Induced drift by a self-propelled swimmer at intermediate Reynolds numbers

Swimming organisms have been proposed to contribute to the mixing of stratified water in the ocean, thereby facilitating the vertical transport of nutrients and dissolved gases. In general, mixing results from increasing the interface available for molecular diffusion between neighboring fluid volumes. At high Reynolds numbers (Re), swimmers generate such interfaces through their turbulent wake structures. At lower Re, however, turbulent mixing becomes ineffective as viscous effects dissipate small-scale fluid motions as heat, and diffusion is not significantly enhanced. In this regime, it appears that the dominant mechanism for mixing by a swimmer is induced drift, i.e., the propagation and stretching of a fluid volume by a moving body's pressure field, which increases the diffusion-enabling interface between the drift volume and surrounding fluid. The ratio of drift volume to body volume is called the “added-mass” coefficient and depends on the shape of the body. Importantly, previous computational analysis suggested that the total drift volume increases at low and intermediate Re, 3 implying that in contrast to turbulent mixing, mixing through induced drift becomes more efficient in viscous conditions. As pointed out by others, the limitation of previous numerical simulations, however, is that the simulated objects were towed through viscous fluid, which is dynamically distinct from a self-propelled swimmer. Using qualitative flow visualization, we here demonstrate the presence of induced drift in self-propelled swimmers operating at intermediate Re (1–100). In these experiments, the spatiotemporal pattern of a fluid volume initially surrounding a juvenile Moon jellyfish ( Aurelia aurita) is visualized using Fluorescein dye (see Fig. 1 ). For details on the experimental methods see supplemental material in Ref. 13

Targeted Manipulation of Abundant and Rare Taxa in the Daphnia magna Microbiota with Antibiotics Impacts Host Fitness Differentially

Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community members. Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism Daphnia magna to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare or abundant members across two temperatures and then measured key host life history metrics and shifts in microbial community composition. We find that removal of abundant taxa had greater impacts on host fitness than did removal of rare taxa and that the abundances of nontarget taxa were impacted by antibiotic treatment, suggesting that no rare keystone taxa exist in the Daphnia magna microbiota but that microbe-microbe interactions may play a role in host fitness. We also find that microbial community composition was impacted by antibiotics differently across temperatures, indicating that ecological context shapes within-host microbial responses and effects on host fitness

Functional Expression of an Orchid Fragrance Gene in Lactococcus lactis

Vanda Mimi Palmer (VMP), an orchid hybrid of Vanda tesselata and Vanda Tan Chay Yan is a highly scented tropical orchid which blooms all year round. Previous studies revealed that VMP produces a variety of isoprenoid volatiles during daylight. Isoprenoids are well known to contribute significantly to the scent of most fragrant plants. They are a large group of secondary metabolites which may possess valuable characteristics such as flavor, fragrance and toxicity and are produced via two pathways, the mevalonate (MVA) pathway or/and the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. In this study, a sesquiterpene synthase gene denoted VMPSTS, previously isolated from a floral cDNA library of VMP was cloned and expressed in Lactococcus lactis to characterize the functionality of the protein. L. lactis, a food grade bacterium which utilizes the mevalonate pathway for isoprenoid production was found to be a suitable host for the characterization of plant terpene synthases. Through recombinant expression of VMPSTS, it was revealed that VMPSTS produced multiple sesquiterpenes and germacrene D dominates its profile

Robust Dropping Criteria for F-norm Minimization Based Sparse Approximate Inverse Preconditioning

Dropping tolerance criteria play a central role in Sparse Approximate Inverse preconditioning. Such criteria have received, however, little attention and have been treated heuristically in the following manner: If the size of an entry is below some empirically small positive quantity, then it is set to zero. The meaning of "small" is vague and has not been considered rigorously. It has not been clear how dropping tolerances affect the quality and effectiveness of a preconditioner $M$. In this paper, we focus on the adaptive Power Sparse Approximate Inverse algorithm and establish a mathematical theory on robust selection criteria for dropping tolerances. Using the theory, we derive an adaptive dropping criterion that is used to drop entries of small magnitude dynamically during the setup process of $M$. The proposed criterion enables us to make $M$ both as sparse as possible as well as to be of comparable quality to the potentially denser matrix which is obtained without dropping. As a byproduct, the theory applies to static F-norm minimization based preconditioning procedures, and a similar dropping criterion is given that can be used to sparsify a matrix after it has been computed by a static sparse approximate inverse procedure. In contrast to the adaptive procedure, dropping in the static procedure does not reduce the setup time of the matrix but makes the application of the sparser $M$ for Krylov iterations cheaper. Numerical experiments reported confirm the theory and illustrate the robustness and effectiveness of the dropping criteria.Comment: 27 pages, 2 figure

ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions

Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70. The binding patterns of both Crp and σ70 are indicative of RNAP holoenzyme DNA footprinting profiles associated with stages during transcription initiation that occur post-recruitment. This is marked by a pronounced advancement of the template strand footprint profile to the +20 position relative to the transcription start site and a multimodal distribution on the nontemplate strand. This trend was also observed in the familial transcription factor, Fnr, but full protection of the motif was seen in the repressor ArcA. Given the time-scale of ChIP studies and that the rate-limiting step in transcription initiation is typically post recruitment, we propose a hypothesis where Crp is absent from the DNA motif but remains associated with RNAP holoenzyme post-recruitment during transcription initiation. The release of Crp from the DNA motif may be a result of energetic changes that occur as RNAP holoenzyme traverses the various stable intermediates towards elongation complex formation

"Suurin osa elämästä on menny siihen, että mun täytyis olla toisenlainen": Herkkyyden kokemuksia nyky-yhteiskunnassa

Artikkelissa tarkastellaan inhimillisten toimintamahdollisuuksien ilmenemistä yksilöllisissä herkkyyden kokemuksissa. Kulttuurinen konteksti on yhteydessä siihen, kuinka ihminen kokee itsensä yhteiskunnassa ja maailmassa. Tutkimuksen teoreettisena viitekehyksenä on filosofi Martha Nussbaumin toimintamahdollisuuksien lähestymistapa (capabilities approach), jossa toiminnan mahdollisuudet nähdään toimijuutta edistävinä etappeina kohti inhimillistä hyvinvointia. Kysymme, 1) millä tavoin herkkyyttä kuvaillaan kokemuksellisena ilmiönä ja 2) miten herkkyyden koetaan vaikuttaneen omiin toimintamahdollisuuksiin. Analysoitava aineistokokonaisuus koostui kirjoitetuista muistoista sekä muisteluryhmän tallennetuista ja litteroiduista ryhmäkeskusteluista. Aineistot analysoitiin sisällönanalyysin avulla. Tulosten perusteella herkkyys voi olla kokijalleen yhtäältä suuri elämän rikkaus ja voimavara, toisaalta tukahduttava kuormituksen ja jopa häpeän lähde. Yksilöllinen kokemusmaailma saattaa ajautua ristiriitaan ympäröivien sosiaalisten, kulttuuristen ja yhteiskunnallisten odotusten sekä vaatimusten kanssa ja johtaa toimijuutta ja hyvinvointia lamaavaan toimintamahdollisuuksien kaventumiseen. Tulokset avaavat näkymiä herkkyyden asemoitumiseen vallitsevissa yhteiskunnallisissa normikäsityksissä ja arvostuksissa sekä siihen, kuinka yksilölliseen herkkyyteen kytkeytyviä toimintavalmiuksia voidaan tukea.© 2023 Kirjoittajat. Tämä työ on lisensoitu Creative Commons Nimeä 4.0 Kansainvälinen Julkinen -lisenssillä.fi=vertaisarvioitu|en=peerReviewed

A Test of Multisession Automatic Action Tendency Retraining to Reduce Alcohol Consumption Among Young Adults in the Context of a Human Laboratory Paradigm.

BACKGROUND: Young adult heavy drinking is an important public health concern. Current interventions have efficacy but with only modest effects, and thus, novel interventions are needed. In prior studies, heavy drinkers, including young adults, have demonstrated stronger automatically triggered approach tendencies to alcohol-related stimuli than lighter drinkers. Automatic action tendency retraining has been developed to correct this tendency and consequently reduce alcohol consumption. This study is the first to test multiple iterations of automatic action tendency retraining, followed by laboratory alcohol self-administration. METHODS: A total of 72 nontreatment-seeking, heavy drinking young adults ages 21 to 25 were randomized to automatic action tendency retraining or a control condition (i.e., sham training ). Of these, 69 (54% male) completed 4 iterations of retraining or the control condition over 5 days with an alcohol drinking session on Day 5. Self-administration was conducted according to a human laboratory paradigm designed to model individual differences in impaired control (i.e., difficulty adhering to limits on alcohol consumption). RESULTS: Automatic action tendency retraining was not associated with greater reduction in alcohol approach tendency or less alcohol self-administration than the control condition. The laboratory paradigm was probably sufficiently sensitive to detect an effect of an experimental manipulation given the range of self-administration behavior observed, both in terms of number of alcoholic and nonalcoholic drinks and measures of drinking topography. CONCLUSIONS: Automatic action tendency retraining was ineffective among heavy drinking young adults without motivation to change their drinking. Details of the retraining procedure may have contributed to the lack of a significant effect. Despite null primary findings, the impaired control laboratory paradigm is a valid laboratory-based measure of young adult alcohol consumption that provides the opportunity to observe drinking topography and self-administration of nonalcoholic beverages (i.e., protective behavioral strategies directly related to alcohol use)