Brain Repair by Cell Replacement via In Situ Neuronal Reprogramming.

Neurodegenerative diseases, characterized by progressive neural loss, have been some of the most challenging medical problems in aging societies. Treatment strategies such as symptom management have little impact on disease progression, while intervention with specific disease mechanisms may only slow down disease progression. One therapeutic strategy that has the potential to reverse the disease phenotype is to replenish neurons and rebuild the pathway lost to degeneration. Although it is generally believed that the central nervous system has lost the capability to regenerate, increasing evidence indicates that the brain is more plastic than previously thought, containing perhaps the biggest repertoire of cells with latent neurogenic programs in the body. This review focuses on key advances in generating new neurons through in situ neuronal reprogramming, which is tied to fundamental questions regarding adult neurogenesis, cell source, and mechanisms for neuronal reprogramming, as well as the ability of new neurons to integrate into the existing circuitry.

Author Correction: Reversing a model of Parkinson's disease with in situ converted nigral neurons.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Reversing a model of Parkinson's disease with in situ converted nigral neurons.

Parkinson's disease is characterized by loss of dopamine neurons in the substantia nigra1. Similar to other major neurodegenerative disorders, there are no disease-modifying treatments for Parkinson's disease. While most treatment strategies aim to prevent neuronal loss or protect vulnerable neuronal circuits, a potential alternative is to replace lost neurons to reconstruct disrupted circuits2. Here we report an efficient one-step conversion of isolated mouse and human astrocytes to functional neurons by depleting the RNA-binding protein PTB (also known as PTBP1). Applying this approach to the mouse brain, we demonstrate progressive conversion of astrocytes to new neurons that innervate into and repopulate endogenous neural circuits. Astrocytes from different brain regions are converted to different neuronal subtypes. Using a chemically induced model of Parkinson's disease in mouse, we show conversion of midbrain astrocytes to dopaminergic neurons, which provide axons to reconstruct the nigrostriatal circuit. Notably, re-innervation of striatum is accompanied by restoration of dopamine levels and rescue of motor deficits. A similar reversal of disease phenotype is also accomplished by converting astrocytes to neurons using antisense oligonucleotides to transiently suppress PTB. These findings identify a potentially powerful and clinically feasible approach to treating neurodegeneration by replacing lost neurons.

The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations.

Mutations in several general pre-mRNA splicing factors have been linked to myelodysplastic syndromes (MDSs) and solid tumors. These mutations have generally been assumed to cause disease by the resultant splicing defects, but different mutations appear to induce distinct splicing defects, raising the possibility that an alternative common mechanism is involved. Here we report a chain of events triggered by multiple splicing factor mutations, especially high-risk alleles in SRSF2 and U2AF1, including elevated R-loops, replication stress, and activation of the ataxia telangiectasia and Rad3-related protein (ATR)-Chk1 pathway. We further demonstrate that enhanced R-loops, opposite to the expectation from gained RNA binding with mutant SRSF2, result from impaired transcription pause release because the mutant protein loses its ability to extract the RNA polymerase II (Pol II) C-terminal domain (CTD) kinase-the positive transcription elongation factor complex (P-TEFb)-from the 7SK complex. Enhanced R-loops are linked to compromised proliferation of bone-marrow-derived blood progenitors, which can be partially rescued by RNase H overexpression, suggesting a direct contribution of augmented R-loops to the MDS phenotype.

Transcription factor OsbZIP10 modulates rice grain quality by regulating OsGIF1.

Understanding and optimizing the process of grain filling helps the quest to maximize rice (Oryza sativa L.) seed yield and quality, yet the intricate mechanisms at play remain fragmented. Transcription factors (TFs) are major players in the gene networks underlying the grain filling process. Here, we employed grain incomplete filling (OsGIF1)/cell wall invertase 2, a key gene involved in grain filling, to explore its upstream TFs and identified a bZIP family TF, OsbZIP10, to be a transcriptional activator of OsGIF1. Rice grains of the knockouts of OsbZIP10 showed increased white-core rates but lower amylose content (AC), leading to better eating and cooking qualities in all genetic backgrounds investigated, though the impact of mutations in OsbZIP10 on grain weight depended on genetic background. Multi-omics analyses suggested that, in addition to OsGIF1, multiple genes involved in different biological processes contributing to grain filling were targeted by OsbZIP10, including OsAGPS1, a gene encoding the ADP-Glc pyrophosphorylase (AGPase) small subunit, and genes contributing to homeostasis of reactive oxygen species. Distinct genetic make-up was observed in OsbZIP10 between japonica and indica rice varieties, with the majority varieties of each subspecies belonging to two different haplotypes that were closely associated with AC. Overexpressing the haplotype linked to high-AC in the low-AC genetic background increased AC. Overall, this study sheds crucial light on the significance of the OsbZIP10-OsGIF1 module in the determination of rice grain quality, offering a potential avenue for genetic engineering of rice to produce seeds with tailored attributes.

KGDiff: towards explainable target-aware molecule generation with knowledge guidance.

Designing 3D molecules with high binding affinity for specific protein targets is crucial in drug design. One challenge is that the atomic interaction between molecules and proteins in 3D space has to be taken into account. However, the existing target-aware methods solely model the joint distribution between the molecules and proteins, disregarding the binding affinities between them, which leads to limited performance. In this paper, we propose an explainable diffusion model to generate molecules that can be bound to a given protein target with high affinity. Our method explicitly incorporates the chemical knowledge of protein-ligand binding affinity into the diffusion model, and uses the knowledge to guide the denoising process towards the direction of high binding affinity. Specifically, an SE(3)-invariant expert network is developed to fit the Vina scoring functions and jointly trained with the denoising network, while the domain knowledge is distilled and conveyed from Vina functions to the expert network. An effective guidance is proposed on both continuous atom coordinates and discrete atom types by taking advantages of the gradient of the expert network. Experiments on the benchmark CrossDocked2020 demonstrate the superiority of our method. Additionally, an atom-level explanation of the generated molecules is provided, and the connections with the domain knowledge are established.

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters.

R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase-H-based approach; this reveals predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. Transcription perturbation experiments further indicate that R-loop induction correlates to transcriptional pausing. Interestingly, we note that most mapped R-loops are each linked to a nearby free RNA end; by using a ribozyme to co-transcriptionally cleave nascent RNA, we demonstrate that such a free RNA end coupled with a G/C-skewed sequence is necessary and sufficient to induce R-loop. These findings provide a topological solution for RNA invasion into duplex DNA and suggest an order for R-loop initiation and elongation in an opposite direction to that previously proposed.

Acetylation of GhCaM7 enhances cotton resistance to Verticillium dahliae.

Protein lysine acetylation is an important post-translational modification mechanism involved in cellular regulation in eukaryotes. Calmodulin (CaM) is a ubiquitous Ca2+ sensor in eukaryotes and is crucial for plant immunity, but it is so far unclear whether acetylation is involved in CaM-mediated plant immunity. Here, we found that GhCaM7 is acetylated upon Verticillium dahliae (V. dahliae) infection and a positive regulator of V. dahliae resistance. Overexpressing GhCaM7 in cotton and Arabidopsis enhances V. dahliae resistance and knocking-down GhCaM7 makes cotton more susceptible to V. dahliae. Transgenic Arabidopsis plants overexpressing GhCaM7 with mutation at the acetylation site are more susceptible to V. dahliae than transgenics overexpressing the wild-type GhCaM7, implying the importance of the acetylated GhCaM7 in response to V. dahliae infection. Yeast two-hybrid, bimolecular fluorescent complementation, luciferase complementation imaging, and coimmunoprecipitation assays demonstrated interaction between GhCaM7 and an osmotin protein GhOSM34 that was shown to have a positive role in V. dahliae resistance. GhCaM7 and GhOSM34 are co-localized in the cell membrane. Upon V. dahliae infection, the Ca2+ content reduces almost instantly in plants with downregulated GhCaM7 or GhOSM34. Down regulating GhOSM34 enhances accumulation of Na+ and increases cell osmotic pressure. Comparative transcriptomic analyses between cotton plants with an increased or reduced expression level of GhCaM7 and wild-type plants indicate the involvement of jasmonic acid signaling pathways and reactive oxygen species in GhCaM7-enabled disease resistance. Together, these results demonstrate the involvement of CaM protein in the interaction between cotton and V. dahliae, and more importantly, the involvement of the acetylated CaM in the interaction.

Impacted spike frequency adaptation associated with reduction of KCNQ2/3 exacerbates seizure activity in temporal lobe epilepsy.

Numerous epilepsy-related genes have been identified in recent decades by unbiased genome-wide screens. However, the available druggable targets for temporal lobe epilepsy (TLE) remain limited. Furthermore, a substantial pool of candidate genes potentially applicable to TLE therapy awaits further validation. In this study, we reveal the significant role of KCNQ2 and KCNQ3, two M-type potassium channel genes, in the onset of seizures in TLE. Our investigation began with a quantitative analysis of two publicly available TLE patient databases to establish a correlation between seizure onset and the downregulated expression of KCNQ2/3. We then replicated these pathological changes in a pilocarpine seizure mouse model and observed a decrease in spike frequency adaptation due to the affected M-currents in dentate gyrus granule neurons. In addition, we performed a small-scale simulation of the dentate gyrus network and confirmed that the impaired spike frequency adaptation of granule cells facilitated epileptiform activity throughout the network. This, in turn, resulted in prolonged seizure duration and reduced interictal intervals. Our findings shed light on an underlying mechanism contributing to ictogenesis in the TLE hippocampus and suggest a promising target for the development of antiepileptic drugs.

Genome­wide analysis of cotton SCAMP genes and functional characterization of GhSCAMP2 and GhSCAMP4 in salt tolerance.

BACKGROUND: Secretory carrier membrane proteins (SCAMPs) form a family of integral membrane proteins and play a crucial role in mediating exocytosis in both animals and plants. While SCAMP genes have been studied in several plant species, their functions in cotton, particularly in response to abiotic stress, have not yet been reported. RESULTS: In this study, a total of 53 SCAMP genes were identified in G. arboreum, G. raimondii, G. hirsutum, and G. barbadense. These genes were classified into five groups based on a phylogenetic analysis with SCAMPs from Arabidopsis thaliana. The main factor driving the expansion of the SCAMP gene family in G. hirsutum is tandem and segmental duplication events. Using MEME, in addition to the conserved SCAMP domain, we identified 3-13 other domains in each GhSCAMP. The cis-element analysis suggested that GhSCAMPs were widely involved in cotton growth and development, and responses to abiotic stresses. RNA sequencing (RNA-Seq) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) results showed that most GhSCAMPs were expressed highly in many tissues and had differential expression responses to drought, cold, and heat stresses. Knock-down of GhSCAMP2 and GhSCAMP4 by virus-induced gene silencing (VIGS) lead to a salt-sensitive phenotype and had a lower content of CAT, POD, and SOD. CONCLUSIONS: This study identified SCAMP genes in four cotton species, enhancing our understanding of the potential biological functions of SCAMPs. Additionally, we demonstrated that GhSCAMP2 and GhSCAMP4 positively regulate cotton tolerance to salt stress.

Triple Templates Directed Synthesis of Nitrogen-Doped Hierarchically Porous Carbons from Pyridine Rich Monomer as Efficient and Reversible SO2 Adsorbents.

Herein, a variety of 2,6-diaminopyridine (DAP) derived nitrogen-doped hierarchically porous carbon (DAP-NHPC-T) prepared from carbonization-induced structure transformation of DAP-Zn-SiO2-P123 nanocomposites are reported, which are facilely prepared from solvent-free co-assembly of block copolymer templates P123 with pyridine-rich monomer of DAP, Zn(NO3)2 and tetramethoxysilane. In the pyrolysis process, P123 and SiO2 templates promote the formation of mesoporous and supermicroporous structures in the DAP-NHPC-T, while high-temperature volatilization of Zn contributed to generation of micropores. The DAP-NHPC-T possess large BET surface areas (≈956-1126 m2 g-1), hierarchical porosity with micro-supermicro-mesoporous feature and high nitrogen contents (≈10.44-5.99 at%) with tunable density of pyridine-based nitrogen sites (≈5.99-3.32 at%), exhibiting good accessibility and reinforced interaction with SO2. Consequently, the DAP-NHPC-T show high SO2 capacity (14.7 mmol g-1, 25 °C and 1.0 bar) and SO2/CO2/N2 IAST selectivities, extraordinary dynamic breakthrough separation efficiency and cycling stability, far beyond any other reported nitrogen-doped metal-free carbon. As verified by in situ spectroscopy and theoretical calculations, the pyridine-based nitrogen sites of the DAP-NHPC-T boost SO2 adsorption via the unique charge transfer, the adsorption mechanism and reaction model have been finally clarified.

Are miRNAs applicable for balancing crop growth and defense trade-off?

Securing agricultural supplies for the increasing population without negative impacts on environment demands new crop varieties with higher yields, better quality, and stronger stress resilience. But breeding such super crop varieties is restrained by growth-defense (G-D) trade-off. MicroRNAs (miRNAs) are versatile regulators of plant growth and immune responses, with several being demonstrated to simultaneously regulate crop growth and defense against biotic stresses and to balance G-D trade-off. Increasing evidence also links miRNAs to the metabolism and signaling of phytohormones, another type of master regulator of plant growth and defense. Here, we synthesize the reported functions of miRNAs in crop growth, development, and responses to bio-stressors, summarize the regulatory scenarios of miRNAs based on their relationship with target(s), and discuss how miRNAs, particularly those involved in crosstalk with phytohormones, can be applied in balancing G-D trade-off in crops. We also propose several open questions to be addressed for adopting miRNAs in balancing crop G-D trade-off.

Biosynthesis and Signaling of Strigolactones Act Synergistically With That of ABA and JA to Enhance Verticillium dahliae Resistance in Cotton (Gossypium hirsutum L.).

Verticillium wilt (VW) caused by the soil-borne fungal pathogen Verticillium dahliae reduces cotton productivity and quality. Numerous studies have explored the genetic and molecular mechanisms regulating VW resistance in cotton, but the role and mechanism of strigolactone (SL) is still elusive. We investigated the function of SL in cotton's immune response to V. dahliae infection by exogenously applying SL analog, blocking or enhancing biosynthesis of endogenous SLs in combination with comparative transcriptome analysis and by exploring cross-talk between SL and other phytohormones. Silencing GhDWARF27 and applying the SL analog GR24 or overexpressing GhDWARF27 decreased and enhanced V. dahliae resistance, respectively. Transcriptome analysis revealed SL-mediated activation of abscisic acid (ABA) and jasmonic acid (JA) biosynthesis and signaling pathways. Enhanced ABA biosynthesis and signaling led to increased activity of antioxidant enzymes and reduced buildup of excess reactive oxygen species. Enhanced JA biosynthesis and signaling facilitated transcription of JA-dependent disease resistance genes. One of the components of the SL signal transduction pathway, GhD53, was found to interact with GhNCED5 and GhLOX2, the key enzymes of ABA and JA biosynthesis, respectively. We revealed the molecular mechanism underlying SL-enabled V. dahliae resistance and provided potential solutions for improving VW resistance in cotton.

Systemic Immune-Inflammation Index and Its Association with the Prevalence of Stroke in the United States Population: A Cross-Sectional Study Using the NHANES Database.

Background: The purpose of this study was to evaluate the ability of the systemic immune-inflammation index (SII) to predict the prevalence of stroke in the American population. Methods: A cross-sectional research study of 53,600 people was carried out utilizing information from the U.S. National Health and Nutrition Examination Survey (NHANES) database. Participants were divided into three groups based on the tertiles of their SII levels: SII-low, SII-median, and SII-high. Logistic regression analysis was used to investigate SII and the prevalence of stroke. Subgroup analyses, sensitivity analyses, and restricted cubic spline (RCS) analysis were also carried out. Results: A total of 2368 patients with stroke were found among the participants in this cross-sectional study. The high SII group had a substantially greater prevalence of stroke compared to the low SII group (odds ratio [OR] = 1.18, 95% confidence interval [CI] 1.01, 1.42). The risk of stroke decreased by 34% for every unit rise in log-transformed SII (OR 1.30, 95% CI 0.99, 1.70). A positive linear connection between SII levels and the prevalence of stroke was revealed using RCS analysis (p for non-linearity = 0.387). Conclusions: This cross-sectional study utilizing large-scale data from NHANES provides the first evidence of a significant association between higher SII levels and increased prevalence of stroke. These findings highlight the relevance of SII as a potential predictive marker for stroke.

Quantitative genomics-enabled selection for simultaneous improvement of lint yield and seed traits in cotton (Gossypium hirsutum L.).

KEY MESSAGE: A Bayesian linkage disequilibrium-based multiple-locus mixed model identified QTLs for fibre, seed and oil traits and predicted breeding worthiness of test lines, enabling their simultaneous improvement in cotton. Improving cotton seed and oil yields has become increasingly important while continuing to breed for higher lint yield. In this study, a novel Bayesian linkage disequilibrium-based multiple-locus mixed model was developed for QTL identification and genomic prediction (GP). A multi-parent population consisting of 256 recombinant inbred lines, derived from four elite cultivars with distinct combinations of traits, was used in the analysis of QTLs for lint percentage, seed index, lint index and seed oil content and their interrelations. All four traits were moderately heritable and correlated but with no large influence of genotype × environment interactions across multiple seasons. Seven to ten major QTLs were identified for each trait with many being adjacent or overlapping for different trait pairs. A fivefold cross-validation of the model indicated prediction accuracies of 0.46-0.62. GP results based on any two-season phenotypes were strongly correlated with phenotypic means of a pooled analysis of three-season experiments (r = 0.83-0.92). When used for selection of improvement in lint, seed and oil yields, GP captured 40-100% of individuals with comparable lint yields of those selected based on the three-season phenotypic results. Thus, this quantitative genomics-enabled approach can not only decipher the genomic variation underlying lint, seed and seed oil traits and their interrelations, but can provide predictions for their simultaneous improvement. We discuss future breeding strategies in cotton that will enhance the entire value of the crop, not just its fibre.

Cardiac magnetic resonance assessment of cardiac function across chronic kidney disease stages.

BACKGROUND: Cardiovascular disease prevalence remains high among chronic kidney disease (CKD) patients. Mechanisms and treatments to improve prognosis remain of paramount important and imaging biomarkers of left ventricular myocardial structure and function have better defined the phenotype of renal cardiomyopathy. The left atrial function and right heart remain are less well reported in CKD. This study used cardiac MRI to assess the interplay of left atrial and right ventricular function. METHODS: In a cross-sectional study, we examined 58 CKD patients (Group I: stages 2-3, n = 25; Group II: stages 4-5, n = 33). Additionally, 26 age-matched healthy controls were included. Comprehensive CMR protocols (1.5T) were employed, encompassing cine imaging, native T1 and T2 mapping, and tissue tracking strain analysis. LV, RV, and LA structure, function, and strain parameters were assessed. RESULTS: Compared to healthy controls, both groups I and II exhibited impaired RV and LA function. RVEDVi and RVESVi showed significant increases in both groups I and II (p < 0.001). All LV, RV, and LA strain parameters were reduced in the patient groups (all p < 0.001). In the univariate binary logistic regression, several parameters, including age, blood pressure, RV volumes and LV/RV strain were found to have a statistically significant association with CKD. In a multivariable model adjusted for other confounders, RV GLS and left atrial strain remained as independent significant predictors. CONCLUSIONS: RV size, LA strain and volume assessed by CMR serve as markers of RV and LA cardiac dysfunction in CKD patients with preserved LVEF. Greater attention should be given to RV and LA dysfunction for early identification of cardiac dysfunction in CKD patients.

Exploring retinal degenerative diseases through CRISPR-based screening.

The CRISPR (Clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein9) system has emerged as a powerful genetic tool, gaining global recognition as a versatile and efficient gene-editing technique. Its transformation into a high-throughput research platform, CRISPR Screening, has demonstrated wide applicability across various fields such as cancer biology, virology, and drug target discovery, resulting in significant advances. However, its potential in studying retinal degenerative diseases remains largely unexplored, despite the urgent need for effective treatments arising from an incomplete understanding of disease mechanisms. This review aims to present a comprehensive overview of the evolution and current state of CRISPR tools and CRISPR screening methodologies. Noteworthy pioneering studies utilizing these technologies are discussed, alongside experimental design guidelines, including positive and negative selection strategies and delivery methods for sgRNAs (single guide RNAs) and Cas proteins. Furthermore, we explore existing in vitro models appropriate for CRISPR screening in retinal research and identify relevant research questions that could be addressed through this approach. It is anticipated that this review will stimulate innovation in retinal research, facilitating a deeper comprehension of retinal pathophysiology and paving the way for groundbreaking therapeutic interventions and enhanced patient outcomes in the management of retinal degenerative disorders.

Diversifying the benzenesulfonamide scaffold for potential V-ATPase inhibitors: synthesis and insecticidal activity evaluation.

Celangulin V is a natural ß-dihydroagarofuran derivative isolated from Celastrus angulatus which shows insecticidal activity in many agricultural pests. Using celangulin V as a molecular probe, we find out a new pesticide target: subunit H of V-ATPase. To explore the potential application of this novel target, lead sulfonamides have been found through virtual screening. Combined with the previous work, 46 sulfonamide derivatives are designed and synthesized. All target compounds are first screened for their insecticidal activities against Mythimna separata. The results of bioassay reveal that most of the designed compounds exhibit significant insecticidal activities against third-instar larvae of M. separata under the concentration of 10 mg/mL, and compound 8.4 shows the highest activity with LC50 value of 1.72 mg/mL, 15-fold smaller than that of celangulin V (25.89 mg/mL). Molecular docking results further indicated that compound 8.4 might serve as a potential inhibitor of the subunit H of V-ATPase. This study provides a potential sulfonamide candidate compound for the M. separata control.

Synthesis, and Insecticidal Activities of Propargyloxy-Diphenyl Oxide-Sulfonamide Derivatives.

Agricultural pests are the primary contributing factor to crop yield reduction, particularly in underdeveloped regions. Despite the significant efficacy of pesticides in pest control, their extensive use has led to the drug-fast of insecticide resistance. Developing of new environmentally friendly plant-based pesticides is an urgent necessity. In this study, a series of diaryl ether compounds containing propargyloxy and sulfonamide groups were designed. The synthesis of these 36 compounds primarily relied on nuclear magnetic resonance for structure determination, while single-crystal X-ray diffraction was employed for certain compounds. Meanwhile, the insecticidal activities against Mythimna separata were also assessed. Some of the compounds exhibited significantly enhanced activity, the LC50 value of the highest activity compound TD8 (0.231 mg/mL) demonstrating respective increases by 100-fold compared to the plant pesticide celangulin V (23.9 mg/mL), and a 5-fold increase with the positive control L-1 (1.261 mg/mL). The interaction between the target compound and the target, as well as the consistency of the target, were verified through symptomological analysis and molecular docking. The structure-activity relationships were also conducted. This study offered a novel trajectory for the advancement and formulation of future pesticides.