Discovering the nuclear localization signal of Werner Helicase Interacting Protein 1.

Our study maps the classic nuclear localization signal (cNLS) domain within WRNIP that directs the protein's nuclear positioning.

KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions.

Tyrosine and serine/threonine kinases are essential regulators of cell processes and are important targets for human therapies. Unfortunately, very little is known about specific kinase-substrate relationships, making it difficult to infer meaning from dysregulated phosphoproteomic datasets or for researchers to identify possible kinases that regulate specific or novel phosphorylation sites. The last two decades have seen an explosion in algorithms to extrapolate from what little is known into the larger unknown-predicting kinase relationships with site-specific substrates using a variety of approaches that include the sequence-specificity of kinase catalytic domains and various other factors, such as evolutionary relationships, co-expression, and protein-protein interaction networks. Unfortunately, a number of limitations prevent researchers from easily harnessing these resources, such as loss of resource accessibility, limited information in publishing that results in a poor mapping to a human reference, and not being updated to match the growth of the human phosphoproteome. Here, we propose a methodological framework for publishing predictions in a unified way, which entails ensuring predictions have been run on a current reference proteome, mapping the same substrates and kinases across resources to a common reference, filtering for the human phosphoproteome, and providing methods for updating the resource easily in the future. We applied this framework on three currently available resources, published in the last decade, which provide kinase-specific predictions in the human proteome. Using the unified datasets, we then explore the role of study bias, the emergent network properties of these predictive algorithms, and comparisons within and between predictive algorithms. The combination of the code for unification and analysis, as well as the unified predictions are available under the resource we named KinPred. We believe this resource will be useful for a wide range of applications and establishes best practices for long-term usability and sustainability for new and existing predictive algorithms.

Optogenetic investigation of BMP target gene expression diversity.

Signaling molecules activate distinct patterns of gene expression to coordinate embryogenesis, but how spatiotemporal expression diversity is generated is an open question. In zebrafish, a BMP signaling gradient patterns the dorsal-ventral axis. We systematically identified target genes responding to BMP and found that they have diverse spatiotemporal expression patterns. Transcriptional responses to optogenetically delivered high- and low-amplitude BMP signaling pulses indicate that spatiotemporal expression is not fully defined by different BMP signaling activation thresholds. Additionally, we observed negligible correlations between spatiotemporal expression and transcription kinetics for the majority of analyzed genes in response to BMP signaling pulses. In contrast, spatial differences between BMP target genes largely collapsed when FGF and Nodal signaling were inhibited. Our results suggest that, similar to other patterning systems, combinatorial signaling is likely to be a major driver of spatial diversity in BMP-dependent gene expression in zebrafish.

Laser-Plasma Spectroscopy of Hydroxyl with Applications.

This article discusses laser-induced laboratory-air plasma measurements and analysis of hydroxyl (OH) ultraviolet spectra. The computations of the OH spectra utilize line strength data that were developed previously and that are now communicated for the first time. The line strengths have been utilized extensively in interpretation of recorded molecular emission spectra and have been well-tested in laser-induced fluorescence applications for the purpose of temperature inferences from recorded data. Moreover, new experiments with Q-switched laser pulses illustrate occurrence of molecular recombination spectra for time delays of the order of several dozen of microseconds after plasma initiation. The OH signals occur due to the natural humidity in laboratory air. Centrifugal stretching of the Franck-Condon factors and r-centroids are included in the process of determining the line strengths that are communicated as a Supplementary File. Laser spectroscopy applications of detailed OH computations include laser-induced plasma and combustion analyses, to name but two applications. This work also includes literature references that address various diagnosis applications.

Laser-Plasma Spatiotemporal Cyanide Spectroscopy and Applications.

This article reports new measurements of laser-induced plasma hypersonic expansion measurements of diatomic molecular cyanide (CN). Focused, high-peak-power 1064 nm Q-switched radiation of the order of 1 TW/cm 2 generated optical breakdown plasma in a cell containing a 1:1 molar gas mixture of N 2 and CO 2 at a fixed pressure of 1.1 × 10 5 Pascal and in a 100 mL/min flow of the mixture. Line-of-sight (LOS) analysis of recorded molecular spectra indicated the outgoing shockwave at expansion speeds well in excess of Mach 5. Spectra of atomic carbon confirmed increased electron density near the shockwave, and, equally, molecular CN spectra revealed higher excitation temperature near the shockwave. Results were consistent with corresponding high-speed shadowgraphs obtained by visualization with an effective shutter speed of 5 nanoseconds. In addition, LOS analysis and the application of integral inversion techniques allow inferences about the spatiotemporal plasma distribution.

Pattern formation mechanisms of self-organizing reaction-diffusion systems.

Embryonic development is a largely self-organizing process, in which the adult body plan arises from a ball of cells with initially nearly equal potency. The reaction-diffusion theory first proposed by Alan Turing states that the initial symmetry in embryos can be broken by the interplay between two diffusible molecules, whose interactions lead to the formation of patterns. The reaction-diffusion theory provides a valuable framework for self-organized pattern formation, but it has been difficult to relate simple two-component models to real biological systems with multiple interacting molecular species. Recent studies have addressed this shortcoming and extended the reaction-diffusion theory to realistic multi-component networks. These efforts have challenged the generality of previous central tenets derived from the analysis of simplified systems and guide the way to a new understanding of self-organizing processes. Here, we discuss the challenges in modeling multi-component reaction-diffusion systems and how these have recently been addressed. We present a synthesis of new pattern formation mechanisms derived from these analyses, and we highlight the significance of reaction-diffusion principles for developmental and synthetic pattern formation.

Engineering DNA recognition and allosteric response properties of TetR family proteins by using a module-swapping strategy.

The development of synthetic biological systems requires modular biomolecular components to flexibly alter response pathways. In previous studies, we have established a module-swapping design principle to engineer allosteric response and DNA recognition properties among regulators in the LacI family, in which the engineered regulators served as effective components for implementing new cellular behavior. Here we introduced this protein engineering strategy to two regulators in the TetR family: TetR (UniProt Accession ID: P04483) and MphR (Q9EVJ6). The TetR DNA-binding module and the MphR ligand-binding module were used to create the TetR-MphR. This resulting hybrid regulator possesses DNA-binding properties of TetR and ligand response properties of MphR, which is able to control gene expression in response to a molecular signal in cells. Furthermore, we studied molecular interactions between the TetR DNA-binding module and MphR ligand-binding module by using mutant analysis. Together, we demonstrated that TetR family regulators contain discrete and functional modules that can be used to build biological components with novel properties. This work highlights the utility of rational design as a means of creating modular parts for cell engineering and introduces new possibilities in rewiring cellular response pathways.

Dementia as a predictor of mortality in adult trauma patients.

BACKGROUND: The specific contribution of dementia towards mortality in trauma patients is not well defined. The purpose of the study was to evaluate dementia as a predictor of mortality in trauma patients when compared to case-matched controls. METHODS: A 5-year retrospective review was conducted of adult trauma patients with a diagnosis of dementia at an American College of Surgeons-verified level I trauma center. Patients with dementia were matched with non-dementia patients and compared on mortality, ICU length of stay, and hospital length of stay. RESULTS: A total of 195 patients with dementia were matched to non-dementia controls. Comorbidities and complications (11.8% vs 12.4%) were comparable between both groups. Dementia patients spent fewer days on the ventilator (1 vs 4.5, P = 0.031). The length of ICU stay (2 days), hospital length of stay (3 days), and mortality (5.1%) were the same for both groups (P > 0.05). CONCLUSIONS: Dementia does not appear to increase the risk of mortality in trauma patients. Further studies should examine post-discharge outcomes in dementia patients.

Effects of sleeve gastrectomy and rs9930506 FTO variants on angiopoietin/Tie-2 system in fat expansion and M1 macrophages recruitment in morbidly obese subjects.

Angiogenesis in inflammation are hallmarks for adipose tissue expansion in obesity. The role of angiopoietin/Tie-2 system in adipose tissue expansion and immune cell recruitment is unclear. We studied the effect of sleeve gastrectomy and the influence of FTO rs9930506 polymorphism on Tie-2, angiopoietin-1 and angiopoietin-2 expression in morbid obesity. Fifteen morbidly obese subjects (4 men and 11 women) aged 24-55 years were followed-up 3 and 6 months after sleeve gastrectomy. Serum sTie-2, angiopoietin-1, angiopoietin-2, and hypoxia-inducible factor-1α concentrations were determined by ELISA. Tie-2 and its ligands in visceral and subcutaneous adipose tissue were localized by immunohistochemistry. Tie-2 expression was measured by flow cytometry in circulating monocytes and infiltrated macrophages. Comparisons before and after sleeve gastrectomy were carried out using ANOVA for repeated measures. rs9930506FTO genotyping was performed by PCR-RFLP. Circulating sTie-2 and angiopoietin-2 were higher before sleeve gastrectomy. Tie-2 and angiopoietin-2 mRNA levels were higher in subcutaneous adipose tissue than visceral and both decreased after surgery. Monocytes and infiltrated macrophages showed a pro-inflammatory phenotype, with increased Tie-2 expression that decreased 3 and 6 months after sleeve gastrectomy. Baseline sTie-2 correlated inversely with adiponectin levels. At baseline the rs9930506FTO AG ó GG genotypes carriers had more 34 kg than genotype carriers of rs9930506 AA. Weight and body mass index decreased at 6 months. We found that angiopoietin/Tie-2 system is mainly expressed in subcutaneous adipose tissue, contributing to expandability, fat accumulation, and monocytes attachment in obesity. Bariatric surgery favorably modifies the pro-angiogenic profile, allowed a reduced angiogenic expression in the circulation and adipose tissue.

Response to Nodal morphogen gradient is determined by the kinetics of target gene induction.

Morphogen gradients expose cells to different signal concentrations and induce target genes with different ranges of expression. To determine how the Nodal morphogen gradient induces distinct gene expression patterns during zebrafish embryogenesis, we measured the activation dynamics of the signal transducer Smad2 and the expression kinetics of long- and short-range target genes. We found that threshold models based on ligand concentration are insufficient to predict the response of target genes. Instead, morphogen interpretation is shaped by the kinetics of target gene induction: the higher the rate of transcription and the earlier the onset of induction, the greater the spatial range of expression. Thus, the timing and magnitude of target gene expression can be used to modulate the range of expression and diversify the response to morphogen gradients.

Cannabinoid-induced actomyosin contractility shapes neuronal morphology and growth.

Endocannabinoids are recently recognized regulators of brain development, but molecular effectors downstream of type-1 cannabinoid receptor (CB1R)-activation remain incompletely understood. We report atypical coupling of neuronal CB1Rs, after activation by endo- or exocannabinoids such as the marijuana component ∆(9)-tetrahydrocannabinol, to heterotrimeric G12/G13 proteins that triggers rapid and reversible non-muscle myosin II (NM II) dependent contraction of the actomyosin cytoskeleton, through a Rho-GTPase and Rho-associated kinase (ROCK). This induces rapid neuronal remodeling, such as retraction of neurites and axonal growth cones, elevated neuronal rigidity, and reshaping of somatodendritic morphology. Chronic pharmacological inhibition of NM II prevents cannabinoid-induced reduction of dendritic development in vitro and leads, similarly to blockade of endocannabinoid action, to excessive growth of corticofugal axons into the sub-ventricular zone in vivo. Our results suggest that CB1R can rapidly transform the neuronal cytoskeleton through actomyosin contractility, resulting in cellular remodeling events ultimately able to affect the brain architecture and wiring.

Rhinovirus 3C protease can localize in the nucleus and alter active and passive nucleocytoplasmic transport.

The degradation of nuclear pore components and disruption of nucleocytoplasmic trafficking during rhinovirus infection have been attributed to viral 2A protease. Here we show for the first time that rhinovirus 3C protease may also have a role. Specifically, we show that 3C and its precursor, 3CD, can target green fluorescent protein to the nucleus of living cells, leading to degradation of nuclear pore components, and that incubation with recombinant 3C disrupts active and passive nucleocytoplasmic transport in a semi-intact cell nuclear transport system dependent on 3C protease activity. 3C may thus contribute to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown.