Identification and Functional Prediction of CircRNAs in Leaves of F1 Hybrid Poplars with Different Growth Potential and Their Parents

Circular RNAs (CircRNAs) regulate plant growth and development; however, their role in poplar heterosis is unclear. We identified 3722 circRNAs in poplar leaves, most of which were intergenic (57.2%) and exonic (40.2%). The expression of circRNAs in F1 hybrids with high growth potential was higher than that in those with low growth potential. Non-additive expression of circRNAs and single-parent expression of circRNAs (SPE-circRNAs) might regulate poplar heterosis through microRNA sponging and protein translation, respectively. DECs among F1 hybrids with different growth potentials might regulate the growth potential of poplar via microRNA sponging. Correlation analysis between circRNA expression and its parent gene expression showed that SPE-M circRNA (circRNAs expressed by male parent only) might regulate poplar heterosis by inhibiting parent gene expression, while other circRNAs might regulate poplar heterosis by enhancing parent gene expression. Weighted correlation network analysis of gene/circRNA expression showed that circRNAs mainly regulate poplar heterosis via carbohydrate metabolism, amino acid metabolism, energy metabolism, and material transport. In addition, we identified seven circRNAs that positively or negatively regulate poplar heterosis. Thus, non-additively expressed circRNAs and SPE circRNAs are involved in regulating poplar heterosis, and DECs among F1 hybrids with different growth potentials were involved in regulating poplar growth potential.

Hallmarks of aging: An expanding universe

Aging is driven by hallmarks fulfilling the following three premises: (1) their age-associated manifestation, (2) the acceleration of aging by experimentally accentuating them, and (3) the opportunity to decelerate, stop, or reverse aging by therapeutic interventions on them. We propose the following twelve hallmarks of aging: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, disabled macroautophagy, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation, and dysbiosis. These hallmarks are interconnected among each other, as well as to the recently proposed hallmarks of health, which include organizational features of spatial compartmentalization, maintenance of homeostasis, and adequate responses to stress.

New Fructokinase, OsFRK3, Regulates Starch Accumulation and Grain Filling in Rice

Plant fructokinase (FRK) guarantees the growth and development of higher plants by participating in carbohydrate metabolism. In this study, a new fructokinase, OsFRK3, was identified using bioinformatics analysis, enzyme assay, bacterial growth assay, and yeast complementation test. Then, we created OsFRK3 knockout transgenic lines (osfrk3-1 and osfrk3-2) by the CRISPR/Cas9 technology. We found that the 1000-grain weight decreased notably (approximately -3.6% and -6.1%, respectively) in osfrk3-1 and osfrk3-2. Evidently decreased grain width, grain thickness, and endosperm filling rate were detected in the osfrk3 mutants (osfrk3-1 and osfrk3-2) compared with those of the WT. In addition, the content of seed total starch was significantly decreased by 3.42 and 4.80% in osfrk3 lines, compared with that in the WT. The level of maltose was significantly reduced in the mutants, while that of sucrose and fructose was obviously increased in the mutants. The transcript levels of OsGBSS1, OsBEIIb, OsPFP1β, and OsAGPL1 were significantly decreased in the osfrk3 mutants. These results suggest that OsFRK3 may positively regulate the accumulation of starch through influencing the sugar metabolism.

Rice lipid transfer protein, OsLTPL23, controls seed germination by regulating starch-sugar conversion and ABA homeostasis

Seed germination is vital for ensuring the continuity of life in spermatophyte. High-quality seed germination usually represents good seedling establishment and plant production. Here, we identified OsLTPL23, a putative rice non-specific lipid transport protein, as an important regulator responsible for seed germination. Subcellular localization analysis confirmed that OsLTPL23 is present in the plasma membrane and nucleus. The knockout mutants of OsLTPL23 were generated by CRISPR/Cas9-mediated genome editing, and osltpl23 lines significantly germinated slower and lower than the Nipponbare (NIP). Starch and soluble sugar contents measurement showed that OsLTPL23 may have alpha-amylase inhibitor activity, and high soluble sugar content may be a causal agent for the delayed seed germination of osltpl23 mutants. Transcript profiles in the germinating seeds exhibited that the abscisic acid (ABA)-responsive genes, OsABI3 and OsABI5, and biosynthesis genes, OsNCED1, OsNCED2, OsNCED3 and OsNCED4, are obviously upregulated in the osltpl23 mutants compared to NIP plants, conversely, ABA metabolism genes OsABA8ox1, OsABA8ox2 and OsABA8ox3 are stepwise decreased. Further investigations found that osltpl23 mutants displays weakened early seedling growth, with elevated gene expresssion of ABA catabolism genes and repressive transcription response of defence-related genes OsWRKY45, OsEiN3, OsPR1a, OsPR1b and OsNPR1. Integrated analysis indicated that OsLTPL23 may exert an favorable effect on rice seed germination and early seedling growth via modulating endogenous ABA homeostasis. Collectively, our study provides important insights into the roles of OsLTPL23-mediated carbohydrate conversion and endogenous ABA pathway on seed germination and early seedling growth, which contributes to high-vigor seed production in rice breeding.

A Systematic Investigation of Lipid Transfer Proteins Involved in Male Fertility and Other Biological Processes in Maize

Plant lipid transfer proteins (LTPs) play essential roles in various biological processes, including anther and pollen development, vegetative organ development, seed development and germination, and stress response, but the research progress varies greatly among Arabidopsis, rice and maize. Here, we presented a preliminary introduction and characterization of the whole 65 LTP genes in maize, and performed a phylogenetic tree and gene ontology analysis of the LTP family members in maize. We compared the research progresses of the reported LTP genes involved in male fertility and other biological processes in Arabidopsis and rice, and thus provided some implications for their maize orthologs, which will provide useful clues for the investigation of LTP transporters in maize. We predicted the functions of LTP genes based on bioinformatic analyses of their spatiotemporal expression patterns by using RNA-seq and qRT-PCR assays. Finally, we discussed the advances and challenges in substrate identification of plant LTPs, and presented the future research directions of LTPs in plants. This study provides a basic framework for functional research and the potential application of LTPs in multiple plants, especially for male sterility research and application in maize.

CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions

Complete and accurate identification of genetic variants associated with specific phenotypes can be challenging when there is a high level of genomic divergence between individuals in a study and the corresponding reference genome. We have applied the Cas9-mediated enrichment coupled to nanopore sequencing to perform a targeted de novo assembly and accurately reconstruct a genomic region of interest. This approach was used to reconstruct a 250-kbp target region on chromosome 5 of the common bean genome (Phaseolus vulgaris) associated with the shattering phenotype. Comparing a non-shattering cultivar (Midas) with the reference genome revealed many single-nucleotide variants and structural variants in this region. We cut five 50-kbp tiled sub-regions of Midas genomic DNA using Cas9, followed by sequencing on a MinION device and de novo assembly, generating a single contig spanning the whole 250-kbp region. This assembly increased the number of Illumina reads mapping to genes in the region, improving their genotypability for downstream analysis. The Cas9 tiling approach for target enrichment and sequencing is a valuable alternative to whole-genome sequencing for the assembly of ultra-long regions of interest, improving the accuracy of downstream genotype-phenotype association analysis.

Assessment of Diagnosis, Prognosis and Immune Infiltration Response to the Expression of the Ferroptosis-Related Molecule HAMP in Clear Cell Renal Cell Carcinoma

BACKGROUND

Hepcidin antimicrobial peptide (HAMP) is a key factor in maintaining iron metabolism, which may induce ferroptosis when upregulated. However, its prognostic value and relation to immune infiltrating cells remains unclear.

METHODS

This study analyzed the expression levels of HAMP in the Oncomine, Timer and Ualcan databases, and examined its prognostic potential in KIRC with R programming. The Timer and GEPIA databases were used to estimate the correlations between HAMP and immune infiltration and the markers of immune cells. The intersection genes and the co-expression PPI network were constructed via STRING, R programming and GeneMANIA, and the hub genes were selected with Cytoscape. In addition, we analyzed the gene set enrichment and GO/KEGG pathways by GSEA.

RESULTS

Our study revealed higher HAMP expression levels in tumor tissues including KIRC, which were related to poor prognosis in terms of OS, DSS and PFI. The expression of HAMP was positively related to the immune infiltration level of macrophages, Tregs, etc., corresponding with the immune biomarkers. Based on the intersection genes, we constructed the PPI network and used the 10 top hub genes. Further, we performed a pathway enrichment analysis of the gene sets, including Huntington's disease, the JAK-STAT signaling pathway, ammonium ion metabolic process, and so on.

CONCLUSION

In summary, our study gave an insight into the potential prognosis of HAMP, which may act as a diagnostic biomarker and therapeutic target related to immune infiltration in KIRC.

Plant pan-genomics and its applications

Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among individuals. The variable DNA sequences, along with the conserved core sequences, compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a species. With rapid progress in genome sequencing technologies, pan-genome research in plants is now accelerating. Here we review recent advances in plant pan-genomics, including major driving forces of structural variations that constitute the variable sequences, methodological innovations for representing the pan-genome, and major successes in constructing plant pan-genomes. We also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources, which have remarkable advantages over numerous previously assembled less-than-perfect genomes, are expected to become new references for genetic studies and plant breeding.

Crosstalk between melatonin and reactive oxygen species in fruits and vegetables post-harvest preservation: An update

Fruits and vegetables contain numerous nutrients, such as vitamins, minerals, phenolic compounds, and dietary fibers. They reduce the incidence of cardiovascular diseases and the risk of certain chronic diseases, and improve the antioxidant and anti-inflammatory capacity. Moreover, melatonin was found in various fruits and vegetables species. Melatonin acts as a multifunctional compound to participate in various physiological processes. In recent years, many advances have been found that melatonin is also appraised as a key modulator on the fruits and vegetables post-harvest preservation. Fruits and vegetables post-harvest usually elicit reactive oxygen species (ROS) generation and accumulation. Excess ROS stimulate cell damage, protein structure destruction, and tissue aging, and thereby reducing their quality. Numerous studies find that exogenous application of melatonin modulates ROS homeostasis by regulating the antioxidant enzymes and non-enzymatic antioxidants systems. Further evidences reveal that melatonin often interacts with hormones and other signaling molecules, such as ROS, nitric oxide (NO), hydrogen sulfide (H₂S), and etc. Among these 'new' molecules, crosstalks of melatonin and ROS, especially the H₂O₂ produced by RBOHs, are provided in fruits and vegetables post-harvest preservation in this review. It will provide reference for complicated integration of both melatonin and ROS as signal molecules in future study.

Combined QTL mapping on bi-parental immortalized heterozygous populations to detect the genetic architecture on heterosis

From bi-parental pure-inbred lines (PIL), immortalized backcross (i.e., IB₁ and IB₂, representing the two directions of backcrossing) and F₂ (i.e., IF₂) populations can be developed. These populations are suitable for genetic studies on heterosis, due to the present of both homozygous and heterozygous genotypes, and in the meantime allow repeated phenotyping trials across multiple locations and years. In this study, we developed a combined approach of quantitative trait locus (QTL) mapping, when some or all of the four immortalized populations (i.e., PIL, IB₁, IB₂, and IF₂) are available. To estimate the additive and dominant effects simultaneously and accurately, suitable transformations are made on phenotypic values from different populations. When IB₁ and IB₂ are present, summation and subtraction are used. When IF₂ and PIL are available, mid-parental values and mid-parental heterosis are used. One-dimensional genomic scanning is performed to detect the additive and dominant QTLs, based on the algorithm of inclusive composite interval mapping (ICIM). The proposed approach was applied to one IF₂ population together with PIL in maize, and identified ten QTLs on ear length, showing varied degrees of dominance. Simulation studies indicated the proposed approach is similar to or better than individual population mapping by QTL detection power, false discovery rate (FDR), and estimated QTL position and effects.

Biological functions, mechanisms, and clinical significance of circular RNA in colorectal cancer

Colorectal cancer (CRC) is a leading cause of cancer-related death worldwide due to the lack of effective diagnosis and prognosis biomarkers and therapeutic targets, resulting in poor patient survival rates. Circular RNA (circRNA) is a type of endogenous non-coding RNA (ncRNA) with a closed-loop structure that plays a crucial role in physiological processes and pathological diseases. Recent studies indicate that circRNAs are involved in the diagnosis, prognosis, drug resistance, and development of tumors, particularly in CRC. Therefore, circRNA could be a potential new target for improving CRC diagnosis, prognosis, and treatment. This review focuses on the origin and biological functions of circRNA, summarizes recent research on circRNA's role in CRC, and discusses the potential use of circRNAs as clinical biomarkers for cancer diagnosis and prognosis, as well as therapeutic targets for CRC treatment.

Zinc restores functionality in porcine prepubertal Sertoli cells exposed to subtoxic cadmium concentration via regulating the Nrf2 signaling pathway

INTRODUCTION

Among substances released into the environment by anthropogenic activities, the heavy metal cadmium (Cd) is known to induce severe testicular injury causing male subfertility/infertility. Zinc (Zn) is another heavy metal that, unlike Cd, is physiologically present in the testis, being essential for spermatogenesis. We aimed to examine the possibility that 50 µM ZnCl₂ could counteract the toxic effects induced by Cd in an in vitro model of porcine prepubertal Sertoli cells (SCs) exposed to both subtoxic (5 μM) and toxic (10 μM) concentrations of CdCl₂ for 48 h.

MATERIALS AND METHODS

Apoptosis, cell cycle, and cell functionality were assessed. The gene expression of Nrf2 and its downstream antioxidant enzymes, ERK1/2, and AKT kinase signaling pathways were evaluated.

MATERIALS AND RESULTS

We found that Zn, in co-treatment with subtoxic and toxic Cd concentration, increased the number of metabolically active SCs compared to Cd exposure alone but restored SC functionality only in co-treatment with subtoxic Cd concentration with respect to subtoxic Cd alone. Exposure of Cd disrupted cell cycle in SCs, and Zn co-treatment was not able to counteract this effect. Cd alone induced SC death through apoptosis and necrosis in a dose-dependent manner, and co-treatment with Zn increased the pro-apoptotic effect of Cd. Subtoxic and toxic Cd exposures activated the Nrf2 signaling pathway by increasing gene expression of Nrf2 and its downstream genes (SOD, HO-1, and GSHPx). Zn co-treatment with subtoxic Cd attenuated upregulation on the Nrf2 system, while with toxic Cd, the effect was more erratic. Studying ERK1/2 and AKT pathways as a target, we found that the phosphorylation ratio of p-ERK1/2 and p-AKT was upregulated by both subtoxic and toxic Cd exposure alone and in co-treatment with Zn.

DISCUSSION

Our results suggest that Zn could counteract Cd effects by increasing the number of metabolically active SCs, fully or partially restoring their functionality by modulating Nrf2, ERK1/2, and AKT pathways. Our SC model could be useful to study the effects of early Cd exposure on immature testis, evaluating the possible protective effects of Zn.

Elabela blunts doxorubicin-induced oxidative stress and ferroptosis in rat aortic adventitial fibroblasts by activating the KLF15/GPX4 signaling

Doxorubicin (DOX) is a chemotherapeutic drug for a variety of malignancies, while its application is restricted by the cardiovascular toxic effects characterized by oxidative stress. Ferroptosis is a novel iron-dependent regulated cell death driven by lipid peroxidation. Our study aimed to investigate the role of Elabela (ELA) in DOX-induced oxidative stress and ferroptosis. In cultured rat aortic adventitial fibroblasts (AFs), stimulation with DOX dramatically induced cytotoxicity with reduced cell viability and migration ability, and enhanced lactate dehydrogenase (LDH) activity. Importantly, ELA and ferrostatin-1 (Fer-1) mitigated DOX-mediated augmentation of reactive oxygen species (ROS) in rat aortic AFs, accompanied by upregulated levels of Nrf2, SLC7A11, GPX4, and GSH. In addition, ELA reversed DOX-induced dysregulation of apoptosis- and inflammation-related factors including Bax, Bcl2, interleukin (IL)-1β, IL6, IL-10, and CXCL1. Intriguingly, knockdown of Krüppel-like factor 15 (KLF15) by siRNA abolished ELA-mediated alleviation of ROS production and inflammatory responses. More importanly, KLF15 siRNA impeded the beneficial roles of ELA in DOX-pretreated rat aortic AFs by suppressing the Nrf2/SLC7A11/GPX4 signaling. In conclusion, ELA prevents DOX-triggered promotion of cytotoxicity, and exerts anti-oxidative and anti-ferroptotic effects in rat aortic AFs via activation of the KLF15/GPX4 signaling, indicating a promising therapeutic value of ELA in antagonizing DOX-mediated cardiovascular abnormality and disorders.

Mitochondrial alternative oxidase enhanced ABA-mediated drought tolerance in Solanum lycopersicum

The phytohormone abscisic acid (ABA) plays essential roles in modulating drought stress responses. Mitochondrial alternative oxidase (AOX) is critical for reactive oxygen species (ROS) scavenging in drought stress responses. However, whether ABA signal in concert with AOX to moderate drought stress response remains largely unclear. In our study, we uncover the positive role of AOX in ABA-mediated drought tolerance in tomato (Solanum lycopersicum). Here, we report that ABA participates in the regulation of alternative respiration, and the increased AOX was found to improve drought tolerance by reducing total ROS accumulation. We also found that transcription factor ABA response element-binding factor 1 (SlAREB1) can directly bind to the promoter of AOX1a to activate its transcription. Virus-induced gene silencing (VIGS) of SlAREB1 compromised the ABA-induced alternative respiratory pathway, disrupted redox homeostasis and decreased plant resistance to drought stress, while overexpression of AOX1a in TRV2-SlAREB1 plants partially rescued the severe drought phenotype. Taken together, our results indicated that AOX1a plays an essential role in ABA-mediated drought tolerance partially in a SlAREB1-dependent manner, providing new insights into how ABA modulates ROS levels to cope with drought stress by AOX.

CLPP Depletion Causes Diplotene Arrest; Underlying Testis Mitochondrial Dysfunction Occurs with Accumulation of Perrault Proteins ERAL1, PEO1, and HARS2

Human Perrault syndrome (PRLTS) is autosomal, recessively inherited, and characterized by ovarian insufficiency with hearing loss. Among the genetic causes are mutations of matrix peptidase CLPP, which trigger additional azoospermia. Here, we analyzed the impact of CLPP deficiency on male mouse meiosis stages. Histology, immunocytology, different OMICS and biochemical approaches, and RT-qPCR were employed in CLPP-null mouse testis. Meiotic chromosome pairing and synapsis proceeded normally. However, the foci number of the crossover marker MLH1 was slightly reduced, and foci persisted in diplotene, most likely due to premature desynapsis, associated with an accumulation of the DNA damage marker γH2AX. No meiotic M-phase cells were detected. Proteome profiles identified strong deficits of proteins involved in male meiotic prophase (HSPA2, SHCBP1L, DMRT7, and HSF5), versus an accumulation of AURKAIP1. Histone H3 cleavage, mtDNA extrusion, and cGAMP increase suggested innate immunity activation. However, the deletion of downstream STING/IFNAR failed to alleviate pathology. As markers of underlying mitochondrial pathology, we observed an accumulation of PRLTS proteins ERAL1, PEO1, and HARS2. We propose that the loss of CLPP leads to the extrusion of mitochondrial nucleotide-binding proteins to cytosol and nucleus, affecting late meiotic prophase progression, and causing cell death prior to M-phase entry. This phenotype is more severe than in mito-mice or mutator-mice.

New Insight into Plant Saline-Alkali Tolerance Mechanisms and Application to Breeding

Saline-alkali stress is a widespread adversity that severely affects plant growth and productivity. Saline-alkaline soils are characterized by high salt content and high pH values, which simultaneously cause combined damage from osmotic stress, ionic toxicity, high pH and HCO₃^-/CO₃^2- stress. In recent years, many determinants of salt tolerance have been identified and their regulatory mechanisms are fairly well understood. However, the mechanism by which plants respond to comprehensive saline-alkali stress remains largely unknown. This review summarizes recent advances in the physiological, biochemical and molecular mechanisms of plants tolerance to salinity or salt- alkali stress. Focused on the progress made in elucidating the regulation mechanisms adopted by plants in response to saline-alkali stress and present some new views on the understanding of plants in the face of comprehensive stress. Plants generally promote saline-alkali tolerance by maintaining pH and Na⁺ homeostasis, while the plants responding to HCO₃^-/CO₃^2- stress are not exactly the same as high pH stress. We proposed that pH-tolerant or sensitive plants have evolved distinct mechanisms to adapt to saline-alkaline stress. Finally, we highlight the areas that require further research to reveal the new components of saline-alkali tolerance in plants and present the current and potential application of key determinants in breed improvement and molecular breeding.

Plant Plasma Membrane Proton Pump: One Protein with Multiple Functions

In plants, the plasma membrane proton pump (PM H⁺-ATPase) regulates numerous transport-dependent processes such as growth, development, basic physiology, and adaptation to environmental conditions. This review explores the multifunctionality of this enzyme in plant cells. The abundance of several PM H⁺-ATPase isogenes and their pivotal role in energizing transport in plants have been connected to the phenomena of pleiotropy. The multifunctionality of PM H⁺-ATPase is a focal point of numerous studies unraveling the molecular mechanisms of plant adaptation to adverse environmental conditions. Furthermore, PM H⁺-ATPase is a key element in plant defense mechanisms against pathogen attack; however, it also functions as a target for pathogens that enable plant tissue invasion. Here, we provide an extensive review of the PM H⁺-ATPase as a multitasking protein in plants. We focus on the results of recent studies concerning PM H⁺-ATPase and its role in plant growth, physiology, and pathogenesis.

Leucine Contributes to Copper Stress Tolerance in Peach (Prunus persica) Seedlings by Enhancing Photosynthesis and the Antioxidant Defense System

Heavy metal contamination has a severe impact on ecological health and plant growth and is becoming increasingly serious globally. Copper (Cu) is a heavy metal that is essential for the growth and development of plants, including peach (Prunus persica L. Batsch); however, an excess is toxic. In plants, amino acids are involved in responses to abiotic and biotic stresses, such as water deficit, extreme temperatures, high salinity, and heavy metal stress. However, the role of leucine in the regulation of heavy metal stress is currently unclear. Therefore, we investigated the effects of exogenous leucine on the growth of peach seedlings under Cu stress. Exogenous leucine improved the leaf ultrastructure and ionic balance and increased the chlorophyll content, the net photosynthetic rate, and the maximum photochemical efficiency. Furthermore, it attenuated Cu-stress-induced oxidative damage via a decrease in reactive oxygen species (ROS) and the regulation of the antioxidant and osmotic systems. These effects, in turn, ameliorated the reductions in cell viability, cellular activity, and biomass under Cu stress. Moreover, exogenous leucine increased the activities of nitrate reductase (NR), glutamine synthetase (GS), and glutamic acid synthetase (GOGAT) and thus improved the nitrogen metabolism efficiency of plants. In conclusion, leucine significantly improved the photosynthetic performance and antioxidant capacity, reduced Cu accumulation, and promoted nitrogen metabolism, which in turn improved the resistance of peach seedlings to Cu stress.

Diagnostic accuracy of metagenomic next-generation sequencing in diagnosing infectious diseases: a meta-analysis

Many common pathogens are difficult or impossible to detect using conventional microbiological tests. However, the rapid and untargeted nature of metagenomic next-generation sequencing (mNGS) appears to be a promising alternative. To perform a systematic review and meta-analysis of evidence regarding the diagnostic accuracy of mNGS in patients with infectious diseases. An electronic literature search of Embase, PubMed and Scopus databases was performed. Quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. Summary receiver operating characteristics (sROC) and the area under the curve (AUC) were calculated; A random-effects model was used in cases of heterogeneity. A total of 20 papers were eligible for inclusion and synthesis. The sensitivity and specificity of diagnostic mNGS were 75% and 68%, respectively. The AUC from the SROC was 85%, corresponding to excellent performance. mNGS demonstrated satisfactory diagnostic performance for infections and yielded an overall detection rate superior to conventional methods.

Pseudouridylation of chloroplast ribosomal RNA contributes to low temperature acclimation in rice

Ribosomal RNAs (rRNAs) undergo many modifications during transcription and maturation; homeostasis of rRNA modifications is essential for chloroplast biogenesis in plants. The chloroplast acts as a hub to sense environmental signals, such as cold temperature. However, how RNA modifications contribute to low temperature responses remains unknown. Here we reveal that pseudouridine (Ψ) modification of rice chloroplast rRNAs mediated by the pseudouridine synthase (OsPUS1) contributes to cold tolerance at seedling stage. Loss-function of OsPUS1 leads to abnormal chloroplast development and albino seedling phenotype at low temperature. We find that OsPUS1 is accumulated upon cold and binds to chloroplast precursor rRNAs (pre-rRNAs) to catalyse the pseudouridylation on rRNA. These modifications on chloroplast rRNAs could be required for their processing, as the reduction of mature chloroplast rRNAs and accumulation of pre-rRNAs are observed in ospus1-1 at low temperature. Therefore, the ribosome activity and translation in chloroplasts is disturbed in ospus1-1. Furthermore, transcriptome and translatome analysis reveals that OsPUS1 balances growth and stress-responsive state, preventing excess reactive oxygen species accumulation. Taken together, our findings unveil a crucial function of Ψ in chloroplast ribosome biogenesis and cold tolerance in rice, with potential applications in crop improvement.

Resveratrol and SIRT1: Antiaging Cornerstones for Oocytes?

It is well-known that there is an enormous variability in the aging-related decline of oocytes' quantity and their developmental competence among mammalian species. The implication of female germline aging is profound from the perspective of evolutionary conservation of the aging mechanism, a topic of continuous and widespread interest that has yet to be fully addressed for the mammalian oocyte. There is a certain need to develop novel antiaging strategies to delay or slow down aging, or even to reverse the aging phenotype in the oocyte. In the past two decades, several antioxidants have been tested for this purpose. Resveratrol is one of these latter-mentioned compounds, which has shown anti-inflammatory and antiaging properties in a dose-dependent manner. Interestingly, resveratrol appears to enhance the activity of so-called Sirtuin 1, too. Therefore, the aim of this review is to summarize and discuss the latest findings related to resveratrol, Sirtuin 1, and their crosstalk and influence on the mammalian oocyte to elucidate the question of whether these factors can delay or slow down reproductive aging.

THP9 enhances seed protein content and nitrogen-use efficiency in maize

Teosinte, the wild ancestor of maize (Zea mays subsp. mays), has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms that are responsible for this trait are unknown^1,2. Here we use trio binning to create a contiguous haplotype DNA sequence of a teosinte (Zea mays subsp. parviglumis) and, through map-based cloning, identify a major high-protein quantitative trait locus, TEOSINTE HIGH PROTEIN 9 (THP9), on chromosome 9. THP9 encodes an asparagine synthetase 4 enzyme that is highly expressed in teosinte, but not in the B73 inbred, in which a deletion in the tenth intron of THP9-B73 causes incorrect splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 significantly increased the seed protein content. Introgression of THP9-teosinte into modern maize inbreds and hybrids greatly enhanced the accumulation of free amino acids, especially asparagine, throughout the plant, and increased seed protein content without affecting yield. THP9-teosinte seems to increase nitrogen-use efficiency, which is important for promoting a high yield under low-nitrogen conditions.

Genome-Wide Identification and Expression Profiling of Heat Shock Protein 20 Gene Family in Sorbus pohuashanensis (Hance) Hedl under Abiotic Stress

Small heat shock proteins (HSP20s) are a significant factor in plant growth and development in response to abiotic stress. In this study, we investigated the role of HSP20s' response to the heat stress of Sorbus pohuashanensis introduced into low-altitude areas. The HSP20 gene family was identified based on the genome-wide data of S. pohuashanensis, and the expression patterns of tissue specificity and the response to abiotic stresses were evaluated. Finally, we identified 38 HSP20 genes that were distributed on 16 chromosomes. Phylogenetic analysis of HSP20s showed that the closest genetic relationship to S. pohuashanensis (SpHSP20s) is Malus domestica, followed by Populus trichocarpa and Arabidopsis thaliana. According to phylogenetic analysis and subcellular localization prediction, the 38 SpHSP20s belonged to 10 subfamilies. Analysis of the gene structure and conserved motifs indicated that HSP20 gene family members are relatively conserved. Synteny analysis showed that the expansion of the SpHSP20 gene family was mainly caused by segmental duplication. In addition, many cis-acting elements connected with growth and development, hormones, and stress responsiveness were found in the SpHSP20 promoter region. Analysis of expression patterns showed that these genes were closely related to high temperature, drought, salt, growth, and developmental processes. These results provide information and a theoretical basis for the exploration of HSP20 gene family resources, as well as the domestication and genetic improvement of S. pohuashanensis.

Low-dose AAV-CRISPR-mediated liver-specific knock-in restored hemostasis in neonatal hemophilia B mice with subtle antibody response

AAV-delivered CRISPR/Cas9 (AAV-CRISPR) has shown promising potentials in preclinical models to efficiently insert therapeutic gene sequences in somatic tissues. However, the AAV input doses required were prohibitively high and posed serious risk of toxicity. Here, we performed AAV-CRISPR mediated homology-independent knock-in at a new target site in mAlb 3'UTR and demonstrated that single dose of AAVs enabled long-term integration and expression of hF9 transgene in both adult and neonatal hemophilia B mice (mF9 -/-), yielding high levels of circulating human Factor IX (hFIX) and stable hemostasis restoration during entire 48-week observation period. Furthermore, we achieved hemostasis correction with a significantly lower AAV dose (2 × 10⁹ vg/neonate and 1 × 10¹⁰ vg/adult mouse) through liver-specific gene knock-in using hyperactive hF9^R338L variant. The plasma antibodies against Cas9 and AAV in the neonatal mice receiving low-dose AAV-CRISPR were negligible, which lent support to the development of AAV-CRISPR mediated somatic knock-in for treating inherited diseases.

Metabolic and Transcriptional Stress Memory in Sorbus pohuashanensis Suspension Cells Induced by Yeast Extract

Plant stress memory can provide the benefits of enhanced protection against additional stress exposure. Here, we aimed to explore the responses of recurrent and non-recurrent yeast extract (YE) stresses in Sorbus pohuashanensis suspension cells (SPSCs) at metabolomics and transcriptional levels. Biochemical analyses showed that the cell wall integrity and antioxidation capacity of SPSCs in the pretreated group were evidently improved. Metabolic analysis showed that there were 39 significantly altered metabolites in the pretreated group compared to the non-pretreated group. Based on the transcriptome analysis, 219 differentially expressed genes were obtained, which were highly enriched in plant-pathogen interaction, circadian rhythm-plant, oxidative phosphorylation, and phenylpropanoid biosynthesis. Furthermore, the correlation analysis of the transcriptome and metabolome data revealed that phenylpropanoid biosynthesis involved in the production of biphenyl phytoalexins may play a critical role in the memory response of SPSC to YE, and the key memory genes were also identified, including PAL1, BIS1, and BIS3. Collectively, the above results demonstrated that the memory responses of SPSC to YE were significant in almost all levels, which would be helpful for better understanding the adaptation mechanisms of medicinal plants in response to biotic stress, and laid a biotechnological foundation to accumulate favorable antimicrobial drug candidates from plant suspension cells.

Salinity and Heavy Metal Tolerance, and Phytoextraction Potential of Ranunculus sceleratus Plants from a Sandy Coastal Beach

The aim of the present study was to evaluate tolerance to salinity and different heavy metals as well as the phytoextraction potential of Ranunculus sceleratus plants from a brackish coastal sandy beach habitat. Four separate experiments were performed with R. sceleratus plants in controlled conditions: (1) the effect of NaCl gradient on growth and ion accumulation, (2) the effect of different Na⁺ and K⁺ salts on growth and ion accumulation, (3) heavy metal tolerance and metal accumulation potential, (4) the effect of different forms of Pb salts (nitrate and acetate) on plant growth and Pb accumulation. A negative effect of NaCl on plant biomass was evident at 0.5 g L^-1 Na⁺ and growth was inhibited by 44% at 10 g L^-1 Na⁺, and this was associated with changes in biomass allocation. The maximum Na⁺ accumulation (90.8 g kg^-1) was found in the stems of plants treated with 10 g kg^-1 Na⁺. The type of anion determined the salinity tolerance of R. sceleratus plants, as Na⁺ and K⁺ salts with an identical anion component had a comparable effect on plant growth: nitrates strongly stimulated plant growth, and chloride treatment resulted in slight but significant growth reduction, but plants treated with nitrites and carbonates died within 4 and 5 weeks after the full treatment, respectively. The shoot growth of R. sceleratus plants was relatively insensitive to treatment with Mn, Cd and Zn in the form of sulphate salts, but Pb nitrate increased it. Hyperaccumulation threshold concentration values in the leaves of R. sceleratus were reached for Cd, Pb and Zn. R. sceleratus can be characterized as a shoot accumulator of heavy metals and a hyperaccumulator of Na⁺. A relatively short life cycle together with a high biomass accumulation rate makes R. sceleratus useful for dynamic constructed wetland systems aiming for the purification of concentrated wastewaters.

From single- to multi-omics: future research trends in medicinal plants

Medicinal plants are the main source of natural metabolites with specialised pharmacological activities and have been widely examined by plant researchers. Numerous omics studies of medicinal plants have been performed to identify molecular markers of species and functional genes controlling key biological traits, as well as to understand biosynthetic pathways of bioactive metabolites and the regulatory mechanisms of environmental responses. Omics technologies have been widely applied to medicinal plants, including as taxonomics, transcriptomics, metabolomics, proteomics, genomics, pangenomics, epigenomics and mutagenomics. However, because of the complex biological regulation network, single omics usually fail to explain the specific biological phenomena. In recent years, reports of integrated multi-omics studies of medicinal plants have increased. Until now, there have few assessments of recent developments and upcoming trends in omics studies of medicinal plants. We highlight recent developments in omics research of medicinal plants, summarise the typical bioinformatics resources available for analysing omics datasets, and discuss related future directions and challenges. This information facilitates further studies of medicinal plants, refinement of current approaches and leads to new ideas.

Wnt/planar cell polarity signaling controls morphogenetic movements of gastrulation and neural tube closure

Gastrulation and neurulation are successive morphogenetic processes that play key roles in shaping the basic embryonic body plan. Importantly, they operate through common cellular and molecular mechanisms to set up the three spatially organized germ layers and to close the neural tube. During gastrulation and neurulation, convergent extension movements driven by cell intercalation and oriented cell division generate major forces to narrow the germ layers along the mediolateral axis and elongate the embryo in the anteroposterior direction. Apical constriction also makes an important contribution to promote the formation of the blastopore and the bending of the neural plate. Planar cell polarity proteins are major regulators of asymmetric cell behaviors and critically involved in a wide variety of developmental processes, from gastrulation and neurulation to organogenesis. Mutations of planar cell polarity genes can lead to general defects in the morphogenesis of different organs and the co-existence of distinct congenital diseases, such as spina bifida, hearing deficits, kidney diseases, and limb elongation defects. This review outlines our current understanding of non-canonical Wnt signaling, commonly known as Wnt/planar cell polarity signaling, in regulating morphogenetic movements of gastrulation and neural tube closure during development and disease. It also attempts to identify unanswered questions that deserve further investigations.

Legume Pangenome: Status and Scope for Crop Improvement

In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major legume crops. These advances have certainly facilitated the identification of novel genetic variants underlying the traits of agronomic importance in many legume crops. Furthermore, these robust sequencing technologies have allowed us to study structural variations across the whole genome in multiple individuals and at the species level using 'pangenome analysis.' This review updates the progress of constructing pangenome assemblies for various legume crops and discusses the prospects for these pangenomes and how to harness the information to improve various traits of economic importance through molecular breeding to increase genetic gain in legumes and tackle the increasing global food crisis.

Exploring People's Knowledge of Genetics and Attitude towards Genetic Testing: A Cross-Sectional Study in a Population with a High Prevalence of Consanguinity

This study investigated people’s knowledge of genetics, attitudes toward genetic testing, and views on consanguinity. This cross-sectional study utilized a validated questionnaire modified from published studies to collect data on people’s knowledge of genetics and attitudes about genetic testing among 1008 respondents from various Saudi Arabian regions. Using SPSS software version 26, data were analyzed using a t-test, ANOVA, and multivariate analysis. p-values of <0.05 were considered statistically significant. About 59.9% of the participants had sufficient knowledge of genetics, and around 50% had a favorable attitude toward genetic testing. Knowledge of genetics is significantly correlated (p ≤ 0.001) with a positive attitude toward genetic testing. Gender, age, level of education, marital status, family income, and family history were significantly correlated with respondents’ understanding of genetics. Gender, family income, residence, and family history were associated with attitudes toward genetic testing at a 0.05 level of significance. There is a need to strengthen peoples’ knowledge of genetics and attitudes toward genetic testing through diverse educational programs and healthcare strategies. Impetus on how to disseminate genetic information on consanguinity and transmission of diseases should be prioritized in regions where consanguineous marriages are high.

Targeting Ferroptosis Holds Potential for Intervertebral Disc Degeneration Therapy

Intervertebral disc degeneration (IVDD) is a common pathological condition responsible for lower back pain, which can significantly increase economic and social burdens. Although considerable efforts have been made to identify potential mechanisms of disc degeneration, the treatment of IVDD is not satisfactory. Ferroptosis, a recently reported form of regulated cell death (RCD), is characterized by iron-dependent lipid peroxidation and has been demonstrated to be responsible for a variety of degenerative diseases. Accumulating evidence suggests that ferroptosis is implicated in IVDD by decreasing viability and increasing extracellular matrix degradation of nucleus pulposus cells, annulus fibrosus cells, or endplate chondrocytes. In this review, we summarize the literature regarding ferroptosis of intervertebral disc cells and discuss its molecular pathways and biomarkers for treating IVDD. Importantly, ferroptosis is verified as a promising therapeutic target for IVDD.

Graph Pangenomes Track Genetic Variants for Crop Improvement

Global climate change and the urgency to transform crops require an exhaustive genetic evaluation. The large polyploid genomes of food crops, such as cereals, make it difficult to identify candidate genes with confirmed hereditary. Although genome-wide association studies (GWAS) have been proficient in identifying genetic variants that are associated with complex traits, the resolution of acquired heritability faces several significant bottlenecks such as incomplete detection of structural variants (SV), genetic heterogeneity, and/or locus heterogeneity. Consequently, a biased estimate is generated with respect to agronomically complex traits. The graph pangenomes have resolved this missing heritability and provide significant details in terms of specific loci segregating among individuals and evolving to variations. The graph pangenome approach facilitates crop improvements through genome-linked fast breeding.

Short-chain fatty acid metabolism and multiple effects on cardiovascular diseases

Cardiovascular diseases (CVDs) are the leading cause of mortality worldwide, and fatty acid metabolism has been well studied. Short-chain fatty acids (SCFAs) have been less discussed than long-chain fatty acids (LCFAs) in CVDs. However, increasing evidence indicates the importance of SCFAs in regulating cardiac function. Here, we summarize the current understanding of SCFAs in hypertension, ischaemic reperfusion, myocardial infarction, atherosclerosis and heart failure. Most SCFAs exert positive effects in regulating related diseases. Butyrate and propionate can reduce blood pressure, improve I/R injury and decrease the risk of coronary artery disease (CAD) and atherosclerosis. Acetate can also play a positive role in regulating hypertension and preventing atherosclerosis, and malonate can improve cardiac function after MI. They affect these diseases by regulating inflammation, the immune system and related G protein-coupled receptors, with multiple neurohumoural regulation participation. In contrast, succinate can accelerate IR injury, increasing mitochondrial ROS production. SCFAs ultimately affect the regulation of different pathophysiological processes in heart failure. Here, we clarified the importance of short-chain fatty acids in the cardiovascular system and their multiple effects in various pathophysiological processes, providing new insights into their promising clinical application. More research should be conducted to further elucidate the underlying mechanism and different effects of single or multiple SCFA supplementation on the cardiovascular system.

Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.)

Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes Os04g0350700 and Os05g0154700 are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes Os06g0254300 and Os03g0168100. The functions of Os06g0254300 and Os03g0168100 are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice.

Transcriptomic Interaction between Young Fecal Transplantation and Perfluorobutanesulfonate in Aged Zebrafish Gonads

The transfer of young fecal microbiota has been found to significantly refresh the reproductive endocrine system and effectively ameliorate the toxicity of perfluorobutanesulfonate (PFBS) in aged zebrafish recipients. However, the mechanisms underlying the antagonistic action of young fecal microbiota against the reproductive endocrine toxicity of PFBS remain largely unknown. In this study, the aged zebrafish were transplanted with feces from young donors and then exposed to PFBS for 14 days. After exposure, the shift in the transcriptomic fingerprint of the gonads was profiled by using high-throughput sequencing, aiming to provide mechanistic clues into the interactive mode of action between young fecal transplantation and PFBS's innate toxicity. The results showed that the gene transcription pattern associated with protein and lipid synthesis in the gonads of the aged individuals was quite different from the young counterparts. It was intriguing that the transplantation of young feces established a youth-like transcriptomic phenotype in the elderly recipients, thus attenuating the functional decline and maintaining a healthy aging state of the gonads. A sex specificity response was clearly observed. Compared to the aged females, more metabolic pathways (e.g., glycine, serine, and threonine metabolism; glyoxylate and dicarboxylate metabolism; pyrimidine metabolism) were significantly enriched in aged males receiving young feces transplants. PFBS dramatically altered the transcriptome of aged testes, while a much milder effect was observable in aged ovaries. Accordingly, a suite of biological processes related to germ cell proliferation were disrupted by PFBS in aged males, including the ECM-receptor interaction, retinol metabolism, and folate biosynthesis. In aged ovaries exposed to PFBS, mainly the fatty acid and arginine biosynthesis pathway was significantly affected. However, these transcriptomic disorders caused by PFBS were largely mitigated in aged gonads by transferring young feces. Overall, the present findings highlighted the potential of young fecal transplantation to prevent the functional compromise of gonads resulting from aging and PFBS.

Epigenetic impact of a 1-week intensive multimodal group program for adolescents with multiple adverse childhood experiences

Adverse childhood experiences (ACEs, i.e., abuse, neglect, household dysfunction) represent a potential risk factor for a wide range of long-lasting diseases and shorter life expectancy. We recently described a 1-week residential group program, based on mindfulness training, artistic expression and EMDR group therapy, that significantly reduced PTSD-related symptoms and increased attention/awareness-related outcomes in adolescent girls with multiple ACEs in a randomized controlled study. Since epigenetic mechanisms (i.e., DNA methylation) have been associated with the long-lasting effects of ACEs, the present report extends these prior findings by exploring genome-wide DNA methylation changes following the program. Saliva samples from all participants (n = 44) were collected and genomic DNA was extracted prior (T1) and following (T2) the intervention. Genome-wide DNA methylation analysis using the MethylationEPIC beadchip array (Illumina) revealed 49 differentially methylated loci (DML; p value < 0.001; methylation change > 10%) that were annotated to genes with roles in biological processes linked to early childhood adversity (i.e., neural, immune, and endocrine pathways, cancer and cardiovascular disease). DNA sequences flanking these DML showed significant enrichment of transcription factor binding sites involved in inflammation, cancer, cardiovascular disease, and brain development. Methylation changes in SIRT5 and TRAPPC2L genes showed associations with changes in trauma-related psychological measures. Results presented here suggest that this multimodal group program for adolescents with multiple victimization modulates the DNA methylome at sites of potential relevance for health and behavioral disorders associated with ACEs.

FSP1, a novel KEAP1/NRF2 target gene regulating ferroptosis and radioresistance in lung cancers

In the study of "A targetable CoQ-FSP1 axis drives ferroptosis- and radiation-resistance in KEAP1 inactive lung cancers" which was published earlier in Nature Communications, the authors have identified a novel KEAP1/NRF2 target gene, FSP1, and demonstrated that FSP1 plays an essential role in NRF2-mediated ferroptosis resistance and radioresistance in KEAP1-deficient lung cancer cells. Currently, many NRF2 target genes have been found to participate in the regulation of ferroptosis, and exactly which one plays a dominant role seems unclear. This study proposes that FSP1 is the key effector in NRF2-mediated ferroptosis resistance and radioresistance in KEAP-deficient lung cancer cells, as we discussed in the manuscript.

Emerging Roles of RNA-Binding Proteins in Inner Ear Hair Cell Development and Regeneration

RNA-binding proteins (RBPs) regulate gene expression at the post-transcriptional level. They play major roles in the tissue- and stage-specific expression of protein isoforms as well as in the maintenance of protein homeostasis. The inner ear is a bi-functional organ, with the cochlea and the vestibular system required for hearing and for maintaining balance, respectively. It is relatively well documented that transcription factors and signaling pathways are critically involved in the formation of inner ear structures and in the development of hair cells. Accumulating evidence highlights emerging functions of RBPs in the post-transcriptional regulation of inner ear development and hair cell function. Importantly, mutations of splicing factors of the RBP family and defective alternative splicing, which result in inappropriate expression of protein isoforms, lead to deafness in both animal models and humans. Because RBPs are critical regulators of cell proliferation and differentiation, they present the potential to promote hair cell regeneration following noise- or ototoxin-induced damage through mitotic and non-mitotic mechanisms. Therefore, deciphering RBP-regulated events during inner ear development and hair cell regeneration can help define therapeutic strategies for treatment of hearing loss. In this review, we outline our evolving understanding of the implications of RBPs in hair cell formation and hearing disease with the aim of promoting future research in this field.

The role of microRNAs in ferroptosis

Ferroptosis is a newly discovered type of programmed cell death, which is closely related to the imbalance of iron metabolism and oxidative stress. Ferroptosis has become an important research topic in the fields of cardiomyopathy, tumors, neuronal injury disorders, and ischemia perfusion disorders. As an important part of non-coding RNA, microRNAs regulate various metabolic pathways in the human body at the post-transcriptional level and play a crucial role in the occurrence and development of many diseases. The present review introduces the mechanisms of ferroptosis and describes the relevant pathways by which microRNAs affect cardiomyopathy, tumors, neuronal injury disorders and ischemia perfusion disorders through regulating ferroptosis. In addition, it provides important insights into ferroptosis-related microRNAs, aiming to uncover new methods for treatment of the above diseases, and discusses new ideas for the implementation of possible microRNA-based ferroptosis-targeted therapies in the future.

Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops

The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.

Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom

In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.

A Ghd7-centered regulatory network provides a mechanistic approximation to optimal heterosis in an elite rice hybrid

Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single-locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F₂ s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement.

Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

BACKGROUND

Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F₁ (BCF₁) hybrids derived from QYSM's parents across three environments and gene-based analyses.

RESULTS

Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF₁ hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM.

CONCLUSIONS

The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis.

Identification of key gene networks controlling polysaccharide accumulation in different tissues of Polygonatum cyrtonema Hua by integrating metabolic phenotypes and gene expression profiles

Plant polysaccharides, a type of important bioactive compound, are involved in multiple plant defense mechanisms, and in particular polysaccharide-alleviated abiotic stress has been well studied. Polygonatum cyrtonema Hua (P. cyrtonema Hua) is a medicinal and edible perennial plant that is used in traditional Chinese medicine and is rich in polysaccharides. Previous studies suggested that sucrose might act as a precursor for polysaccharide biosynthesis. However, the role of sucrose metabolism and transport in mediating polysaccharide biosynthesis remains largely unknown in P. cyrtonema Hua. In this study, we investigated the contents of polysaccharides, sucrose, glucose, and fructose in the rhizome, stem, leaf, and flower tissues of P. cyrtonema Hua, and systemically identified the genes associated with the sucrose metabolism and transport and polysaccharide biosynthesis pathways. Our results showed that polysaccharides were mainly accumulated in rhizomes, leaves, and flowers. Besides, there was a positive correlation between sucrose and polysaccharide content, and a negative correlation between glucose and polysaccharide content in rhizome, stem, leaf, and flower tissues. Then, the transcriptomic analyses of different tissues were performed, and differentially expressed genes related to sucrose metabolism and transport, polysaccharide biosynthesis, and transcription factors were identified. The analyses of the gene expression patterns provided novel regulatory networks for the molecular basis of high accumulation of polysaccharides, especially in the rhizome tissue. Furthermore, our findings explored that polysaccharide accumulation was highly correlated with the expression levels of SUS, INV, SWEET, and PLST, which are mediated by bHLH, bZIP, ERF, ARF, C2H2, and other genes in different tissues of P. cyrtonema Hua. Herein, this study contributes to a comprehensive understanding of the transcriptional regulation of polysaccharide accumulation and provides information regarding valuable genes involved in the tolerance to abiotic stresses in P. cyrtonema Hua.

Deciphering the role of transforming growth factor-beta 1 as a diagnostic-prognostic-therapeutic candidate against hepatocellular carcinoma

Transforming growth factor-beta (TGF-β) is a multifunctional cytokine that performs a dual role as a tumor suppressor and tumor promoter during cancer progression. Among different ligands of the TGF-β family, TGF-β1 modulates most of its biological outcomes. Despite the abundant expression of TGF-β1 in the liver, steatosis to hepatocellular carcinoma (HCC) progression triggers elevated TGF-β1 levels, contributing to poor prognosis and survival. Additionally, elevated TGF-β1 levels in the tumor microenvironment create an immunosuppressive stage via various mechanisms. TGF-β1 has a prime role as a diagnostic and prognostic biomarker in HCC. Moreover, TGF-β1 is widely studied as a therapeutic target either as monotherapy or combined with immune checkpoint inhibitors. This review provides clinical relevance and up-to-date information regarding the potential of TGF-β1 in diagnosis, prognosis, and therapy against HCC.

Control of Grain Shape and Size in Rice by Two Functional Alleles of OsPUB3 in Varied Genetic Background

Grain shape and size are key determinants of grain appearance quality and yield in rice. In our previous study, a grain shape QTL, qGS1-35.2, was fine-mapped using near-isogenic lines (NILs) derived from a cross between Zhenshan 97 (ZS97) and Milyang 46 (MY46). One annotated gene, OsPUB3, was found to be the most likely candidate gene. Here, knockout and overexpression experiments were performed to investigate the effects of OsPUB3 on grain shape and size. Four traits were tested, including grain length, grain width, grain weight, and the ratio of grain length to width. Knockout of OsPUB3 in NIL^ZS97, NIL^MY46, and another rice cultivar carrying the OsPUB3^MY46 allele all caused decreases in grain width and weight and increases in the ratio of grain length to width. Results also showed that the magnitude of the mutational effects varied depending on the target allele and the genetic background. Moreover, it was found that NIL^ZS97 and NIL^MY46 carried different functional alleles of OsPUB3, causing differences in grain shape rather than grain weight. In the overexpression experiment, significant differences between transgenic-positive and transgenic-negative plants were detected in all four traits. These results indicate that OsPUB3 regulates grain shape and size through a complex mechanism and is a good target for deciphering the regulatory network of grain shape. This gene could be used to improve grain appearance quality through molecular breeding as well.

Involvement of JMJ15 in the dynamic change of genome-wide H3K4me3 in response to salt stress

Post-translational histone modifications play important roles in regulating chromatin structure and transcriptional regulation. Histone 3 lysine 4 trimethylation (H3K4me3) is a prominent histone modification mainly associated with gene activation. Here we showed that a histone demethylase, JMJ15, belonging to KDM5/JARID group, is involved in salt stress response in Arabidopsis thaliana. Jmj15 loss-of-function mutants displayed increased sensitivity to salt stress. Moreover, knockout of JMJ15 impaired the salt responsive gene expression program and affected H3K4me3 levels of many stress-related genes under salt-stressed condition. Importantly, we demonstrated that JMJ15 regulated the expression level of two WRKY transcription factors, WRKY46 and WRKY70, which were negatively involved in abiotic stress tolerance. Furthermore, JMJ15 directly bound to and demethylated H3K4me3 mark in the promoter and coding regions of WRKY46 and WRKY70, thereby repressing these two WRKY gene expression under salt stress. Overall, our study revealed a novel molecular function of the histone demethylase JMJ15 under salt stress in plants.

Salt stress resilience in plants mediated through osmolyte accumulation and its crosstalk mechanism with phytohormones

Salinity stress is one of the significant abiotic stresses that influence critical metabolic processes in the plant. Salinity stress limits plant growth and development by adversely affecting various physiological and biochemical processes. Enhanced generation of reactive oxygen species (ROS) induced via salinity stress subsequently alters macromolecules such as lipids, proteins, and nucleic acids, and thus constrains crop productivity. Due to which, a decreasing trend in cultivable land and a rising world population raises a question of global food security. In response to salt stress signals, plants adapt defensive mechanisms by orchestrating the synthesis, signaling, and regulation of various osmolytes and phytohormones. Under salinity stress, osmolytes have been investigated to stabilize the osmotic differences between the surrounding of cells and cytosol. They also help in the regulation of protein folding to facilitate protein functioning and stress signaling. Phytohormones play critical roles in eliciting a salinity stress adaptation response in plants. These responses enable the plants to acclimatize to adverse soil conditions. Phytohormones and osmolytes are helpful in minimizing salinity stress-related detrimental effects on plants. These phytohormones modulate the level of osmolytes through alteration in the gene expression pattern of key biosynthetic enzymes and antioxidative enzymes along with their role as signaling molecules. Thus, it becomes vital to understand the roles of these phytohormones on osmolyte accumulation and regulation to conclude the adaptive roles played by plants to avoid salinity stress.

Identification of nine mutant genes and establishment of three prediction models of organ tropism metastases of non-small cell lung cancer

BACKGROUND

Most Non-small cell lung cancer (NSCLC) patients tend to have metastases at the initial diagnosis. However, limited knowledge has been established regarding which factors, are associated with its metastases. This study aims to identify more biomarkers associated with its organ tropism metastasis and to establish models for prediction of its metastatic organs.

METHODS

We performed targeted next-generation sequencing (NGS) to detect genes related to lung cancer in 272 patients with primary advanced NSCLC from Northeast China. We adopted Fisher test, multivariate logistic regression analysis to identify metastasis-related gene mutations and to establish prediction models.

RESULTS

Mutations of EGFR (p = 0.0003, OR = 2.554) (especially EGFR L858R [p = 0.02, OR = 2.009]), ATM (p = 0.008, OR = 11.032), and JAK2 (p = 0.009, OR = Inf) were positively and of TP53 exon4mut (p = 0.001, OR = 0.173) was negatively correlated with lung metastasis, and those of CSF1R (p = 0.01, OR = Inf), KIT (p = 0.03, OR = 4.746), MYC (p = 0.05, OR = 7.938), and ERBB2 (p = 0.02, OR = 2.666) were positively correlated with pleural dissemination; those of TP53 (p = 0.01, OR = 0.417) was negatively, while of SMAD4 (p = 0.03, OR = 4.957) was positively correlated with brain metastasis of NSCLC. Additionally, smoking history (p = 0.004, OR = 0.004) was negatively correlated with pleural dissemination of NSCLC. Furthermore, models for prediction of lung metastasis (AUC = 0.706), pleural dissemination (AUC = 0.651), and brane metastasis (AUC = 0.629) were established.

CONCLUSION

Taken together, this study revealed nine mutant genes and smoking history associated with organ tropism metastases of NSCLC and provided three models for the prediction of metastatic organs. This study enables us to predict the organs to which non-small cell lung cancer metastasizes before it does develop.