.05), the SI was 0.25 +/- 0.12 ( p 0.05). Conclusions In clinical practice, pelvic tilting along the long axis in VDHE view results in non-favourable hip changes in the NA, SI and SC on the underside and favourable on the upperside, and the internal or external femoral rotation did not affect these variables.info:eu-repo/semantics/publishedVersio

Taken by strum: ukuleles and participatory music-making in Hamilton, Aotearoa/New Zealand

Ethnographic study of ukulele playing in Hamilton, N

Effect of Carvacrol on Salmonella Saintpaul Biofilms on Stainless Steel Surface

Purpose: To evaluate the effect of carvacrol against Salmonella Saintpaul biofilms on stainless steel surface.Methods: The effects of carvacrol on planktonic cells were evaluated by determining the minimum inhibitory concentration and minimal bactericidal concentration. The action of carvacrol on Salmonella Saintpaul biofilms on stainless steel surface was evaluated on established biofilm and on biofilm formation by counting the number of bacterial cells that adhered to the surface using scanning electron microscopy.Results: The antimicrobial activity of carvacrol in planktonic cells of Salmonella Saintpaul was observed. The highest inhibitory effect of carvacrol was observed on biofilm formation at different subinhibitory concentrations.Conclusion: Carvacrol reduced the number of bacterial cells that adhered to stainless steel surface, making it a potential compound for Salmonella Saintpaul control.Keywords: Salmonella spp, Biofilm, Planktonic cells, Carvacrol, Stainless stee

Stereotyping starlings are more 'pessimistic'.

Negative affect in humans and animals is known to cause individuals to interpret ambiguous stimuli pessimistically, a phenomenon termed 'cognitive bias'. Here, we used captive European starlings (Sturnus vulgaris) to test the hypothesis that a reduction in environmental conditions, from enriched to non-enriched cages, would engender negative affect, and hence 'pessimistic' biases. We also explored whether individual differences in stereotypic behaviour (repetitive somersaulting) predicted 'pessimism'. Eight birds were trained on a novel conditional discrimination task with differential rewards, in which background shade (light or dark) determined which of two covered dishes contained a food reward. The reward was small when the background was light, but large when the background was dark. We then presented background shades intermediate between those trained to assess the birds' bias to choose the dish associated with the smaller food reward (a 'pessimistic' judgement) when the discriminative stimulus was ambiguous. Contrary to predictions, changes in the level of cage enrichment had no effect on 'pessimism'. However, changes in the latency to choose and probability of expressing a choice suggested that birds learnt rapidly that trials with ambiguous stimuli were unreinforced. Individual differences in performance of stereotypies did predict 'pessimism'. Specifically, birds that somersaulted were more likely to choose the dish associated with the smaller food reward in the presence of the most ambiguous discriminative stimulus. We propose that somersaulting is part of a wider suite of behavioural traits indicative of a stress response to captive conditions that is symptomatic of a negative affective state

Autobiographical memory and hierarchical search strategies in depressed and non-depressed participants

Background: There is a growing body of literature showing individuals with depression and other trauma-related disorders (e.g., posttraumatic stress disorder) recall more overgeneral and less specific autobiographical memories compared to normal participants. Although the mechanisms underlying overgeneral memory are quite clear, the search strategy operated within the autobiographical knowledge base, at time of recollection, requires further exploration. The current study aimed to examine the hierarchical search sequence used to recall autobiographical memories in depressed and non-depressed participants, with a view to determining whether depressed participants exhibited truncated search strategies. Methods: Thirteen depressed and an equal number of non-depressed participants retrieved 15 memories each, in response to 15 commonly used cue words. Participants reported the first memory that entered in their mind. All memory descriptions were recorded and later transcribed verbatim for content analysis.Results: Depressed participants retrieved autobiographical memories faster, produced shorter memory descriptions and were less likely to recall positive memories than non-depressed participants. Non-depressed participants were more likely to commence retrieval by accessing lifetime period knowledge followed by general event and event specific knowledge, whereas depressed participants showed a tendency to terminate retrieval at the general event level. Conclusions: It is concluded that depressed participants do adhere to the same hierarchical search strategy as non-depressed participants when retrieving specific autobiographical memories, but that they terminate their search early, resulting in overgeneral memories

Synthesis of (±)-3,4-dimethoxybenzyl- 4-methyloctanoate as a novel internal standard for capsinoid determination by HPLC-ESI-MS/MS(QTOF)

Capsinoids exhibit health-promoting properties and are therefore compounds of interest for medical and food sciences. They are minor compounds present in relatively high concentrations in only a few number of pepper cultivars. It is desirable to quantify capsinoids to provide selected cultivars with high capsinoid contents, which can then be employed as health food product. Quantifying low concentrations of capsinoids from pepper fruit requires a precise and selective analytical technique such as HPLC coupled to electrospray ionization - mass spectrometry, with development of an internal standard essential. In this work, the synthesis method of a novel compound analogue of capsinoids, the (±)-3,4-dimethoxybenzyl-4-methyloctanoate, which could be a suitable internal standard for capsinoid determination by electrospray ionization - mass spectrometry is described. (±)-3,4-dimethoxybenzyl-4-methyloctanoate was stable under the analysis conditions and exerted chemical and physical properties similar to those of capsinoids. This internal standard will provide an accurate capsinoid determination by electrospray ionization - mass spectrometry, thus facilitating the pepper breeding programs, screening pepper cultivars and a better understanding of capsinoid biosynthetic pathway

Efficient public-key cryptography with bounded leakage and tamper resilience

We revisit the question of constructing public-key encryption and signature schemes with security in the presence of bounded leakage and tampering memory attacks. For signatures we obtain the first construction in the standard model; for public-key encryption we obtain the first construction free of pairing (avoiding non-interactive zero-knowledge proofs). Our constructions are based on generic building blocks, and, as we show, also admit efficient instantiations under fairly standard number-theoretic assumptions. The model of bounded tamper resistance was recently put forward by Damgård et al. (Asiacrypt 2013) as an attractive path to achieve security against arbitrary memory tampering attacks without making hardware assumptions (such as the existence of a protected self-destruct or key-update mechanism), the only restriction being on the number of allowed tampering attempts (which is a parameter of the scheme). This allows to circumvent known impossibility results for unrestricted tampering (Gennaro et al., TCC 2010), while still being able to capture realistic tampering attack

Fast and flexible selection with a single switch

Selection methods that require only a single-switch input, such as a button click or blink, are potentially useful for individuals with motor impairments, mobile technology users, and individuals wishing to transmit information securely. We present a single-switch selection method, "Nomon," that is general and efficient. Existing single-switch selection methods require selectable options to be arranged in ways that limit potential applications. By contrast, traditional operating systems, web browsers, and free-form applications (such as drawing) place options at arbitrary points on the screen. Nomon, however, has the flexibility to select any point on a screen. Nomon adapts automatically to an individual's clicking ability; it allows a person who clicks precisely to make a selection quickly and allows a person who clicks imprecisely more time to make a selection without error. Nomon reaps gains in information rate by allowing the specification of beliefs (priors) about option selection probabilities and by avoiding tree-based selection schemes in favor of direct (posterior) inference. We have developed both a Nomon-based writing application and a drawing application. To evaluate Nomon's performance, we compared the writing application with a popular existing method for single-switch writing (row-column scanning). Novice users wrote 35% faster with the Nomon interface than with the scanning interface. An experienced user (author TB, with > 10 hours practice) wrote at speeds of 9.3 words per minute with Nomon, using 1.2 clicks per character and making no errors in the final text.Comment: 14 pages, 5 figures, 1 table, presented at NIPS 2009 Mini-symposi