A real-time biochemical assay for quantitative analyses of APOBEC-catalyzed DNA deamination.

Over the past decade, the connection between APOBEC3 cytosine deaminases and cancer mutagenesis has become increasingly apparent. This growing awareness has created a need for biochemical tools that can be used to identify and characterize potential inhibitors of this enzyme family. In response to this challenge, we have developed a Real-time APOBEC3-mediated DNA Deamination assay. This assay offers a single-step set-up and real-time fluorescent read-out, and it is capable of providing insights into enzyme kinetics. The assay also offers a high-sensitivity and easily scalable method for identifying APOBEC3 inhibitors. This assay serves as a crucial addition to the existing APOBEC3 biochemical and cellular toolkit and possesses the versatility to be readily adapted into a high-throughput format for inhibitor discovery.

An incoherent feed-forward loop involving bHLH transcription factors, Auxin and CYCLIN-Ds regulates style radial symmetry establishment in Arabidopsis.

The bilateral-to-radial symmetry transition occurring during the development of the Arabidopsis thaliana female reproductive organ (gynoecium) is a crucial biological process linked to plant fertilization and seed production. Despite its significance, the cellular mechanisms governing the establishment and breaking of radial symmetry at the gynoecium apex (style) remain unknown. To fill this gap, we employed quantitative confocal imaging coupled with MorphoGraphX analysis, in vivo and in vitro transcriptional experiments, and genetic analysis encompassing mutants in two bHLH transcription factors necessary and sufficient to promote transition to radial symmetry, SPATULA (SPT) and INDEHISCENT (IND). Here, we show that defects in style morphogenesis correlate with defects in cell-division orientation and rate. We showed that the SPT-mediated accumulation of auxin in the medial-apical cells undergoing symmetry transition is required to maintain cell-division-oriented perpendicular to the direction of organ growth (anticlinal, transversal cell division). In addition, SPT and IND promote the expression of specific core cell-cycle regulators, CYCLIN-D1;1 (CYC-D1;1) and CYC-D3;3, to support progression through the G1 phase of the cell cycle. This transcriptional regulation is repressed by auxin, thus forming an incoherent feed-forward loop mechanism. We propose that this mechanism fine-tunes cell division rate and orientation with the morphogenic signal provided by auxin, during patterning of radial symmetry at the style.

Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores.

Phase separation of biomolecules underlies the formation and regulation of various membraneless condensates in cells. How condensates function reliably while surrounded by heterogeneous and dynamic mixtures of biomolecular components with specific and nonspecific interactions is yet to be understood. Studying multicomponent biomolecular mixtures with designer peptides has recently become an attractive avenue for learning about physicochemical principles governing cellular condensates. In this work, we employed long-timescale atomistic simulations of multicomponent tripeptide mixtures with all residue substitutions to illuminate the nature of direct and water-mediated interactions in a prototypical cellular condensate environment. We find that peptide mixtures form clusters with inverse hydrophobic order. Most multivalent and charged residues are localized in the cluster's core, with a large fraction of nonaromatic hydrophobic residues remaining on the surface. This inverse hydrophobic order in peptide clusters is partly driven by the expulsion of nonspecifically bound water molecules following peptide cluster growth. The growth of clusters is also accompanied by the formation of increasing numbers of specific water-mediated interactions between polar and charged residues. While the present study focused on the condensation of short peptide motifs, the general findings and analysis techniques should be helpful for future studies on larger peptides and protein condensation.

An Online Mindfulness-Based Group Intervention for Tics: A Pilot Randomized Controlled Trial.

BACKGROUND: Current treatments for Tourette syndrome (TS) and persistent tic disorder (PTD) are often insufficiently effective, inaccessible, and frequently associated with adverse events. Thus, we must continue to develop and test effective, accessible, and safe treatment options. OBJECTIVE: We aimed to conduct a pilot randomized controlled trial (RCT) comparing a novel, videoconference-delivered group mindfulness-based intervention for tics (MBIT) to videoconference-delivered group psychoeducation, relaxation, and supportive therapy (PRST) for adults with TS or PTD. METHODS: Thirty-two adults with TS or PTD were randomly assigned to receive 8 weeks of either MBIT or PRST. Tic severity, tic-related impairment, and global improvement were assessed by a trained, independent evaluator who was masked to treatment condition at baseline (week 0), posttreatment (week 9), 1-month follow-up, and 6-month follow-up. All study procedures were conducted online via secure videoconferencing. RESULTS: Twenty-eight participants began treatment and were included in analyses. MBIT, relative to PRST, was associated with a significantly greater decline in tic severity (d = 0.85) and tic-related impairment (d = 0.99) from baseline to posttreatment. Treatment response was significantly higher in MBIT (69%) than in PRST (13%). Neither treatment resulted in serious adverse effects. The durability of treatment outcomes is also reported and discussed. CONCLUSIONS: The results from this pilot RCT suggest that videoconference-delivered group MBIT may be an efficacious, accessible, and safe intervention for adults with tics. Future research is necessary to confirm these preliminary findings. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Involvement of Type 10 17ß-Hydroxysteroid Dehydrogenase in the Pathogenesis of Infantile Neurodegeneration and Alzheimer's Disease.

Type 10 17ß-hydroxysteroid dehydrogenase (17ß-HSD10) is the HSD17B10 gene product playing an appreciable role in cognitive functions. It is the main hub of exercise-upregulated mitochondrial proteins and is involved in a variety of metabolic pathways including neurosteroid metabolism to regulate allopregnanolone homeostasis. Deacetylation of 17ß-HSD10 by sirtuins helps regulate its catalytic activities. 17ß-HSD10 may also play a critical role in the control of mitochondrial structure, morphology and dynamics by acting as a member of the Parkin/PINK1 pathway, and by binding to cyclophilin D to open mitochondrial permeability pore. 17ß-HSD10 also serves as a component of RNase P necessary for mitochondrial tRNA maturation. This dehydrogenase can bind with the Aß peptide thereby enhancing neurotoxicity to brain cells. Even in the absence of Aß, its quantitative and qualitative variations can result in neurodegeneration. Since elevated levels of 17ß-HSD10 were found in brain cells of Alzheimer's disease (AD) patients and mouse AD models, it is considered to be a key factor in AD pathogenesis. Since data underlying Aß-binding-alcohol dehydrogenase (ABAD) were not secured from reported experiments, ABAD appears to be a fabricated alternative term for the HSD17B10 gene product. Results of this study would encourage researchers to solve the question why elevated levels of 17ß-HSD10 are present in brains of AD patients and mouse AD models. Searching specific inhibitors of 17ß-HSD10 may find candidates to reduce senile neurodegeneration and open new approaches for the treatment of AD.

Forecasting West Nile Virus With Graph Neural Networks: Harnessing Spatial Dependence in Irregularly Sampled Geospatial Data.

Machine learning methods have seen increased application to geospatial environmental problems, such as precipitation nowcasting, haze forecasting, and crop yield prediction. However, many of the machine learning methods applied to mosquito population and disease forecasting do not inherently take into account the underlying spatial structure of the given data. In our work, we apply a spatially aware graph neural network model consisting of GraphSAGE layers to forecast the presence of West Nile virus in Illinois, to aid mosquito surveillance and abatement efforts within the state. More generally, we show that graph neural networks applied to irregularly sampled geospatial data can exceed the performance of a range of baseline methods including logistic regression, XGBoost, and fully-connected neural networks.

Living and post-mortem CT scans in the gross anatomy lab: A study investigating differences in first-year medical students' exam performance and perceptions.

Basic competency in radiological imaging is essential for physicians to identify and manage diseases. An optimal place in which to include imaging in the medical curriculum is during anatomy as students can correlate the 3D anatomy from their body donors with the 2D cross-sectional anatomy. The goal of this project was to enhance first-year medical students' knowledge of cross-sectional imaging in the gross anatomy lab and to investigate whether there are benefits to learning cross sectional imaging via scans from body donors versus living individuals. Student participant performance was evaluated on laboratory practical examinations, CT image questions and spatial anatomical knowledge in the thorax and abdomen sections of gross anatomy. Students learned the cross-sectional imaging during dissections where they accessed the images relevant to their study on Pacsbin, a web-based Digital Imaging and Communication in Medicine viewer, via iPads. Results showed no statistically significant differences in practical examination scores, spatial anatomical knowledge, or identification of anatomical structures on CT image questions between participants who learned from images on body donors versus living individuals. In a questionnaire given at the end of the course, participants cited that the CT images improved their anatomical and imaging knowledge and that they felt better prepared to use imaging software and interpret diagnostic imaging results upon entering clerkships. While there were no differences in academic performance between the groups, positive outcomes regarding student perceptions of anatomical and imaging knowledge and preparedness for use of imaging software were identified in this study.

The Use of Musculoskeletal Fitness Measures as Indicators of Performance in Police Occupational Tasks.

Fitness testing is employed by some law enforcement agencies to assure performance in occupational tasks. The aim of this study was to investigate associations between musculoskeletal fitness assessment scores and performance in police occupational tasks. Retrospective data from 106 law enforcement officers who completed five musculoskeletal fitness assessments (vertical jump (VJ), hand grip strength, leg back dynamometer, 1-minute push-ups and sit-ups) and three routine occupational tasks (1.22m fence jump (FJ), 8.5m victim drag (VD) with 101kg and a get-up (GU)) were collected. A standard multiple regression was performed to determine if the results in fitness assessments were predictive of performance in the occupational tasks. Models combining all fitness assessments significantly predicted performance in FJ (F(5,88)=12.228, p<0.001; adjusted R2=0.38), VD (F(5,88)=9.407, p<0.001; adjusted R2=0.31) and GU (F(5,87)=14.319, p<0.001; adjusted R2=0.42). Further analysis of individual predictors highlighted that performance in the VJ test was a significant contributor for all models, uniquely predicting 15% of FJ (p<0.001), 4% of VD (p=0.03) and 8% of GU (p=0.001) performance. Grip strength uniquely contributed 3% to performance in the VD (p=0.05) and performance in the sit-up test contributed 8% to GU performance (p=0.001). Performance in police-specific occupational tasks requires a combination of muscular strength, power, and endurance. These musculoskeletal fitness components should be ideally assessed in recruitment and return-to work practices to ensure officers can safely and optimally perform their occupational requirements.

A real-time biochemical assay for quantitative analyses of APOBEC-catalyzed DNA deamination.

Over the past decade, the connection between APOBEC3 cytosine deaminases and cancer mutagenesis has become increasingly apparent. This growing awareness has created a need for biochemical tools that can be used to identify and characterize potential inhibitors of this enzyme family. In response to this challenge, we have developed a Real-time APOBEC3-mediated DNA Deamination (RADD) assay. This assay offers a single-step set-up and real-time fluorescent read-out, and it is capable of providing insights into enzyme kinetics and also offering a high-sensitivity and easily scalable method for identifying APOBEC3 inhibitors. This assay serves as a crucial addition to the existing APOBEC3 biochemical and cellular toolkit and possesses the versatility to be readily adapted into a high-throughput format for inhibitor discovery.

Assessing cell viability with dynamic optical coherence microscopy.

Assessing cell viability is important in many fields of research. Current optical methods to assess cell viability typically involve fluorescent dyes, which are often less reliable and have poor permeability in primary tissues. Dynamic optical coherence microscopy (dOCM) is an emerging tool that provides label-free contrast reflecting changes in cellular metabolism. In this work, we compare the live contrast obtained from dOCM to viability dyes, and for the first time to our knowledge, demonstrate that dOCM can distinguish live cells from dead cells in murine syngeneic tumors. We further demonstrate a strong correlation between dOCM live contrast and optical redox ratio by metabolic imaging in primary mouse liver tissue. The dOCM technique opens a new avenue to apply label-free imaging to assess the effects of immuno-oncology agents, targeted therapies, chemotherapy, and cell therapies using live tumor tissues.

Building Environmental and Sociological Predictive Intelligence to Understand the Seasonal Threat of SARS-CoV-2 in Human Populations.

Current modeling practices for environmental and sociological modulated infectious diseases remain inadequate to forecast the risk of outbreak(s) in human populations, partly due to a lack of integration of disciplinary knowledge, limited availability of disease surveillance datasets, and overreliance on compartmental epidemiological modeling methods. Harvesting data knowledge from virus transmission (aerosols) and detection (wastewater) of SARS-CoV-2, a heuristic score-based environmental predictive intelligence system was developed that calculates the risk of COVID-19 in the human population. Seasonal validation of the algorithm was uniquely associated with wastewater surveillance of the virus, providing a lead time of 7-14 days before a county-level outbreak. Using county-scale disease prevalence data from the United States, the algorithm could predict COVID-19 risk with an overall accuracy ranging between 81% and 98%. Similarly, using wastewater surveillance data from Illinois and Maryland, the SARS-CoV-2 detection rate was greater than 80% for 75% of the locations during the same time the risk was predicted to be high. Results suggest the importance of a holistic approach across disciplinary boundaries that can potentially allow anticipatory decision-making policies of saving lives and maximizing the use of available capacity and resources.

Enhanced Dye-Sensitized Mechanosensation Utilizing Pulsed and Digitally Modulated Light.

The generation of pressure perturbations in matter stimulated by pulsed light is a method widely recognized as the photoacoustic or light-induced thermoelastic effect. In a series of psychophysical experiments, the robustness of the tactile perception generated with a variety of light sources is examined: a diverging pulsed laser used for photoacoustic tomography optical parameter oscillation (OPO), a miniature diode laser (MDL), and a commercial digital light processing (DLP) projector. It is demonstrated that participants can accurately detect, categorically describe the sensations, and discern the direction of pulsed light travel. High detection accuracy is reported as follows: (d' = 4.95 (OPO); d' = 2.78 (modulated MDL); d' = 2.99 (DLP)) of the stimulus on glabrous skin coated with a thin layer of dye absorber. For all light sources, the predominant sensation is felt as vibration at the distal phalanx (i.e., fingertip, 55.21-57.29%) and the proximal phalanx (41.67-44.79%). At the fingertip, thermal sensations are perceived less frequently than mechanical ones. Moreover, these haptic effects are preserved under a wide range of pulse widths, spot sizes, optical energies, and wavelengths of the light sources. This form of sensory stimulation demonstrates a generalizable non-contact, non-optogenetic, in situ activation of the mechanosensory system.

Human Paleodemography and Paleoecology of the North Pacific Rim from the Mid to Late Holocene.

Using 14 proxy human population time series from around the North Pacific (Alaska, Hokkaido and the Kuril Islands), we evaluate the possibility that the North Pacific climate and marine ecosystem includes a millennial-scale regime shift cycle affecting subsistence and migration. We develop both visual and statistical methods for addressing questions about relative population growth and movement in the past. We introduce and explore the use of a Time Iterative Moran I (TIMI) spatial autocorrelation method to compare time series trends quantitatively - a method that could prove useful in other paleoecological analyses. Results reveal considerable population dynamism around the North Pacific in the last 5000 years and strengthen a previously reported inverse correlation between Northeast and Northwest Pacific proxy population indices. Visual and TIMI analyses suggest multiple, overlapping explanations for the variability, including the potential that oscillating ecological regime shifts affect the North Pacific basin. These results provide an opening for coordinated research to unpack the interrelated social, cultural and environmental dynamics around the subarctic and arctic North Pacific at different spatial and temporal scales by international teams of archaeologists, historians, paleoecologists, paleoceanographers, paleoclimatologists, modelers and data management specialists.