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

Variation in Food Prices and SNAP Adequacy for Purchasing the Thrifty Food Plan

Whether Supplemental Nutrition Assistance Program (SNAP) benefits are adequate to provide food security for eligible households is an important and timely policy question. While the nominal value of SNAP benefits is fixed across states (except for Hawaii and Alaska), variation in food prices across geographic areas is dramatic, and the real value of SNAP benefits varies widely across the U.S. Our research provides new evidence on geographic variation in the adequacy of SNAP benefits to purchase the Thrifty Food Plan (TFP). Using multiple methods to estimate the cost of the Thrifty Food Plan (TFP) faced by households across the nation, and several measures of the SNAP benefits available to them, we consistently find that a substantial fraction of SNAP-recipient households receive benefits that are insufficient to purchase the TFP. Our primary estimates indicate that SNAP benefits (plus 30 percent of income) are insufficient for approximately 20-30 percent of households to purchase the TFP. Sufficiency rates increase monotonically as we expand the distance within which the household is assumed to be able to shop. For households who are unable to afford the TFP, average dollar shortfalls between the cost of the TFP and SNAP benefits (plus 30 percent of income) are often as large as $150 per month. When shoppers are assumed to be able to purchase the TFP at the minimum-cost store in the area, SNAP benefits are sufficient for over 90 percent of households. However, this assumption seems unlikely to hold for many SNAP households

Trace Mineral Clearance from Plasma and Liver Following Injection is Affected by Cattle Breed

Trace mineral supplementation during times of stress and critical production periods may prove beneficial to overall animal health and performance. A decrease in trace mineral status may negatively impact reproduction, immunity, and general performance of the animal. Little research is available inquiring into breed differences on trace mineral status and clearance. This study concluded that Multimin®90 appeared to be an effective way to improve the trace mineral status, specifically of liver copper (Cu) and selenium (Se), of Angus and Simmental calves when compared to controls receiving sterilized saline

Effects of Original XPC on Newly Weaned Beef Steer Nutrient Digestibility and Response to a Vaccination Challenge

The study was designed to determine the effects of Diamond V Original XPC, a yeast fermentation product, in the diets of newly weaned beef steers on nutrient digestibility and response to a vaccination challenge. Although no overall performance benefit was noted, XPC improved total tract CP digestibility. Steers fed XPC at 14 g/d exhibited lesser concentrations of APP, greater DMI, and more efficient rumination post-vaccination. Further research is needed to determine the optimal supplementation rate of XPC to newly received beef cattle

How do Norwegian second-grade teachers use guided reading? The quantity and quality of practices

This paper documents how teachers use guided reading practices in Norwegian second-grade class-rooms. In a two-part study consisting of teachers’ self-reports (Study 1) and video-observations of guid-ed reading sessions (Study 2), we analyzed the frequency and characteristics of guided reading practic-es. Findings from Study 1 indicate that guided reading is a common practice of Norwegian second-grade teachers and that discussing word meaning, text, and pictures are the most frequently addressed liter-acy components. Findings from Study 2 illustrate that the teachers regularly make optimal use of the before-reading phase, while the after-reading phase is relatively lacking. The observational data also indicate that teachers are more likely to simply check students’ understanding of word meaning rather than to work in-depth with vocabulary. Likewise, teachers were more likely to supply help in the de-coding process rather than scaffold students’ decoding with strategies. In sum, the data indicate that teachers may not fully use the benefits that guided reading instruction can afford. We discuss how to help educators use more of the potential of guided reading, arguing that the benefits of guided reading can be strengthened by (1) more in-depth planning, (2) greater use of strategies, and (3) routines for observing and assessing.publishedVersio

Exogenous Estrogen Boosts Circulating Estradiol Concentrations and Calcium Uptake by Duodenal Tissue in Heat-Stressed Hens

In the hen, heat stress (HS) disrupts shell calcification and reproductive processes, including hormone synthesis and egg production. Two studies were conducted to investigate palliative effects of exogenous estrogen or dietary vitamin D3 on Ca homeostasis and reproductive physiology during HS. Study 1: Hy-Line W36 hens were randomly assigned to thermoneutral (TN) or HS treatments and to 1 of 7 estrogen treatments: zero (control) or one Compudose 200 implant given 1, 2, 3, 8, 9, or 10 d before onset of HS. With no implant, HS reduced plasma estradiol (E2) and total Ca absorbed (CaT) by duodenal cells (P \u3c 0.05). In TN hens with implants, plasma E2 tripled within 24 h (P \u3c 0.05) and remained elevated (P \u3c 0.05) through d 9. In HS hens with implants, plasma E2 rose 6-fold (P \u3c 0.05) to equal TN+E2 concentrations and remained elevated through d 10. In TN and HS hens with implants, the rate of Ca absorption (CaTR) and CaT increased dramatically; the responses were quadratic and essentially identical. Study 2: Hy-Line W36 hens were provided diets formulated either according to NRC requirements (NRC, 1994), or with the addition of 22,000 IU/kg vitamin D3 (+VD hens). A 24-h HS episode was imposed 2 wk after initiation of the dietary regimen. Duodenal samples were collected for Ca absorption assays after the 24-h HS episode. Both CaTR and CaT in +VD hens were approximately 3-fold higher than in hens in the NVD group (P = 0.102). The results lead to the conclusion that exogenous estrogen, high levels of dietary vitamin D, or both, before a HS episode, are efficacious in alleviating at least some of the effects of HS and should be further investigated

Consanguinity and rare mutations outside of MCCC genes underlie nonspecific phenotypes of MCCD.

Purpose3-Methylcrotonyl-CoA carboxylase deficiency (MCCD) is an autosomal recessive disorder of leucine catabolism that has a highly variable clinical phenotype, ranging from acute metabolic acidosis to nonspecific symptoms such as developmental delay, failure to thrive, hemiparesis, muscular hypotonia, and multiple sclerosis. Implementation of newborn screening for MCCD has resulted in broadening the range of phenotypic expression to include asymptomatic adults. The purpose of this study was to identify factors underlying the varying phenotypes of MCCD.MethodsWe performed exome sequencing on DNA from 33 cases and 108 healthy controls. We examined these data for associations between either MCC mutational status, genetic ancestry, or consanguinity and the absence or presence/specificity of clinical symptoms in MCCD cases.ResultsWe determined that individuals with nonspecific clinical phenotypes are highly inbred compared with cases that are asymptomatic and healthy controls. For 5 of these 10 individuals, we discovered a homozygous damaging mutation in a disease gene that is likely to underlie their nonspecific clinical phenotypes previously attributed to MCCD.ConclusionOur study shows that nonspecific phenotypes attributed to MCCD are associated with consanguinity and are likely not due to mutations in the MCC enzyme but result from rare homozygous mutations in other disease genes.Genet Med 17 8, 660-667