Global identification of SWI/SNF targets reveals compensation by EP400.

Mammalian SWI/SNF chromatin remodeling complexes move and evict nucleosomes at gene promoters and enhancers to modulate DNA access. Although SWI/SNF subunits are commonly mutated in disease, therapeutic options are limited by our inability to predict SWI/SNF gene targets and conflicting studies on functional significance. Here, we leverage a fast-acting inhibitor of SWI/SNF remodeling to elucidate direct targets and effects of SWI/SNF. Blocking SWI/SNF activity causes a rapid and global loss of chromatin accessibility and transcription. Whereas repression persists at most enhancers, we uncover a compensatory role for the EP400/TIP60 remodeler, which reestablishes accessibility at most promoters during prolonged loss of SWI/SNF. Indeed, we observe synthetic lethality between EP400 and SWI/SNF in cancer cell lines and human cancer patient data. Our data define a set of molecular genomic features that accurately predict gene sensitivity to SWI/SNF inhibition in diverse cancer cell lines, thereby improving the therapeutic potential of SWI/SNF inhibitors.

ecDNA party bus: Bringing the enhancer to you.

Recent work from Zhu et al. (2021) reveals that extrachromosomal DNA circles harboring enhancers can serve as mobile regulatory elements that interact with chromosomal oncogenes, stimulating high-level gene activity and contributing to tumor heterogeneity and cancer progression.

Wild animals suppress the spread of socially transmitted misinformation.

Understanding the mechanisms by which information and misinformation spread through groups of individual actors is essential to the prediction of phenomena ranging from coordinated group behaviors to misinformation epidemics. Transmission of information through groups depends on the rules that individuals use to transform the perceived actions of others into their own behaviors. Because it is often not possible to directly infer decision-making strategies in situ, most studies of behavioral spread assume that individuals make decisions by pooling or averaging the actions or behavioral states of neighbors. However, whether individuals may instead adopt more sophisticated strategies that exploit socially transmitted information, while remaining robust to misinformation, is unknown. Here, we study the relationship between individual decision-making and misinformation spread in groups of wild coral reef fish, where misinformation occurs in the form of false alarms that can spread contagiously through groups. Using automated visual field reconstruction of wild animals, we infer the precise sequences of socially transmitted visual stimuli perceived by individuals during decision-making. Our analysis reveals a feature of decision-making essential for controlling misinformation spread: dynamic adjustments in sensitivity to socially transmitted cues. This form of dynamic gain control can be achieved by a simple and biologically widespread decision-making circuit, and it renders individual behavior robust to natural fluctuations in misinformation exposure.

STAT3 is a master regulator of epithelial identity and KRAS-driven tumorigenesis.

A dichotomy exists regarding the role of signal transducer and activator of transcription 3 (STAT3) in cancer. Functional and genetic studies demonstrate either an intrinsic requirement for STAT3 or a suppressive effect on common types of cancer. These contrasting actions of STAT3 imply context dependency. To examine mechanisms that underlie STAT3 function in cancer, we evaluated the impact of STAT3 activity in KRAS-driven lung and pancreatic cancer. Our study defines a fundamental and previously unrecognized function of STAT3 in the maintenance of epithelial cell identity and differentiation. Loss of STAT3 preferentially associates with the acquisition of mesenchymal-like phenotypes and more aggressive tumor behavior. In contrast, persistent STAT3 activation through Tyr705 phosphorylation confers a differentiated epithelial morphology that impacts tumorigenic potential. Our results imply a mechanism in which quantitative differences of STAT3 Tyr705 phosphorylation, as compared with other activation modes, direct discrete outcomes in tumor progression.

An out-of-equilibrium definition of protein turnover.

Protein turnover (PT) has been formally defined only in equilibrium conditions, which is ill-suited to quantify PT during dynamic processes that occur during embryogenesis or (extra) cellular signaling. In this Hypothesis, we propose a definition of PT in an out-of-equilibrium regime that allows the quantification of PT in virtually any biological context. We propose a simple mathematical and conceptual framework applicable to a broad range of available data, such as RNA sequencing coupled with pulsed-SILAC datasets. We apply our framework to a published dataset and show that stimulation of mouse dendritic cells with LPS leads to a proteome-wide change in PT. This is the first quantification of PT out-of-equilibrium, paving the way for the analysis of biological systems in other contexts.

Exploring the role of transcriptional and post-transcriptional processes in mRNA co-expression.

Co-expression of two or more genes at the single-cell level is usually associated with functional co-regulation. While mRNA co-expression-measured as the correlation in mRNA levels-can be influenced by both transcriptional and post-transcriptional events, transcriptional regulation is typically considered dominant. We review and connect the literature describing transcriptional and post-transcriptional regulation of co-expression. To enhance our understanding, we integrate four datasets spanning single-cell gene expression data, single-cell promoter activity data and individual transcript half-lives. Confirming expectations, we find that positive co-expression necessitates promoter coordination and similar mRNA half-lives. Surprisingly, negative co-expression is favored by differences in mRNA half-lives, contrary to initial predictions from stochastic simulations. Notably, this association manifests specifically within clusters of genes. We further observe a striking compensation between promoter coordination and mRNA half-lives, which additional stochastic simulations suggest might give rise to the observed co-expression patterns. These findings raise intriguing questions about the functional advantages conferred by this compensation between distal kinetic steps.

Cell cycle perturbation uncouples mitotic progression and invasive behavior in a post-mitotic cell.

The acquisition of the post-mitotic state is crucial for the execution of many terminally differentiated cell behaviors during organismal development. However, the mechanisms that maintain the post-mitotic state in this context remain poorly understood. To gain insight into these mechanisms, we used the genetically and visually accessible model of C. elegans anchor cell (AC) invasion into the vulval epithelium. The AC is a terminally differentiated uterine cell that normally exits the cell cycle and enters a post-mitotic state before initiating contact between the uterus and vulva through a cell invasion event. Here, we set out to identify the set of negative cell cycle regulators that maintain the AC in this post-mitotic, invasive state. Our findings revealed a critical role for CKI-1 (p21CIP1/p27KIP1) in redundantly maintaining the post-mitotic state of the AC, as loss of CKI-1 in combination with other negative cell cycle regulators-including CKI-2 (p21CIP1/p27KIP1), LIN-35 (pRb/p107/p130), FZR-1 (Cdh1/Hct1), and LIN-23 (ß-TrCP)-resulted in proliferating ACs. Remarkably, time-lapse imaging revealed that these ACs retain their ability to invade. Upon examination of a node in the gene regulatory network controlling AC invasion, we determined that proliferating, invasive ACs do so by maintaining aspects of pro-invasive gene expression. We therefore report that the requirement for a post-mitotic state for invasive cell behavior can be bypassed following direct cell cycle perturbation.

Mesoderm induction and patterning: Insights from neuromesodermal progenitors.

The discovery of mesoderm inducing signals helped usher in the era of molecular developmental biology, and today the mechanisms of mesoderm induction and patterning are still intensely studied. Mesoderm induction begins during gastrulation, but recent evidence in vertebrates shows that this process continues after gastrulation in a group of posteriorly localized cells called neuromesodermal progenitors (NMPs). NMPs reside within the post-gastrulation embryonic structure called the tailbud, where they make a lineage decision between ectoderm (spinal cord) and mesoderm. The majority of NMP-derived mesoderm generates somites, but also contributes to lateral mesoderm fates such as endothelium. The discovery of NMPs provides a new paradigm in which to study vertebrate mesoderm induction. This review will discuss mechanisms of mesoderm induction within NMPs, and how they have informed our understanding of mesoderm induction more broadly within vertebrates as well as animal species outside of the vertebrate lineage. Special focus will be given to the signaling networks underlying NMP-derived mesoderm induction and patterning, as well as emerging work on the significance of partial epithelial-mesenchymal states in coordinating cell fate and morphogenesis.

Evaluating Chat Generative Pre-trained Transformer Responses to Common Pediatric In-toeing Questions.

OBJECTIVE: Chat generative pre-trained transformer (ChatGPT) has garnered attention in health care for its potential to reshape patient interactions. As patients increasingly rely on artificial intelligence platforms, concerns about information accuracy arise. In-toeing, a common lower extremity variation, often leads to pediatric orthopaedic referrals despite observation being the primary treatment. Our study aims to assess ChatGPT's responses to pediatric in-toeing questions, contributing to discussions on health care innovation and technology in patient education. METHODS: We compiled a list of 34 common in-toeing questions from the "Frequently Asked Questions" sections of 9 health care-affiliated websites, identifying 25 as the most encountered. On January 17, 2024, we queried ChatGPT 3.5 in separate sessions and recorded the responses. These 25 questions were posed again on January 21, 2024, to assess its reproducibility. Two pediatric orthopaedic surgeons evaluated responses using a scale of "excellent (no clarification)" to "unsatisfactory (substantial clarification)." Average ratings were used when evaluators' grades were within one level of each other. In discordant cases, the senior author provided a decisive rating. RESULTS: We found 46% of ChatGPT responses were "excellent" and 44% "satisfactory (minimal clarification)." In addition, 8% of cases were "satisfactory (moderate clarification)" and 2% were "unsatisfactory." Questions had appropriate readability, with an average Flesch-Kincaid Grade Level of 4.9 (±2.1). However, ChatGPT's responses were at a collegiate level, averaging 12.7 (±1.4). No significant differences in ratings were observed between question topics. Furthermore, ChatGPT exhibited moderate consistency after repeated queries, evidenced by a Spearman rho coefficient of 0.55 ( P = 0.005). The chatbot appropriately described in-toeing as normal or spontaneously resolving in 62% of responses and consistently recommended evaluation by a health care provider in 100%. CONCLUSION: The chatbot presented a serviceable, though not perfect, representation of the diagnosis and management of pediatric in-toeing while demonstrating a moderate level of reproducibility in its responses. ChatGPT's utility could be enhanced by improving readability and consistency and incorporating evidence-based guidelines. LEVEL OF EVIDENCE: Level IV-diagnostic.

Predictors of Persistent Limp Following Proximal Femoral Varus Osteotomy for Perthes Disease.

INTRODUCTION: One of the most popular containment procedures for Legg-Calvé-Perthes disease (LCPD) is proximal femur varus osteotomy (PFO). While generally successful in achieving containment, PFO can cause limb length discrepancy, abductor weakness, and (of most concern for families) a persistent limp. While many studies have focused on radiographic outcomes following containment surgery, none have analyzed predictors of this persistent limp. The aim of this study was to determine clinical, radiographic, and surgical risk factors for persistent limp 2 years after PFO in children with LCPD. METHODS: A retrospective review of a prospectively collected multicenter database was conducted for patients aged 6 to 11 years at disease onset with unilateral early-stage LCPD (Waldenström I) who underwent PFO. Limp status (no, mild, and severe), age, BMI, and pain scores were obtained at initial presentation, 3-month, and 2-year postoperative visits. Preoperative and follow-up radiographs were used to measure traditional morphologic hip metrics including acetabular index (AI), lateral center-edge angle (LCEA), and femoral neck-shaft angle (NSA). Univariate analysis as well as multivariate logistic regression models were used to analyze factors associated with mild and severe limp at the 2-year visit. RESULTS: A total of 95 patients met the inclusion criteria, and of these 50 patients underwent concomitant greater trochanter apophysiodesis (GTA) at the time of PFO. At the 2-year visit, there were 38 patients (40%) with a mild or severe limp. Multivariate logistic regression revealed no significant radiographic factors associated with a persistent limp. However, lower 2-year BMI and undergoing GTA were associated with decreased rates of persistent limp regardless of age ( P <0.05). When stratifying by age of disease onset, apophysiodesis appeared to be protective against any severity of limp in patients aged 6 to 8 years old ( P = 0.03), but not in patients 8 years or older ( P = 0.49). CONCLUSIONS: Persistent limp following PFO is a frustrating problem that was seen in 40% of patients at 2 years. However, lower follow-up BMI and performing a greater trochanter apophysiodesis, particularly in patients younger than 8 years of age, correlated with a lower risk of postoperative limp.

Stable isotopes reveal trophic ontogeny in Cisco (Coregonus artedi).

Cisco (Coregonus artedi) are a widespread, cold-water zooplanktivore native to North America. Although Cisco are generally referred to as an "obligate zooplanktivore," there is some evidence that the species exhibits considerable variability in trophic niche. Here, we assessed how Cisco body size relates to trophic position, that is, trophic ontogeny. We analysed 13C and 15N isotopes from Cisco ranging from 127 to 271 mm in body length (n = 66) from Trout Lake, Vilas County, Wisconsin, USA. 15N isotopes showed smaller Cisco had a trophic position of ~3, which steadily increased to ~3.5 for larger Cisco. Further, 13C isotope signatures showed Cisco transitioned to be more pelagically reliant (lower 13C signatures). Using gillnet catch data, we found that larger Cisco were using deeper habitats than smaller Cisco. Our results support that Cisco have significant variability in trophic niche even though they are traditionally thought of as an obligate planktivore. Overall, we emphasize that researchers should be cautious when generalizing Cisco trophic function, particularly when considering the broader food web.

Graphitic Carbon Nitride as a Photocatalyst for Decarboxylative C(sp2)-C(sp3) Couplings via Nickel Catalysis.

The development of robust and reliable methods for the construction of C(sp2)-C(sp3) bonds is vital for accessing an increased array of structurally diverse scaffolds in drug discovery and development campaigns. While significant advances towards this goal have been achieved using metallaphotoredox chemistry, many of these methods utilise photocatalysts based on precious-metals due to their efficient redox processes and tuneable properties. However, due to the cost, scarcity, and toxicity of these metals, the search for suitable replacements should be a priority. Here, we show the use of commercially available heterogeneous semiconductor graphitic carbon nitride (gCN) as a photocatalyst, combined with nickel catalysis, for the cross-coupling between aryl halide and carboxylic acid coupling partners. gCN has been shown to engage in single-electron-transfer (SET) and energy-transfer (EnT) processes for the formation of C-X bonds, and in this manuscript we overcome previous limitations to furnish C-C over C-O bonds using carboxylic acids. A broad scope of both aryl halides and carboxylic acids is presented, and recycling of the photocatalyst demonstrated. The mechanism of the reaction is also investigated.

A fishy tail: Insights into the cell and molecular biology of neuromesodermal cells from zebrafish embryos.

Vertebrate embryos establish their primary body axis in a conserved progressive fashion from the anterior to the posterior. During this process, a posteriorly localized neuromesodermal cell population called neuromesodermal progenitors (NMps) plays a critical role in contributing new cells to the spinal cord and mesoderm as the embryo elongates. Defects in neuromesodermal population development can cause severe disruptions to the formation of the body posterior to the head. Given their importance during development and their potential, some of which has already been realized, for revealing new methods of in vitro tissue generation, there is great interest in better understanding NMp biology. The zebrafish model system has been instrumental in advancing our understanding of the molecular and cellular attributes of the NM cell population and its derivatives. In this review, we focus on our current understanding of the zebrafish NM population and its contribution to body axis formation, with particular emphasis on the lineage potency, morphogenesis, and niche factors that promote or inhibit differentiation.

Myogenic regulatory factors Myod and Myf5 are required for dorsal aorta formation and angiogenic sprouting.

The vertebrate embryonic midline vasculature forms in close proximity to the developing skeletal muscle, which originates in the somites. Angioblasts migrate from bilateral positions along the ventral edge of the somites until they meet at the midline, where they sort and differentiate into the dorsal aorta and the cardinal vein. This migration occurs at the same time that myoblasts in the somites are beginning to differentiate into skeletal muscle, a process which requires the activity of the basic helix loop helix (bHLH) transcription factors Myod and Myf5. Here we examined vasculature formation in myod and myf5 mutant zebrafish. In the absence of skeletal myogenesis, angioblasts migrate normally to the midline but form only the cardinal vein and not the dorsal aorta. The phenotype is due to the failure to activate vascular endothelial growth factor ligand vegfaa expression in the somites, which in turn is required in the adjacent angioblasts for dorsal aorta specification. Myod and Myf5 cooperate with Hedgehog signaling to activate and later maintain vegfaa expression in the medial somites, which is required for angiogenic sprouting from the dorsal aorta. Our work reveals that the early embryonic skeletal musculature in teleosts evolved to organize the midline vasculature during development.

Sexual dimorphism in bidirectional SR-mitochondria crosstalk in ventricular cardiomyocytes.

Calcium transfer into the mitochondrial matrix during sarcoplasmic reticulum (SR) Ca2+ release is essential to boost energy production in ventricular cardiomyocytes (VCMs) and match increased metabolic demand. Mitochondria from female hearts exhibit lower mito-[Ca2+] and produce less reactive oxygen species (ROS) compared to males, without change in respiration capacity. We hypothesized that in female VCMs, more efficient electron transport chain (ETC) organization into supercomplexes offsets the deficit in mito-Ca2+ accumulation, thereby reducing ROS production and stress-induced intracellular Ca2+ mishandling. Experiments using mitochondria-targeted biosensors confirmed lower mito-ROS and mito-[Ca2+] in female rat VCMs challenged with ß-adrenergic agonist isoproterenol compared to males. Biochemical studies revealed decreased mitochondria Ca2+ uniporter expression and increased supercomplex assembly in rat and human female ventricular tissues vs male. Importantly, western blot analysis showed higher expression levels of COX7RP, an estrogen-dependent supercomplex assembly factor in female heart tissues vs males. Furthermore, COX7RP was decreased in hearts from aged and ovariectomized female rats. COX7RP overexpression in male VCMs increased mitochondrial supercomplexes, reduced mito-ROS and spontaneous SR Ca2+ release in response to ISO. Conversely, shRNA-mediated knockdown of COX7RP in female VCMs reduced supercomplexes and increased mito-ROS, promoting intracellular Ca2+ mishandling. Compared to males, mitochondria in female VCMs exhibit higher ETC subunit incorporation into supercomplexes, supporting more efficient electron transport. Such organization coupled to lower levels of mito-[Ca2+] limits mito-ROS under stress conditions and lowers propensity to pro-arrhythmic spontaneous SR Ca2+ release. We conclude that sexual dimorphism in mito-Ca2+ handling and ETC organization may contribute to cardioprotection in healthy premenopausal females.

Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages - United States, January 2022-May 2023.

CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including the Omicron variant. This report summarizes U.S. trends in variant proportions from national genomic surveillance during January 2022-May 2023. During this period, the Omicron variant remained predominant, with various descendant lineages reaching national predominance (>50% prevalence). During the first half of 2022, BA.1.1 reached predominance by the week ending January 8, 2022, followed by BA.2 (March 26), BA.2.12.1 (May 14), and BA.5 (July 2); the predominance of each variant coincided with surges in COVID-19 cases. The latter half of 2022 was characterized by the circulation of sublineages of BA.2, BA.4, and BA.5 (e.g., BQ.1 and BQ.1.1), some of which independently acquired similar spike protein substitutions associated with immune evasion. By the end of January 2023, XBB.1.5 became predominant. As of May 13, 2023, the most common circulating lineages were XBB.1.5 (61.5%), XBB.1.9.1 (10.0%), and XBB.1.16 (9.4%); XBB.1.16 and XBB.1.16.1 (2.4%), containing the K478R substitution, and XBB.2.3 (3.2%), containing the P521S substitution, had the fastest doubling times at that point. Analytic methods for estimating variant proportions have been updated as the availability of sequencing specimens has declined. The continued evolution of Omicron lineages highlights the importance of genomic surveillance to monitor emerging variants and help guide vaccine development and use of therapeutics.

Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.

We have used a variety of theoretical and experimental techniques to study the role of four basic amino acids-Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid-on the structure, flexibility and sequence-dependent stability of DNA. We found that the presence of organic ions stabilizes the duplexes and significantly reduces the difference in stability between AT- and GC-rich duplexes with respect to the control conditions. This suggests that these amino acids, ingredients of the primordial soup during abiogenesis, could have helped to equalize the stability of AT- and GC-rich DNA oligomers, facilitating a general non-catalysed self-replication of DNA. Experiments and simulations demonstrate that organic ions have an effect that goes beyond the general electrostatic screening, involving specific interactions along the grooves of the double helix. We conclude that organic ions, largely ignored in the DNA world, should be reconsidered as crucial structural elements far from mimics of small inorganic cations.

Strength is in engagement: The rise of an online scientific community during the COVID-19 pandemic.

Many scientists, confined to home office by COVID-19, have been gathering in online communities, which could become viable alternatives to physical meetings and conferences.

Surgically Correctable Congenital Anomalies: Reducing Morbidity and Mortality in the First 8000 Days of Life.

BACKGROUND: Congenital anomalies are a leading cause of morbidity and mortality worldwide. We aimed to review the common surgically correctable congenital anomalies with recent updates on the global disease burden and identify the factors affecting morbidity and mortality. METHOD: A literature review was done to assess the burden of surgical congenital anomalies with emphasis on those that present within the first 8000 days of life. The various patterns of diseases were analyzed in both low- and middle-income countries (LMIC) and high-income countries (HIC). RESULTS: Surgical problems such as digestive congenital anomalies, congenital heart disease and neural tube defects are now seen more frequently. The burden of disease weighs more heavily on LMIC. Cleft lip and palate has gained attention and appropriate treatment within many countries, and its care has been strengthened by global surgical partnerships. Antenatal scans and timely diagnosis are important factors affecting morbidity and mortality. The frequency of pregnancy termination following prenatal diagnosis of a congenital anomaly is lower in many LMIC than in HIC. CONCLUSION: Congenital heart disease and neural tube defects are the most common congenital surgical diseases; however, easily treatable gastrointestinal anomalies are underdiagnosed due to the invisible nature of the condition. Current healthcare systems in most LMICs are still unprepared to tackle the burden of disease caused by congenital anomalies. Increased investment in surgical services is needed.

Less pain reported 5 years after cementless compared to cemented unicompartmental knee replacement: an analysis of pain, neuropathy, and co-morbidity scores.

PURPOSE: To compare patient-reported pain scores and assess the influence of neuropathy and co-morbidity, on knee pain following cemented and cementless medial unicompartmental knee replacement (UKR) 5 years after surgery. METHOD: In this longitudinal study, 262 cemented and 262 cementless Oxford UKR performed for the same indications and with the same techniques were recruited. Patients were reviewed at five years, evaluating patient-reported pain and association with clinical outcomes. Intermittent and Constant Osteoarthritis Pain (ICOAP), PainDETECT (PD), Charnley score, Oxford Knee Score (OKS) and American Knee Society Score (AKSS) were compared. RESULTS: In both cohorts, intermittent pain was more common than constant pain (47% vs 21%). Cementless knees reported significantly less pain than cemented (ICOAP-Total 5/100 vs 11/100, p < 0.0001). A greater proportion of cementless knees experienced no pain at all (ICOAP = 0/100, 61% vs 43%, p < 0.0001) and 75% fewer experienced severe or extreme pain. Pain sub-scores in PD, OKS and AKSS follow this trend. Pain was unlikely to be neuropathic (PD positive: 5.26%), but patients reporting high levels of 'strongest' pain were three times more likely to be neuropathic. Patients with co-morbidities (Charnley C) experienced greater pain than those without (Charnley A+B) across all knee-specific scores, despite scores being knee specific. CONCLUSION: Both cemented and cementless UKR in this study had substantially less pain than that reported in literature following TKR. Cementless UKR had significantly less pain than cemented UKR in all scores. Two-thirds of patients with a cementless UKR had no pain at all at 5 years, and pain experienced was most likely to be mild and intermittent with no patients in severe or extreme pain. Patients with cementless UKR that had higher levels of pain were more likely to have co-morbidity or evidence or neuropathic pain. It is unclear why cementless UKR have less pain than cemented; further study is necessary.