The clinical efficacy of Medial Sustain Nail(MSN) and Proximal femoral nail anti-rotation(PFNA) for fixation of medial comminuted trochanteric fractures: a prospective randomized controlled trial.

PURPOS: To evaluate the clinical efficacy of the Medial Sustain Nail (MSN) for medial comminuted trochanteric fractures fixation in comparison to Proximal Femoral Nail Antirotation (PFNA) through a clinical study. METHODS: A non-inferiority randomized controlled trial was conducted at a single centre between July 2019 and July 2020. Fifty patients diagnosed comminuted trochanteric fractures were randomly assigned to either the MSN group (n = 25) or the PFNA group (n = 25). A total of forty-three patients were included in the final study analysis. The primary outcome measure was Short Form 36 health surgery physical component summary (SF-36 PCS) score. Secondary outcomes included the Oxford Hip Scores (OHS), weight bearing, complication relate to implant and so on. This study was not blined to surgeons, but to patients and data analysts. RESULTS: The MSN demonstrated significantly better functional outcomes as measured by SF-36 PCS and OHS at six months postoperative compared to PFNA (p < 0.05). Union of fractures in the MSN group reached 90.9% at three months after surgery, whereas the PFNA group achieved a union rate of 57.1% (p < 0.05). Furthermore, weight-bearing time of MSN group was earlier than PFNA group (p < 0.05). Additionally, complications related to implant usage were more prevalent in the PFNA group (33.3%) compared to the MSN group (4.5%) (p < 0.05). CONCLUSION: MSN exhibited superior quality of life outcomes compared to PFNA at six months postoperative. This indicates that MSN effectively reconstructs medial femoral support in patients with comminuted trochanteric fractures, which facilitates early weight-bearing and accelerates the recovery process. TRIAL REGISTRATION: Trial registration number: NCT01437176, Date of the trial registration:2011-9-1, Date of commencement of the study:2011-9, Date of enrolment/recruitment of the study subjects:2019-7.

The Lnc-ENST00000602558/IGF1 axis as a predictor of response to treatment with tripterygium glycosides in rheumatoid arthritis patients.

AIMS: Growing clinical evidence suggests that not all patients with rheumatoid arthritis (RA) benefit to the same extent by treatment with tripterygium glycoside (TG), which highlights the need to identify RA-related genes that can be used to predict drug responses. In addition, single genes as markers of RA are not sufficiently accurate for use as predictors. Therefore, there is a need to identify paired expression genes that can serve as biomarkers for predicting the therapeutic effects of TG tablets in RA. METHODS: A total of 17 pairs of co-expressed genes were identified as candidates for predicting an RA patient's response to TG therapy, and genes involved in the Lnc-ENST00000602558/GF1 axis were selected for that purpose. A partial-least-squares (PLS)-based model was constructed based on the expression levels of Lnc-ENST00000602558/IGF1 in peripheral blood. The model showed high efficiency for predicting an RA patient's response to TG tablets. RESULTS: Our data confirmed that genes co-expressed in the Lnc-ENST00000602558/IGF1 axis mediate the efficacy of TG in RA treatment, reduce tumor necrosis factor-α induced IGF1 expression, and decrease the inflammatory response of MH7a cells. CONCLUSION: We found that genes expressed in the Lnc-ENST00000602558/IGF1 axis may be useful for identifying RA patients who will not respond to TG treatment. Our findings provide a rationale for the individualized treatment of RA in clinical settings.

GhERF.B4-15D: A Member of ERF Subfamily B4 Group Positively Regulates the Resistance against Verticillium dahliae in Upland Cotton.

Verticillium wilt is a fungal disease in upland cotton and exerts a significant effect on growth and potential productivity. This disease is mainly caused by V. dahliae Kleb. Ethylene response factor (ERF) is one of the superfamilies of transcription factors that is involved in the development and environmental adaption of crops. A total of 30 ERF.B4 group members were detected in upland cotton and divided into 6 subgroups. Gene structures, conserved motifs, and domain analysis revealed that members in each subgroup are highly conserved. Further, the 30 GhERF.B4 group members were distributed on 18 chromosomes, and 36 gene synteny relationships were found among them. GhERF.B4 genes were ubiquitously expressed in various tissues and developmental stages of cotton. Amongst them, GhERF.B4-15D was predominantly expressed in roots, and its expression was induced by V. dahliae infection. In addition, GhERF.B4-15D responded to methyl jasmonate (MeJA), methyl salicylate (MeSA), and ethylene (ET) phytohormones. It was also found that the V. dahliae resistance was enhanced due to overexpression of GhERF.B4-15D in Arabidopsis thaliana. On the contrary, interference of GhERF.B4-15D by virus-induced gene silencing (VIGS) technology decreased the V. dahliae resistance level in upland cotton. The subcellular localization experiment showed that GhERF.B4-15D was located in the nucleus. Yeast two-hybrid (Y2H) and luciferase complementation (LUC) approaches demonstrated that GhERF.B4-15D interacted with GhDREB1B. Additionally, the V. dahliae resistance was significantly decreased in GhDREB1B knockdowns. Our results showed that GhERF.B4-15D plays a role during V. dahliae infection in cotton.

Interactions between Verticillium dahliae and cotton: pathogenic mechanism and cotton resistance mechanism to Verticillium wilt.

Cotton is widely grown in many countries around the world due to the huge economic value of the total natural fiber. Verticillium wilt, caused by the soil-borne pathogen Verticillium dahliae, is the most devastating disease that led to extensive yield losses and fiber quality reduction in cotton crops. Developing resistant cotton varieties through genetic engineering is an effective, economical, and durable strategy to control Verticillium wilt. However, there are few resistance gene resources in the currently planted cotton varieties, which has brought great challenges and difficulties for breeding through genetic engineering. Further revealing the molecular mechanism between V. dahliae and cotton interaction is crucial to discovering genes related to disease resistance. In this review, we elaborated on the pathogenic mechanism of V. dahliae and the resistance mechanism of cotton to Verticillium wilt. V. dahliae has evolved complex mechanisms to achieve pathogenicity in cotton, mainly including five aspects: (1) germination and growth of microsclerotia; (2) infection and successful colonization; (3) adaptation to the nutrient-deficient environment and competition of nutrients; (4) suppression and manipulation of cotton immune responses; (5) rapid reproduction and secretion of toxins. Cotton has evolved multiple physiological and biochemical responses to cope with V. dahliae infection, including modification of tissue structures, accumulation of antifungal substances, homeostasis of reactive oxygen species (ROS), induction of Ca2+ signaling, the mitogen-activated protein kinase (MAPK) cascades, hormone signaling, and PAMPs/effectors-triggered immune response (PTI/ETI). This review will provide an important reference for the breeding of new cotton germplasm resistant to Verticillium wilt through genetic engineering.

Experimental Research on Improving Activity of Calcinated Coal Gangue via Increasing Calcium Content.

In this investigation, non-spontaneous combustion coal gangue was activated by two methods: (1) low-temperature calcination and (2) calcium addition. Differences in the activity of the activated coal gangue were studied at various calcination temperatures and amounts of calcium addition. Meanwhile, the cementation activity of the activated coal gangue was evaluated according to the activity effect analysis. Furthermore, the influences of the activated coal gangue on the cementation activity of cement were investigated. The results indicated that the activities of the activated coal gangue increased at a temperature between 500 °C and 700 °C. The calcium addition method can also increase the activity of coal gangue, with the effect being better when the gangue is mixed with slag. The addition of calcium and the calcination of coal gangue can promote the production of active minerals such as metakaolin, which is the main reason for the increased cementation activity.

Identification of metal ion-binding sites in RNA structures using deep learning method.

Metal ion is an indispensable factor for the proper folding, structural stability and functioning of RNA molecules. However, it is very difficult for experimental methods to detect them in RNAs. With the increase of experimentally resolved RNA structures, it becomes possible to identify the metal ion-binding sites in RNA structures through in-silico methods. Here, we propose an approach called Metal3DRNA to identify the binding sites of the most common metal ions (Mg2+, Na+ and K+) in RNA structures by using a three-dimensional convolutional neural network model. The negative samples, screened out based on the analysis for binding surroundings of metal ions, are more like positive ones than the randomly selected ones, which are beneficial to a powerful predictor construction. The microenvironments of the spatial distributions of C, O, N and P atoms around a sample are extracted as features. Metal3DRNA shows a promising prediction power, generally surpassing the state-of-the-art methods FEATURE and MetalionRNA. Finally, utilizing the visualization method, we inspect the contributions of nucleotide atoms to the classification in several cases, which provides a visualization that helps to comprehend the model. The method will be helpful for RNA structure prediction and dynamics simulation study. Availability and implementation: The source code is available at https://github.com/ChunhuaLiLab/Metal3DRNA.

Analysis of PAT1 subfamily members in the GRAS family of upland cotton and functional characterization of GhSCL13-2A in Verticillium dahliae resistance.

KEY MESSAGE: GhSCL13-2A, a member of the PAT1 subfamily in the GRAS family, positively regulates cotton resistance to Verticillium dahliae by mediating the jasmonic acid and salicylic acid signaling pathways and accumulation of reactive oxygen species. Verticillium wilt (VW) is a devastating disease of upland cotton (Gossypium hirsutum) that is primarily caused by the soil-borne fungus Verticillium dahliae. Scarecrow-like (SCL) proteins are known to be involved in plant abiotic and biotic stress responses, but their roles in cotton defense responses are still unclear. In this study, a total of 25 GhPAT1 subfamily members in the GRAS family were identified in upland cotton. Gene organization and protein domain analysis showed that GhPAT1 members were highly conserved. GhPAT1 genes were widely expressed in various tissues and at multiple developmental stages, and they were responsive to jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signals. Furthermore, GhSCL13-2A was induced by V. dahliae infection. V. dahliae resistance was enhanced in Arabidopsis thaliana by ectopic overexpression of GhSCL13-2A, whereas cotton GhSCL13-2A knockdowns showed increased susceptibility. Levels of reactive oxygen species (ROS) and JA were also increased and SA content was decreased in GhSCL13-2A knockdowns. At the gene expression level, PR genes and SA signaling marker genes were down-regulated and JA signaling marker genes were upregulated in GhSCL13-2A knockdowns. GhSCL13-2A was shown to be localized to the cell membrane and the nucleus. Yeast two-hybrid and luciferase complementation assays indicated that GhSCL13-2A interacted with GhERF5. In Arabidopsis, V. dahliae resistance was enhanced by GhERF5 overexpression; in cotton, resistance was reduced in GhERF5 knockdowns. This study revealed a positive role of GhSCL13-2A in V. dahliae resistance, establishing it as a strong candidate gene for future breeding of V. dahliae-resistant cotton cultivars.

Intramedullary nailing versus plating fixation for the treatment of midshaft clavicular fractures: A meta-analysis of randomized controlled trials.

PURPOSE: This study was to test the hypothesis that intramedullary (IM) nailing fixation of midshaft clavicle fractures could result in better clinical outcomes and lower complications rates than plating fixation. METHODS: PubMed, Embase, and the Cochrane Library database were used to search all English language published randomized controlled trials (RCTs) of midshaft clavicle fractures using plating versus IM nailing. The characteristics of the study participants were collected. Outcomes of postoperative shoulder functional measurements, operative data and complications rates were meta-analyzed. RESULTS: Eight hundred and ninety-five patients in ten RCTs and three quasi-RCTs were involved in the meta-analysis. The results of meta-analysis of these studies showed that the functional outcome evaluated by the Constant Shoulder and Disabilities of the Arm, Shoulder and Hand (DASH) scores after accepting IM nailing was significantly better than that of plating fixation at one year post-operatively (P < 0.01), with the heterogeneity of 43% and 91%, respectively. Sensitivity analyses of the pooled results of Constant and DASH scores displayed that the functional advantage of IM nailing fixation comes from the subgroup of locked IM nailing. Further, regarding the operative statistics, operative time, blood loss and wound length were significantly less in the IM nailing group than the plating group (P < 0.001). The rates of infection, major complications and complications-related revision surgery were significantly higher in the plating group than the IM nailing group; however, there were no significantly statistical differences in other complications, e.g., nonunion, refracture after hardware removal, implant failure, symptomatic hardware, etc. (P > 0.05). CONCLUSION: The observations in this review suggested that IM nailing, especially locked IM nailing, could provide better shoulder functional outcome at one-year follow-up. Moreover, IM nailing fixation could effectively reduce operative time, blood loss, rates of infection, major complications, and revision surgery than plating. Further high-quality clinical trials with large samples and consistent designs are still needed to verify the long-term functional advantage of locked and unlocked IM nailing for midshaft clavicle fractures. LEVEL OF EVIDENCE: Level II.

A Novel Anatomical Locking Guide Plate for Treating Acetabular Transverse Posterior Wall Fracture: A Finite Element Analysis Study.

OBJECTIVE: To improve the treatment of the acetabular transverse posterior wall fracture (ATPWF), a novel anatomical locking guidance plate (NALGP) was designed and compared with traditional fixations using finite element analysis. METHODS: The ATPWF model was constructed using the three-dimensional finite element model of the half pelvis via the Mimics software and three internal devices were used to fix this model: the posterior-column locking plate with anterior-column screws (PCLP), double-column locking plates (DCLP), and NALGP. Next, mesh division was conducted by solid 187 tetrahedral elements in the workbench software. After defining the boundary condition and material properties, each assembly model was loaded in an increasing manner with a downward vertical force of 200, 400, and 600 N, respectively. The loading force was directed at 45 degrees upward in the coronal plane and 25 degrees backward in the sagittal plane. Finally, the stress distribution and stress peak of plates and screws were measured and evaluated, and the displacement of fracture fragments under different loading force was assessed among the three groups. RESULTS: For stress distribution, it was found that the stress mainly acted on the posterior-column plate, especially concentrated at the middle and lower section of the plate in all three groups after fixation on the ATPWF. In addition, most stresses of screws appeared on the lag screws instead of the common screws. The common screws in the NALGP group experienced larger stresses under all loading force, while those in the DCLP group withstood less stresses compared to those in the PCLP group. For the displacement of fracture fragments, the NALGP group were found to have less fracture fragment displacements than the PCLP group, but had comparable results to DCLP at both the transverse fracture and the posterior wall fracture sites. CONCLUSION: The newly-designed fixation device showed superiorities on fracture stabilization over PCLP, but had comparable stability to DCLP. This suggests that the DCLP might be unnecessary for treating ATPWF in some instances because it might cause bigger surgical trauma and blood loss.

Prognostic prediction of systemic immune-inflammation status for patients with colorectal cancer: a novel pyroptosis-related model.

Pyroptosis and related gasdermin family proteins play an important role in the tumorigenesis of colorectal cancer (CRC). However, the prognostic roles of pyroptosis-related genes (PRGs) and their relation to infiltrates of immune cells in the pathogenesis of CRC remain unclear. Using this study, we set up a prognostic gene pattern on the basis of 13 PRGs (AIM2, CASP1, CASP5, CASP6, CASP8, CASP9, ELANE, GPX4, GSDMD, NLRP7, NOD2, PJVK, and PRKACA) for CRC patients. A comprehensive bioinformatics analysis based on these genes was then performed. With the good AUC prediction value of the ROC curves, the group with high hazard first had a poorer survival prognosis than the group with low hazard. Second, we found that PRGs were significantly related to inflammation-associated genes and immune-associated genes in CRC. Then, we identified a correlation of PRGs with immune infiltrations in CRC. For instance, the abundances of resting NK cells resting and neutrophils were higher in the low hazard group than in the high hazard group. Overall, this work indicated that PRGs contributed to generate heterogeneity of the tumor microenvironment (TME) in CRC. This prognostic PRG model may provide a starting point for the early diagnosis and medication use of CRC.

Analysis of the PRA1 Genes in Cotton Identifies the Role of GhPRA1.B1-1A in Verticillium dahliae Resistance.

Verticillium wilt in cotton (Gossypium hirsutum) is primarily caused by Verticillium dahliae. Previous data suggest that prenylated RAB acceptors (PRAs) play essential roles in environmental plant adaptation, although the potential roles of PRA1 in cotton are unclear. Therefore, in this study, PRA1 family members were identified in G. hirsutum, and their roles in biotic and abiotic stresses were analyzed. Thirty-seven GhPRA1 family members were identified in upland cotton, which were divided into eight groups. Gene structure and domain analyses revealed that the sequences of GhPRA1 members in each group were highly conserved. Many environmental stress-related and hormone-response cis-acting elements were identified in the GhPRA1 promoter regions, indicating that they may respond to biotic and abiotic stresses. Expression analysis revealed that GhPRA1 members were widely expressed in upland cotton. The GhPRA1 genes responded to abiotic stress: drought, cold, salt, and heat stress. GhPRA1.B1-1A expression increased after V. dahliae infection. Furthermore, the functional role of GhPRA1.B1-1A was confirmed by overexpression in Arabidopsis thaliana, which enhanced the resistance to V. dahliae. In contrast, V. dahliae resistance was significantly weakened via virus-induced gene silencing of GhPRA1.B1-1A in upland cotton. Simultaneously, reactive oxygen species accumulation; the H2O2, salicylic acid, and jasmonic acid contents; and callose deposition were significantly decreased in cotton plants with GhPRA1.B1-1A silencing. These findings contribute to a better understanding of the biological roles of GhPRA1 proteins and provide candidate genes for cotton breeders for breeding V. dahliae-resistant cultivars.

Computational methods, databases and tools for synthetic lethality prediction.

Synthetic lethality (SL) occurs between two genes when the inactivation of either gene alone has no effect on cell survival but the inactivation of both genes results in cell death. SL-based therapy has become one of the most promising targeted cancer therapies in the last decade as PARP inhibitors achieve great success in the clinic. The key point to exploiting SL-based cancer therapy is the identification of robust SL pairs. Although many wet-lab-based methods have been developed to screen SL pairs, known SL pairs are less than 0.1% of all potential pairs due to large number of human gene combinations. Computational prediction methods complement wet-lab-based methods to effectively reduce the search space of SL pairs. In this paper, we review the recent applications of computational methods and commonly used databases for SL prediction. First, we introduce the concept of SL and its screening methods. Second, various SL-related data resources are summarized. Then, computational methods including statistical-based methods, network-based methods, classical machine learning methods and deep learning methods for SL prediction are summarized. In particular, we elaborate on the negative sampling methods applied in these models. Next, representative tools for SL prediction are introduced. Finally, the challenges and future work for SL prediction are discussed.

Identification and expression analysis of arabinogalactan protein genes in cotton reveal the function of GhAGP15 in Verticillium dahliae resistance.

Verticillium wilt, primarily caused by the fungal pathogen Verticillium dahliae, is a serious disease in cotton. Arabinogalactan proteins (AGPs), a class of hydroxyproline-rich glycoproteins, have been widely implicated in plant growth and environmental adaptation. The purpose of this study is to identify and characterize AGP members in cotton plants and explore their roles in responding to environmental stressors. In total, 65 GhAGP members were identified in upland cotton (Gossypium hirsutum), along with 43, 35, and 37 AGP members that were also identified in G. barbadense, G. arboreum, and G. raimondii, respectively. According to gene structure and protein domains analysis, GhAGP genes in upland cotton are highly conserved. Meanwhile, tandem duplication events have occurred frequently throughout cotton's evolutionary history. Expression analysis showed that GhAGP genes were widely expressed during growth and development and in response to abiotic stressors. Many cis-elements related to hormonal responses and environmental stressors were detected in GhAGP promoter regions. GhAGP genes participate in responding to cold, drought, and salt stress, and were sensitive to ET signaling. Furthermore, the expression level of GhAGP15 was elevated during V. dahliae infection and resistance against V. dahliae in upland cotton was significantly weakened by silencing GhAGP15 using a virus-induced gene silencing (VIGS) approach. Our results further suggest that the function of GhAGP15 in V. dahliae resistance might be involved in regulation of the JA, SA, and reactive oxygen species (ROS) pathways. The comprehensive analysis of AGP genes in cotton performed in this study provides a basic framework for further functional research of these genes.

Semaphorin3A regulates mitochondrial apoptosis in RAW264.7 cells in vitro.

Osteoclasts apoptosis plays vital roles in abnormal bone remodeling-associated diseases. It's reported that Semaphorin3A (Sema3A) may affect osteoarthritis progression through osteoclasts function, while the specific mechanism remains unclear. To determine the effect of Sema3A on osteoclasts, we detected the apoptosis of RAW264.7 cells treated with Sema3A and explored the potential pathways in vitro. Firstly, Cell Counting Kit-8 (CCK8) assay was performed to assess the proliferation to screen out the appropriate concentration of Sema3A. Then, apoptosis was evaluated after cells were incubated with Sema3A for 0, 2, 6, 12, 24 and 48 h, respectively, by Terminal Deoxynucleotidyl Transferase dUTP nick end labeling (TUNEL) staining and flow cytometry. Finally, phosphorylation of Nrf2 and CREB, mitochondrial apoptosis-related markers and JNK/AKT/ERK pathway activation were examined by qRT-PCR and Western blot. As a result, flow cytometry and TUNEL staining revealed that RAW264.7 cells apoptosis was promoted by Sema3A-treated. Meanwhile, Western blot showed that cleaved-caspase-3 and cleaved-caspase-9 were highly expressed in Sema3A-treated RAW264.7 cells, and the ERK/JNK/AKT pathways were significantly inhibited by Sema3A in RAW264.7 cells. In a word, we demonstrated that Sema3A induces apoptosis of RAW264.7 cells probably by promoting mitochondrial apoptosis, which may provide a potential target for therapeutic strategies.

Relationship between delayed luminescence emission and mitochondrial status in Saccharomyces cerevisiae.

Delayed luminescence (DL) is gradually used in various detection of biological systems as a rapid detection technique, however, its biological mechanism was still not clear. In this study, a new model of DL detection system for liquid biological samples is established to investigate the DL emission of Saccharomyces cerevisiae cells cultured in different glucose concentrations. We analyzed the relationship between the DL emission and cell growth, cell vitality, mitochondrial morphology, mitochondrial DNA (mtDNA) copy number, adenosine triphosphate (ATP), oxygen consumption rate (OCR), as well as mitochondria membrane potential (MMP) in S. cerevisiae cells cultured with 0.01, 0.05, 0.15, 3, 10 and 20 g/L glucose respectively. It was found that the DL emission had strong correlation with mitochondrial morphology, OCR, and MMP. The results suggested that DL is an indicator of mitochondria status under different glucose supply conditions, and may be an effective method to detect mitochondrial metabolism related disorders.

LSM12 facilitates the progression of colorectal cancer by activating the WNT/CTNNB1 signaling pathway.

Aberrant activation of the WNT signaling pathway is a joint event in colorectal cancer (CRC), but the molecular mechanism is still unclear. Recently, RNA-splicing factor LSM12 (like-Sm protein 12) is highly expressed in CRC tissues. This study aimed to verify whether LSM12 is involved in regulating CRC progression via regulating the WNT signaling pathway. Here, we found that LSM12 is highly expressed in CRC patient-derived tissues and cells. LSM12 is involved in the proliferation, invasion, and apoptosis of CRC cells, similar to the function of WNT signaling in CRC. Furthermore, protein interaction simulation and biochemical experiments proved that LSM12 directly binds to CTNNB1 (also known as ß-Catenin) and regulates its protein stability to affect the CTTNB1-LEF1-TCF1 transcriptional complex formation and the associated WNT downstream signaling pathway. LSM12 depletion in CRC cells decreased the in vivo tumor growth through repression of cancer cell growth and acceleration of cancer cell apoptosis. Taken together, we suggest that the high expression of LSM12 is a novel factor leading to aberrant WNT signaling activation, and that strategies targeting this molecular mechanism may contribute to developing a new therapeutic method for CRC.

Evolutionary and Characteristic Analysis of RING-DUF1117 E3 Ubiquitin Ligase Genes in Gossypium Discerning the Role of GhRDUF4D in Verticillium dahliae Resistance.

Verticillium wilt, primarily induced by the soil-borne fungus Verticillium dahliae, is a serious threat to cotton fiber production. There are a large number of really interesting new gene (RING) domain-containing E3 ubiquitin ligases in Arabidopsis, of which three (At2g39720 (AtRHC2A), At3g46620 (AtRDUF1), and At5g59550 (AtRDUF2)) have a domain of unknown function (DUF) 1117 domain in their C-terminal regions. This study aimed to detect and characterize the RDUF members in cotton, to gain an insight into their roles in cotton's adaptation to environmental stressors. In this study, a total of 6, 7, 14, and 14 RDUF (RING-DUF1117) genes were detected in Gossypium arboretum, G. raimondii, G. hirsutum, and G. barbadense, respectively. These RDUF genes were classified into three groups. The genes in each group were highly conserved based on gene structure and domain analysis. Gene duplication analysis revealed that segmental duplication occurred during cotton evolution. Expression analysis revealed that the GhRDUF genes were widely expressed during cotton growth and under abiotic stresses. Many cis-elements related to hormone response and environment stressors were identified in GhRDUF promoters. The predicted target miRNAs and transcription factors implied that GhRDUFs might be regulated by gra-miR482c, as well as by transcription factors, including MYB, C2H2, and Dof. The GhRDUF genes responded to cold, drought, and salt stress and were sensitive to jasmonic acid, salicylic acid, and ethylene signals. Meanwhile, GhRDUF4D expression levels were enhanced after V. dahliae infection. Subsequently, GhRDUF4D was verified by overexpression in Arabidopsis and virus-induced gene silencing treatment in upland cotton. We observed that V. dahliae resistance was significantly enhanced in transgenic Arabidopsis, and weakened in GhRDUF4D silenced plants. This study conducted a comprehensive analysis of the RDUF genes in Gossypium, hereby providing basic information for further functional studies.

Evolution and Characterization of Acetyl Coenzyme A: Diacylglycerol Acyltransferase Genes in Cotton Identify the Roles of GhDGAT3D in Oil Biosynthesis and Fatty Acid Composition.

Cottonseed oil is rich in unsaturated fatty acids (UFAs) and serves as an edible oil in human nutrition. Reports suggest that acyl-coenzyme A: diacylglycerol acyltransferases (DGAT) and wax ester synthase/DGAT (WSD1) genes encode a key group of enzymes that catalyze the final step for triacylglycerol biosynthesis and enable an important rate-limiting process. However, their roles in oil biosynthesis and the fatty acid profile of cotton seed are poorly understood. Therefore, the aim of this study was to identify and characterize DGAT and WSD1 genes in cotton plants and examine their roles in oil biosynthesis, the fatty acid profile of cotton seeds, and abiotic stress responses. In this study, 36 GhDGAT and GhWSD1 genes were identified in upland cotton (G. hirsutum) and found to be clustered into four groups: GhDGAT1, GhDGAT2, GhDGAT3, and GhWSD1. Gene structure and domain analyses showed that the GhDGAT and GhWSD1 genes in each group are highly conserved. Gene synteny analysis indicated that segmental and tandem duplication events occurred frequently during cotton evolution. Expression analysis revealed that GhDGAT and GhWSD1 genes function widely in cotton development and stress responses; moreover, several environmental stress and hormone response-related cis-elements were detected in the GhDGAT and GhWSD1 promoter regions. The predicted target transcription factors and miRNAs imply an extensive role of GhDGAT and GhWSD1 genes in stress responses. Increases in GhDGAT3 gene expression with increases in cottonseed oil accumulation were observed. Transformation study results showed that there was an increase in C18:1 content and a decrease in C18:2 and C18:3 contents in seeds of Arabidopsis transgenic plants overexpressing GhDGAT3D compared with that of control plants. Overall, these findings contributed to the understanding of the functions of GhDGAT and GhWSD1 genes in upland cotton, providing basic information for further research.

EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA-protein interaction prediction.

BACKGROUND: Non-coding RNA (ncRNA) and protein interactions play essential roles in various physiological and pathological processes. The experimental methods used for predicting ncRNA-protein interactions are time-consuming and labor-intensive. Therefore, there is an increasing demand for computational methods to accurately and efficiently predict ncRNA-protein interactions. RESULTS: In this work, we presented an ensemble deep learning-based method, EDLMFC, to predict ncRNA-protein interactions using the combination of multi-scale features, including primary sequence features, secondary structure sequence features, and tertiary structure features. Conjoint k-mer was used to extract protein/ncRNA sequence features, integrating tertiary structure features, then fed into an ensemble deep learning model, which combined convolutional neural network (CNN) to learn dominating biological information with bi-directional long short-term memory network (BLSTM) to capture long-range dependencies among the features identified by the CNN. Compared with other state-of-the-art methods under five-fold cross-validation, EDLMFC shows the best performance with accuracy of 93.8%, 89.7%, and 86.1% on RPI1807, NPInter v2.0, and RPI488 datasets, respectively. The results of the independent test demonstrated that EDLMFC can effectively predict potential ncRNA-protein interactions from different organisms. Furtherly, EDLMFC is also shown to predict hub ncRNAs and proteins presented in ncRNA-protein networks of Mus musculus successfully. CONCLUSIONS: In general, our proposed method EDLMFC improved the accuracy of ncRNA-protein interaction predictions and anticipated providing some helpful guidance on ncRNA functions research. The source code of EDLMFC and the datasets used in this work are available at https://github.com/JingjingWang-87/EDLMFC .