Cdk8/CDK19 promotes mitochondrial fission through Drp1 phosphorylation and can phenotypically suppress pink1 deficiency in Drosophila.

Cdk8 in Drosophila is the orthologue of vertebrate CDK8 and CDK19. These proteins have been shown to modulate transcriptional control by RNA polymerase II. We found that neuronal loss of Cdk8 severely reduces fly lifespan and causes bang sensitivity. Remarkably, these defects can be rescued by expression of human CDK19, found in the cytoplasm of neurons, suggesting a non-nuclear function of CDK19/Cdk8. Here we show that Cdk8 plays a critical role in the cytoplasm, with its loss causing elongated mitochondria in both muscles and neurons. We find that endogenous GFP-tagged Cdk8 can be found in both the cytoplasm and nucleus. We show that Cdk8 promotes the phosphorylation of Drp1 at S616, a protein required for mitochondrial fission. Interestingly, Pink1, a mitochondrial kinase implicated in Parkinson's disease, also phosphorylates Drp1 at the same residue. Indeed, overexpression of Cdk8 significantly suppresses the phenotypes observed in flies with low levels of Pink1, including elevated levels of ROS, mitochondrial dysmorphology, and behavioral defects. In summary, we propose that Pink1 and Cdk8 perform similar functions to promote Drp1-mediated fission.

Next-generation DNA sequencing of Panax samples revealed new genotypes: Burrows-Wheeler Aligner, Python-based abundance and clustering analysis.

Background: There are two major species of the Panax genus, namely Panax ginseng and Panax quinquefolius. Other than the nucleic acid test and nucleic acid amplification test, DNA sequencing can be used to authenticate the species of ginseng samples, especially when their physical forms cannot be used for differentiation. Method: In this work, next generation sequencing was used to obtain millions of reads from fourteen ginseng samples (root, powder, and granule). Then Gaussian Mixture clustering analysis was applied to analyze the reads from each sample. Results and Discussion: A new genotype has been revealed in this study. Two samples have been authenticated with certainty, while the others may be hybrid in nature as revealed by the clustering results.

Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening.

STING is an innate immune sensor that traffics across many cellular compartments to carry out its function of detecting cyclic di-nucleotides and triggering defense processes. Mutations in factors that regulate this process are often linked to STING-dependent human inflammatory disorders. To systematically identify factors involved in STING trafficking, we performed a genome-wide optical pooled screen and examined the impact of genetic perturbations on intracellular STING localization. Based on subcellular imaging of STING protein and trafficking markers in 45 million cells perturbed with sgRNAs, we defined 464 clusters of gene perturbations with similar cellular phenotypes. A higher-dimensional focused optical pooled screen on 262 perturbed genes which assayed 11 imaging channels identified 73 finer phenotypic clusters. In a cluster containing USE1, a protein that mediates Golgi to ER transport, we found a gene of unknown function, C19orf25. Consistent with the known role of USE1, loss of C19orf25 enhanced STING signaling. Other clusters contained subunits of the HOPS, GARP and RIC1-RGP1 complexes. We show that HOPS deficiency delayed STING degradation and consequently increased signaling. Similarly, GARP/RIC1-RGP1 loss increased STING signaling by delaying STING exit from the Golgi. Our findings demonstrate that genome-wide genotype-phenotype maps based on high-content cell imaging outperform other screening approaches, and provide a community resource for mining for factors that impact STING trafficking as well as other cellular processes observable in our dataset.

Plant and soil responses to tillage practices change arbuscular mycorrhizal fungi populations during crop growth.

Background: Tillage practices can substantially affect soil properties depending on crop stage. The interaction between tillage and crop growth on arbuscular mycorrhizal fungi (AMF) communities remains unclear. We investigated the interactions between four tillage treatments (CT: conventional tillage, RT: reduced tillage, NT: no tillage with mulch, and SS: subsoiling with mulch), maintained for 25 years, and two wheat growth stages (elongation stage and grain filling stage) on AMF diversity and community composition. Results: The AMF community composition strongly changed during wheat growth, mainly because of changes in the relative abundance of dominant genera Claroideoglomus, Funneliformi, Rhizophagu, Entrophospora, and Glomus. Co-occurrence network analysis revealed that the grain filling stage had a more complex network than the elongation stage. Redundancy analysis results showed that keystone genera respond mainly to changes in soil organic carbon during elongation stage, whereas the total nitrogen content affected the keystone genera during grain filling. Compared with CT, the treatments with mulch, i.e., NT and SS, significantly changed the AMF community composition. The change of AMF communities under different tillage practices depended on wheat biomass and soil nutrients. NT significantly increased the relative abundances of Glomus and Septoglomus, while RT significantly increased the relative abundance of Claroideoglomus. Conclusion: Our findings indicate that the relative abundance of dominant genera changed during wheat growth stages. Proper tillage practices (e.g., NT and SS) benefit the long-term sustainable development of the Loess Plateau cropping systems.

Improved all-cause mortality with left bundle branch area pacing compared to biventricular pacing in cardiac resynchronization therapy: a meta-analysis.

BACKGROUND: Left bundle branch area pacing (LBBAP) has emerged as a physiological alternative pacing strategy to biventricular pacing (BIVP) in cardiac resynchronization therapy (CRT). We aimed to assess the impact of LBBAP vs. BIVP on all-cause mortality and heart failure (HF)-related hospitalization in patients undergoing CRT. METHODS: Studies comparing LBBAP and BIVP for CRT in patients with HF with reduced left ventricular ejection fraction (LVEF) were included. The coprimary outcomes were all-cause mortality and HF-related hospitalization. Secondary outcomes included procedural and fluoroscopy time, change in QRS duration, and change in LVEF. RESULTS: Thirteen studies (12 observational and 1 RCT, n = 3239; LBBAP = 1338 and BIVP = 1901) with a mean follow-up duration of 25.8 months were included. Compared to BIVP, LBBAP was associated with a significant absolute risk reduction of 3.2% in all-cause mortality (9.3% vs 12.5%, RR 0.7, 95% CI 0.57-0.86, p < 0.001) and an 8.2% reduction in HF-related hospitalization (11.3% vs 19.5%, RR 0.6, 95% CI 0.5-0.71, p < 0.00001). LBBAP also resulted in reductions in procedural time (mean weighted difference- 23.2 min, 95% CI - 42.9 to - 3.6, p = 0.02) and fluoroscopy time (- 8.6 min, 95% CI - 12.5 to - 4.7, p < 0.001) as well as a significant reduction in QRS duration (mean weighted difference:- 25.3 ms, 95% CI - 30.9 to - 19.8, p < 0.00001) and a greater improvement in LVEF of 5.1% (95% CI 4.4-5.8, p < 0.001) compared to BIVP in the studies that reported these outcomes. CONCLUSION: In this meta-analysis, LBBAP was associated with a significant reduction in all-cause mortality as well as HF-related hospitalization when compared to BIVP. Additional data from large RCTs is warranted to corroborate these promising findings.

The impact of three learning methods on dental students' satisfaction and knowledge acquisition.

OBJECTIVES: Health professionals' education presents unique challenges including clinical application of knowledge and interprofessional collaboration. Additionally, institutions suffer from faculty shortages while class sizes increase. Therefore, educators seek innovative andragogical techniques utilizing minimal resources. Several active learning methods have been introduced as a solution. The aim of this study is to assess the impact of lecture (LBL), case (CBL), and team (TBL) based learning on the students' satisfaction and knowledge attainment. METHODS: A total of 134 sophomore dental students are taught pediatric dentistry course using LBL, CBL, and TBL techniques. At the end of the course, students are invited to participate in a satisfaction survey. Statistical analysis is conducted using a two-sided chi-square goodness of fit test. Students' comments are used for qualitative analysis. Final exam analysis is administered via Examsoft software. RESULTS: A total of 98% of the students participated in the survey out of which 83% met the inclusion criteria (N = 110). Students chose LBL as the method that helped them learn in a comprehensive way, provided the most comfortable environment, and presented the overall highest satisfaction with statistically significant difference (p value = 0.001). LBL questions scored the highest point biserial and discrimination index. The percentage of correct answers and difficulty level was highest for TBL. CONCLUSION: Students preferred LBL over the other learning methods. Final exam psychometrics showed favorable results for LBL and TBL. Students could potentially benefit from combining both techniques. However, more research is needed to assess the effectiveness of various teaching methods on the short- and long-term learning outcomes.

Acute Heart Valve Emergencies.

Within the cardiac intensive care unit, prompt recognition of severe acute valvular lesions is essential because hemodynamic collapse can occur rapidly, especially when cardiac chambers have not had time for compensatory remodeling. Within this context, optimal medical management, considerations for temporary mechanical circulatory support and decisive treatments strategies are addressed. Fundamental concepts include an appreciation for how sudden changes in flow and pressure gradients between cardiac chambers can impact hemodynamic and echocardiographic findings differently compared to similarly severe chronic lesions, as well as understanding the main causes for decompensated heart failure and cardiogenic shock for each valvular abnormality.

The continued financial effect of COVID: Increasing costs for non-elective major lower extremity amputations.

Background: The COVID-19 pandemic necessitated changes in processes of care, which significantly impacted surgical care. This study evaluated the impact of these changes on patient outcomes and costs for non-elective major lower extremity amputations (LEA). Methods: The 2019-2021 Florida Agency for Health Care Administration database was queried for adult patients who underwent non-elective major LEA. Per-patient inflation-adjusted costs were collected. Patient cohorts were established based on Florida COVID-19 mortality rates: COVID-heavy (CH) included nine months with the highest mortality, COVID-light (CL) included nine months with the lowest mortality, and pre-COVID (PC) included nine months before COVID (2019). Outcomes included in-hospital patient outcomes and hospitalization cost. Results: 6132 patients were included (1957 PC, 2104 CH, and 2071 CL). Compared to PC, there was increased patient acuity at presentation, but morbidity (31%), mortality (4%), and length of stay (median 12 [8-17] days) were unchanged during CH and CL. Additionally, costs significantly increased during the pandemic; median total cost rose 9%, room costs increased by 16%, ICU costs rose by 15%, and operating room costs rose by 15%. When COVID-positive patients were excluded, cost of care was still significantly higher during CH and CL. Conclusions: Despite maintaining pre-pandemic standards, as evidenced by unchanged outcomes, the pandemic led to increased costs for patients undergoing non-elective major LEA. This was likely due to increased patient acuity, resource strain, and supply chain shortages during the pandemic. Key message: While patient outcomes for non-elective major lower extremity amputations remained consistent during the COVID-19 pandemic, healthcare costs significantly increased, likely due to increased patient acuity and heightened pressures on resources and supply chains. These findings underscore the need for informed policy changes to mitigate the financial impact on patients and healthcare systems for future public health emergencies.

Fluoroscopy-Assisted Computer Navigation Accurately Determines Cup Position and Leg Length for Anterior Hip Arthroplasty.

BACKGROUND: Recently, fluoroscopy-assisted computer navigation has been developed to assess intraoperative cup inclination/anteversion and leg-length discrepancy (LLD) in the operating room. However, there is a relative dearth of studies investigating the accuracy of this software compared with postoperative radiographs. MATERIALS AND METHODS: We prospectively enrolled 211 navigated anterior total hip arthroplasties using fluoroscopy-assisted computer navigation software. Intraoperative navigated measurements were compared with postoperative anteroposterior radiographs to assess accuracy of cup inclination/anteversion and LLD. Continuous variables were analyzed using the Student's t test, and categorical variables were analyzed using Fisher's exact test. RESULTS: On postoperative radiographs, 94.3% of cups (199 of 211) were positioned within the Lewinnek "safe zone," compared with 99.1% navigated intraoperatively (P=.01). Eighty-two percent of hips (174 of 211) were navigated intraoperatively to LLDs within ±2 mm; on postoperative radiographs, 65% of hips (138 of 211) had LLDs within ±2 mm (P=.0001). Intraoperatively, 100% of hips (211 of 211) were navigated to LLDs within ±5 mm; similarly, on postoperative radiographs, 98% of hips (207 of 211) had LLDs within ±5 mm (P=.12). CONCLUSION: A novel fluoroscopy-assisted computer navigation platform accurately assessed intraoperative cup position and LLD during anterior total hip arthroplasty. Careful attention to fluoroscopic technique, positioning of radiographic landmarks, and knowledge of the limitations of fluoroscopy, including parallax effect, are important concepts that surgeons should incorporate into their decision algorithm. [Orthopedics. 202x;4x(x):xx-xx.].

CROPseq-multi: a versatile solution for multiplexed perturbation and decoding in pooled CRISPR screens.

Forward genetic screens seek to dissect complex biological systems by systematically perturbing genetic elements and observing the resulting phenotypes. While standard screening methodologies introduce individual perturbations, multiplexing perturbations improves the performance of single-target screens and enables combinatorial screens for the study of genetic interactions. Current tools for multiplexing perturbations are incompatible with pooled screening methodologies that require mRNA-embedded barcodes, including some microscopy and single cell sequencing approaches. Here, we report the development of CROPseq-multi, a CROPseq1-inspired lentiviral system to multiplex Streptococcus pyogenes (Sp) Cas9-based perturbations with mRNA-embedded barcodes. CROPseq-multi has equivalent per-guide activity to CROPseq and low lentiviral recombination frequencies. CROPseq-multi is compatible with enrichment screening methodologies and optical pooled screens, and is extensible to screens with single-cell sequencing readouts. For optical pooled screens, an optimized and multiplexed in situ detection protocol improves barcode detection efficiency 10-fold, enables detection of recombination events, and increases decoding efficiency 3-fold relative to CROPseq. CROPseq-multi is a widely applicable multiplexing solution for diverse SpCas9-based genetic screening approaches.

Experimental evidence for Parthanatos-like mode of cell death of heat-damaged human skin fibroblasts in a cell culture-based in vitro burn model.

The cellular mechanisms of burn conversion of heat damaged tissue are center of many studies. Even if the molecular mechanisms of heat-induced cell death are controversially discussed in the current literature, it is widely accepted that caspase-mediated apoptosis plays a central role. In the current study we wanted to develop further information on the nature of the mechanism of heat-induced cell death of fibroblasts in vitro. We found that heating of human fibroblast cultures (a 10 s rise from 37 °C to 67 °C followed by a 13 s cool down to 37 °C) resulted in the death of about 50% of the cells. However, the increase in cell death started with a delay, about one hour after exposure to heat, and reached the maximum after about five hours. The lack of clear evidence for an active involvement of effector caspase in the observed cell death mechanism and the lack of observation of the occurrence of hypodiploid nuclei contradict heat-induced cell death by caspase-mediated apoptosis. Moreover, a dominant heat-induced increase in PARP1 protein expression, which correlated with a time-delayed ATP synthesis inhibition, appearance of double-strand breaks and secondary necrosis, indicate a different type of cell death than apoptosis. Indeed, increased translocation of Apoptosis Inducing Factor (AIF) and Macrophage Migration Inhibitory Factor (MIF) into cell nuclei, which correlates with the mentioned enhanced PARP1 protein expression, indicate PARP1-induced, AIF-mediated and MIF-activated cell death. With regard to the molecular actors involved, the cellular processes and temporal sequences, the mode of cell death observed in our model is very similar to the cell death mechanism via Parthanatos described in the literature.

Prolonged Ileus Due to Underlying Shigella Infection After Bilateral Open Inguinal Hernia Repair.

We present a rare case of prolonged ileus caused by underlying Shigella infection after surgical hernia repair. Infectious disease is an uncommon cause of postoperative prolonged ileus in adults. Our 48-year-old male patient underwent bilateral open inguinal hernia repair and open umbilical hernia repair without complication at an academic institution, with same-day discharge. Eight days later, he presented to the emergency department with complaints of severe cramping abdominal pain, nausea, emesis, and watery diarrhea. Physical examination, computed tomography scan of the abdomen and pelvis, and abdominal X-ray were initially concerning for bowel obstruction. The patient was admitted to the general surgery service. Concern for ileus with underlying gastritis arose after a small bowel follow-through showed contrast eventually reaching the rectum. A subsequent gastrointestinal pathogens panel was positive for Shigella. The patient's symptoms resolved after appropriate antibiotic treatment. Shigellosis and other infectious diseases should be considered in the differential diagnosis of postoperative prolonged ileus.

Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine.

Biofluids contain molecules in circulation and from nearby organs that can be indicative of disease states. Characterizing the proteome of biofluids with DIA-MS is an emerging area of interest for biomarker discovery; yet, there is limited consensus on DIA-MS data analysis approaches for analyzing large numbers of biofluids. To evaluate various DIA-MS workflows, we collected urine from a clinically heterogeneous cohort of prostate cancer patients and acquired data in DDA and DIA scan modes. We then searched the DIA data against urine spectral libraries generated using common library generation approaches or a library-free method. We show that DIA-MS doubles the sample throughput compared to standard DDA-MS with minimal losses to peptide detection. We further demonstrate that using a sample-specific spectral library generated from individual urines maximizes peptide detection compared to a library-free approach, a pan-human library, or libraries generated from pooled, fractionated urines. Adding urine subproteomes, such as the urinary extracellular vesicular proteome, to the urine spectral library further improves the detection of prostate proteins in unfractionated urine. Altogether, we present an optimized DIA-MS workflow and provide several high-quality, comprehensive prostate cancer urine spectral libraries that can streamline future biomarker discovery studies of prostate cancer using DIA-MS.

Management Strategies for Malignant Left-Sided Colonic Obstruction: A Systematic Review and Network Meta-analysis of Randomized Controlled Trials and Propensity Score Matching Studies.

BACKGROUND: The optimal treatment strategy for left-sided malignant colonic obstruction remains controversial. Emergency colonic resection has been the standard of care; however, self-expanding metallic stenting as a bridge to surgery may offer short-term advantages, although oncological concerns exist. Decompressing stoma may provide a valid alternative, with limited evidence. OBJECTIVE: To perform a systematic review and Bayesian arm random effects model network meta-analysis comparing the approaches for management of malignant left-sided colonic obstruction. DATA SOURCES: A systematic review was conducted from inception to August 22, 2023, of PubMed, Embase, Cochrane Library, and Google Scholar databases. STUDY SELECTION: Randomized controlled trials and propensity score matched studies. INTERVENTIONS: Emergency colonic resection, self-expanding metallic stent, decompressing stoma. MAIN OUTCOME MEASURES: Oncologic efficacy, morbidity, successful minimally invasive surgery, primary anastomosis, and permanent stoma rates. RESULTS: Nineteen articles from 5225 identified met our inclusion criteria. Stenting (risk ratio 0.57, 95% credible interval: 0.33, 0.79) and decompressing stomas (risk ratio 0.46, 95% credible interval: 0.18, 0.92) both resulted in a significant reduction in the permanent stoma rate. Stenting facilitated minimally invasive surgery more frequently (risk ratio 4.10, 95% credible interval: 1.45, 13.13) and had lower overall morbidity (risk ratio 0.58, 95% credible interval: 0.35, 0.86). A pairwise analysis of primary anastomosis rates showed an increase in stenting (risk ratio 1.40, 95% credible interval: 1.31, 1.49) as compared with emergency resection. There was a significant decrease in the 90-day mortality with stenting (risk ratio 0.63, 95% credible interval: 0.41, 0.95) when compared with resection. There were no differences in disease-free and overall survival rates, respectively. LIMITATIONS: There is a lack of randomized controlled trial and propensity score matching data comparing short and long-term outcomes for diverting stomas compared to self-expanding metallic stents. Two trials compared self-expanding metallic stents and diverting stomas in left-sided malignant colonic obstruction. CONCLUSION: This study provides high-level evidence that bridge-to-surgery strategy is safe for the management of left-sided malignant colonic obstruction, and may facilitate minimally invasive surgery, increase primary anastomosis rates, and reduce permanent stoma rates and postoperative morbidity as compared to emergency colonic resection.

Global density equations for interacting particle systems with stochastic resetting: From overdamped Brownian motion to phase synchronization.

A wide range of phenomena in the natural and social sciences involve large systems of interacting particles, including plasmas, collections of galaxies, coupled oscillators, cell aggregations, and economic "agents." Kinetic methods for reducing the complexity of such systems typically involve the derivation of nonlinear partial differential equations for the corresponding global densities. In recent years, there has been considerable interest in the mean field limit of interacting particle systems with long-range interactions. Two major examples are interacting Brownian particles in the overdamped regime and the Kuramoto model of coupled phase oscillators. In this paper, we analyze these systems in the presence of local or global stochastic resetting, where the position or phase of each particle independently or simultaneously resets to its original value at a random sequence of times generated by a Poisson process. In each case, we derive the Dean-Kawasaki (DK) equation describing hydrodynamic fluctuations of the global density and then use a mean field ansatz to obtain the corresponding nonlinear McKean-Vlasov (MV) equation in the thermodynamic limit. In particular, we show how the MV equation for global resetting is driven by a Poisson noise process, reflecting the fact that resetting is common to all of the particles and, thus, induces correlations that cannot be eliminated by taking a mean field limit. We then investigate the effects of local and global resetting on nonequilibrium stationary solutions of the macroscopic dynamics and, in the case of the Kuramoto model, the reduced dynamics on the Ott-Antonsen manifold.

Phylogenomics and the rise of the angiosperms.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Theoretical model of femtosecond coherence spectroscopy of vibronic excitons in molecular aggregates.

When used as pump pulses in transient absorption spectroscopy measurements, femtosecond laser pulses can produce oscillatory signals known as quantum beats. The quantum beats arise from coherent superpositions of the states of the sample and are best studied in the Fourier domain using Femtosecond Coherence Spectroscopy (FCS), which consists of one-dimensional amplitude and phase plots of a specified oscillation frequency as a function of the detection frequency. Prior works have shown ubiquitous amplitude nodes and π phase shifts in FCS from excited-state vibrational wavepackets in monomer samples. However, the FCS arising from vibronic-exciton states in molecular aggregates have not been studied theoretically. Here, we use a model of vibronic-exciton states in molecular dimers based on displaced harmonic oscillators to simulate FCS for dimers in two important cases. Simulations reveal distinct spectral signatures of excited-state vibronic-exciton coherences in molecular dimers that may be used to distinguish them from monomer vibrational coherences. A salient result is that, for certain relative orientations of the transition dipoles, the key resonance condition between the electronic coupling and the frequency of the vibrational mode may yield strong enhancement of the quantum-beat amplitude and, perhaps, also cause a significant decrease of the oscillation frequency to a value far lower than the vibrational frequency. Future studies using these results will lead to new insights into the excited-state coherences generated in photosynthetic pigment-protein complexes.