Temperature-sensitive control of protein activity by conditionally splicing inteins

Conditional or temperature-sensitive (TS) alleles represent useful tools with which to investigate gene function. Indeed, much of our understanding of yeast has relied on temperature-sensitive mutations which, when available, also provide important insights into other model systems. However, the rarity of temperature-sensitive alleles and difficulty in identifying them has limited their use. Here we describe a system to generate temperature-sensitive alleles based on conditionally active inteins. We have identified temperature-sensitive splicing variants of the yeast Saccharomyces cerevisiae vacuolar ATPase subunit (VMA) intein inserted within Gal4 and transferred these into Gal80. We show that Gal80-intein(TS) is able to efficiently provide temporal regulation of the Gal4/upstream activation sequence (UAS) system in a temperature-dependent manner in Drosophila melanogaster. Given the minimal host requirements necessary for temperature-sensitive intein splicing, this technique has the potential to allow the generation and use of conditionally active inteins in multiple host proteins and model systems, thereby widening the use of temperature-sensitive alleles for functional protein analysis.     

Burn trauma alters calcium transporter protein expression in the heart.

We have shown previously that burn trauma produces significant cardiac dysfunction, which is first evident 8 h postburn and is maximal 24 h postburn. Because calcium handling by the cardiomyocyte is essential for cardiac function, one mechanism by which burn injury may cause cardiac abnormalities is via calcium dyshomeostasis. We hypothesized that major burn injury alters cardiomyocyte calcium handling through changes in calcium transporter expression. Sprague-Dawley rats were given either burn injury or no burn injury (controls). Cardiomyocyte intracellular calcium and sodium were quantified at various times postburn by fura 2-AM or sodium-binding benzofuran isophthalate fluorescent indicators, respectively. In addition, hearts freeze-clamped at various times postburn (2, 4, 8, and 24 h) were used for Western blot analysis using antibodies against the sarcoplasmic reticulum calcium-ATPase (SERCA), the L-type calcium-channel, the ryanodine receptor, the sodium/calcium exchanger, or the sodium-potassium-ATPase. Intracellular calcium levels were elevated significantly 8-24 h postburn, and intracellular sodium was increased significantly 4 through 24 h postburn. Expression of SERCA was significantly reduced 1-8 h postburn, whereas L-type calcium-channel expression was diminished 1 and 2 h postburn (P < 0.05) but returned toward control levels 4 h postburn. Ryanodine receptor protein was significantly reduced at 1 and 2 h postburn, returning to baseline by 4 h postburn. Sodium/calcium exchanger expression was significantly elevated 2 h postburn but was significantly reduced 24 h postburn. An increase in sodium-potassium-ATPase expression occurred 2-24 h postburn. These data confirm that burn trauma alters calcium transporter expression, likely contributing to cardiomyocyte calcium loading and cardiac contractile dysfunction.     

The evolutionary history of seahorses (Syngnathidae: Hippocampus): molecular data suggest a West Pacific origin and two invasions of the Atlantic Ocean

Sequence data derived from four markers (the nuclear RP1 and Aldolase and the mitochondrial 16S rRNA and cytochrome b genes) were used to determine the phylogenetic relationships among 32 species belonging to the genus Hippocampus. There were marked differences in the rate of evolution among these gene fragments, with Aldolase evolving the slowest and the mtDNA cytochrome b gene the fastest. The RP1 gene recovered the highest number of nodes supported by >70% bootstrap values from parsimony analysis and >95% posterior probabilities from Bayesian inference. The combined analysis based on 2317 nucleotides resulted in the most robust phylogeny. A distinct phylogenetic split was identified between the pygmy seahorse, Hippocampus bargibanti, and a clade including all other species. Three species from the western Pacific Ocean included in our study, namely H. bargibanti, H. breviceps, and H. abdominalis occupy basal positions in the phylogeny. This and the high species richness in the region suggests that the genus evolved somewhere in the West Pacific. There is also fairly strong molecular support for the remaining species being subdivided into three main evolutionary lineages: two West Pacific clades and a clade of species present in both the Indo-Pacific and the Atlantic Ocean. The phylogeny obtained herein suggests at least two independent colonization events of the Atlantic Ocean, once before the closure of the Tethyan seaway, and once afterwards.     

Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'

Background  

The frequency of a haplotype comprising one allele at each of two loci can be expressed as a cubic equation (the 'Hill equation'), the solution of which gives that frequency. Most haplotype and linkage disequilibrium analysis programs use iteration-based algorithms which substitute an estimate of haplotype frequency into the equation, producing a new estimate which is repeatedly fed back into the equation until the values converge to a maximum likelihood estimate (expectation-maximisation).     

Habitat‐mediated timing of migration in polar bears: an individual perspective

Migration phenology is largely determined by how animals respond to seasonal changes in environmental conditions. Our perception of the relationship between migratory behavior and environmental cues can vary depending on the spatial scale at which these interactions are measured. Understanding the behavioral mechanisms behind population‐scale movements requires knowledge of how individuals respond to local cues. We show how time‐to‐event models can be used to predict what factors are associated with the timing of an individual's migratory behavior using data from GPS collared polar bears (Ursus maritimus) that move seasonally between sea ice and terrestrial habitats. We found the concentration of sea ice that bears experience at a local level, along with the duration of exposure to these conditions, was most associated with individual migration timing. Our results corroborate studies that assume thresholds of >50% sea ice concentration are necessary for suitable polar bear habitat; however, continued periods (e.g., days to weeks) of exposure to suboptimal ice concentrations during seasonal melting were required before the proportion of bears migrating to land increased substantially. Time‐to‐event models are advantageous for examining individual movement patterns because they account for the idea that animals make decisions based on an accumulation of knowledge from the landscapes they move through and not simply the environment they are exposed to at the time of a decision. Understanding the migration behavior of polar bears moving between terrestrial and marine habitat, at multiple spatiotemporal scales, will be a major aspect of quantifying observed and potential demographic responses to climate‐induced environmental changes.     

Teaching cardiac electrophysiology modeling to undergraduate students: laboratory exercises and GPU programming for the study of arrhythmias and spiral wave dynamics

As part of a 3-wk intersession workshop funded by a National Science Foundation Expeditions in Computing award, 15 undergraduate students from the City University of New York(1) collaborated on a study aimed at characterizing the voltage dynamics and arrhythmogenic behavior of cardiac cells for a broad range of physiologically relevant conditions using an in silico model. The primary goal of the workshop was to cultivate student interest in computational modeling and analysis of complex systems by introducing them through lectures and laboratory activities to current research in cardiac modeling and by engaging them in a hands-on research experience. The success of the workshop lay in the exposure of the students to active researchers and experts in their fields, the use of hands-on activities to communicate important concepts, active engagement of the students in research, and explanations of the significance of results as the students generated them. The workshop content addressed how spiral waves of electrical activity are initiated in the heart and how different parameter values affect the dynamics of these reentrant waves. Spiral waves are clinically associated with tachycardia, when the waves remain stable, and with fibrillation, when the waves exhibit breakup. All in silico experiments were conducted by simulating a mathematical model of cardiac cells on graphics processing units instead of the standard central processing units of desktop computers. This approach decreased the run time for each simulation to almost real time, thereby allowing the students to quickly analyze and characterize the simulated arrhythmias. Results from these simulations, as well as some of the background and methodology taught during the workshop, is presented in this article along with the programming code and the explanations of simulation results in an effort to allow other teachers and students to perform their own demonstrations, simulations, and studies.     

In vivo adenosine receptor preconditioning reduces myocardial infarct size via subcellular ERK signaling

The protective effects of adenosine receptor acute preconditioning (PC) are well known; however, the signaling mechanism mediating this effect has not been determined in in vivo models. The purpose of this study was to determine the role of the extracellular signal-regulated kinase (ERK) pathway in mediating adenosine PC in in vivo rat myocardium. Open-chest rats were submitted to 25 min of coronary artery occlusion and 2 h of reperfusion. ERK activation was assessed by measuring total and dually phosphorylated p44/42 ERK isoforms in nuclear and/or myofilament, mitochondrial, cytosolic, and membrane fractions. Adenosine receptor PC with the A1/A2a agonist 1S-[1a,2b,3b,4a(S*)]-4-[7-[[2-(3-chloro-2-thienyl)-1-methylpropyl]amino]-3H-imidazo[4,5-b]pyridyl-3-yl]cyclopentane carboxamide (AMP-579) reduced infarct size from 49 +/- 3% to 29 +/- 3%, an effect that was blocked by the mitogen-activated protein kinase-ERK inhibitor U-0126. ERK isoforms were present in all fractions, with the greatest expression in the cytosolic fraction and the least in the mitochondrial fraction. AMP-579 treatment increased preischemic p44/42 ERK phosphorylation in all fractions 2.7- to 6.9-fold. Reperfusion increased ERK isoform activation in all fractions, but there were no differences between control and AMP-579 hearts. Preischemic increases in phospo-p44/p42 ERK with AMP-579 were blunted by U-0126, although only in mitochondrial and membrane compartments. The PC effects of AMP-579 on infarct size and ERK were blunted by both the A1 antagonist 8-cyclopentyl-1,3-dipropylxanthine and, surprisingly, the A2a antagonist ZM-241385. These results indicate that the unique adenosine receptor agonist AMP-579 exerts its beneficial effects in vivo via both A1 and A2a receptor modulation of subcellular ERK isoform signaling.     

Crystal structure of the protease-resistant core domain of Yersinia pestis virulence factor YopR

Yersinia pestis, the causative agent of the plague, employs a type III secretion system (T3SS) to secrete and translocate virulence factors into to the cytoplasm of mammalian host cells. One of the secreted virulence factors is YopR. Little is known about the function of YopR other than that it is secreted into the extracellular milieu during the early stages of infection and that it contributes to virulence. Hoping to gain some insight into the function of YopR, we determined the crystal structure of its protease-resistant core domain, which consists of residues 38-149 out of 165 amino acids. The core domain is composed of five alpha-helices that display unexpected structural similarity with one domain of YopN, a central regulator of type III secretion in Y. pestis. This finding raises the possibility that YopR may play a role in the regulation of type III secretion.     

An early event in adipogenesis, the nuclear selection of the CCAAT enhancer-binding protein {beta} (C/EBP{beta}) mRNA by HuR and its translocation to the cytosol

HuR is a ligand for nuclear mRNAs containing adenylate-uridylate-rich elements in the 3'-untranslated region. Once bound to the mRNA, HuR is recognized by adapter proteins that then facilitate nuclear export of the complex. In the cytosol, HuR is thought to function to control stability and translation of its ligand message. In the 3T3-L1 cells HuR is constitutively expressed and localized predominantly to the nucleus in the preadipocytes. However, within 30 min of exposure to the differentiation stimulus the HuR content in the cytosol increases, consistent with HuR regulating the availability of relevant mRNAs for translation. Using in vitro RNA gel shifts, we have demonstrated that the CCAAT enhancer-binding protein beta (C/EBPbeta) message is a ligand for HuR. Within 2 h of initiation of the differentiation process, HuR complexes containing C/EBPbeta mRNA could be isolated from the cytosolic compartment. Importantly, the process appears to be highly selective, as cyclin D1, which contains a putative HuR binding site and is expressed on the same time frame as C/EBPbeta, was not found in the immunoprecipitated messenger ribonucleoprotein complexes. The proximity of this event to adipogenic stimuli and the importance of C/EBPbeta to the differentiation process have led us to hypothesize a role for HuR in the regulation of the onset of adipogenesis. In support of this hypothesis, small interfering RNA suppression of HuR protein content resulted in an inhibition of C/EBPbeta protein expression and an attenuation of the differentiation process.