DNA-based ForceChrono probes for deciphering single-molecule force dynamics in living cells.

Understanding cellular force transmission dynamics is crucial in mechanobiology. We developed the DNA-based ForceChrono probe to measure force magnitude, duration, and loading rates at the single-molecule level within living cells. The ForceChrono probe circumvents the limitations of in vitro single-molecule force spectroscopy by enabling direct measurements within the dynamic cellular environment. Our findings reveal integrin force loading rates of 0.5-2 pN/s and durations ranging from tens of seconds in nascent adhesions to approximately 100 s in mature focal adhesions. The probe's robust and reversible design allows for continuous monitoring of these dynamic changes as cells undergo morphological transformations. Additionally, by analyzing how mutations, deletions, or pharmacological interventions affect these parameters, we can deduce the functional roles of specific proteins or domains in cellular mechanotransduction. The ForceChrono probe provides detailed insights into the dynamics of mechanical forces, advancing our understanding of cellular mechanics and the molecular mechanisms of mechanotransduction.

Effect of heat-reinforcing needling on hypoxia-inducible factor 1α and glycolysis activity in rabbits with cold syndrome of rheumatoid arthritis. / çƒ­è¡¥é’ˆæ³•å¯¹ç±»é£Žæ¹¿å ³èŠ‚ç‚Žå¯’è¯å®¶å ”è†å ³èŠ‚æ»‘è†œç»„ç»‡ç¼ºæ°§è¯±å¯¼å› å­1αå’Œç³–é µè§£æ´»æ€§çš„å½±å“.

OBJECTIVES: To observe the effect of heat-reinforcing needling (HRN) on synovial inflammation, hypoxia-inducible factor-1α (HIF-1α) and glycolytic activity in serum and synovial tissue in rabbits with cold syndrome of rheumatoid arthritis (RA), so as to explore its mechanisms underlying improvement of RA. METHODS: A total of 32 rabbits were randomly divided into normal, model, inhibitor and HRN groups, with 8 rabbits in each group. The RA with cold syndrome model was induced by injecting ovalbumin dry powder and Freund's complete adjuvant combined with cold freezing. Rabbits in the inhibitor group were intraperitoneally injected with 2-methoxyestradiol (2.5 mg/kg), rabbits in the HRN group were received HRN at bilateral "Zusanli" (ST36) for 30 min. The treatments were conducted once daily for 14 consecutive days. After the interventions, the knee circumference and pain threshold were measured. The contents of nicotinamide adenine dinucleotide phosphoric (NADPH), Hexokinase II (HK2) and 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 3 (PFKFB3) in serum of rabbits were detected by ELISA. The pathological morphology of synovial tissue of the knee joints were observed by HE staining. The positive expressions of tumor necrosis factor (TNF-α), interleukin (IL)-1ß, IL-6 and IL-17 in synovial tissue of knee joint were detected by immunohistochemistry. The content of lactic acid in synovial tissue of rabbit knee joint was detected by spectrophotometry. The expression levels of HIF-1α, pyruvate kinase 2 (PKM2) and lactate dehydrogenase (LDHA) in synovial tissue of knee joint were detected by Western blot. RESULTS: After intervention, compared with the normal group, the knee circumference was significantly enlarged (P<0.05), the pain threshold was significantly decreased (P<0.05)；the synovial tissue of knee joints showed significant cell proliferation and inflammatory infiltration, the pathological score was significantly increased (P<0.05)；positive expressions of TNF-α, IL-1ß, IL-6 and IL-17, the content of lactic acid in synovial tissue, the contents of NADPH, HK2 and PFKFB3 in serum, and the protein expression levels of HIF-1α, PKM2 and LDHA in synovial tissue were increased (all P<0.05) in the model group. Compared with model group, the circumference of knee joint was significantly decreased (P<0.05), the pain threshold was significantly increased (P<0.05)；in synovial tissue, the pathological score was decreased (P<0.05)；the positive expressions of TNF-α, IL-1ß, IL-6 and IL-17 in synovial tissue were decreased (P<0.05), the lactic acid content in synovial tissue was decreased (P<0.05)；the contents of NADPH, HK2 and PFKFB3 in serum and the protein expression levels of HIF-1α, PKM2 and LDHA in synovial tissue were decreased (P<0.05) in inhibitor group and HRN group. Compared with the inhibitor group, the synovial pathological score was significantly increased (P<0.05), positive expressions of TNF-α, IL-1ß, IL-6 and IL-17, the content of lactic acid in synovial tissue, the contents of NADPH, HK2 and PFKFB3 in serum, and the protein expression levels of HIF-1α, PKM2 and LDHA in synovial tissue were increased (all P<0.05) in HRN group. CONCLUSIONS: HRN can increase the pain threshold, reduce the knee circumference and inhibit the inflammatory response in rabbits with cold syndrome of RA. The possible mechanism is related to the down-regulation of HIF-1α and glycolysis activity.

Maize Autophagy-Related Protein ZmATG3 Confers Tolerance to Multiple Abiotic Stresses.

Abiotic stresses pose a major increasing problem for the cultivation of maize. Autophagy plays a vital role in recycling and re-utilizing nutrients and adapting to stress. However, the role of autophagy in the response to abiotic stress in maize has not yet been investigated. Here, ZmATG3, which is essential for ATG8-PE conjugation, was isolated from the maize inbred line B73. The ATG3 sequence was conserved, including the C-terminal domains with HPC and FLKF motifs and the catalytic domain in different species. The promoter of the ZmATG3 gene contained a number of elements involved in responses to environmental stresses or hormones. Heterologous expression of ZmATG3 in yeast promoted the growth of strain under salt, mannitol, and low-nitrogen stress. The expression of ZmATG3 could be altered by various types of abiotic stress (200 mM NaCl, 200 mM mannitol, low N) and exogenous hormones (500 µM ABA). GUS staining analysis of ZmATG3-GUS transgenic Arabidopsis revealed that GUS gene activity increased after abiotic treatment. ZmATG3-overexpressing Arabidopsis plants had higher osmotic and salinity stress tolerance than wild-type plants. Overexpression of ZmATG3 up-regulated the expression of other AtATGs (AtATG3, AtATG5, and AtATG8b) under NaCl, mannitol and LN stress. These findings demonstrate that overexpression of ZmATG3 can improve tolerance to multiple abiotic stresses.

Selective hydrogenation of vanillin over a graphene-encapsulated nitrogen-doped bimetallic magnetic Ni/Fe@NDC nano-catalyst.

One of the main obstacles to the development of sustainable biomass feedstocks today is the research of selective hydrogenation of biomass platform compounds for the synthesis of high-value chemicals. This work reports on the synthesis of a Ni/Fe bimetallic catalyst with nitrogen-doped carbon serving as the carrier, hydrogen serving as the primary donor, and isopropanol serving as the reaction medium and serving as a secondary donor. Vanillin was catalytically hydrogenated to produce 4-methylguaiacol, a complete hydrogenation product, under a reaction temperature of 200 °C for four hours. A single product with a good yield (95.26% conversion and selectivity up to 99%) was achieved by the moderate conditions, offering a potential route for the catalytic hydrogenation of biomass platform compounds.

Flexible Thermoelectric Device Based on Protrusion-Structured Liquid Metal Elastomer for Gravity Heat Pipe.

Monitoring the temperature of the coal gangue mountains is fundamental to preventing their spontaneous combustion. However, the existing temperature monitoring systems fail to achieve stable, pollution-free temperature monitoring without affecting vegetation growth in these mountains. To address this issue, this work proposes a flexible thermoelectric device (FTD) based on a protrusion-structured liquid metal elastomer (LME). Utilizing a high-thermal-conductivity LME, the FTD adheres closely to the surface of the gravity heat pipe (GHP), ensuring compatibility between FTD and the curved surface of the GHP. Simultaneously, employing a low-thermal-conductivity elastomer helps concentrate heat onto FTD, thereby enhancing thermoelectric power generation efficiency. Additionally, the impact of the shape, size, and height of the protrusion structure at the cold end of the GHP on its efficiency was also investigated. The practical application of FTD on GHP was demonstrated.

Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles.

The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.

Rapid Preparation Triggered by Visible Light for Tough Hydrogel Sensors with Low Hysteresis and High Elasticity: Mechanism, Use and Recycle-by-Design.

Hydrogels have emerged as promising candidates for flexible devices and water resource management. However, further applications of conventional hydrogels are restricted due to their limited performance and lack of a recycling strategy. Herein, a tough, flexible, and recyclable hydrogel sensor via a visible-light-triggered polymerization is rapidly created. The Zn2+ crosslinked terpolymer is in situ polymerized using g-C3N4 as the sole initiator to form in situ chain entanglements, endowing the hydrogels with low hysteresis and high elasticity. In the use phase, the hydrogel sensor exhibited high ion conductivity, excellent mechanical properties, fast responsiveness, high sensitivity, and remarkable anti-fatigue ability, making it exceptionally effective in accurately monitoring complex human movements. At the end-of-life (EOL), leveraging the synergy between the photodegradation capacity of g-C3N4 and the adsorption function of the hydrogel matrix, the post-consumer hydrogel is converted into water remediation materials, which not only promoted the rapid degradation of organic pollutants, but also facilitated collection and reuse. This innovative strategy combined in situ entangling reinforcement and tailored recycle-by-design that employed g-C3N4 as key blocks in the hydrogel to achieve high performance in the use phase and close the loop through the reutilization at EOL, highlighting the cost-effective synthesis, specialized structure, and life cycle management.

MnS-BaS Heterostructures as Effective Catalysts for Oxygen Reduction Reaction.

The inadequate electrical conductivity of metal sulfides, along with their tendency to agglomerate, has hindered their use in energy storage and catalysis. The construction of a heterojunction can ameliorate these deficiencies to some extent. In this paper, MnS-BaS heterojunction catalysts were prepared by a hydrothermal method, which is a simple and inexpensive process. The MnS-BaS heterojunction catalysts exhibited superior performance owing to the strong synergistic interaction between MnS and BaS. Density functional theory (DFT) calculations reveal strong interactions at the heterojunction interface and significant electron transfer between MnS and BaS, which further modulates the electronic structure of Mn. The elevation of the center of the d-band enhances the adsorption of oxygen and oxygen-containing intermediates on the catalyst, thus promoting the oxygen reduction reaction (ORR). The practical application of MnS-BaS catalysts was tested by assembling zinc-air batteries. This study provides a rational strategy for designing transition metal catalysts that are efficient and low cost.

Successful Outcome of a Patient with Concomitant Pancreatic and Renal Carcinoma Receiving Secoisolariciresinol Diglucoside Therapy Alone: A Case Report.

Introduction: Pancreatic cancer (PC) is among the deadliest malignancies. Kidney cancer (KC) is a common malignancy globally. Chemo- or radio-therapies are not very effective to control PC or KC, and overdoses often cause severe site reactions to the patients. As a result, novel treatment strategies with high efficacy but without toxic side effects are urgently desired. Secoisolariciresinol diglucoside (SDG) belongs to plant lignans with potential anticancer activities, but clinical evidence is not available in PC or KC treatment. Patient Concerns: We report a rare case of an 83-year-old female patient with pancreatic and kidney occupying lesions that lacked the conditions to receive surgery or chemo- or radiotherapy. Diagnosis: Pancreatic and kidney cancers. Interventions: We gave dietary SDG to the patient as the only therapeutics. Outcomes: SDG effectively halted progression of both PC and KC. All clinical manifestations, including bad insomnia, loss of appetite, stomach symptoms, and skin itching over the whole body, all disappeared. The initial massive macroscopic hematuria became microscopic and infrequent, and other laboratory results also gradually returned to normal. Most of the cancer biomarkers, initially high such as CEA, CA199, CA724, CA125, came down rapidly, among which CA199 changed most radically. This patient has had progression-free survival of one year so far. Conclusion: These results demonstrate the potent inhibitory effects of SDG on PC and KC of this patient and provide promising novel therapeutics for refractory malignant tumors.

Engineering of Cas12a nuclease variants with enhanced genome-editing specificity.

The clustered regularly interspaced short palindromic repeat (CRISPR)-Cas12a system is a powerful tool in gene editing; however, crRNA-DNA mismatches might induce unwanted cleavage events, especially at the distal end of the PAM. To minimize this limitation, we engineered a hyper fidelity AsCas12a variant carrying the mutations S186A/R301A/T315A/Q1014A/K414A (termed HyperFi-As) by modifying amino acid residues interacting with the target DNA and crRNA strand. HyperFi-As retains on-target activities comparable to wild-type AsCas12a (AsCas12aWT) in human cells. We demonstrated that HyperFi-As has dramatically reduced off-target effects in human cells, and HyperFi-As possessed notably a lower tolerance to mismatch at the position of the PAM-distal region compared with the wild type. Further, a modified single-molecule DNA unzipping assay at proper constant force was applied to evaluate the stability and transient stages of the CRISPR/Cas ribonucleoprotein (RNP) complex. Multiple states were sensitively detected during the disassembly of the DNA-Cas12a-crRNA complexes. On off-target DNA substrates, the HyperFi-As-crRNA was harder to maintain the R-loop complex state compared to the AsCas12aWT, which could explain exactly why the HyperFi-As has low off-targeting effects in human cells. Our findings provide a novel version of AsCas12a variant with low off-target effects, especially capable of dealing with the high off-targeting in the distal region from the PAM. An insight into how the AsCas12a variant behaves at off-target sites was also revealed at the single-molecule level and the unzipping assay to evaluate multiple states of CRISPR/Cas RNP complexes might be greatly helpful for a deep understanding of how CRISPR/Cas behaves and how to engineer it in future.

The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.

The subtle differences in the chemical structures of double-stranded (ds) RNA and DNA lead to significant variations in their biological roles and medical implications, largely due to their distinct biophysical properties, such as bending stiffness. Although it is well known that A-form dsRNA is stiffer than B-form dsDNA under physiological salt conditions, the underlying cause of this difference remains unclear. In this study, we employ high-precision magnetic-tweezer experiments along with molecular dynamics simulations and reveal that the relative bending stiffness between dsRNA and dsDNA is primarily determined by the structure- and salt-concentration-dependent ion distribution around their helical structures. At near-physiological salt conditions, dsRNA shows a sparser ion distribution surrounding its phosphate groups compared to dsDNA, causing its greater stiffness. However, at very high monovalent salt concentrations, phosphate groups in both dsRNA and dsDNA become fully neutralized by excess ions, resulting in a similar intrinsic bending persistence length of approximately 39 nm. This similarity in intrinsic bending stiffness of dsRNA and dsDNA is coupled to the analogous fluctuations in their total groove widths and further coupled to the similar fluctuation of base-pair inclination, despite their distinct A-form and B-form helical structures.

Heat-sensitive moxibustion combined with Xiangwu powder for erectile dysfunction with kidney deficiency and blood stasis: a randomized controlled trial. / çƒ­æ•ç¸è”åˆé¦™èœˆæ•£æ²»ç–—è‚¾è™šè¡€ç˜€åž‹å‹ƒèµ·åŠŸèƒ½éšœç¢ï¼šéšæœºå¯¹ç §è¯•éªŒ.

OBJECTIVES: To observe the clinical efficacy of heat-sensitive moxibustion combined with Xiangwu powder in treating erectile dysfunction with kidney deficiency and blood stasis. METHODS: A total of 80 patients with erectile dysfunction of kidney deficiency and blood stasis were randomly divided into a comprehensive group (40 cases, 1 case dropped out) and a Chinese herb group (40 cases, 2 cases dropped out). In the Chinese herb group, Xiangwu powder was applied orally, one dose per day. On the basis of the Chinese herb group, heat-sensitive moxibustion was applied after detecting the heat-sensitive points in the areas of Guanyuan (CV 4), Zhongji (CV 3), Qihai (CV 6) and bilateral Xuehai (SP 10), Sanyinjiao (SP 6) in the comprehensive group, once a day, 5 times a week. Both groups were treated for 4 weeks. The international index of erectile function-5 (IIEF-5) score, erectile hardness score (EHS), nocturnal penile tumescence and rigidity (NPTR) indexes (nocturnal penile erection frequency, total duration of penile erection, duration of penile head hardness ≥60%, duration of penile root hardness ≥60%, percentage change in penile head circumference, percentage change in penile root circumference), TCM syndrome score, and penile vascular function indexes (peak systolic velocity [PSV], end diastolic velocity [EDV], and resistance index [RI] of penile cavernosal artery) were compared in the patients of the two groups before and after treatment, and the clinical efficacy was evaluated. RESULTS: After treatment, the IIEF-5 scores, EHS, PSV, RI, and NPTR indexes were increased compared with those before treatment (P<0.01), while the TCM syndrome scores and EDV were decreased compared with those before treatment (P<0.01) in the two groups.The IIEF-5 score, EHS, PSV, RI, and NPTR indexes in the comprehensive group were ascended compared with those in the Chinese herb group (P<0.01), while the TCM syndrome score and EDV in the comprehensive group were lower than those in the traditional Chinese herb group (P<0.01). The total effective rate of the comprehensive group was 94.9% (37/39), which was higher than 78.9% (30/38, P<0.05) of the Chinese herb group. CONCLUSIONS: The combination of heat-sensitive moxibustion and Xiangwu powder can effectively treat erectile dysfunction of kidney deficiency and blood stasis, improve patients' erectile function, enhance their erection hardness, and improve their penile vascular function and clinical symptoms.

Reveal the kernel dehydration mechanisms in maize based on proteomic and metabolomic analysis.

BACKGROUND: Kernel dehydration is an important factor for the mechanized harvest in maize. Kernel moisture content (KMC) and kernel dehydration rate (KDR) are important indicators for kernel dehydration. Although quantitative trait loci and genes related to KMC have been identified, where most of them only focus on the KMC at harvest, these are still far from sufficient to explain all genetic variations, and the relevant regulatory mechanisms are still unclear. In this study, we tried to reveal the key proteins and metabolites related to kernel dehydration in proteome and metabolome levels. Moreover, we preliminarily explored the relevant metabolic pathways that affect kernel dehydration combined proteome and metabolome. These results could accelerate the development of further mechanized maize technologies. RESULTS: In this study, three maize inbred lines (KB182, KB207, and KB020) with different KMC and KDR were subjected to proteomic analysis 35, 42, and 49 days after pollination (DAP). In total, 8,358 proteins were quantified, and 2,779 of them were differentially expressed proteins in different inbred lines or at different stages. By comparative analysis, K-means cluster, and weighted gene co-expression network analysis based on the proteome data, some important proteins were identified, which are involved in carbohydrate metabolism, stress and defense response, lipid metabolism, and seed development. Through metabolomics analysis of KB182 and KB020 kernels at 42 DAP, 18 significantly different metabolites, including glucose, fructose, proline, and glycerol, were identified. CONCLUSIONS: In sum, we inferred that kernel dehydration could be regulated through carbohydrate metabolism, antioxidant systems, and late embryogenesis abundant protein and heat shock protein expression, all of which were considered as important regulatory factors during kernel dehydration process. These results shed light on kernel dehydration and provide new insights into developing cultivars with low moisture content.

Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population.

Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F1 hybrid populations, it also provides a valuable basis for further molecular biology and breeding research.

Chemical synthesis of carbon dots with blue, green and red emission for dopamine reversible switching probes.

Carbon dots (CDs) possess the merits such as energy efficiency, green sustainability and environmental friendliness, comparing with top-down synthesis methods at higher pressure or temperature condition. Here, a variety of emission states CDs were prepared by using the method of room temperature chemistry by selecting green raw materials such as glucose, p-phthalaldehyde and m-diethylaminophenol. The luminescence mechanism was studied in detail. The luminescent center of blue emitting carbon dots (B-CDs) and green emitting carbon dots (G-CDs) is CO bond, and the increased contents of CO bond lead to the creation of new energy levels between the energy gaps of HOMO and LUMO levels, which results in the red shift of luminescence wavelength. The emission state of red emitting carbon dots (R-CDs) is due to the formation of amino N. In addition, R-CDs have an exclusive respond to dopamine (DA) and are regarded as good fluorescent probes for detecting DA. Furthermore, the addition of ascorbic acid (AA) restores the luminescence of R-CDs quenched by DA. Therefore, R-CDs has great application potential as a selective fluorescent "turn on-off" probe.

Stereoisomeric Non-Fullerene Acceptors-Based Organic Solar Cells.

Chiral alkyl chains are ubiquitously observed in organic semiconductor materials and can regulate solution processability and active layer morphology, but the effect of stereoisomers on photovoltaic performance has rarely been investigated. For the racemic Y-type acceptors widely used in organic solar cells, it remains unknown if the individual chiral molecules separate into the conglomerate phase or if racemic phase prevails. Here, the photovoltaic performance of enantiomerically pure Y6 derivatives, (S,S)/(R,R)-BTP-4F, and their chiral mixtures are compared. It is found that (S,S) and (R,R)-BTP-4F molecule in the racemic mixtures tends to interact with its enantiomer. The racemic mixtures enable efficient light harvesting, fast hole transfer, and long polaron lifetime, which is conducive to charge generation and suppresses the recombination losses. Moreover, abundant charge diffusion pathways provided by the racemate contribute to efficient charge transport. As a result, the racemate system maximizes the power output and minimizes losses, leading to a higher efficiency of 18.16% and a reduced energy loss of 0.549 eV, as compared to the enantiomerically pure molecules. This study demonstrates that the chirality of non-fullerene acceptors should receive more attention and be designed rationally to enhance the efficiency of organic solar cells.

A Q-learning method based on coarse-to-fine potential energy surface for locating transition state and reaction pathway.

Transition state (TS) on the potential energy surface (PES) plays a key role in determining the kinetics and thermodynamics of chemical reactions. Inspired by the fact that the dynamics of complex systems are always driven by rare but significant transition events, we herein propose a TS search method in accordance with the Q-learning algorithm. Appropriate reward functions are set for a given PES to optimize the reaction pathway through continuous trial and error, and then the TS can be obtained from the optimized reaction pathway. The validity of this Q-learning method with reasonable settings of Q-value table including actions, states, learning rate, greedy rate, discount rate, and so on, is exemplified in 2 two-dimensional potential functions. In the applications of the Q-learning method to two chemical reactions, it is demonstrated that the Q-learning method can predict consistent TS and reaction pathway with those by ab initio calculations. Notably, the PES must be well prepared before using the Q-learning method, and a coarse-to-fine PES scanning scheme is thus introduced to save the computational time while maintaining the accuracy of the Q-learning prediction. This work offers a simple and reliable Q-learning method to search for all possible TS and reaction pathway of a chemical reaction, which may be a new option for effectively exploring the PES in an extensive search manner.

Genetic architecture of ear traits based on association mapping and co-expression networks in maize inbred lines and hybrids.

Ear traits are key contributors to grain yield in maize; therefore, exploring their genetic basis facilitates the improvement of grain yield. However, the underlying molecular mechanisms of ear traits remain obscure in both inbred lines and hybrids. Here, two association panels, respectively, comprising 203 inbred lines (IP) and 246 F1 hybrids (HP) were employed to identify candidate genes for six ear traits. The IP showed higher phenotypic variation and lower phenotypic mean than the HP for all traits, except ear tip-barrenness length. By conducting a genome-wide association study (GWAS) across multiple environments, 101 and 228 significant single-nucleotide polymorphisms (SNPs) associated with six ear traits were identified in the IP and HP, respectively. Of these significant SNPs identified in the HP, most showed complete-incomplete dominance and over-dominance effects for each ear trait. Combining a gene co-expression network with GWAS results, 186 and 440 candidate genes were predicted in the IP and HP, respectively, including known ear development genes ids1 and sid1. Of these, nine candidate genes were detected in both populations and expressed in maize ear and spikelet tissues. Furthermore, two key shared genes (GRMZM2G143330 and GRMZM2G171139) in both populations were found to be significantly associated with ear traits in the maize Goodman diversity panel with high-density variations. These findings advance our knowledge of the genetic architecture of ear traits between inbred lines and hybrids and provide a valuable resource for the genetic improvement of ear traits in maize. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01426-9.

Identification of the Maize LEA Gene Family and Its Relationship with Kernel Dehydration.

Maize, the most widely planted and highest yielding of the three major crops in the world, requires the development and breeding of new varieties to accommodate the shift towards mechanized harvesting. However, the moisture content of kernels during harvest poses a significant challenge to mechanized harvesting, leading to seed breakage and increased storage costs. Previous studies highlighted the importance of LEA (Late Embryogenesis Abundant) members in regulating kernel dehydration. In this study, we aimed to gain a better understanding of the relationship between the LEA family and grain dehydration in maize. Through expression pattern analysis of maize, we identified 52 LEA genes (ZmLEAs) distributed across 10 chromosomes, organized into seven subgroups based on phylogenetic analysis, gene structure, and conserved motifs. Evolutionary and selective pressure analysis revealed that the amplification of ZmLEA genes primarily resulted from whole-genome or fragment replication events, with strong purifying selection effects during evolution. Furthermore, the transcriptome data of kernels of two maize inbred lines with varying dehydration rates at different developmental stages showed that 14 ZmLEA genes were expressed differentially in the two inbreds. This suggested that the ZmLEA genes might participate in regulating the kernel dehydration rate (KDR) in maize. Overall, this study enhances our understanding of the ZmLEA family and provides a foundation for further research into its role in regulating genes associated with grain dehydration in maize.

Construction and validation of a immune-related prognostic gene DHRS1 in hepatocellular carcinoma based on bioinformatic analysis.

A member of the short-chain dehydrogenase/reductase superfamily (DHRS1, SDR19C1) is a member of the short-chain dehydrogenase/reductase superfamily and a potential predictor of hepatocellular carcinoma (HCC). However, the role of DHRS1 in HCC immunity remains unclear. We systematically analyzed the association between DHRS1 and HCC immunity with transcriptional and clinical data from the Tumor Immune Estimation Resource, an integrated repository portal for tumor immune system interactions, and cBioPortal databases. Six DHRS1-associated immunomodulators strongly correlated with survival and were uncovered by exploiting univariate and multivariate Cox analyses. We created a risk score for each patient by adding the points from each immunomodulator and then classified them into high and low risk categories. Survival analysis were used to compare the overall survival between the 2 groups, and the receiver operating characteristic curve was applied to assess the accuracy of the risk score. Data from our center were adopted as the external validation set, the risk score was calculated using the risk coefficient of the 6 genes in the training cohort, and survival analysis were executed to verify the experimental group results. A nomogram was ultimately constructed with the R package. Our data revealed a correlation between the levels of immune cell infiltration and either the DHRS1 gene copy numbers or mRNA levels in HCC. Second, we generated a signature based on the 6 DHRS1-related immunomodulators (KDR, TNFRSF4, CD276, TNFSF4, SLAMF6, and SIGLEC9). We postulate that the generated risk scores would serve as an independent indicator of HCC prognosis, with an area under the receiver operating characteristic curve for the risk score of 0.743. We further established external validation sets to reconfirm the predictive validity of the risk score. Finally, a prognostic nomogram and calibration curve were created. The DHRS1 gene may exert an impact on HCC immunity. We posit that the nominated immune signature based on DHRS1-associated immunomodulators could constitute a promising prognostic biomarker in HCC.