Large Scale Dynamical Model of Macrophage/HIV Interactions

Properties emerge from the dynamics of large-scale molecular networks that are not discernible at the individual gene or protein level. Mathematical models - such as probabilistic Boolean networks - of molecular systems offer a deeper insight into how these emergent properties arise. Here, we introduce a non-linear, deterministic Boolean model of protein, gene, and chemical interactions in human macrophage cells during HIV infection. Our model is composed of 713 nodes with 1583 interactions between nodes and is responsive to 38 different inputs including signaling molecules, bacteria, viruses, and HIV viral particles. Additionally, the model accurately simulates the dynamics of over 50 different known phenomena, including molecular events associated with viral infection, endocytosis, transport, replication, budding, and cellular release. Statistical analyses of the model reveal network components with significant potential to influence molecular systems in both normal and infected macrophages, many of which have been confirmed in cell and animal models of HIV infection. We designed a Probabilistic Confidence Interval analysis for Boolean models (PCIB), demonstrating that our model emulates approximately 82% of a mass spectrometry dataset, collected from 7 macrophage samples infected with HIV across 67 proteins known to be central to the HIV infection process. The reproducibility of our model will facilitate guided hypothesis creation for future in vitro and in vivo studies. Additionally, the model allows for protein signaling interactions in human macrophages during HIV infection to be studied from a non-reductionist point of view

Investigating COMT Influence on the Proactive-Reactive Stress Coping Axis in Zebrafish

Individuals of the same species often display differences in correlated suites of behaviors which are made conspicuous when challenges – stressful, fear-inducing, etc. – are presented. In many species, a specific suite of behaviors (risk-aversion, aggression, exploration, learning, and memory) characterize an alternative set of stress coping styles (proactive and reactive). Such behaviors are regulated in the brain by specific neurotransmitters along with proteins that regulate them. One neurotransmitter regulator protein, catechol-O-methyltransferase (COMT) shows higher baseline whole-brain expression in proactive relative to reactive animals. However, it is not known whether its expression is a cause or a consequence of the stress coping style. In this ongoing study, I am testing the hypothesis that alteration of comta activity will lead to changes in stress coping behavior. Specifically, I attempted to knockout comtain zebrafish embryos using CRISPR/Cas9 with the intent of comparing stress-related behaviors and comtabrain-gene expression between mutant and control individuals in each stress coping style. I predict knocking out comtawill result in proactive zebrafish displaying similar stress-related behaviors as their reactive conspecifics and that reactive individuals will display elevated stress-related behaviors compared to controls. Across 155 breeding attempts, I found that approximately 23.75% (285/1200) of treatment embryos survived to 72 hours post-fertilization. High resolution melt analysis revealed 78.25% (18/23) to have variants in the target region, of which 11/18 (84.6%) showed successful mutations by Sanger sequencing. I intend to generate an F1 line in which to compare stress-related behaviors and comtabrain-gene expression by in situ hybridization

The Impact of Technological Developments on the Rules of Attorney Ethics Regarding Attorney–Client Privilege, Confidentiality, and Social Media

This article focuses on the development of the law of ethics and technology. Emphasis is placed on how technological developments have affected the rules and means by which lawyers practice law and certain ethical pitfalls that have developed hand-in-hand with technological advancements. Topics examined include: (1) the ways by which electronic communication has increased the potential for the attorney–client privilege to be waived and the resulting impact on the present-day practice of law; (2) the effect of social media on lawyers’ ethical obligations, including counseling clients regarding the client’s use of social media and the lawyer’s own use of social media; and (3) the impact of cloud computing on a lawyer’s obligation to protect client confidences. The authors examine the development of these technological effects on the practice of law through an examination of the evolution of the American Bar Association, its Model Rules of Professional Conduct, and state ethics opinions and representative case law

Spectrophotometric investigation of products formed following the initial one-electron electrochemical reduction of nicotinamide adenine dinucleotide (NAD+)

On electrolysis of NAD+ in aqueous solution at a potential corresponding to the initial one-electron reduction of NAD+ to a free radical, a greenish-yellow color appears which fades when electrolysis is complete. Literature ultraviolet absorption data for the resulting dimer show considerable variation. When the electrolysis is conducted in darkness, the colored product has [epsilon]340 of approx. 5700 M-1 [middle dot] cm-1 and [epsilon]259 of approx. 31000 M-1 [middle dot] cm-1. On ultraviolet and visible illumination, the color disappears, the 340-nm peak decreases and the 259-nm peak increases. On only visible illumination, the color disappears, both peaks increases, the dimer's polarographic oxidation wave decreases and the wave due to 1-substituted nicotinamide reduction increases. The data suggest that the dimer decomposes to NAD+ and 1,4-NADH.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24167/1/0000425.pd

Electrode technique

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42710/1/18_2005_Article_BF01969579.pd

But Is It Myopia? Risk Aversion and the Efficiency of Stock-Based Managerial Incentives

This paper points out that stock incentives do not lead to myopia unless they result in more emphasis on the short-term than would occur under an optimal contract. It shows that myopia findings relative to the standard used throughout the literature (first-best efficiency) are often reversed when evaluated relative to the relevant standard of optimal contracting. Results reported by the previous literature to be myopia often in fact have excessive emphasis on the long-term. The paper solves in closed-form for the region in parameter space which gives rise to these reversals and shows that it can be arbitrarily largehttp://deepblue.lib.umich.edu/bitstream/2027.42/49369/5/2008Jan16JCarmel.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/49369/1/Visiting-Carmel.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/49369/4/Visiting-Carmel.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/49369/7/1108_2008Jan16JCarmel.pd

Duplication of clostridial binding domains for enhanced macromolecular delivery into neurons

Neurological diseases constitute a quarter of global disease burden and are expected to rise worldwide with the ageing of human populations. There is an increasing need to develop new molecular systems which can deliver drugs specifically into neurons, non-dividing cells meant to last a human lifetime. Neuronal drug delivery must rely on agents which can recognise neurons with high specificity and affinity. Here we used a recently introduced ‘stapling’ system to prepare macromolecules carrying duplicated binding domains from the clostridial family of neurotoxins. We engineered individual parts of clostridial neurotoxins separately and combined them using a strong alpha-helical bundle. We show that combining two identical binding domains of tetanus and botulinum type D neurotoxins, in a sterically defined way by protein stapling, allows enhanced intracellular delivery of molecules into neurons. We also engineered a botulinum neurotoxin type C variant with a duplicated binding domain which increased enzymatic delivery compared to the native type C toxin. We conclude that duplication of the binding parts of tetanus or botulinum neurotoxins will allow production of high avidity agents which could deliver imaging reagents and large therapeutic enzymes into neurons with superior efficiency

Validation of Landsat 8 high resolution Sea Surface Temperature using surfers

This is the final version. Available on open access from Elsevier via the DOI in this record.Nearshore coastal waters are highly dynamic in both space and time. They can be difficult to sample using conventional methods due to their shallow depth, tidal variability, and the presence of strong currents and breaking waves. High resolution satellite sensors can be used to provide synoptic views of Surface Temperature (ST), but the performance of such ST products in the nearshore zone is poorly understood. Close to the shoreline, the ST pixels can be influenced by mixed composition of water and land, as a result of the sensor’s spatial resolution. This can cause thermal adjacency effects due to the highly different diurnal temperature cycles of water bodies and land. Previously, temperature data collected during surfing sessions has been proposed for validation of moderate resolution (1 km pixel size) satellite ST products. In this paper we use surfing temperature data to validate three high resolution (100 m resampled to 30 m pixel size) ST products derived from the Thermal InfraRed Sensor (TIRS) on board Landsat 8 (L8). ST was derived from Collection 1 and 2 Level 1 data (C1L1 and C2L1) using the Thermal Atmospheric Correction Tool (TACT), and was obtained from the standard Collection 2 Level 2 product (USGS C2L2). This study represents one of the first evaluations of the new C2 products, both L1 and L2, released by USGS at the end of 2020. Using automated matchup and image quality control, 88 matchups between L8/TIRS and surfers were identified, distributed across the NorthWestern semihemisphere. The unbiased Root Mean Squared Difference (uRMSD) between satellite and in situ measurements was generally < 2 K, with warm biases (Mean Average Difference, MAD) of 1.7 K (USGS C2L2), 1.3 K (TACT C1L1) and 0.8 K (TACT C2L1). Large interquartile ranges of ST in 5 × 5 satellite pixels around the matchup location were found for several images, especially for the summer matchups around the Californian coast. By filtering on target stability the number of matchups reduced to 31, which halved the uRMSD across the three methods (to around 1.1K), MAD were much lower, i.e. 1.1 K (USGS C2L2), 0.6 K (TACT C1L1), and 0.2 K (TACT C2L1). The larger biases of the C2L2 product compared to TACT C2L1 are caused as a result of: (1) a lower emissivity value for water targets used in USGS C2L2, and (2) differences in atmospheric parameter retrieval, mainly from differences in upwelling atmospheric radiance and lower atmospheric transmittance retrieved by USGS C2L2. Additionally, tiling artefacts are present in the C2L2 product, which originate from a coarser atmospheric correction process. Overall, the L8/TIRS derived ST product compares well with in situ measurements made while surfing, and we found the best performing ST product for nearshore coastal waters to be the Collection 2 Level 1 data processed with TACT.UK Research and InnovationFederal Belgian Science Policy Office (BELSPO)Lost Bird Foundatio

Electrochemical reduction of uridine in dimethyl sulfoxide: effect of the ribose group

The easier electrochemical reduction of uridine (1-[beta]-D-ribofuranosyluracil) in dimethyl sulfoxide as compared to uracil (2, 4-dihydroxypyrimidine) by ca. 0.1 V is explicable on the basis of the electron-withdrawing effect of the ribose group. This effect and possible steric hindrance by the ribose group markedly affect the reaction sequence following the initial one-electron reduction to generate a radical anion, which abstracts a proton from the parent uridine (father--son reaction) to form the neutral uridine free radical and the uridine anion. With increasing uridine concentration, further reduction and protonation reactions are favored, resulting in an increase in the effective faradaic n from ca. 0.5 to 0.8. The availability of only one proton-donating site on uridine, ie, that on N(3), allows explication of the behavior of other hydroxypyrimidines such as uracil.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24369/1/0000638.pd

Comparative adsorption of adenine and nicotinamide adenine dinucleotide (NAD+) at an aqueous solution | mercury interface

The relative extent of adsorption of adenine and NAD+ at the 10-[mu]M level from a solution of pH 4.8 and 0.5 M ionic strength (McIlvaine buffer) has been measured as a function of potential by an inverse normal pulse polarographic technic at a dropping mercury electrode (d.m.e.). Normalization of the pulse polarographic current resulting from pre-concentration of the electroactive species through adsorption compared to the current expected for a simple diffusion-controlled electron-transfer indicates that NAD+ is strongly adsorbed over a broader potential range than adenine, and that its surface concentration is slightly greater; causes for such behavior are considered. Other normalization approaches indicate NAD+ to be strongly adsorbed but comparably to adenine when account is taken of the relative effective areas occupied on adsorption.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25046/1/0000474.pd