Acute dietary zinc deficiency in rats exacerbates myocardial ischaemia-reperfusion injury through depletion of glutathione.

Zinc (Zn) plays an important role in maintaining the anti-oxidant status within the heart, and helps to counter the acute redox stress that occurs during myocardial ischaemia and reperfusion. Individuals with low zinc (Zn) levels are at greater risk of developing an acute myocardial infarction; however, the impact of this on the extent of myocardial injury is unknown. The present study aimed to compare the effects of dietary zinc depletion with in vitro removal of Zn (TPEN) on the outcome of acute myocardial infarction and vascular function. Male Sprague-Dawley rats were fed either a zinc adequate (ZA; 35mg Zn/kg diet) or zinc deficient (ZD; < 1mg Zn/kg diet) diet for two weeks prior to heart isolation. Perfused hearts were subjected to a thirty-minute ischaemia/two-hour reperfusion (I/R) protocol, during which time ventricular arrhythmias were recorded and after which infarct size was measured, along with markers of anti-oxidant status. In separate experiments hearts were challenged with the Zn chelator TPEN (10μM) prior to ischaemia onset. Both dietary and TPEN-induced Zn depletion significantly extended infarct size; dietary Zn depletion was associated with reduced total cardiac glutathione (GSH) levels, while TPEN decreased cardiac SOD-1 levels. TPEN, but not dietary Zn depletion also suppressed ventricular arrhythmias and depressed vascular responses to nitric oxide (NO). These findings demonstrate that both modes of zinc depletion worsen the outcome from I/R but through different mechanisms. Dietary Zn deficiency, resulting in reduced cardiac GSH, is the most appropriate model for determining the role of endogenous Zn in I/R injury

Topographic variation in soil erosion and accumulation determined with meteoric ¹⁰Be:Soil erosion and accumulation determined with meteoric 10Be

Understanding natural soil redistribution processes is essential for measuring the anthropogenic impact on landscapes. Although meteoric beryllium-10 (10Be) has been used to determine erosion processes within the Pleistocene and Holocene, fewer studies have used the isotope to investigate the transport and accumulation of the resulting sediment. Here we use meteoric 10Be in hilltop and valley site soil profiles to determine sediment erosion and deposition processes in the Christina River Basin (Pennsylvania, USA). The data indicate natural erosion rates of 14 to 21 mm 10−3yr and soil ages of 26 000 to 57 000 years in hilltop sites. Furthermore, valley sites indicate an alteration in sediment supply due to climate change (from the Pleistocene to the Holocene) within the last 60 000 years and sediment deposition of at least 0.5-2 m during the Wisconsinan glaciation. The change in soil erosion rate was most likely induced by changes in geomorphic processes; probably solifluction and slope wash during the cold period, when ice advanced into the mid latitudes of North America. This study shows the value of using meteoric10Be to determine sediment accumulation within the Quaternary and quantifies major soil redistribution occurred under natural conditions in this region

Biolayer interferometry for DNA-protein interactions

Biolayer interferometry (BLI) is a widely utilized technique for determining macromolecular interaction dynamics in real time. Using changes in the interference pattern of white light reflected off a biosensor tip, BLI can determine binding parameters for protein-protein (e.g., antibody-substrate kinetics) or protein-small molecule (e.g., drug discovery) interactions. However, a less-appreciated application for BLI analysis is DNA-protein interactions. DNAbinding proteins play an immense role in cellular biology, controlling critical processes including transcription, DNA replication, and DNA repair. Understanding how proteins interact with DNA often provides important insight into their biological function, and novel technologies to assay DNA-protein interactions are of broad interest. Currently, a detailed protocol utilizing BLI for DNA-protein interactions is lacking. In the following protocol, we describe the use of BLI and biotinylated-DNA probes to determine the binding kinetics of a transcription factor to a specific DNA sequence. The experimental steps include the generation of biotinylated-DNA probes, the execution of the BLI experiment, and data analysis by scientific graphing and statistical software (e.g., GraphPad Prism). Although the example experiment used throughout this protocol involves a prokaryotic transcription factor, this technique can be easily translated to any DNA-binding protein. Pitfalls and potential solutions for investigating DNA-binding proteins by BLI are also presented

Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields

We compare the free energies of adsorption (∆Aads) and the structural preferences of amino acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ between the force fields, the trends in the free energy of adsorption with amino acids are similar across the studied force fields. ∆Aads positively correlates with amino acid–graphene and negatively correlates with graphene–water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that while the thermodynamics of adsorption of proteins and peptides would be described consistently across different force fields, the structural preferences of peptides and proteins on graphene will be force field dependent. </div

Discovering the DNA-Binding Consensus of the HB8 Transcriptional Regulator TTHA1359

Transcription regulatory proteins, also known as transcription factors, function as molecular switches modulating the first step in gene expression, transcription initiation. Cyclic-AMP receptor proteins (CRPs) and fumarate and nitrate reduction regulators (FNRs) compose the CRP/FNR superfamily of transcription factors, regulating gene expression in response to a spectrum of stimuli. In the present work, a reverse-genetic methodology was applied to the study of TTHA1359, one of four CRP/FNR superfamily transcription factors in the model organism HB8. Restriction Endonuclease Protection, Selection, and Amplification (REPSA) followed by next-generation sequencing techniques and bioinformatic motif discovery allowed identification of a DNA-binding consensus for TTHA1359, 5\u27-AWTGTRA(N)TYACAWT-3\u27, which TTHA1359 binds to with high affinity. By bioinformatically mapping the consensus to the HB8 genome, several potential regulatory TTHA1359-binding sites were identified and validated in vitro. The findings contribute to the knowledge of TTHA1359 regulatory activity within HB8 and demonstrate the effectiveness of a reverse-genetic methodology in the study of putative transcription factors

In vivo activation of human immunodeficiency virus type 1 long terminal repeat by UV type A (UV-A) light plus psoralen and UV-B light in the skin of transgenic mice

UV irradiation has been shown to activate the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) in cell culture; however, only limited studies have been described in vivo. UV light has been categorized as UV-A (400 to 315 nm), -B (315 to 280 nm), or -C (less than 280 nm); the longer wavelengths are less harmful but more penetrative. Highly penetrative UV-A radiation constitutes the vast majority of UV sunlight reaching the earth\u27s surface but is normally harmless. UV-B irradiation is more harmful but less prevalent than UV-A. In this report, the HIV-1 LTR-luciferase gene in the skin of transgenic mice was markedly activated when exposed to UV-B irradiation. The LTR in the skin of transgenic mice pretreated topically with a photosensitizing agent (psoralen) was also activated to similar levels when exposed to UV-A light. A 2-h exposure to sunlight activated the LTR in skin treated with psoralen, whereas the LTR in skin not treated with psoralen was activated after 7 h of sunlight exposure. The HIV-1 LTR-beta-galactosidase reporter gene was preferentially activated by UV-B irradiation in a small population of epidermal cells. The transgenic mouse models carrying HIV-1 LTR-luciferase and LTR-beta-galactosidase reporter genes have been used to demonstrate the in vivo UV-induced activation of the LTR and might be used to evaluate other environmental factors or pharmacologic substances that might potentially activate the HIV-1 LTR in vivo