Histological and Single-nucleus Transcriptome Analyses Unveil the Specialized Functions of Ligular Sclerenchyma Cells and Key Regulators of Leaf Angle in Maize.

Leaf angle (LA) is a crucial factor affecting planting density and yield in maize. However, the regulatory mechanisms underlying LA formation remain largely unknown. In this study, we conducted a comparative histological analysis of the ligular region across various maize inbred lines, revealing that LA size is significantly influenced by a two-step regulatory process involving initial cell elongation followed by subsequent lignification in the ligular adaxial sclerenchyma cells (SC). We performed both bulk and single-nucleus RNA sequencing, generated a comprehensive transcriptomic atlas of the ligular region, and identified numerous genes enriched in the hypodermal cells that may influence their specialization into SC. Furthermore, we functionally characterized two genes encoding atypical basic helix-loop-helix (bHLH) transcription factors, bHLH30 and its homolog bHLH155, respectively, which are highly expressed in the elongated adaxial cells. Genetic analyses revealed that bHLH30 and bHLH155 positively regulate LA expansion, and molecular experiments demonstrated their ability to activate the transcription of genes involved in cell elongation and lignification of SC. These findings highlight the specialized functions of ligular adaxial SC in LA regulation by restricting the further extension of ligular cells and enhancing mechanical strength. The transcriptomic atlas of ligular region at single -nucleus resolution not only deepens our understanding of LA regulation but also identifies numerous potential targets for optimizing plant architecture in modern maize breeding.

Adaptive promising zone design for cancer immunotherapy with heterogeneous delayed treatment effect.

Indirect mechanisms of cancer immunotherapies result in delayed treatment effects that vary among patients. Consequently, the use of the log-rank test in trial design and analysis can lead to significant power loss and pose additional challenges for interim decisions in adaptive designs. In this paper, we describe patients' survival using a piecewise proportional hazard model with random lag time and propose an adaptive promising zone design for cancer immunotherapy with heterogeneous delayed effects. We provide solutions for calculating conditional power and adjusting the critical value for the log-rank test with interim data. We divide the sample space into three zones - unfavourable, promising, and favourable -based on re-estimations of the survival parameters, the log-rank test statistic at the interim analysis, and the initial and maximum sample sizes. If the interim results fall into the promising zone, the sample size is increased; otherwise, it remains unchanged. We show through simulations that our proposed approach has greater overall power than the fixed sample design and similar power to the matched group sequential trial. Furthermore, we confirm that critical value adjustment effectively controls the type I error rate inflation. Finally, we provide recommendations on the implementation of our proposed method in cancer immunotherapy trials.

Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis.

Coding transcript-derived siRNAs (ct-siRNAs) produced from specific endogenous loci can suppress the translation of their source genes to balance plant growth and stress response. In this study, we generated Arabidopsis mutants with deficiencies in RNA decay and/or post-transcriptional gene silencing (PTGS) pathways and performed comparative sRNA-seq analysis, revealing that multiple RNA decay and PTGS factors impede the ct-siRNA selective production. Genes that produce ct-siRNAs often show increased or unchanged expression and typically have higher GC content in sequence composition. The growth and development of plants can perturb the dynamic accumulation of ct-siRNAs from different gene loci. Two nitrate reductase genes, NIA1 and NIA2, produce massive amounts of 22-nt ct-siRNAs and are highly expressed in a subtype of mesophyll cells where DCL2 exhibits higher expression relative to DCL4, suggesting a potential role of cell-specific expression of ct-siRNAs. Overall, our findings unveil the multifaceted factors and features involved in the selective production and regulation of ct-siRNAs and enrich our understanding of gene silencing process in plants.

Group sequential design with maximin efficiency robust test for immunotherapy with generalized delayed treatment effect.

The delayed treatment effect is a common feature of immunotherapy, characterized by a gradual onset of action ranging from no effect to full effect. In this study, we propose a generalized delayed treatment effect function to depict the delayed effective process precisely and flexibly. To reduce potential power loss caused by the delayed treatment effect in a group sequential trial, we employ the maximin efficiency robust test, which enhances power robustness across a range of possible delays. We present novel approaches based on the Markov chain method for determining group sequential boundaries, calculating the power function, and estimating the maximum sample size through iterative regressions between the square root of the maximum sample size and the normal quantile of power. Extensive simulation studies validate the effectiveness of our approaches, particularly in balanced trials, demonstrating the validity of group sequential boundaries and the accuracy of maximum sample size estimations. Additionally, we utilize a real trial as an example to compare our considered trial with group sequential trials using the log-rank and generalized piecewise weighted log-rank tests. The results show significantly reduced maximum sample sizes, highlighting the economic advantage of our approach.

Variation in vitamin D status in infants and children: a two-year cross-sectional study in Shanghai, China.

BACKGROUND: Vitamin D deficiency (VDD) is a public health problem. The variation in vitamin D status across regions and populations remains unclear, and there is a lack of consensus regarding the screening for VDD in individuals. METHODS: Children who visited the hospital from January 2019 to December 2020 were included in this study. Serum 25-hydroxyvitamin D (25(OH)D) concentrations were measured using an enzyme-linked immunosorbent assay. The cutoffs for serum 25(OH)D concentrations to define deficiency, insufficiency, and sufficiency were < 20 ng/mL, 20-30 ng/mL, and ≥ 30 ng/mL, respectively. RESULTS: A total of 7285 children aged 0-11 years were assessed; the mean 25(OH)D level was 31.4 ng/mL, and the median 25(OH)D level was 30.7 (interquartile range 24.4, 37.5) ng/mL. The 25(OH)D level declined with age in clinical visiting children aged 0-11 years, but maintained a consistently high level in health examination children aged 4-11 years. The percentages of 25(OH)D < 20 ng/mL and 25(OH)D < 30 ng/mL were 10.0% and 43.8%, respectively. Higher percentages of VDD were found in clinical visiting children than in health examination children within the 6-11-year group (53.3% vs. 14.7%) and winter (44.3% vs. 15.4%). CONCLUSION: Low vitamin D status (deficiency and insufficiency) was more common in clinic-visiting children than in health examinations, especially in schoolchildren and in the winter. The study implies the positive effects of vitamin D assessments included in child health checkups to optimize vitamin D status.

Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings.

Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs at this time. Although several studies have reported about organ-specific development and expression induced by light, a systematic analysis of cell-type-specific differentiation and the associated transcriptional regulation is still lacking. Here we obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis thaliana seedlings. Informative cells from shoot and root tissues were grouped into 48 different cell clusters and finely annotated using multiple markers. With the determination of comprehensive developmental trajectories, we demonstrate light modulation of cell fate determination during guard cell specialization and vasculature development. Comparison of expression atlases between wild type and the pifq mutant indicates that phytochrome-interacting factors (PIFs) are involved in distinct developmental processes in endodermal and stomatal lineage cells via controlling cell-type-specific expression of target genes. These results provide information concerning the light signalling networks at the cell-type resolution, improving our understanding of how light regulates plant development at the cell-type and genome-wide levels. The obtained information could serve as a valuable resource for comprehensively investigating the molecular mechanism of cell development and differentiation in response to light.

Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus.

Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation in crop engineering. Pluripotent callus cells develop into fertile shoots through shoot regeneration. The molecular basis of the shoot regeneration process in crop callus remains largely elusive. This study pioneers the exploration of the spatial transcriptome of tomato callus during shoot regeneration. The findings reveal the presence of highly heterogeneous cell populations within the callus, including epidermis, vascular tissue, shoot primordia, inner callus, and outgrowth shoots. By characterizing the spatially resolved molecular features of shoot primordia and surrounding cells, specific factors essential for shoot primordia formation are identified. Notably, chlorenchyma cells, enriched in photosynthesis-related processes, play a crucial role in promoting shoot primordia formation and subsequent shoot regeneration. Light is shown to promote shoot regeneration by inducing chlorenchyma cell development and coordinating sugar signaling. These findings significantly advance our understanding of the cellular and molecular aspects of shoot regeneration in tomato callus and demonstrate the immense potential of spatial transcriptomics in plant biology.

DeepTree: Modeling Trees with Situated Latents.

In this paper, we propose DeepTree, a novel method for modeling trees based on learning developmental rules for branching structures instead of manually defining them. We call our deep neural model "situated latent" because its behavior is determined by the intrinsic state -encoded as a latent space of a deep neural model- and by the extrinsic (environmental) data that is "situated" as the location in the 3D space and on the tree structure. We use a neural network pipeline to train a situated latent space that allows us to locally predict branch growth only based on a single node in the branch graph of a tree model. We use this representation to progressively develop new branch nodes, thereby mimicking the growth process of trees. Starting from a root node, a tree is generated by iteratively querying the neural network on the newly added nodes resulting in the branching structure of the whole tree. Our method enables generating a wide variety of tree shapes without the need to define intricate parameters that control their growth and behavior. Furthermore, we show that the situated latents can also be used to encode the environmental response of tree models, e.g., when trees grow next to obstacles. We validate the effectiveness of our method by measuring the similarity of our tree models and by procedurally generated ones based on a number of established metrics for tree form.

FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing.

Motivation: Direct RNA-seq (dRNA-seq) using Oxford Nanopore Technology (ONT) has revolutionized transcript mapping by offering enhanced precision due to its long-read length. Unlike traditional techniques, dRNA-seq eliminates the need for PCR amplification, reducing the impact of GC bias, and preserving valuable base physical information, such as RNA modification and poly(A) length estimation. However, the rapid advancement of ONT devices has set higher standards for analytical software, resulting in potential challenges of software incompatibility and reduced efficiency. Results: We present a novel workflow, called FASTdRNA, to manipulate dRNA-seq data efficiently. This workflow comprises two modules: a data preprocessing module and a data analysis module. The preprocessing data module, dRNAmain, encompasses basecalling, mapping, and transcript counting, which are essential for subsequent analyses. The data analysis module consists of a range of downstream analyses that facilitate the estimation of poly(A) length, prediction of RNA modifications, and assessment of alternative splicing events across different conditions with duplication. The FASTdRNA workflow is designed for the Snakemake framework and can be efficiently executed locally or in the cloud. Comparative experiments have demonstrated its superior performance compared to previous methods. This innovative workflow enhances the research capabilities of dRNA-seq data analysis pipelines by optimizing existing processes and expanding the scope of analysis. Availability and implementation: The workflow is freely available at https://github.com/Tomcxf/FASTdRNA under an MIT license. Detailed install and usage guidance can be found in the GitHub repository.

Vitamin D status among infants and children in Shanghai, China: A hospital-based study.

The variation in vitamin D status is still unclear. We aim to describe the vitamin D status among healthy infants and children in Shanghai (31° N latitude), one of the largest cities in China. We conducted a hospital-based, 2-year retrospective observational study and recruited children for health examination at the Tongren Hospital affiliated with Shanghai Jiao Tong University School of Medicine from January 2019 to December 2020. Serum 25-hydroxyvitamin D (25(OH)D) levels were measured using an enzyme-linked immunosorbent assay. A total of 6164 children aged 0-11 years were included. Of these, 94.4% of the serum 25(OH)D measurements at first assessment were within the range of 12-50 ng/mL. The median 25(OH)D level was 31.3 (IQR 25.6, 38.1) ng/mL, the percentages of 25(OH)D < 20 ng/mL and 25(OH)D < 30 ng/mL were 10.0% and 43.8%, respectively. Low vitamin D status (deficiency and insufficiency) differed significantly by age group (infants, toddlers, preschoolers, and schoolers) and seasonality (all p < .001), but not by gender. For the sub-group (n = 855) of children with repeated assessments, their low 25(OH)D levels increased significantly whether after about a 7-month (n = 351) or 12-month (n = 504) interval, and the increments of median 25(OH)D levels were 8.1 ng/mL and 2.1 ng/mL respectively (p < .001). This study documents the vitamin D status in Shanghai, showing that low vitamin D status is common in infants and children and suggesting that the assessment of 25(OH)D level is necessary for individuals who are at risk for deficiency or excess.

A comparative study of adaptive trial designs for dose optimization.

Recently, the US Food and Drug Administration Oncology Center of Excellence initiated Project Optimus to reform the dose optimization and dose selection paradigm in oncology drug development. The agency pointed out that the current paradigm for dose selection-based on the maximum tolerated dose (MTD)-is not sufficient for molecularly targeted therapies and immunotherapies, for which efficacy may not increase after the dose reaches a certain level. In these cases, it is more appropriate to identify the optimal biological dose (OBD) that optimizes the risk-benefit tradeoff of the drug. Project Optimus has spurred tremendous interest and urgent need for guidance on designing dose optimization trials. In this article, we review several representative dose optimization designs, including model-based and model-assisted designs, and compare their operating characteristics based on 10,000 randomly generated scenarios with various dose-toxicity and dose-efficacy curves and some fixed representative scenarios. The results show that, compared with model-based designs, model-assisted methods have advantages of easy-to-implement, robustness, and high accuracy to identify OBD. Some guidance is provided to help biostatisticians and clinicians to choose appropriate dose optimization methods in practice.

Metagenomic profiles of planktonic bacteria and resistome along a salinity gradient in the Pearl River Estuary, South China.

Estuarine ecosystems undergo pronounced and intricate changes due to the mixing of freshwater and saltwater. Additionally, urbanization and population growth in estuarine regions result in shifts in the planktonic bacterial community and the accumulation of antibiotic resistance genes (ARGs). The dynamic changes in bacterial communities, environmental factors, and carriage of ARGs from freshwater to seawater, as well as the complex interrelationships among these factors, have yet to be fully elucidated. Here, we conducted a comprehensive study based on metagenomic sequencing and full-length 16S rRNA sequencing, covering the entire Pearl River Estuary (PRE) in Guangdong, China. The abundance and distribution of the bacterial community, ARGs, mobile genetic elements (MGEs), and bacterial virulence factors (VFs) were analyzed on a site-by-site basis through sampling along the salinity gradient in PRE, from upstream to downstream. The structure of the planktonic bacterial community undergoes continuous changes in response to variations in estuarine salinity, with the phyla Proteobacteria and Cyanobacteria being dominant bacterial throughout the entire region. The diversity and abundance of ARGs and MGEs gradually decreased with the direction of water flow. A large number of ARGs were carried by potentially pathogenic bacteria, especially in Alpha-proteobacteria and Beta-proteobacteria. Multi-drug resistance genes have the highest abundance and subtypes in PRE. In addition, ARGs are more linked to some MGEs than to specific bacterial taxa and disseminate mainly by HGT and not by vertical transfer in the bacterial communities. Various environmental factors, such as salinity and nutrient concentrations, have a significantly impact on the community structure and distribution of bacteria. In conclusion, our results represent a valuable resource for further investigating the intricate interplay between environmental factors and anthropogenic disturbances on bacterial community dynamics. Moreover, they contribute to a better understanding of the relative impact of these factors on the dissemination of ARGs.

An R-R-type MYB transcription factor promotes non-climacteric pepper fruit carotenoid pigment biosynthesis.

Carotenoids are major accessory pigments in the chloroplast, and they also act as phytohormones and volatile compound precursors to influence plant development and confer characteristic colours, affecting both the aesthetic and nutritional value of fruits. Carotenoid pigmentation in ripening fruits is highly dependent on developmental trajectories. Transcription factors incorporate developmental and phytohormone signalling to regulate the biosynthesis process. By contrast to the well-established pathways regulating ripening-related carotenoid biosynthesis in climacteric fruit, carotenoid regulation in non-climacteric fruit is poorly understood. Capsanthin is the primary carotenoid of non-climacteric pepper (Capsicum) fruit; its biosynthesis is tightly associated with fruit ripening, and it confers red pigmentation to the ripening fruit. In the present study, using a coexpression analysis, we identified an R-R-type MYB transcription factor, DIVARICATA1, and demonstrated its role in capsanthin biosynthesis. DIVARICATA1 encodes a nucleus-localised protein that functions primarily as a transcriptional activator. Functional analyses showed that DIVARICATA1 positively regulates carotenoid biosynthetic gene (CBG) transcript levels and capsanthin levels by directly binding to and activating CBG promoter transcription. Furthermore, an association analysis revealed a significant positive association between DIVARICATA1 transcription level and capsanthin content. ABA promotes capsanthin biosynthesis in a DIVARICATA1-dependent manner. Comparative transcriptomic analysis of DIVARICATA1 in Solanaceae plants showed that its function likely differs among species. Moreover, the pepper DIVARICATA1 gene could be regulated by the ripening regulator MADS-RIN. The present study illustrates the transcriptional regulation of capsanthin biosynthesis and offers a target for breeding peppers with high red colour intensity.

The hTERT-p50 homodimer inhibits PLEKHA7 expression to promote gastric cancer invasion and metastasis.

Although accumulating evidence has highlighted the molecular mechanisms by which hTERT promotes tumour cell invasion and metastasis, the molecular mechanisms of the properties enabling hTERT to contribute to invasion and metastasis have not been clearly illustrated. Here, we report that hTERT promotes gastric cancer invasion and metastasis by recruiting p50 to synergistically inhibit PLEKHA7 expression. We observed that the expression of PLEKHA7 in gastric cancer was significantly negatively associated with the TNM stage and lymphatic metastasis and that decreased PLEKHA7 expression dramatically increased invasion and metastasis in gastric cancer cells. Further mechanistic research showed that hTERT directly regulates PLEKHA7 expression by binding p50 and recruiting the hTERT/p50 complex to the PLEKHA7 promoter. Increased hTERT dramatically decreased PLEKHA7 expression and promoted invasion and metastasis in gastric cancer cells. The hTERT-mediated invasion/metastasis properties at least partially depended on PLEKHA7. Our work uncovers a novel molecular mechanism underlying invasion/metastasis in gastric cancer orchestrated by hTERT and p50.

Kinetic Controlled Chirality Transfer and Induction in 2D Hydrogen-Bonding Assemblies of Glycylglycine on Au(111).

Chirality transfer is of vital importance that dominates the structure and functionality of biological systems and living matters. External physical stimulations, e.g. polarized light and mechanical forces, can trigger the chirality symmetry breaking, leading to the appearance of the enantiomeric entities created from a chiral self-assembly of achiral molecule. Here, several 2D assemblies with different chirality, synthesized on Au(111) surface by using achiral building blocks - glycylglycine (digly), the simplest polypeptide are reported. By delicately tuning the kinetic factors, i.e., one-step slow/rapid deposition, or stepwise slow deposition with mild annealing, achiral square hydrogen-bond organic frameworks (HOF), homochiral rhombic HOF and racemic rectangular assembly are achieved, respectively. Chirality induction and related symmetry broken in assemblies are introduced by the handedness (H-bond configurations in principle) of the assembled motifs and then amplified to the entire assemblies via the interaction between motifs. The results show that the chirality transfer and induction of biological assemblies can be tuned by altering the kinetic factors instead of applying external forces, which may offer an in-depth understanding and practical approach to peptide chiral assembly on the surfaces and can further facilitate the design of desired complex biomolecular superstructures.

Distribution and Transmission of Colistin Resistance Genes mcr-1 and mcr-3 among Nontyphoidal Salmonella Isolates in China from 2011 to 2020.

Mobile colistin resistance (mcr) genes are present mainly in plasmids and can disseminate clonally or horizontally via either plasmids or insertion sequences in different genomic locations among the Enterobacteriaceae. A nationwide large-scale study on mcr prevalence and transmission in nontyphoidal Salmonella isolates is still lacking. Here, we identified 140 mcr-positive Salmonella isolates out of 7,106 isolates from 29 provinces in China from 2011 to 2020. We aligned short reads to putative plasmids from long-read hybrid assemblies and predicted the plasmid backbones of non-long-read sequencing isolates to elucidate mcr transmission patterns. The mcr-1 and mcr-3 genes are transmitted on similar high-risk clones (sequence type 34 [ST34]) but through plasmids of various replicon types. Furthermore, the ban on colistin use in food animals can lead to a decrease in the mcr-positive Salmonella prevalence among diarrheal patients, related mainly to IncHI2A_IncHI2 plasmids. We provide a framework for plasmid data incorporation into genomic surveillance systems, contributing to a better understanding of mcr spread and transmission. IMPORTANCE Nontyphoidal Salmonella is one of four major causative agents of diarrheal diseases globally, with most cases of salmonellosis being mild. Antimicrobial treatments are required for cases of life-threatening infections, and colistin is one of the last-line antibiotics for the treatment of multidrug-resistant Salmonella infections. However, the efficacy of colistin has been compromised by the emergence of various mcr genes. To elucidate the transmission of mcr genes in Salmonella isolates, our study analyzed 7,106 Salmonella strains from 29 provinces in China from 2011 to 2020. The results showed that mcr genes are transmitted on similar high-risk clones (ST34) but through plasmids of various replicon types. In addition, our data illustrated that the ban on the use of colistin in food animals led to a significant decrease in mcr-positive isolates. Our findings offer an essential step toward a more comprehensive understanding of the spread and transmission of mcr genes.

A novel protein domain is important for photosystem II complex assembly and photoautotrophic growth in angiosperms.

Photosystem II (PSII) is a multi-subunit protein complex of the photosynthetic electron transport chain that is vital to photosynthesis. Although the structure, composition, and function of PSII have been extensively studied, its biogenesis mechanism remains less understood. Thylakoid rhodanese-like (TROL) provides an anchor for leaf-type ferredoxin:NADP+ oxidoreductase. Here, we report the chacterizaton of a second type of TROL protein, TROL2, encoded by seed plant genomes whose function has not previously been reported. We show that TROL2 is a PSII assembly cofactor with essential roles in the establishment of photoautotrophy. TROL2 contains a 45-amino-acid domain, termed the chlorotic lethal seedling (CLS) domain, that is both necessary and sufficient for TROL2 function in PSII assembly and photoautotrophic growth. Phylogenetic analyses suggest that TROL2 may have arisen from ancestral TROL1 via gene duplication before the emergence of seed plants and acquired the CLS domain via evolution of the sequence encoding its N-terminal portion. We further reveal that TROL2 (or CLS) forms an assembly cofactor complex with the intrinsic thylakoid membrane protein LOW PSII ACCUMULATION2 and interacts with small PSII subunits to facilitate PSII complex assembly. Collectively, our study not only shows that TROL2 (CLS) is essential for photoautotrophy in angiosperms but also reveals its mechanistic role in PSII complex assembly, shedding light on the molecular and evolutionary mechanisms of photosynthetic complex assemblyin angiosperms.

(-)-Gossypol enhances the anticancer activity of epirubicin via downregulating survivin in hepatocellular carcinoma.

Epirubicin (EPI)-based transarterial chemoembolization is an effective therapy for advanced hepatocellular carcinoma (HCC). However, EPI-induced survivin expression limits its tumor-killing potential in HCC. Interestingly, (-)-gossypol ((-)-Gsp), a male contraceptive, suppresses various malignancies. More importantly, (-)-Gsp also holds promise for enhancing the antitumor effects of chemotherapy in numerous cancer types. In the present study, we demonstrated for the first time that (-)-Gsp-sensitized EPI inhibited cell growth and induced apoptosis of HCC cells in vitro. Furthermore, (-)-Gsp sensitized EPI by attenuating the EPI-elevated survivin protein levels. Mechanistic studies showed that EPI stimulated survivin protein synthesis by promoting translation initiation, which was alleviated by (-)-Gsp mainly through suppressing the AKT-4EBP1/p70S6K-survivin and ERK-4EBP1-survivin pathways. HCC xenograft experiments in nude mice also showed that (-)-Gsp treatment acted synergistically with EPI to repress xenograft tumor growth. Overall, our proof-of-concept results may pave the way for novel strategies for the treatment of HCC based on the combination of EPI and (-)-Gsp.