Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression

Numerous transcription factors (TFs) encode information about upstream signals in the dynamics of their activation, but how downstream genes decode these dynamics remains poorly understood. Using microfluidics to control the nucleocytoplasmic translocation dynamics of the budding yeast TF Msn2, we elucidate the principles that govern how different promoters convert dynamical Msn2 input into gene expression output in single cells. Combining modeling and experiments, we classify promoters according to their signal-processing behavior and reveal that multiple, distinct gene expression programs can be encoded in the dynamics of Msn2. We show that both oscillatory TF dynamics and slow promoter kinetics lead to higher noise in gene expression. Furthermore, we show that the promoter activation timescale is related to nucleosome remodeling. Our findings imply a fundamental trade-off: although the cell can exploit different promoter classes to differentially control gene expression using TF dynamics, gene expression noise fundamentally limits how much information can be encoded in the dynamics of a single TF and reliably decoded by promoters

Concept Maps in the Family Science Classroom

This presentation will illustrate the usefulness and variability of concept maps in family science classrooms. This poster will define concept maps, demonstrate examples of effective use of concept maps in teaching family science, and delineate scholarly-based information on how to maximize their effectiveness. It also will illustrate the importance of student involvement in constructing and using this visual aid

Shape and Interaction Decoupling for Colloidal Pre-Assembly

Creating materials with a structural hierarchy that is independently controllable at a range of scales requires breaking naturally occurring hierarchies. Breaking natural hierarchies is possible if building block attributes can be decoupled from the structure of pre-assembled, mesoscale building blocks that form the next level in the structural hierarchy. Here, we show that pre-assembled colloidal structures achieving geometric and interaction decoupling can be prepared in emulsions of silica superballs, which are cubic-like particles with rounded edges. We show that, for clusters of up to nine particles, colloidal superballs pack consistently like spheres, despite the presence of shape anisotropy and facets in the cubic-like particles. We compare our results with clusters prepared with magnetic superballs and find good qualitative agreement, suggesting that the cluster geometries are solely determined by the shape of the constituent particles. Our findings demonstrate that highly shape-anisotropic building blocks, under suitable conditions, can be pre-assembled into structures that are not found in bulk, thereby achieving a decoupling that can be further exploited for hierarchical materials development.Comment: 22 pages, 7 figure

Clusters of polyhedra in spherical confinement

What is the best way to pack objects into a container? This simple question, one that is relevant to everyday life, biology, and nanoscience, is easy to state but surprisingly difficult to answer. Here, we use computational methods to determine dense packings of a set of polyhedra inside a sphere, for up to 60 constituent packers. Our dense packings display a wide variety of symmetries and structures, and indicate that the presence of the spherical container suppresses packing effects due to polyhedral shape. Our results have implications for a range of biological phenomena and experimental applications, including blood clotting, cell aggregation, drug delivery, colloidal engineering, and the creation of metamaterials

Hur stor behöver en ettårig öring eller lax vara? : förslag till en strategi för att sortera ut ensomrig fisk på hösten som blir smolt till våren

Ett av de svåraste momenten inom kompensationsodling av lax och havsöring är att bedöma om fisken är tillräckligt stor för att utvecklas till ettårig smolt. Syftet med detta projekt var att testa en sorteringsstrategi för att förenkla denna bedömning för odlingspersonalen. Strategin gick ut på att ensomrig lax och öring på hösten delades upp i olika storleksklasser och under den kommande våren undersöktes deras prestanda som ettårig smolt i vandringsbassänger och i en bäck. På sensommaren eller hösten året innan odlad fisk ska vandra ut i havet startar den fysiologiska utvecklingen till smolt om fisken nått en viss kritisk storlek. Den exakta tidpunkten för när storleken ska ha uppnåtts är dock oklar vilket gör det svårt för personal på odlingarna att veta när fisken ska sorteras. Resultatet från detta projektvisade att en lax som är minst 10 cm lång i november med hög sannolikhet kommer att bli smolt till våren. Dessa laxar uppträdde i de flesta avseenden som en vandringsfärdig smolt följande vår och betedde sig mycket likt den tvååriga laxsmolten. Dock förekom det en storleksrelaterad predationsrisk i bäcken efter utsättning där ettårig lax drabbades i större utsträckning än tvåårig lax. Vi föreslår en strategi där laxen sorteras i tre storleksklasser i månadsskiftet augusti-september. Om någon av de tre storleksklasserna i medeltal ligger nära 10 cm i november föreslås en andra sortering för att plocka ut fisk större än 10 cm. All fisk mindre än 10 cm bör hållas kvar i odlingen och sättas ut som tvåårig smolt. För ettårig öring var resultaten mer komplexa. I vandringsbassängerna uppvisade fisk i storleksintervallet 10–16 cm ett beteende som indikerade att de var vandringsfärdiga smolt. Efter utsättningen i bäcken vandrade de dock mycket långsamt och predationen från i första hand skrattmås och fiskmås var hög, speciellt för de minsta öringarna. Jämfört med tvåårig öring var det få ettåriga individer som klarade att lämna bäcken efter utsättning. Om detta berodde på att de inte utvecklats till smolt eller om deras vandring i bäcken påverkades av predationsrisken i bäcken är oklart. Mer data behövs för att förstå den storleksrelaterade tröskeleffekten hos ettårig öring innan förslag på sorteringsrutiner kan ges. Vi föreslår att utsättningen av speciellt öring men också lax bör ske i en miljö med stort vattendjup och högt flöde för att minimera predationsrisken från i första hand fåglar

COSMO Wave 1 Initial Findings: Mental Health and Wellbeing

Over 2 in 5 (44%) 16/17 year olds in England report elevated psychological distress, 9%pts higher than the 35% reporting distress at age 17-18 in the Our Future cohort study (2017) and 21%pts higher than the 23% at age 16-17 in the Next Steps cohort study (2007). Higher proportions of elevated psychological distress were seen among those who reported having long COVID, bad/’severe long COVID’, or who had to shield during the pandemic. For instance, 66% of those with severe long COVID, which largely affected ability to carry out daily activities, reported high psychological distress. Those who experienced major life events during the pandemic, such as being seriously ill and suffering from food affordability issues, were also more likely to report elevated psychological distress. There are stark patterns in signs of poor mental health by gender: Those who identify as female report elevated psychological distress (54%), self-harm (23%) and suicide attempts (11%), compared to those who identify as male (33% report distress, 11% report self-harm and 5% report attempting suicide). Those who identify as ‘non-binary+’ report high psychological distress (69%) and they are considerably more likely to have self- harmed (61%) or to have attempted suicide (35%) than their peers who identify as male or female. Over 2 in 5 (44%) young people with a parent who has high psychological distress also report high distress, compared to 30% of those with a parent who does not report high distress. Half of the pupils from comprehensive or grammar schools rated their school’s mental health support as ‘not very good’ or ‘not at all good’ compared to just a quarter of those attending independent schools. Half of young people said that they are now less motivated to study and learn as a result of the pandemic, with those who reported high psychological distress 31%pts more likely to say so (68% compared to 37% of other participants)

COSMO Wave 1 Initial Findings: Lockdown Learning

There were substantial gaps between state and private secondary schools in the intensity of remote learning during the first lockdown in 2020, with the private sector much better placed to adapt quickly. 96% of independent school pupils had live online lessons in the first lockdown, compared to 65% of state school pupils. While state sector provision improved in the second period of school closures in early 2021, inequalities opened up within the state sector. Grammar schools (96%) and comprehensive schools with more affluent intakes (95%) caught up the most, compared to 80% at schools with the most deprived intakes. Barriers to remote learning – such as lack of access to a suitable device for learning or sharing a device, lack of a quiet space in the home, lack of support from teachers or parents – were all more likely to be experienced by young people from lower socio-economic backgrounds, and those who experienced those barriers reported working fewer hours during lockdowns. Those without a device worked on average 8 hours per week in lockdown 1, those with just a mobile phone 10 hours, and those with a laptop or tablet 14 hours. While many pupils without suitable devices received support through school and government distribution programmes, over half (53%) of those who lacked a device at the beginning of the pandemic had still not received one by the end of the second period of school closures. Problems with internet access showed a different pattern, complicated by the fact that more intensive online learning was associated with more internet problems. Having internet issues was not associated with working fewer hours. Patterns by ethnicity and race were mixed. Overall there were few differences in the amount of time spent learning by ethnic background. While young people from Black and Asian backgrounds were more likely to receive tutoring and had parents more confident with support for learning, they were also more likely to need to share devices and less likely to have a quiet place to study

Briefing No. 7 - Attainment and Assessment

Pupils from independent schools were much more likely to report that their Teacher Assessed Grades (TAGs) were higher than they expected (43%) than those in state schools (34% for those in state grammars and 29% in state comprehensives). They were also much less likely to report that they were lower than they expected (at 7%, compared to 15% of those in state grammars and 23% in state comprehensives). A third of young people reported that they felt that teachers were biased against certain groups in their teacher assessment. This figure was higher among those from ethnic minority backgrounds and lower among those with more socio-economically advantaged backgrounds. Pupils who had particularly disrupted experiences during the COVID-19 pandemic received lower GCSE Teacher Assessed Grades (TAGs) than their peers whose disruption was more moderate. One-to-one or small group tutoring as catch-up provision was most likely to be offered to those from less advantaged backgrounds and those who had lower prior attainment. Boys were more likely to be offered tutoring but, as they were less likely to take it up, there was no gender difference in reported receipt of tutoring. Those who received one-to-one and small group tutoring appeared to perform slightly better in their GCSE TAGs than their peers who were offered this tutoring but did not take it up. However, only just over a quarter of the sample reported that they have received one-to-one or small group tutoring, meaning it is unlikely to have made a big difference to learning lost at the cohort level