The ribotoxic stress response drives UV-mediated cell death.

While ultraviolet (UV) radiation damages DNA, eliciting the DNA damage response (DDR), it also damages RNA, triggering transcriptome-wide ribosomal collisions and eliciting a ribotoxic stress response (RSR). However, the relative contributions, timing, and regulation of these pathways in determining cell fate is unclear. Here we use time-resolved phosphoproteomic, chemical-genetic, single-cell imaging, and biochemical approaches to create a chronological atlas of signaling events activated in cells responding to UV damage. We discover that UV-induced apoptosis is mediated by the RSR kinase ZAK and not through the DDR. We identify two negative-feedback modules that regulate ZAK-mediated apoptosis: (1) GCN2 activation limits ribosomal collisions and attenuates ZAK-mediated RSR and (2) ZAK activity leads to phosphodegron autophosphorylation and its subsequent degradation. These events tune ZAK's activity to collision levels to establish regimes of homeostasis, tolerance, and death, revealing its key role as the cellular sentinel for nucleic acid damage.

Acute inorganic nitrate ingestion does not impact oral microbial composition, cognitive function, or high-intensity exercise performance in female team-sport athletes.

The purpose of this study was to investigate the effects of acute nitrate (NO3-)-rich beetroot juice ingestion on explosive and high-intensity exercise performance, oral microbiota composition, and cognitive flexibility (i.e., function), before and after maximal intermittent running exercise. Fifteen women team-sport athletes were assigned in a randomized, double-blind, crossover design to consume concentrated NO3--depleted beetroot juice (PL; 0.1 mmol NO3-) and NO3--rich beetroot juice (BR; 12.0 mmol NO3-) 2.5 h prior to performing a battery of exercise performance tasks and cognitive testing before and after the Yo-Yo intermittent recovery level 1 (YYIR1) running test. Resting plasma [NO3-] and plasma nitrite ([NO2-]) were elevated following BR (P < 0.001). BR did not impact global composition or relative abundance of taxa in the oral microbiome (P > 0.05) or cognitive flexibility before or after exercise (P > 0.05). There was no significant difference in performance during 20-m (PRE, PL: 4.38 ± 0.27 vs. BR: 4.38 ± 0.32 s; POST, PL: 4.45 ± 0.29 vs. BR: 4.43 ± 0.35 s) and 10-m sprints (PRE, PL 2.78 ± 0.15 vs. BR 2.79 ± 0.18 s; POST, PL: 2.82 ± 0.16 vs. BR: 2.81 ± 0.19 s), isokinetic handgrip dynamometry, medicine ball throw, horizontal countermovement jump, or YYIR1 (PL: 355 ± 163 m vs. BR: 368 ± 184 m) between BR and PL (P > 0.05). These findings indicate that acute dietary NO3- may not influence the oral microbiome, explosive and high-intensity exercise performance, or cognitive function in women team-sport athletes.

PESPIP: Software to fit complex molecular and many-body potential energy surfaces with permutationally invariant polynomials.

We wish to describe a potential energy surface by using a basis of permutationally invariant polynomials whose coefficients will be determined by numerical regression so as to smoothly fit a dataset of electronic energies as well as, perhaps, gradients. The polynomials will be powers of transformed internuclear distances, usually either Morse variables, exp(-ri,j/λ), where λ is a constant range hyperparameter, or reciprocals of the distances, 1/ri,j. The question we address is how to create the most efficient basis, including (a) which polynomials to keep or discard, (b) how many polynomials will be needed, (c) how to make sure the polynomials correctly reproduce the zero interaction at a large distance, (d) how to ensure special symmetries, and (e) how to calculate gradients efficiently. This article discusses how these questions can be answered by using a set of programs to choose and manipulate the polynomials as well as to write efficient Fortran programs for the calculation of energies and gradients. A user-friendly interface for access to monomial symmetrization approach results is also described. The software for these programs is now publicly available.

pyXPCSviewer: an open-source interactive tool for X-ray photon correlation spectroscopy visualization and analysis.

pyXPCSviewer, a Python-based graphical user interface that is deployed at beamline 8-ID-I of the Advanced Photon Source for interactive visualization of XPCS results, is introduced. pyXPCSviewer parses rich X-ray photon correlation spectroscopy (XPCS) results into independent PyQt widgets that are both interactive and easy to maintain. pyXPCSviewer is open-source and is open to customization by the XPCS community for ingestion of diversified data structures and inclusion of novel XPCS techniques, both of which are growing demands particularly with the dawn of near-diffraction-limited synchrotron sources and their dedicated XPCS beamlines.

Assessing optimal: inequalities in codon optimization algorithms.

BACKGROUND: Custom genes have become a common resource in recombinant biology over the last 20 years due to the plummeting cost of DNA synthesis. These genes are often "optimized" to non-native sequences for overexpression in a non-native host by substituting synonymous codons within the coding DNA sequence (CDS). A handful of studies have compared native and optimized CDSs, reporting different levels of soluble product due to the accumulation of misfolded aggregates, variable activity of enzymes, and (at least one report of) a change in substrate specificity. No study, to the best of our knowledge, has performed a practical comparison of CDSs generated from different codon optimization algorithms or reported the corresponding protein yields. RESULTS: In our efforts to understand what factors constitute an optimized CDS, we identified that there is little consensus among codon-optimization algorithms, a roughly equivalent chance that an algorithm-optimized CDS will increase or diminish recombinant yields as compared to the native DNA, a near ubiquitous use of a codon database that was last updated in 2007, and a high variability of output CDSs by some algorithms. We present a case study, using KRas4B, to demonstrate that a median codon frequency may be a better predictor of soluble yields than the more commonly utilized CAI metric. CONCLUSIONS: We present a method for visualizing, analyzing, and comparing algorithm-optimized DNA sequences for recombinant protein expression. We encourage researchers to consider if DNA optimization is right for their experiments, and work towards improving the reproducibility of published recombinant work by publishing non-native CDSs.

Dietary Lutein and Cognitive Function in Adults: A Meta-Analysis of Randomized Controlled Trials.

Emerging literature suggests that dietary lutein may have important functions in cognitive health, but there is not enough data to substantiate its effects in human cognition. The current study was intended to determine the overall effect of lutein on the main domains of cognition in the adult population based on available placebo randomized-controlled trials. Literature searches were conducted in PubMed, AGRICOLA, Scopus, MEDLINE, and EMBASE on 14 November 2020. The effect of lutein on complex attention, executive function and memory domains of cognition were assessed by using an inverse-variance meta-analysis of standardized mean differences (SMD) (Hedge's g method). Dietary lutein was associated with slight improvements in cognitive performance in complex attention (SMD 0.02, 95% CI -0.27 to 0.31), executive function (SMD 0.13, 95% CI -0.26 to 0.51) and memory (SMD 0.03, 95% CI -0.26 to 0.32), but its effect was not significant. Change-from-baseline analysis revealed that lutein consumption could have a role in maintaining cognitive performance in memory and executive function. Although dietary lutein did not significantly improve cognitive performance, the evidence across multiple studies suggests that lutein may nonetheless prevent cognitive decline, especially executive function. More intervention studies are needed to validate the role of lutein in preventing cognitive decline and in promoting brain health.

Blastic plasmacytoid dendritic cell neoplasm in a young patient.

Blastic plasmacytoid dendritic cell neoplasm is a rare hematologic neoplasm originating from plasmacytoid dendritic cell precursors that has an aggressive disease course with typically poor prognosis. Herein, we report a man in his early twenties who presented with rapid onset of violaceous nodules and purpuric papules and macules that began on his chest before spreading to his arms, back, face, scalp, and legs. He also exhibited systemic symptoms including weight loss and night sweats. He was diagnosed with blastic plasmacytoid dendritic cell neoplasm and began treatment with aggressive multidrug therapy. Thus far his treatment has resulted in complete resolution of his cutaneous manifestations.

Full-dimensional, ab initio potential energy surface for glycine with characterization of stationary points and zero-point energy calculations by means of diffusion Monte Carlo and semiclassical dynamics.

A full-dimensional, permutationally invariant potential energy surface (PES) for the glycine amino acid is reported. A precise fit to energies and gradients calculated at the density functional theory (DFT)/B3LYP level of electronic-structure theory with Dunning's aug-cc-pVDZ basis set is performed involving 20 000 low-energy points and associated Cartesian gradients plus about 50 000 additional higher-energy points. The fact that newly calculated DFT/B3LYP energies for the main stationary points are close to the coupled-cluster single-double-triple [CCSD(T)] values, recently reported in the literature, provides reassurance about the accuracy of the constructed PES. Eight conformers and numerous saddle points are identified and characterized by describing geometries, relative stability, and harmonic frequencies. Stochastic and dynamical approaches are employed to study the vibrational ground state. Specifically, diffusion Monte Carlo simulations and approximate quantum dynamics, performed by means of the adiabatic switching semiclassical initial value representation technique, provide zero-point energies in excellent agreement with each other. The PES we report is sufficiently complete to permit spectroscopic and dynamical studies on glycine, which may be of interest to the biochemical and astrochemistry communities.

Investigation of secondary metabolism in the industrial butanol hyper-producer Clostridium saccharoperbutylacetonicum N1-4.

Clostridium saccharoperbutylacetonicum N1-4 (Csa) is a historically significant anaerobic bacterium which can perform saccharolytic fermentations to produce acetone, butanol, and ethanol (ABE). Recent genomic analyses have highlighted this organism's potential to produce polyketide and nonribosomal peptide secondary metabolites, but little is known regarding the identity and function of these metabolites. This study provides a detailed bioinformatic analysis of seven biosynthetic gene clusters (BGCs) present in the Csa genome that are predicted to produce polyketides/nonribosomal peptides. An RNA-seq-based untargeted transcriptomic approach revealed that five of seven BGCs were expressed during ABE fermentation. Additional characterization of a highly expressed nonribosomal peptide synthetase gene led to the discovery of its associated metabolite and its biosynthetic pathway. Transcriptomic analysis suggested an association of this nonribosomal peptide synthetase gene with butanol tolerance, which was supported by butanol challenge assays.

Coupling efficiency in light-driven hybrid P450BM3 and CYP119 enzymes.

The light-driven hybrid P450 enzyme approach utilizing the photochemical properties of a covalently attached Ru(II)-diimine photosensitizer was extended to the archaeal Sulfolobus acidocaldarius CYP119 enzyme leading to high photocatalytic activity in the hydroxylation of the chromogenic substrate, 11-nitrophenoxyundecanoic acid. The determined kcat was greater than those reported with various natural redox partners. In addition, the sacrificial electron donor, diethyldithiocarbamate, used in the photocatalytic reaction is shown to play a dual role. It acts as an efficient quencher of the Ru(II) excited state leading to a highly reducing species necessary to inject electrons into the heme. It is also known for its antioxidant properties and is shown herein to be a useful probe to determine coupling efficiency in the light-driven hybrid enzymes.

Natural products from anaerobes.

Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode unexpected biosynthetic potential for natural products, however, chemical data on natural products from the anaerobic world are extremely limited. Here, we review the current body of work on natural products isolated from strictly anaerobic microbes, including recent genome mining efforts to discover polyketides and non-ribosomal peptides from anaerobes. These known natural products of anaerobes have demonstrated interesting molecular scaffolds, biosynthetic logic, and/or biological activities, making anaerobes a promising reservoir for future natural product discovery.

Development of a High-Efficiency Transformation Method and Implementation of Rational Metabolic Engineering for the Industrial Butanol Hyperproducer Clostridium saccharoperbutylacetonicum Strain N1-4.

While a majority of academic studies concerning acetone, butanol, and ethanol (ABE) production by Clostridium have focused on Clostridium acetobutylicum, other members of this genus have proven to be effective industrial workhorses despite the inability to perform genetic manipulations on many of these strains. To further improve the industrial performance of these strains in areas such as substrate usage, solvent production, and end product versatility, transformation methods and genetic tools are needed to overcome the genetic intractability displayed by these species. In this study, we present the development of a high-efficiency transformation method for the industrial butanol hyperproducer Clostridium saccharoperbutylacetonicum strain N1-4 (HMT) ATCC 27021. Following initial failures, we found that the key to creating a successful transformation method was the identification of three distinct colony morphologies (types S, R, and I), which displayed significant differences in transformability. Working with the readily transformable type I cells (transformation efficiency, 1.1 × 106 CFU/µg DNA), we performed targeted gene deletions in C. saccharoperbutylacetonicum N1-4 using a homologous recombination-mediated allelic exchange method. Using plasmid-based gene overexpression and targeted knockouts of key genes in the native acetone-butanol-ethanol (ABE) metabolic pathway, we successfully implemented rational metabolic engineering strategies, yielding in the best case an engineered strain (Clostridium saccharoperbutylacetonicum strain N1-4/pWIS13) displaying an 18% increase in butanol titers and 30% increase in total ABE titer (0.35 g ABE/g sucrose) in batch fermentations. Additionally, two engineered strains overexpressing aldehyde/alcohol dehydrogenases (encoded by adh11 and adh5) displayed 8.5- and 11.8-fold increases (respectively) in batch ethanol production. IMPORTANCE: This paper presents the first steps toward advanced genetic engineering of the industrial butanol producer Clostridium saccharoperbutylacetonicum strain N1-4 (HMT). In addition to providing an efficient method for introducing foreign DNA into this species, we demonstrate successful rational engineering for increasing solvent production. Examples of future applications of this work include metabolic engineering for improving desirable industrial traits of this species and heterologous gene expression for expanding the end product profile to include high-value fuels and chemicals.

Interplay of Nitrogen-Atom Inversion and Conformational Inversion in Enantiomerization of 1H-1-Benzazepines.

A series of 2,4-disubstituted 1H-1-benzazepines, 2a-d, 4, and 6, were studied, varying both the substituents at C2 and C4 and at the nitrogen atom. The conformational inversion (ring-flip) and nitrogen-atom inversion (N-inversion) energetics were studied by variable-temperature NMR spectroscopy and computations. The steric bulk of the nitrogen-atom substituent was found to affect both the conformation of the azepine ring and the geometry around the nitrogen atom. Also affected were the Gibbs free energy barriers for the ring-flip and the N-inversion. When the nitrogen-atom substituent was alkyl, as in 2a-c, the geometry of the nitrogen atom was nearly planar and the azepine ring was highly puckered; the result was a relatively high-energy barrier to ring-flip and a low barrier to N-inversion. Conversely, when the nitrogen-atom substituent was a hydrogen atom, as in 2d, 4, and 6, the nitrogen atom was significantly pyramidalized and the azepine ring was less puckered; the result here was a relatively high energy barrier to N-inversion and a low barrier to ring-flip. In these N-unsubstituted compounds, it was found computationally that the lowest-energy stereodynamic process was ring-flip coupled with N-inversion, as N-inversion alone had a much higher energy barrier.

Adjuvant cationic liposomes presenting MPL and IL-12 induce cell death, suppress tumor growth, and alter the cellular phenotype of tumors in a murine model of breast cancer.

Dendritic cells (DC) process and present antigens to T lymphocytes, inducing potent immune responses when encountered in association with activating signals, such as pathogen-associated molecular patterns. Using the 4T1 murine model of breast cancer, cationic liposomes containing monophosphoryl lipid A (MPL) and interleukin (IL)-12 were administered by intratumoral injection. Combination multivalent presentation of the Toll-like receptor-4 ligand MPL and cytotoxic 1,2-dioleoyl-3-trmethylammonium-propane lipids induced cell death, decreased cellular proliferation, and increased serum levels of IL-1ß and tumor necrosis factor (TNF)-α. The addition of recombinant IL-12 further suppressed tumor growth and increased expression of IL-1ß, TNF-α, and interferon-γ. IL-12 also increased the percentage of cytolytic T cells, DC, and F4/80(+) macrophages in the tumor. While single agent therapy elevated levels of nitric oxide synthase 3-fold above basal levels in the tumor, combination therapy with MPL cationic liposomes and IL-12 stimulated a 7-fold increase, supporting the observed cell cycle arrest (loss of Ki-67 expression) and apoptosis (TUNEL positive). In mice bearing dual tumors, the growth of distal, untreated tumors mirrored that of liposome-treated tumors, supporting the presence of a systemic immune response.

Comparing Peer-Taught Student Tutors to Faculty-Taught Student Tutors in Educating Medical Students on Musculoskeletal Ultrasound.

INTRODUCTION: In recent years, medical education has witnessed a shift in the integration of ultrasound into the preclinical years of medical school. Given the exponential increase in accessibility to ultrasound technology, students now have the opportunity to create peer learning groups in which ultrasound concepts can be taught from peer to peer, empowering students to work together to integrate ultrasound concepts early in their preclinical education. This project investigates the efficacy of peer-taught student tutors (PTSTs) in imparting the fundamentals of basic ultrasound techniques to first-year medical students in the setting of identifying and labeling upper extremity musculoskeletal (MSK) anatomy.  Methods: First-year medical students were instructed to identify volar forearm structures with an ultrasound probe. Students and instructors were given access to an ultrasound probe, ultrasound gel, an iPad, and a standardized patient. Students were taught either by an ultrasound instructor (UI) or PTST. After a hands-on demonstration by a UI or PTST, participating students were told to take screenshots and label their images as accurately as possible, identifying the aforementioned volar structures on a standardized patient without any feedback. The labeled screenshot images of volar structures were graded based on the ability to clearly visualize the intended structures.  Results: The results of this study compare the efficacy of PTSTs as educators of basic sonographic identification techniques with that of UI faculty members. A chi-square analysis was performed between the images obtained by the UI and PTST students, and there was no statistically significant difference in identification accuracy between the groups (p = 0.7538, 0.1977, 0.1812, 0.301). When using the Mann-Whitney U rank test, there remained no statistically significant difference between the accuracy of the students taught by STs compared to students taught by UIs (p = 0.7744, 0.09538, 0.07547, 0.1846). Another finding showed that students belonging to both teaching groups were generally not able to infer the pathology of volar wrist structures when given pathology identification questions regarding upper extremity ultrasound. Using chi-square with Yates correction, there is no sufficient evidence to justify an association between the ability to answer pathology-based ultrasound questions and instructor type (p = p = 0.6299, 0.8725). CONCLUSIONS: This study supports the interpretation that the capability of first-year medical students to learn novice MSK sonographic identification is independent of whether the educator is a PTST or UI. This interpretation reveals a promising avenue toward the integration of the fundamentals of ultrasound identification early in medical education with little to no concern for the exhaustion of institutional resources. Along with the other well-documented benefits of the utilization of STs in medical school, a peer tutoring system centered on ultrasound skills designed in the way this study describes can be an effective, resource-sparing system that enhances medical students' sonographic capabilities early in their preclinical years.

3D bioprinting: a review and potential applications for Mohs micrographic surgery.

Mohs Micrographic Surgery (MMS) is effective for treating common cutaneous malignancies, but complex repairs may often present challenges for reconstruction. This paper explores the potential of three-dimensional (3D) bioprinting in MMS, offering superior outcomes compared to traditional methods. 3D printing technologies show promise in advancing skin regeneration and refining surgical techniques in dermatologic surgery. A PubMed search was conducted using the following keywords: "Three-dimensional bioprinting" OR "3-D printing" AND "Mohs" OR "Mohs surgery" OR "Surgery." Peer-reviewed English articles discussing medical applications of 3D bioprinting were included, while non-peer-reviewed and non-English articles were excluded. Patients using 3D MMS models had lower anxiety scores (3.00 to 1.7, p < 0.0001) and higher knowledge assessment scores (5.59 or 93.25% correct responses), indicating better understanding of their procedure. Surgical residents using 3D models demonstrated improved proficiency in flap reconstructions (p = 0.002) and knowledge assessment (p = 0.001). Additionally, 3D printing offers personalized patient care through tailored surgical guides and anatomical models, reducing intraoperative time while enhancing surgical. Concurrently, efforts in tissue engineering and regenerative medicine are being explored as potential alternatives to address organ donor shortages, eliminating autografting needs. However, challenges like limited training and technological constraints persist. Integrating optical coherence tomography with 3D bioprinting may expedite grafting, but challenges remain in pre-printing grafts for complex cases. Regulatory and ethical considerations are paramount for patient safety, and further research is needed to understand long-term effects and cost-effectiveness. While promising, significant advancements are necessary for full utilization in MMS.

Immune checkpoint inhibitor associated epidermal necrosis, beyond SJS and TEN: a review of 98 cases.

Immune checkpoint inhibitor (ICI) therapies carry the risk of major immune-related adverse events (irAEs). Among the most severe irAEs is epidermal necrosis that may clinically mimic Stevens-Johnson syndrome (SJS) and toxic epidermal necrosis (TEN). The aim of this study was to provide a summary of the clinical and histological features of ICI-associated epidermal necrosis, with a special focus on factors associated with fatal outcomes in cases of extensive disease. A total of 98 cases, 2 new cases and 96 reported on PubMed and in the literature, of ICI-associated epidermal necrosis were assessed. Development of epidermal necrosis occurred between 1 day and 3 years after starting ICI therapy, with an average onset of 13.8 weeks for patients with limited (< 30% BSA) and 11.3 weeks for those with extensive (≥ 30% BSA) involvement, and a median onset of 5.8 weeks and 4 weeks respectively. A preceding rash was seen in 52 cases and was more common in extensive cases. Mucosal involvement was only reported in 65% of extensive cases but was significantly associated with fatal reactions. Co-administration of cytotoxic chemotherapy was associated with more extensive disease. Recovery was observed in 96% and 65% of those with limited and extensive involvement respectively and no specific therapy was associated with improved survival. Young age was significantly associated with poor outcomes in extensive disease, the average age of surviving patients was 64.5 years old versus 55.1 years old for deceased patients, p < 0.01. Both superficial perivascular and interface/lichenoid inflammatory infiltrates were commonly seen. These findings suggest that ICI-associated epidermal necrosis should be considered a distinct clinical entity from drug-induced SJS/TEN.