Search for Daily Modulation of MeV Dark Matter Signals with DAMIC-M.

Dark matter (DM) particles with sufficiently large cross sections may scatter as they travel through Earth's bulk. The corresponding changes in the DM flux give rise to a characteristic daily modulation signal in detectors sensitive to DM-electron interactions. Here, we report results obtained from the first underground operation of the DAMIC-M prototype detector searching for such a signal from DM with MeV-scale mass. A model-independent analysis finds no modulation in the rate of 1 e^{-} events with sidereal period, where a DM signal would appear. We then use these data to place exclusion limits on DM in the mass range [0.53,2.7] MeV/c^{2} interacting with electrons via a dark photon mediator. Taking advantage of the time-dependent signal we improve by ∼2 orders of magnitude on our previous limit obtained from the total rate of 1 e^{-} events, using the same dataset. This daily modulation search represents the current strongest limit on DM-electron scattering via ultralight mediators for DM masses around 1 MeV/c^{2}.

Adsorption in Action: Molecular Dynamics as a Tool to Study Adsorption at the Surface of Fine Plastic Particles in Aquatic Environments.

The presence of microscopic fine plastic particles (FPPs) in aquatic environments continues to be a societal issue of great concern. Further, the adsorption of pollutants and other macromolecules onto the surface of FPPs is a well-known phenomenon. To establish the adsorption behavior of pollutants and the adsorption capacity of different plastic materials, batch adsorption experiments are typically carried out, wherein known concentrations of a pollutant are added to a known amount of plastic. These experiments can be time-consuming and wasteful by design, and in this work, an alternative theoretical approach to considering the problem is reviewed. As a theoretical tool, molecular dynamics (MD) can be used to probe and understand adsorbent-adsorbate interactions at the molecular scale while also providing a powerful visual picture of how the adsorption process occurs. In recent years, numerous studies have emerged that used MD as a theoretical tool to study adsorption on FPPs, and in this work, these studies are presented and discussed across three main categories: (i) organic pollutants, (ii) inorganic pollutants, and (iii) biological macromolecules. Emphasis is placed on how MD-calculated interaction energies can align with experimental data from batch adsorption experiments, and particular consideration is given to how MD can complement existing approaches. This work demonstrates that MD can provide significant insight into the adsorption behavior of different pollutants, but modern approaches are lacking a generalized formula for theoretically predicting adsorption behavior. With more data, MD could be used as a robust, initial assessment tool for the prioritization of chemical pollutants in the context of the microplastisphere, meaning that less time-consuming and potentially wasteful experiments would need to be carried out. With additional refinement, modern simulations will facilitate an improved understanding of chemical adsorption in aquatic environments.

First Constraints from DAMIC-M on Sub-GeV Dark-Matter Particles Interacting with Electrons.

We report constraints on sub-GeV dark matter particles interacting with electrons from the first underground operation of DAMIC-M detectors. The search is performed with an integrated exposure of 85.23 g days, and exploits the subelectron charge resolution and low level of dark current of DAMIC-M charge-coupled devices (CCDs). Dark-matter-induced ionization signals above the detector dark current are searched for in CCD pixels with charge up to 7e^{-}. With this dataset we place limits on dark matter particles of mass between 0.53 and 1000 MeV/c^{2}, excluding unexplored regions of parameter space in the mass ranges [1.6,1000] MeV/c^{2} and [1.5,15.1] MeV/c^{2} for ultralight and heavy mediator interactions, respectively.

ProtView: A Versatile Tool for In Silico Protease Evaluation and Selection in a Proteomic and Proteogenomic Context.

Many tools have been created to generate in silico proteome digests with different protease enzymes and provide useful information for selecting optimal digest schemes for specific needs. This can save on time and resources and generate insights on the observable proteome. However, there remains a need for a tool that evaluates digest schemes beyond protein and amino acid coverages in the proteomic domain. Here, we present ProtView, a versatile in silico protease combination digest evaluation workflow that maps in silico-digested peptides to both protein and genome references, so that the potential observable portions of the proteome, transcriptome, and genome can be identified. The proteomic identification and quantification of evidence for transcriptional, co-transcriptional, post-transcriptional, translational, and post-translational regulation can all be examined in silico with ProtView prior to an experiment. Benchmarking against biological data comparing multiple proteases shows that ProtView can correctly estimate performances among the digest schemes. ProtView provides this information in a way that is easy to interpret, allowing for digest schemes to be evaluated before carrying out an experiment, in context that can optimize both proteomic and proteogenomic experiments. ProtView is available at https://github.com/SSPuliasis/ProtView.

Uptake of oomycete RXLR effectors into host cells by clathrin-mediated endocytosis.

Filamentous (oomycete and fungal) plant pathogens deliver cytoplasmic effector proteins into host cells to facilitate disease. How RXLR effectors from the potato late blight pathogen Phytophthora infestans enter host cells is unknown. One possible route involves clathrin-mediated endocytosis (CME). Transient silencing of NbCHC, encoding clathrin heavy chain, or the endosome marker gene NbAra6 encoding a Rab GTPase in the model host Nicotiana benthamiana, attenuated P. infestans infection and reduced translocation of RXLR effector fusions from transgenic pathogen strains into host cells. By contrast, silencing PP1c isoforms, susceptibility factors not required for endocytosis, reduced infection but did not attenuate RXLR effector uptake. Endosome enrichment by ultracentrifugation and sucrose gradient fractionation revealed co-localization of RXLR effector Pi04314-RFP with clathrin-coated vesicles. Immunopurification of clathrin- and NbAra6-associated vesicles during infection showed that RXLR effectors Pi04314-RFP and AvrBlb1-RFP, but not apoplastic effector PiSCR74-RFP, were co-immunoprecipitated during infection with pathogen strains secreting these effectors. Tandem mass spectrometry analyses of proteins co-immunoprecipitated with NbAra6-GFP during infection revealed enrichment of host proteins associated with endocytic vesicles alongside multiple pathogen RXLR effectors, but not apoplastic effectors, including PiSCR74, which do not enter host cells. Our data show that the uptake of P. infestans RXLR effectors into plant cells occurs via CME.

Ultrasound Visualization and Recording of Transient Myocardial Vibrations.

OBJECTIVE: A new visualization and recording method used to assess and quantitate autogenic high-velocity motions in myocardial walls to provide a new description of cardiac function is described. METHODS: The regional motion display (RMD) is based on high-speed difference ultrasound B-mode images and spatiotemporal processing to record propagating events (PEs). Sixteen normal participants and one patient with cardiac amyloidosis were imaged at rates of 500-1000/s using the Duke Phased Array Scanner, T5. RMDs were generated using difference images and spatially integrating these to display velocity as function of time along a cardiac wall. RESULTS: In normal participants, RMDs revealed four discrete PEs with average onset timing with respect to the QRS complex of -31.7, +46, +365 and +536 ms. The late diastolic PE propagated apex to base in all participants at an average velocity of 3.4 m/s by the RMD. The RMD of the amyloidosis patient revealed significant changes in the appearance of PEs compared with normal participants. The late diastolic PE propagated at 5.3 m/s from apex to base. All four PEs lagged the average timing of normal participants. CONCLUSION: The RMD method reliably reveals PEs as discrete events and successfully allows reproducible measurement of PE timing and the velocity of at least one PE. The RMD method is applicable to live, clinical high-speed studies and may offer a new approach to characterization of cardiac function.

S-acylation stabilizes ligand-induced receptor kinase complex formation during plant pattern-triggered immune signaling.

Plant receptor kinases are key transducers of extracellular stimuli, such as the presence of beneficial or pathogenic microbes or secreted signaling molecules. Receptor kinases are regulated by numerous post-translational modifications.1,2,3 Here, using the immune receptor kinases FLS24 and EFR,5 we show that S-acylation at a cysteine conserved in all plant receptor kinases is crucial for function. S-acylation involves the addition of long-chain fatty acids to cysteine residues within proteins, altering their biochemical properties and behavior within the membrane environment.6 We observe S-acylation of FLS2 at C-terminal kinase domain cysteine residues within minutes following the perception of its ligand, flg22, in a BAK1 co-receptor and PUB12/13 ubiquitin ligase-dependent manner. We demonstrate that S-acylation is essential for FLS2-mediated immune signaling and resistance to bacterial infection. Similarly, mutating the corresponding conserved cysteine residue in EFR suppressed elf18-triggered signaling. Analysis of unstimulated and activated FLS2-containing complexes using microscopy, detergents, and native membrane DIBMA nanodiscs indicates that S-acylation stabilizes, and promotes retention of, activated receptor kinase complexes at the plasma membrane to increase signaling efficiency.

Photochemical Fingerprinting Is a Sensitive Probe for the Detection of Synthetic Cannabinoid Receptor Agonists; toward Robust Point-of-Care Detection.

With synthetic cannabinoid receptor agonist (SCRA) use still prevalent across Europe and structurally advanced generations emerging, it is imperative that drug detection methods advance in parallel. SCRAs are a chemically diverse and evolving group, which makes rapid detection challenging. We have previously shown that fluorescence spectral fingerprinting (FSF) has the potential to provide rapid assessment of SCRA presence directly from street material with minimal processing and in saliva. Enhancing the sensitivity and discriminatory ability of this approach has high potential to accelerate the delivery of a point-of-care technology that can be used confidently by a range of stakeholders, from medical to prison staff. We demonstrate that a range of structurally distinct SCRAs are photochemically active and give rise to distinct FSFs after irradiation. To explore this in detail, we have synthesized a model series of compounds which mimic specific structural features of AM-694. Our data show that FSFs are sensitive to chemically conservative changes, with evidence that this relates to shifts in the electronic structure and cross-conjugation. Crucially, we find that the photochemical degradation rate is sensitive to individual structures and gives rise to a specific major product, the mechanism and identification of which we elucidate through density-functional theory (DFT) and time-dependent DFT. We test the potential of our hybrid "photochemical fingerprinting" approach to discriminate SCRAs by demonstrating SCRA detection from a simulated smoking apparatus in saliva. Our study shows the potential of tracking photochemical reactivity via FSFs for enhanced discrimination of SCRAs, with successful integration into a portable device.

Eliminating Transition State Calculations for Faster and More Accurate Reactivity Prediction in Sulfa-Michael Additions Relevant to Human Health and the Environment.

Fast and accurate computational approaches to predicting reactivity in sulfa-Michael additions are required for high-throughput screening in toxicology (e.g., predicting excess aquatic toxicity and skin sensitization), chemical synthesis, covalent drug design (e.g., targeting cysteine), and data set generation for machine learning. The kinetic glutathione chemoassay is a time-consuming in chemico method used to extract kinetic data in the form of log(k GSH) for organic electrophiles. In this work, we use density functional theory to compare the use of transition states (TSs) and enolate intermediate structures following C-S bond formation in the prediction of log(k GSH) for a diverse group of 1,4 Michael acceptors. Despite the widespread use of transition state calculations in the literature to predict sulfa-Michael reactivity, we observe that intermediate structures show much better performance for the prediction of log(k GSH), are faster to calculate, and easier to obtain than TSs. Furthermore, we show how linear combinations of atomic charges from the isolated Michael acceptors can further improve predictions, even when using inexpensive semiempirical quantum chemistry methods. Our models can be used widely in the chemical sciences (e.g., in the prediction of toxicity relevant to the environment and human health, synthesis planning, and the design of cysteine-targeting covalent inhibitors), and represent a low-cost, sustainable approach to reactivity assessment.

Comparing the Performances of Force Fields in Conformational Searching of Hydrogen-Bond-Donating Catalysts.

Here, we compare the relative performances of different force fields for conformational searching of hydrogen-bond-donating catalyst-like molecules. We assess the force fields by their predictions of conformer energies, geometries, low-energy, nonredundant conformers, and the maximum numbers of possible conformers. Overall, MM3, MMFFs, and OPLS3e had consistently strong performances and are recommended for conformationally searching molecules structurally similar to those in this study.

Indoor Skydiving: An Emerging Cause of Anterior Shoulder Dislocations.

Background: The risks of indoor skydiving have not been extensively studied. Indoor skydiving facilities are often used for corporate events and parties and by relatively inexperienced participants who may not appreciate the risks involved. The abducted and externally rotated shoulder position, combined with nearby walls, tight spaces, and the strong airstream, has resulted in a pattern of shoulder dislocation injuries. Case Report: A 26-year-old male presented with recurrent left shoulder instability after developing an engaging Hill-Sachs lesion following traumatic anterior shoulder dislocation while indoor skydiving. He entered the wind tunnel with his arms abducted and externally rotated. The wind created an upward force that held his arms in this position. As he reached with his left arm for the side of the tunnel to exit, his arm was forced into further external rotation, dislocating the shoulder. The patient was treated arthroscopically with a remplissage procedure and repair of the glenoid labrum. Postoperatively, he resumed his active lifestyle and sports without further dislocations or instability. Conclusion: Indoor skydiving may pose a high risk of anterior dislocation because the shoulder is forced into abduction and external rotation in the free-fall position. We advise caution before participation in indoor skydiving by any individual, but especially those with a history of shoulder instability.

Acetyl-CoA-carboxylase 1 (ACC1) plays a critical role in glucagon secretion.

Dysregulated glucagon secretion from pancreatic alpha-cells is a key feature of type-1 and type-2 diabetes (T1D and T2D), yet our mechanistic understanding of alpha-cell function is underdeveloped relative to insulin-secreting beta-cells. Here we show that the enzyme acetyl-CoA-carboxylase 1 (ACC1), which couples glucose metabolism to lipogenesis, plays a key role in the regulation of glucagon secretion. Pharmacological inhibition of ACC1 in mouse islets or αTC9 cells impaired glucagon secretion at low glucose (1 mmol/l). Likewise, deletion of ACC1 in alpha-cells in mice reduced glucagon secretion at low glucose in isolated islets, and in response to fasting or insulin-induced hypoglycaemia in vivo. Electrophysiological recordings identified impaired KATP channel activity and P/Q- and L-type calcium currents in alpha-cells lacking ACC1, explaining the loss of glucose-sensing. ACC-dependent alterations in S-acylation of the KATP channel subunit, Kir6.2, were identified by acyl-biotin exchange assays. Histological analysis identified that loss of ACC1 caused a reduction in alpha-cell area of the pancreas, glucagon content and individual alpha-cell size, further impairing secretory capacity. Loss of ACC1 also reduced the release of glucagon-like peptide 1 (GLP-1) in primary gastrointestinal crypts. Together, these data reveal a role for the ACC1-coupled pathway in proglucagon-expressing nutrient-responsive endocrine cell function and systemic glucose homeostasis.

Inner retinal thickening affects microperimetry thresholds in the presence of photoreceptor thinning in patients with RPGR retinitis pigmentosa.

BACKGROUND: Loss of photoreceptors cause degeneration in areas of the retina beyond the photoreceptors. The pattern of changes has implications for disease monitoring and measurement of functional changes. The aim of the study was to study the changes in inner retinal structure associated with photoreceptor disease, and the impact of these on microperimetry threshold. METHODS: This retrospective cohort study was conducted on optical coherence tomography (OCT) images and microperimetry tests collected between 2013 and 2019. 22 eyes with RPGR retinitis pigmentosa completed both OCT imaging and microperimetry assessment. 18 control eyes underwent OCT imaging. Photoreceptor layer and inner retinal thickness calculated for different eccentric areas were obtained. The relationship between the photoreceptor layer and inner retinal thickness, and microperimetry threshold was explored. RESULTS: Central 1° photoreceptor layer and inner retinal thickness were 96±34 and 139±75 µm in RPGR patients, and 139±15 and 62±14 µm in controls. Photoreceptor layer thickness differed between patient and control groups across increasing visual field areas (p<0.01, Kruskal-Wallis 1-way ANOVA), whereas the inner retinal thickness significantly differed between groups for the central 1° and 3° only. Microperimetry thresholds were explained by a combination of photoreceptor thickness (coefficient 0.15, 95% CI 0.13 to 0.18) and inner retinal thickness (coefficient 0.05, 95% CI 0.03 to 0.06). CONCLUSION: OCT shows evidence of remodelling in the inner retinal layers secondary to photoreceptor disease. This appears to have an impact on microperimetry threshold measurements.

Diving for the Basketball: An Isolated Popliteus Rupture in an Adolescent Female with 6 Year Follow-Up.

Popliteus tendon injuries most often occur in a traumatic setting with damage to multiple other knee structures. Isolated popliteal injuries, however, are rare. To our knowledge, there are no cases of a female pediatric patient with an intrasubstance popliteal tendon rupture in the current literature. This case report aims to illustrate symptoms, imaging, and treatment of an isolated popliteal tendon rupture in an adolescent female. An athletic 14-year-old female presented with right knee pain 4 weeks after a basketball injury in which she dove for the ball and fell, twisting and striking her knee. She had diffuse pain on both sides of the right knee for 3 weeks and pain with running, jumping or twisting. The knee exam was otherwise unremarkable. A right knee MRI demonstrated a complete rupture of the popliteal tendon. No other knee injuries were visualized. The patient was treated non-operatively and gradually returned to normal activities and sports at 6 weeks post injury. On 6-year follow up, the patient had no residual pain or instability and was able to play basketball without difficulty. Isolated popliteal tendon ruptures are extremely rare and difficult to diagnose given non-specific clinical exam findings. While these ruptures can be difficult to visualize on MRI, imaging can help to clarify the diagnosis by ruling out other injuries with similar clinical presentations. In the case of this young and active patient, diagnosis and full recovery without limitations were achieved with 6 weeks of conservative management.

Density Functional Theory in the Prediction of Mutagenicity: A Perspective.

As a field, computational toxicology is concerned with using in silico models to predict and understand the origins of toxicity. It is fast, relatively inexpensive, and avoids the ethical conundrum of using animals in scientific experimentation. In this perspective, we discuss the importance of computational models in toxicology, with a specific focus on the different model types that can be used in predictive toxicological approaches toward mutagenicity (SARs and QSARs). We then focus on how quantum chemical methods, such as density functional theory (DFT), have previously been used in the prediction of mutagenicity. It is then discussed how DFT allows for the development of new chemical descriptors that focus on capturing the steric and energetic effects that influence toxicological reactions. We hope to demonstrate the role that DFT plays in understanding the fundamental, intrinsic chemistry of toxicological reactions in predictive toxicology.

Reactivity prediction in aza-Michael additions without transition state calculations: the Ames test for mutagenicity.

Animal testing remains a contentious ethical issue in predictive toxicology. Thus, a fast, versatile, low-cost quantum chemical model is presented for predicting the risk of Ames mutagenicity in a series of 1,4 Michael acceptor type compounds. This framework eliminates the need for transition state calculations, and uses an intermediate structure to probe the reactivity of aza-Michael acceptors. This model can be used in a variety of settings e.g., the design of targeted covalent inhibitors and polyketide biosyntheses.

S-acylation in plants: an expanding field.

S-acylation is a common yet poorly understood fatty acid-based post-translational modification of proteins in all eukaryotes, including plants. While exact roles for S-acylation in protein function are largely unknown the reversibility of S-acylation indicates that it is likely able to play a regulatory role. As more studies reveal the roles of S-acylation within the cell it is becoming apparent that how S-acylation affects proteins is conceptually different from other reversible modifications such as phosphorylation or ubiquitination; a new mind-set is therefore required to fully integrate these data into our knowledge of plant biology. This review aims to highlight recent advances made in the function and enzymology of S-acylation in plants, highlights current and emerging technologies for its study and suggests future avenues for investigation.