measuring-mrna-levels-over-time-during-yeast-s-cerevisiae-hypoxic

Measuring mRNA Levels Over Time During the Yeast <em>S. cerevisiae</em> Hypoxic Response

Complex changes in gene expression typically mediate a large portion of a cellular response. Each gene may change expression with unique kinetics as the ...

Rowan University

Phosphatidylinositol 4,5-bisphosphate (PIP2) is a key down-stream substrate of the endothelin signaling pathway and plays a role in regulating protein function at the membrane-cytoskeletal interface. However, the dynamic properties of distinct pools of PIP2 are poorly understood, especially for PIP2 that is bound to cytoskeletal proteins. We investigated the effects of endothelin-1 (ET-1) stimulation on protein-bound PIP2 in cardiac muscle. Isolated rat myocytes and homogenized mouse ventricles were exposed to 10 nM ET-1 for varying time periods and protein-bound PIP2 was analyzed using an anti-PIP2 antibody and Western blotting. Several cytoskeletal proteins were found to contain tightly bound PIP2, including profilin-1 (approximately 15 kDa), capZ (approximately 32 kDa), gCap39, (approximately 39 kDa) and alpha-actinin (approximately 106 kDa). Interestingly, ET-1 pretreatment reduced the amount of PIP2 bound to profilin-1 by 46% after 15 mins, followed by a recovery to near basal levels after 60 mins. ET-1 had no effect on capZ-, gCap39-, or alpha-actinin-bound PIP2 levels. To further explore the dynamics of PIP2 binding, brefeldin-A (BFA) was used to disrupt PIP2 binding to ADP-ribosylation factors and to impair receptor internalization. Pretreatment with 1 microM BFA increased the PIP2 signal on profilin-1 x 54% after 15 mins, followed by a decline to subbasal levels after 60 mins. Like ET-1, BFA had no effect on levels of PIP2 bound to capZ or to alpha-actinin. Taken together, the data indicate that profilin-1 binds PIP2 dynamically and may serve as a key regulator of the balance between cytoskeletal integrity and PIP2 availability for Ca2+/PKC signaling in the heart.

Endothelin-1 mobilizes profilin-1-bound PIP2 in cardiac muscle.

Endothelin-1 (ET-1) mediates physiological responses via endothelin A (ET(A)) and B (ET(B)) receptors, which may form homo- and heterodimers with unknown function. Here, we investigated ET-receptor dimerization using fluorescence resonance energy transfer (FRET) between receptors tagged with CFP (donor) and receptors tagged with tetracysteine-FlAsH (fluorescein arsenical hairpin) (acceptor) expressed in HEK293 cells. FRET efficiencies were 15%, 22%, and 27% for ET(A)/ET(A), ET(B)/ET(B), and ET(A)/ET(B), respectively, and dimerization was further supported by coimmunoprecipitation. For all dimer pairs, the natural but nonselective ligand ET-1 rapidly (<or=30 s) reduced FRET by >50%, but did not detectably reduce coimmunoprecipitation. ET-1 stimulated a transient increase in intracellular Ca(2+) ([Ca(2+)](i)) lasting 1-2 min for both homodimer pairs, and these ET-1 actions on FRET and [Ca(2+)](i) elevation were blocked by the appropriate subtype-selective antagonist. In contrast, ET(A)/ET(B) heterodimers mediated a sustained [Ca(2+)](i) increase lasting >10 min, and required a combination of ET(A) and ET(B) antagonists to block the observed FRET and [Ca(2+)](i) responses. The sensitive CFP/FlAsH FRET assay used here provides new insights into endothelin-receptor dimer function, and represents a unique approach to characterize G-protein-coupled receptor oligomers, including their pharmacology.

Endothelin receptor dimers evaluated by FRET, ligand binding, and calcium mobilization.

G protein-coupled receptors (GPCRs), including endothelin receptor A (ETA) and B (ETB), may form dimers or higher-order oligomers that profoundly influence signaling. Here we examined a PDZ finger motif within the C-terminus of ETA and its role in heterodimerization with ETB, and in homodimerization with itself, when expressed in HEK293 cells. Receptor dimerization was monitored by (i) fluorescence resonance energy transfer (FRET) between cyan fluorescent protein (CFP) (FRET donor) and tetracysteine/FlAsH (FRET acceptor) fused to the C-termini of ET receptors, and (ii) coimmunoprecipitation of ET receptors after mild detergent solubilization. Mutations in a PDZ finger motif at threonine403/serine404 eliminated FRET and reduced coimmunoprecipitation of heterodimers and homodimers. Functional consequences were evaluated by measuring mobilization of intracellular Ca2+ and internalization of receptors in response to a 10 nmol/L ET-1 challenge. PDZ mutations converted a sustained Ca2+ signal mediated by ETA:ETB heterodimers into a transient response, similar to that observed for homodimers or monomers. Heterodimers containing PDZ mutations were seen to internalize in a similar time domain (approximately 5 min) to the transient Ca2+ elevation and with similar kinetics to internalization of ETA homodimers or monomers. Without the PDZ mutations, heterodimers did not internalize over 15 min, suggesting the intriguing possibility that sustained Ca2+ signaling was a consequence (at least in part) of delayed internalization. The results are consistent with structural models of ETA-receptor dimerization that place threonine403/serine404 of the PDZ finger motif at the interaction interface between heterodimers and homodimers. Sustained Ca2+ signaling and delayed endocytosis of ETA:ETB heterodimers argues strongly for a unique dimer interface that impacts transmembrane signaling and internalization.

Sustained Ca2+ signaling and delayed internalization associated with endothelin receptor heterodimers linked through a PDZ finger.

Histone deacetylase (HDAC) enzymes modify the acetylation state of histones and other important proteins. Aberrant HDAC enzyme function has been implicated in many diseases, and the discovery and development of drugs targeting these enzymes is becoming increasingly important. In this article, the authors report the evaluation of homogeneous, single-addition, bioluminogenic HDAC enzyme activity assays that offer less assay interference by compounds in comparison to fluorescence-based formats. The authors assessed the key operational assay properties including sensitivity, scalability, reproducibility, signal stability, robustness (Z'), DMSO tolerance, and pharmacological response to standard inhibitors against HDAC-1, HDAC-3/NcoR2, HDAC-6, and SIRT-1 enzymes. These assays were successfully miniaturized to a 10 µL assay volume, and their suitability for high-throughput screening was tested in validation experiments using 640 drugs approved by the Food and Drug Administration and the Hypha Discovery MycoDiverse natural products library, which is a collection of 10 049 extracts and fractions from fermentations of higher fungi and contains compounds that are of low molecular weight and wide chemical diversity. Both of these screening campaigns confirmed that the bioluminogenic assay was high-throughput screening compatible and yielded acceptable performance in confirmation, counter, and compound/extract and fraction concentration-response assays.

A bioluminogenic HDAC activity assay: validation and screening.

Although we feel, see, and experience our hands as our own (body or hand ownership), recent research has shown that illusory hand ownership can be induced for fake or virtual hands and may be useful for neuroprosthetics and brain-computer interfaces. Despite the vast amount of behavioral data on illusory hand ownership, neuroimaging studies are rare, in particular electrophysiological studies. Thus, while the neural systems underlying hand ownership are relatively well described, the spectral signatures of body ownership as measured by electroencephalography (EEG) remain elusive. Here we induced illusory hand ownership in an automated, computer-controlled manner using virtual reality while recording 64-channel EEG and found that illusory hand ownership is reflected by a body-specific modulation in the mu-band over fronto-parietal cortex. In a second experiment in the same subjects, we then show that mu as well as beta-band activity in highly similar fronto-parietal regions was also modulated during a motor imagery task often used in paradigms employing non-invasive brain-computer interface technology. These data provide insights into the electrophysiological brain mechanisms of illusory hand ownership and their strongly overlapping mechanisms with motor imagery in fronto-parietal cortex. They also highlight the potential of combining high-resolution EEG with virtual reality setups and automatized stimulation protocols for systematic, reproducible stimulus presentation in cognitive neuroscience, and may inform the design of non-invasive brain-computer interfaces.

Shared electrophysiology mechanisms of body ownership and motor imagery.

Despite its widespread clinical use in load-bearing orthopedic implants, polyether-ether-ketone (PEEK) is often associated with poor osseointegration. In this study, a surface-porous PEEK material (PEEK-SP) was created using a melt extrusion technique. The porous layer was 399.6±63.3 μm thick and possessed a mean pore size of 279.9±31.6 μm, strut spacing of 186.8±55.5 μm, porosity of 67.3±3.1% and interconnectivity of 99.9±0.1%. Monotonic tensile tests showed that PEEK-SP preserved 73.9% of the strength (71.06±2.17 MPa) and 73.4% of the elastic modulus (2.45±0.31 GPa) of as-received, injection-molded PEEK. PEEK-SP further demonstrated a fatigue strength of 60.0 MPa at one million cycles, preserving 73.4% of the fatigue resistance of injection-molded PEEK. Interfacial shear testing showed the pore layer shear strength to be 23.96±2.26 MPa. An osseointegration model in the rat revealed substantial bone formation within the pore layer at 6 and 12 weeks via microcomputed tomography and histological evaluation. Ingrown bone was more closely apposed to the pore wall and fibrous tissue growth was reduced in PEEK-SP when compared to non-porous PEEK controls. These results indicate that PEEK-SP could provide improved osseointegration while maintaining the structural integrity necessary for load-bearing orthopedic applications.

High-strength, surface-porous polyether-ether-ketone for load-bearing orthopedic implants.

Ever since John Hughlings Jackson first described the so-called 'dreamy state' during temporal lobe epilepsy, that is, the sense of an abnormal familiarity (déjà vu) or vivid memory-like hallucinations from the past (experiential hallucinations), these phenomena have been studied and repeatedly linked to mesial temporal lobe structures. However, little is known about the lateralising value of either déjà vu or experiential hallucinations.

Lateralising value of experiential hallucinations in temporal lobe epilepsy.

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206-L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina-sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding.

Recent advances in neuroscience and engineering have led to the development of technologies that permit the control of external devices through real-time decoding of brain activity (brain-machine interfaces; BMI). Though the feeling of controlling bodily movements (sense of agency; SOA) has been well studied and a number of well-defined sensorimotor and cognitive mechanisms have been put forth, very little is known about the SOA for BMI-actions. Using an on-line BMI, and verifying that our subjects achieved a reasonable level of control, we sought to describe the SOA for BMI-mediated actions. Our results demonstrate that discrepancies between decoded neural activity and its resultant real-time sensory feedback are associated with a decrease in the SOA, similar to SOA mechanisms proposed for bodily actions. However, if the feedback discrepancy serves to correct a poorly controlled BMI-action, then the SOA can be high and can increase with increasing discrepancy, demonstrating the dominance of visual feedback on the SOA. Taken together, our results suggest that bodily and BMI-actions rely on common mechanisms of sensorimotor integration for agency judgments, but that visual feedback dominates the SOA in the absence of overt bodily movements or proprioceptive feedback, however erroneous the visual feedback may be.

Visual Feedback Dominates the Sense of Agency for Brain-Machine Actions.

The ability to control the surface topography of orthopedic implant materials is desired to improve osseointegration but is often at the expense of mechanical performance in load bearing environments. Here we investigate the effects of surface modifications, roughness and porosity, on the mechanical properties of a set of polymers with diverse chemistry and structure. Both roughness and surface porosity resulted in samples with lower strength, failure strain and fatigue life due to stress concentrations at the surface; however, the decrease in ductility and fatigue strength were greater than the decrease in monotonic strength. The fatigue properties of the injection molded polymers did not correlate with yield strength as would be traditionally observed in metals. Rather, the fatigue properties and the capacity to maintain properties with the introduction of surface porosity correlated with the fracture toughness of the polymers. Polymer structure impacted the materials relative capacity to maintain monotonic and cyclic properties in the face of surface texture and porosity. Generally, amorphous polymers with large ratios of upper to lower yield points demonstrated a more significant drop in ductility and fatigue strength with the introduction of porosity compared to crystalline polymers with smaller ratios in their upper to lower yield strength. The latter materials have more effective dissipation mechanisms to minimize the impact of surface porosity on both monotonic and cyclic damage.

Impact of surface porosity and topography on the mechanical behavior of high strength biomedical polymers.

Despite its widespread use in orthopaedic implants such as soft tissue fasteners and spinal intervertebral implants, polyetheretherketone (PEEK) often suffers from poor osseointegration. Introducing porosity can overcome this limitation by encouraging bone ingrowth; however, the corresponding decrease in implant strength can potentially reduce the implant's ability to bear physiologic loads. We have previously shown, using a single pore size, that limiting porosity to the surface of PEEK implants preserves strength while supporting in vivo osseointegration. However, additional work is needed to investigate the effect of pore size on both the mechanical properties and cellular response to PEEK.

Do Surface Porosity and Pore Size Influence Mechanical Properties and Cellular Response to PEEK?

The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.

Estimating species richness using environmental DNA.

Organisms making repeated simple decisions are faced with a tradeoff between urgent and cautious strategies. While animals can adopt a statistically optimal policy for this tradeoff, findings about human decision-makers have been mixed. Some studies have shown that people can optimize this "speed-accuracy tradeoff", while others have identified a systematic bias towards excessive caution. These issues have driven theoretical development and spurred debate about the nature of human decision-making. We investigated a potential resolution to the debate, based on two factors that routinely differ between human and animal studies of decision-making: the effects of practice, and of longer-term feedback. Our study replicated the finding that most people, by default, are overly cautious. When given both practice and detailed feedback, people moved rapidly towards the optimal policy, with many participants reaching optimality with less than 1 h of practice. Our findings have theoretical implications for cognitive and neural models of simple decision-making, as well as methodological implications.

People adopt optimal policies in simple decision-making, after practice and guidance.

Surface porous polyether-ether-ketone has the ability to maintain the tensile monotonic and cyclic strength necessary for many load bearing orthopedic applications while providing a surface that facilitates bone ingrowth; however, the relevant deformation behavior of the pore architecture in response to various loading conditions is not yet fully characterized or understood. The focus of this study was to examine the compressive and wear behavior of the surface porous architecture using micro Computed Tomography (micro CT). Pore architectures of various depths (~0.5-2.5mm) and pore sizes (212-508µm) were manufactured using a melt extrusion and porogen leaching process. Compression testing revealed that the pore architecture deforms in the typical three staged linear elastic, plastic, and densification stages characteristic of porous materials. The experimental moduli and yield strengths decreased as the porosity increased but there was no difference in properties between pore sizes. The porous architecture maintained a high degree of porosity available for bone-ingrowth at all strains. Surface porous samples showed no increase in wear rate compared to injection molded samples, with slight pore densification accompanying wear.

Local deformation behavior of surface porous polyether-ether-ketone.

Recently, Veksler, Myers, and Gluck (2015) proposed model flexibility analysis as a method that "aids model evaluation by providing a metric for gauging the persuasiveness of a given fit" (p. 755) Model flexibility analysis measures the complexity of a model in terms of the proportion of all possible data patterns it can predict. We show that this measure does not provide a reliable way to gauge complexity, which prevents model flexibility analysis from fulfilling either of the 2 aims outlined by Veksler et al. (2015): absolute and relative model evaluation. We also show that model flexibility analysis can even fail to correctly quantify complexity in the most clear cut case, with nested models. We advocate for the use of well-established techniques with these characteristics, such as Bayes factors, normalized maximum likelihood, or cross-validation, and against the use of model flexibility analysis. In the discussion, we explore 2 issues relevant to the area of model evaluation: the completeness of current model selection methods and the philosophical debate of absolute versus relative model evaluation. (PsycINFO Database Record

Model flexibility analysis does not measure the persuasiveness of a fit.

Evidence accumulation models of decision-making have led to advances in several different areas of psychology. These models provide a way to integrate response time and accuracy data, and to describe performance in terms of latent cognitive processes. Testing important psychological hypotheses using cognitive models requires a method to make inferences about different versions of the models which assume different parameters to cause observed effects. The task of model-based inference using noisy data is difficult, and has proven especially problematic with current model selection methods based on parameter estimation. We provide a method for computing Bayes factors through Monte-Carlo integration for the linear ballistic accumulator (LBA; Brown and Heathcote, 2008), a widely used evidence accumulation model. Bayes factors are used frequently for inference with simpler statistical models, and they do not require parameter estimation. In order to overcome the computational burden of estimating Bayes factors via brute force integration, we exploit general purpose graphical processing units; we provide free code for this. This approach allows estimation of Bayes factors via Monte-Carlo integration within a practical time frame. We demonstrate the method using both simulated and real data. We investigate the stability of the Monte-Carlo approximation, and the LBA's inferential properties, in simulation studies.

Bayes factors for the linear ballistic accumulator model of decision-making.

Constant decision-making underpins much of daily life, from simple perceptual decisions about navigation through to more complex decisions about important life events. At many scales, a fundamental task of the decision-maker is to balance competing needs for caution and urgency: fast decisions can be more efficient, but also more often wrong. We show how a single mathematical framework for decision-making explains the urgency/caution balance across decision-making at two very different scales. This explanation has been applied at the level of neuronal circuits (on a time scale of hundreds of milliseconds) through to the level of stable personality traits (time scale of years).

Article	Year
Endothelin-1 mobilizes profilin-1-bound PIP2 in cardiac muscle. Experimental biology and medicine (Maywood, N.J.)\| PubMed ID: 16741017	2006
Endothelin receptor dimers evaluated by FRET, ligand binding, and calcium mobilization. Biophysical journal\| PubMed ID: 18424490	2008
Sustained Ca2+ signaling and delayed internalization associated with endothelin receptor heterodimers linked through a PDZ finger. Canadian journal of physiology and pharmacology\| PubMed ID: 18758500	2008
A bioluminogenic HDAC activity assay: validation and screening. Journal of biomolecular screening\| PubMed ID: 21832257	2011
Shared electrophysiology mechanisms of body ownership and motor imagery. NeuroImage\| PubMed ID: 22995776	2013
High-strength, surface-porous polyether-ether-ketone for load-bearing orthopedic implants. Acta biomaterialia\| PubMed ID: 25463499	2015
Lateralising value of experiential hallucinations in temporal lobe epilepsy. Journal of neurology, neurosurgery, and psychiatry\| PubMed ID: 25587072	2015
Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular ecology resources\| PubMed ID: 26032773	2016
Visual Feedback Dominates the Sense of Agency for Brain-Machine Actions. PloS one\| PubMed ID: 26066840	2015
Impact of surface porosity and topography on the mechanical behavior of high strength biomedical polymers. Journal of the mechanical behavior of biomedical materials\| PubMed ID: 26986085	2016
Do Surface Porosity and Pore Size Influence Mechanical Properties and Cellular Response to PEEK? Clinical orthopaedics and related research\| PubMed ID: 27154533	2016
Estimating species richness using environmental DNA. Ecology and evolution\| PubMed ID: 27516876	2016
People adopt optimal policies in simple decision-making, after practice and guidance. Psychonomic bulletin & review\| PubMed ID: 27562760	2017
Local deformation behavior of surface porous polyether-ether-ketone. Journal of the mechanical behavior of biomedical materials\| PubMed ID: 27694015	2017
Model flexibility analysis does not measure the persuasiveness of a fit. Psychological review\| PubMed ID: 28150957	2017
Bayes factors for the linear ballistic accumulator model of decision-making. Behavior research methods\| PubMed ID: 28455795	2017
Need for closure is associated with urgency in perceptual decision-making. Memory & cognition\| PubMed ID: 28585159	2017

Nathan Evans

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