Search

Abstract The recent surge in the plant-based protein market has resulted in high demands for soybean genotypes with improved grain yield, seed protein and oil content, and essential amino acids (EAAs). Given the quantitative nature of these traits, complex interactions among seed components, as well as between seed components and environmental factors and management practices, add complexity to the development of desired genotypes. In this study, the across-environment seed protein stability of 449 genetically diverse plant introductions was assessed, revealing that genotypes may display varying sensitivities to such environmental stimuli. The EAAs valine, phenylalanine, and threonine showed the highest variable importance toward the variation in stability, while both seed protein and oil contents were among the explanatory variables with the lowest importance. In addition, 56 single nucleotide polymorphism (SNP) markers were significantly associated with various seed components. Despite the strong phenotypic Pearson’s correlation observed among most seed components, many independent genomic regions associated with one or few seed components were identified. These findings provide insights for improving the seed concentration of specific EAAs and reducing the negative correlation between seed protein and oil contents.

Human adenoviruses (HAdVs) are major respiratory pathogens. Specifically, human adenovirus type 4 (HAdV4) and human adenovirus type 7 (HAdV7) are known for causing fever and pneumonia, with documented cases of fatalities among the population. In recent years, HAdV4/HAdV7 has been implicated in causing substantial outbreaks, leading to increased morbidity in multiple countries. Most HAdV4 and HAdV7 infections have been reported in North America, Asia, Europe, Africa, South America, Oceania, and the Middle East. Most fatalities occurred in North America (the United States) and Asia (China and Singapore). Engineered recombinant adenoviruses have played a crucial role as vaccine vectors. In this study, we constructed a recombinant adenovirus, Ad4ITRmut-Ad7E3, and evaluated it in vitro and in vivo. We observed that the replication rate of Ad4ITRmut-Ad7E3 was lower than that of the RI-67 strain, indicating that the mutation of inverted terminal repeats (ITRs) weakened the replication ability of HAdV4. Immunization of BALB/c mice with the bivalent Ad4ITRmut-Ad7E3 vaccine strain, administered by intraperitoneal injection and oral gavage, resulted in the elicitation of neutralizing antibodies targeting HAdV4 and HAdV7. This finding not only provides a novel method and technique for the efficient construction of a polyvalent recombinant adenovirus vaccine candidate against HAdV4 and HAdV7 but also against other prevalent adenovirus serotypes such as HAdV3, HAdV11, HAdV14, and HAdV55, from various regions.

The human JC polyomavirus (JCV) is a widespread, neurotropic, opportunistic pathogen responsible for progressive multifocal leukoencephalopathy (PML) as well as other diseases in immunosuppressed individuals, including granule cell neuronopathy, JCV-associated nephropathy, encephalitis, and meningitis in rare cases. JCV classification is still unclear, where the ICTV (International Committee on Taxonomy of Viruses) has grouped all the strains into human polyomavirus 2, with no classification on clade and subclade levels. Therefore, JCV strains were previously classified using different genomic regions, e.g., full-length, VP1, and the V-T intergenic region etc., and the strains were grouped into several types related to various geographic locations and human ethnicities. However, neither of these classifications and nomenclature contemplates all the groups described so far. Herein, we evaluated all the available full-length coding genomes, VP1, and large T antigen nucleotide sequences of JCV reported during 1993–2023 and classified them into four major phylogenetic clades, i.e., GI-GIV, where GI is further grouped into two types GI.1 and GI.2 with five sub-clades each (GI.1/GI.2 a-e), GII into three (GII a-c), GIII as a separate clade, and GIV into seven sub-clades (GIV a-g). Similarly, the phylogeographic network analysis indicated four major clusters corresponding to GI-GIV clades, each with multiple subclusters and mutational sub-branches corresponding to the subclades. GI and GIV clusters are connected via GI.1-e reported from Europe and America, GII, GIII and GIV clusters are connected by GII-b and GII-c strains reported from Africa, while GIV cluster strains are connected to the Russia-Italy JCV haplotype. Furthermore, we identified JCV-variant-GS/B-Germany-1997 (GenBank ID: AF004350.1) as an inter-genotype recombinant having major and minor parents in the GI.1-e and GII-a clades, respectively. Additionally, the amino acid variability analysis revealed high entropy across all proteins. The large T antigen exhibited the highest variability, while the small t antigen showed the lowest variability. Our phylogenetic and phylogeographic analyses provide a new approach to genotyping and sub-genotyping and present a comprehensive classification system of JCV strains based on their genetic characteristics and geographic distribution, while the genetic recombination and amino acid variability can help identify pathogenicity and develop effective preventive and control measures against JCV infections.

Summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant disease with a poor prognosis due to inefficient diagnosis and tenacious drug resistance. Obg-like ATPase 1 (OLA1) is overexpressed in many malignant tumors. The molecular mechanism of OLA1 underlying gemcitabine (GEM)-induced drug resistance was investigated in this study. An enhanced expression of OLA1 was observed in a GEM acquired resistant pancreatic cancer cell lines and in patients with pancreatic cancer. Overexpressed OLA1 showed poor overall survival rates in patients with pancreatic cancer. Dysregulation of the OLA1 reduced expression of CD44+/CD133+, and improved the sensitivity of pancreatic cancer cells to GEM. OLA1 highly expression facilitated the formation of the OLA1/Sonic Hedgehog (SHH)/Hedgehog-interacting protein (HHIP) complex in nuclei, resulting in the inhibition of negative feedback of Hedgehog signaling induced by HHIP. This study suggests that OLA1 may be developed as an innovative drug target for an effective therapy of pancreatic cancer.

The three-dimensional (3D) kidney organoid is a breakthrough model for recapitulating renal morphology and function in vitro, which is grown from stem cells and resembles mammalian kidney organogenesis. Currently, protocols for cultivating this model from induced pluripotent stem cells (iPSCs) and patient-derived adult stem cells (ASCs) have been widely reported. In recent years, scientists have focused on combining cutting-edge bioengineering and bioinformatics technologies to improve the developmental accuracy of kidney organoids and achieve high-throughput experimentation. As a remarkable tool for mechanistic research of the renal system, kidney organoid has both potential and challenges. In this review, we have described the evolution of kidney organoid establishment methods and highlighted the latest progress leading to a more sophisticated kidney transformation research model. Finally, we have summarized the main applications of renal organoids in exploring kidney disease.

To break the high additional mass ratio requirement of traditional vibration absorbing materials/devices, and overcome the shortcoming of the narrow operating frequency band of conventional local resonance metamaterial dampers, this paper proposes a lightweight multi-scale material/structure integrated elastic metamaterial for broadband vibration absorption. By replacing the mass components in the macroscopic metamaterial vibration absorber with a composite mass body filled with microscopic particle materials, a multi-scale structure/material integrated design between the macroscopic oscillator and microscopic particle is realized. The macroscopic oscillator absorbs low-frequency vibration, while the microscopic particle cluster absorbs medium–high frequency vibration, thereby achieving a broadband vibration absorption covering the low-medium–high ranges. Based on the band gap theory and the multiphase flow theory of gas-particle, this paper systematically analyzes the band gap effect of multi-scale metamaterials and the dissipation capacity of medium–high frequency caused by particle damping. The structure exhibits commendable vibration damping performance. The multi-scale integrated vibration damper retains the lightweight and sub-wavelength characteristics of the traditional local resonance unit cells, while greatly broadening the working bandwidth, and having potential applications in low-frequency broadband vibration reduction of various mechanical equipment.

ObjectiveIn past decades, the role of high-risk HPV (HR-HPV) infection in cancer pathogenesis has been extensively studied. The viral E7 protein expressed in pre-malignant cells has been identified as an ideal target for immunological intervention. However, the cultivation of HPV in vitro remains a significant challenge, as well as the lack of methods for expressing the HPV E7 protein and generating replication-competent recombinant viral particles, which posed a major obstacle to further exploration of the function and carcinogenic mechanisms of the E7 oncoprotein. Therefore, it is imperative to investigate novel methodologies to construct replication-competent recombinant viral particles that express the HPV E7 protein to facilitate the study of its function.MethodsWe initiated the construction of recombinant viral particles by utilizing the ccdB-Kan forward/reverse screening system in conjunction with the Red/ExoCET recombinant system. We followed the infection of C33A cells with the obtained recombinant virus to enable the continuous expression of HPV16 E7. Afterwards, the total RNA was extracted and performed transcriptome sequencing using RNA-Seq technology to identify differentially expressed genes associated with HPV-induced oncogenicity.ResultsWe successfully established replicative recombinant viral particles expressing HPV16 E7 stably and continuously. The C33A cells were infected with recombinant viral particles to achieve overexpression of the E7 protein. Subsequently, RNA-Seq analysis was conducted to assess the changes in host cell gene expression. The results revealed an upregulation of the CD36 gene, which is associated with the HPV-induced oncogenic pathways, including PI3K-Akt and p53 signaling pathway. qRT-PCR analysis further identified that the upregulation of the CD36 gene due to the expression of HPV16 E7.ConclusionThe successful expression of HPV16 E7 in cells demonstrates that the replicated recombinant virus retains the replication and infection abilities of Ad4, while also upregulating the CD36 gene involved in the PI3K-Akt signaling and p53 pathways, thereby promoting cell proliferation. The outcome of this study provides a novel perspective and serves as a solid foundation for further exploration of HPV-related carcinogenesis and the development of replicative HPV recombinant vaccines capable of inducing protective immunity against HPV.

Head and neck squamous cell carcinomas (HNSCCs) are highly aggressive tumors with rapid progression and poor prognosis. Human papillomavirus (HPV) infection has been identified as one of the most important carcinogens for HNSCC. As an early event in HNSCC, infection with HPV leads to altered immune profiles in the tumor microenvironment (TME). The TME plays a key role in the progression and transformation of HNSCC. However, the TME in HNSCC is a complex and heterogeneous mix of tumor cells, fibroblasts, different types of infiltrating immune cells, and extracellular matrix. Biomarkers relevant to the TME, and the biological role of these biomarkers, remain poorly understood. To this end, we performed comprehensive analysis of the RNA sequencing (RNA-Seq) data from tumor tissue of 502 patients with HNSCC and healthy tissue of 44 control samples. In total, we identified 4,237 differentially expressed genes, including 2,062 upregulated and 2,175 downregulated genes. Further in-depth bioinformatic analysis suggested 19 HNSCC tumor tissue-specific genes. In the subsequent analysis, we focused on the biomarker candidates shown to be significantly associated with unfavorable patient survival: ITGA5, PLAU, PLAUR, SERPINE1, TGFB1, and VEGFC. We found that the expression of these genes was negatively regulated by DNA methylation. Strikingly, all of these potential biomarkers are profoundly involved in the activation of the epithelial–mesenchymal transition (EMT) pathway in HNSCCs. In addition, these targets were found to be positively correlated with the immune invasion levels of CD4+ T cells, macrophages, neutrophils, and dendritic cells, but negatively correlated with B-cell infiltration and CD8+ T-cell invasion. Notably, our data showed that the expression levels of ITGA5, PLAU, PLAUR, SERPINE1, and TGFB1 were significantly overexpressed in HPV-positive HNSCCs compared to normal controls, indicating the potential role of these biomarkers as transformation and/or malignant progression markers for HNSCCs in patients with HPV infection. Taken together, the results of our study propose ITGA5, PLAU, PLAUR, SERPINE1, and TGFB1 as potential prognostic biomarkers for HNSCCs, which might be involved in the HPV-related TME remodeling of HNSCC. Our findings provide important implications for the development and/or improvement of patient stratification and customized immunotherapies in HNSCC.

Abstract Background High-fat diet (HFD)-induced obesity causes immune cells to infiltrate adipose tissue, leading to chronic inflammation and metabolic syndrome. Brown adipose tissue (BAT) can dissipate the energy produced by lipid oxidation as heat, thereby counteracting obesity. Aerobic exercise activates BAT, but the specific underlying mechanism is still unclear. Methods Male C57BL/6 J mice were divided into a normal diet control group (NC group) and HFD group (H group). After becoming obese, the animals in the H group were subdivided into a control group (HC group) and an exercise group (HE group, with treadmill training). After 4 weeks, the mRNA profile of BAT was determined, and then differentially expressed key genes and pathways were verified in vitro. Results Relative to the NC group, the genes upregulated in the HC group coded mainly for proteins involved in immune system progression and inflammatory and immune responses, while the downregulated genes regulated lipid metabolism and oxidation–reduction. Relative to the HC group, the genes upregulated in the HE group coded for glycolipid metabolism, while those that were downregulated were involved in cell death and apoptosis. VEGF and other signaling pathways were enhanced by aerobic exercise. Interaction analysis revealed that the gene encoding cyclooxygenase 2 (COX2) of the VEGF signaling pathway is central to this process, which was verified by a sympathetic activator (isoprenaline hydrochloride) and COX2 inhibitor (NS-398). Conclusions In mice with HFD-induced obesity, four weeks of aerobic exercise elevated BAT mass and increased the expression of genes related to glycolipid metabolism and anti-inflammatory processes. Several pathways are involved, with COX2 in the VEGF signaling pathway playing a key role.

High-risk human papillomavirus infection may develop into a persistent infection that is highly related to the progression of various cancers, including cervical cancer and head and neck squamous cell carcinomas. The most common high-risk subtypes are HPV16 and HPV18. The oncogenic viral proteins expressed by high-risk HPVs E6/E7 are tightly involved in cell proliferation, differentiation, and cancerous transformation since E6/E7 mRNAs are derived from the same pre-mRNA. Hence, the alternative splicing in the E6/E7-coding region affects the balance of the E6/E7 expression level. Interrupting the balance of E6 and E7 levels results in cell apoptosis. Therefore, it is crucial to understand the regulation of E6/E7 splice site selection and the interaction of splicing enhancers and silencers with cellular splicing factors. In this review, we concluded the relationship of different E6/E7 transcripts with cancer progression, the known splicing sites, and the identified cis-regulatory elements within high-risk HPV E6/E7-coding region. Finally, we also reviewed the role of various splicing factors in the regulation of high-risk HPV oncogenic E6/E7 mRNA splicing.

Cervical cancer is one of the most common gynecological malignancies and is related to human papillomavirus (HPV) infection, especially high-risk type HPV16 and HPV18. Aberrantly expressed genes are involved in the development of cervical cancer, which set a genetic basis for patient prognosis. In this study, we identified a set of aberrantly expressed key genes from The Cancer Genome Atlas (TCGA) database, which could be used to accurately predict the survival rate of patients with cervical squamous cell carcinoma (CESC). A total of 3,570 genes that are differentially expressed between normal and cancerous samples were analyzed by the algorithm of weighted gene co-expression network analysis (WGCNA): 1,606 differentially expressed genes (DEGs) were upregulated, while 1,964 DEGs were downregulated. Analysis of these DEGs divided them into 7 modules including 76 hub genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis revealed a significant increase of genes related to cell cycle, DNA replication, p53 signaling pathway, cGMP-PKG signaling pathway, and Fanconi anemia (FA) pathway in CESC. These biological activities are previously reported to associate with cervical cancer or/and HPV infection. Finally, we highlighted 5 key genes (EMEMP2, GIMAP4, DYNC2I2, FGF13-AS1, and GIMAP1) as robust prognostic markers to predict patient’s survival rate (p = 3.706e-05) through univariate and multivariate regression analyses. Thus, our study provides a novel option to set up several biomarkers for cervical cancer prognosis and anticancer drug targets.

The dopamine D3 receptor (D3R) is an important central nervous system target for treating various neurological diseases. D3R antagonists modulate the improvement of psychostimulant addiction and relapse, while D3R agonists can enhance the response to dopaminergic stimulation and have potential applications in treating Parkinson’s disease, which highlights the importance of identifying novel D3R ligands. Therefore, we performed auto dock Vina-based virtual screening and D3R-binding-affinity assays to identify human D3R ligands with diverse structures. All molecules in the ChemDiv library (>1,500,000) were narrowed down to a final set of 37 molecules for the binding assays. Twenty-seven compounds exhibited over 50% inhibition of D3R at a concentration of 10 μM, and 23 compounds exhibited over 70% D3R inhibition at a concentration of 10 μM. Thirteen compounds exhibited over 80% inhibition of D3R at a concentration of 10 μM and the IC50 values were measured. The IC50 values of the five compounds with the highest D3R-inhibition rates ranged from 0.97 μM to 1.49 μM. These hit compounds exhibited good structural diversity, which prompted us to investigate their D3R-binding modes. After trial and error, we combined unbiased molecular dynamics simulation (MD) and molecular mechanics generalized Born surface area (MM/GBSA) binding free-energy calculations with the reported protein–ligand-binding pose prediction method using induced-fit docking (IFD) and binding pose metadynamics (BPMD) simulations into a self-consistent and computationally efficient method for predicting and verifying the binding poses of the hit ligands to D3R. Using this IFD-BPMD-MD-MM/GBSA method, we obtained more accurate and reliable D3R–ligand-binding poses than were obtained using the reported IFD-BPMD method. This IFD-BPMD-MD-MM/GBSA method provides a novel paradigm and reference for predicting and validating other protein–ligand binding poses.

In this study, finite element analysis (FEA) has been conducted for an improved grouted corrugated duct (GCD) connection design with a reserved recess in bridge footing. This study aims to understand the damage progression mechanism and to evaluate the contribution of each component in the improved GCD connection design. Numerical model based on the experimental results are first created, validated and calibrated. It is found that the confining effect (support and friction force) provided by recess sidewall keeps the connection in good integrity. It also prevents early deformation and early development of transverse cracks along the connection interface, which further avoids the damage concentration at connection joint, transfers the plastic hinge region. Parametric study is then carried out by considering different recess depths, cushion thicknesses, recess diameters, and mortar strengths. The effect of recess details on mechanical behavior is thus studied. Recess depth can be designed as 6–20% of the column section size to ensure a higher upper limit of overall strength and ductility, and it also influences the stress distribution area of the joint local. The stiffness and strength of recess control the local damage, while has limited impact on the overall performance. In addition, preliminary suggestions on the GCD design of recess depth, thickness of mortar cushion, recess diameter, the strength of mortar are proposed.

A combined numerical-experiment investigation on the flow and acoustic field of an electronic expansion valve (EEV) is conducted in this paper. In an electronic expansion valve (EEV) under refrigeration condition, it is usually complex about internal flow. There are high pressure gradient and velocity gradient in the flow field, and it also involves the process of flashing phase change, physical property change, and heat transfer, which is difficult to simulate directly. After many explorations in this paper, the flow field of EEV under refrigeration condition is simulated by a four-step computational fluid dynamics (CFD). On this basis, the noise of EEV which is induced by the internal turbulent flow and propagates outward through the shell of EEV is simulated by a Hybrid Method. Numerical simulations of the mass flow rate (MFR) and sound pressure level (SPL) are verified by experimental data. Then, the characteristics of the internal flow field causing the external acoustic radiation are analyzed and used to create an improved design that can reduce the SPL while the MFR hardly changes.

Abstract Background Human papillomavirus (HPV) is an established risk factor for oropharyngeal squamous cell carcinoma (OSCC). The aim was to establish cell lines from HPV-positive tonsil carcinomas to be used for treatment development. Methods Fresh samples from 23 HPV-positive tonsil carcinomas were cultivated in vitro. The established cell line was analyzed for viral characteristics, cell karyotype, TP53 status, and growth capabilities in nude mice. In vitro studies of sensitivities to radiation, cisplatin and cetuximab were performed. Results After 19 months (eight passages), one cell line, LU-HNSCC-26, was established in vitro and also grew as xenografts. The tumor was from a 48 year old non-smoking man with non-keratinizing, p16 positive tonsil OSCC, stage T2N0M0 with HPV16. It contained 19.5 (CV% 3.7) HPV16 copies/cell (passage 8). The complete HPV16 genome sequence was obtained. Episomal HPV16 was present with an E2/E7 ratio of 1.1 (CV% 2.6). In addition, HPV16 mRNA specific for the intact E2 gene was detected. The viral expression manifested 1.0 (CV% 0.1) E7 mRNA copies per HPV16 genome. The karyotype was determined and the cell line demonstrated wild type TP53. The ID50 for radiation was 0.90 Gy and the IC50 for cisplatin was 0.99 μmol/L. The cell line was inhibited to a maximum of 18% by cetuximab. Conclusions We established an in vitro tonsil carcinoma cell line containing episomal HPV16. This is an important step towards efficient treatment development.

This review summarizes the history and current state of the known genetic basis for soybean resistance to Soybean mosaic virus (SMV), and examines how the integration of molecular markers has been utilized in breeding for crop improvement. SVM causes yield loss and seed quality reduction in soybean based on the SMV strain and the host genotype. Understanding the molecular underpinnings of SMV–soybean interactions and the genes conferring resistance to SMV has been a focus of intense research interest for decades. Soybean reactions are classified into three main responses: resistant, necrotic, or susceptible. Significant progress has been achieved that has greatly increased the understanding of soybean germplasm diversity, differential reactions to SMV strains, genotype–strain interactions, genes/alleles conferring specific reactions, and interactions among resistance genes and alleles. Many studies that aimed to uncover the physical position of resistance genes have been published in recent decades, collectively proposing different candidate genes. The studies on SMV resistance loci revealed that the resistance genes are mainly distributed on three chromosomes. Resistance has been pyramided in various combinations for durable resistance to SMV strains. The causative genes are still elusive despite early successes in identifying resistance alleles in soybean; however, a gene at the Rsv4 locus has been well validated.

Soybean production in the U.S. Mid-South relies heavily on irrigation with 85% of soybean surfaces irrigated in Arkansas. Reduction in irrigation due to water quantity restrictions will significantly affect soybean seed yield, making variety selection increasingly important. The objective of the study was to assess if irrigation onsets at different reproductive stages affect wilting, seed yield, and key agronomic traits on determinate maturity group 5 (MG 5) soybean. One-hundred sixty-five F4-derived populations of recombinant inbred lines with determinate growth habit, similar maturity, and contrasting wilting potential were planted in an augmented strip-plot design in four environments as a single replicate. Four irrigation onsets were applied at R1 (initiation flower), R2 (full bloom), R3 (initiation pod), and R4 (full pod) using an atmometer. Results indicated significant differences in wilting and yield but no significant differences in maturity, protein, oil concentration, and 100-seed weight across different irrigation onsets. There was no significant difference between the fast and slow wilting genotypes across different irrigation onsets for each trait. Allowable depletions measured in this study indicated that both fast and slow wilting soybean genotype determinate MG5 can tolerate high allowable depletion with no significant yield penalty at R3 growth stage in silt loam soil.

Breast cancer is one of the most common malignant tumors in women worldwide. Early diagnosis, treatment, and prognosis of breast cancer are global challenges. Identification of valid predictive diagnosis and prognosis biomarkers and drug targets are crucial for breast cancer prevention. This study characterizes differentially expressed genes (DEGs) based on the TCGA database by using DESeq2, edgeR, and limma. A total of 2032 DEGs, including 1026 up-regulated genes and 1006 down-regulated genes were screened. Followed with WGCNA, PPI analysis, GEPIA 2, and HPA database verification, thirteen hub genes including CDK1, BUB1, BUB1B, CDC20, CCNB2, CCNB1, KIF2C, NDC80, CDCA8, CENPF, BIRC5, AURKB, PLK1, MAD2L1, and CENPE were obtained, and they may serve as potential therapeutic targets of breast cancer. Especially, overexpression of CCNB1 and PLK1 are strongly associated with the low survival rate of breast cancer patients, demonstrating their potentiality as prognostic markers. Moreover, CCNB1 and PLK1 are highly expressed in all breast cancer stages, suggesting that they could be further studied as potential drug targets. Taken together, our study highlights CCNB1 and PLK1 as potential anti-breast cancer drug targets and prognostic markers.

Edamame is a food-grade soybean [Glycine max (L.) Merr.] that is harvested immature between the R6 and R7 reproductive stages. To be labeled as a premium product, the edamame market demands large pod size and intense green color. A staggered harvest season is critical for the commercial industry to post-harvest process the crop in a timely manner. Currently, there is little information to assist in predicting the optimum time to harvest edamame when the pods are at their collective largest size and greenest color. The objectives of this study were to assess the impact of cultivar, planting date, and harvest date on edamame color, pod weight, and a newly minted Edamame Harvest Quality Index combining both aforementioned factors. And to predict edamame harvest quality based on phenological stages, thermal units, and planting dates. We observed that pod color and weight depended on the cultivar, planting date, and harvest date combination. Our results also indicated that edamame quality is increased with delayed planting dates and that quality was dependent on harvest date with a quadratic negative response to delaying harvest. Maximum quality depended on cultivar and planting and harvest dates, but it remained stable for an interval of 18–27 days around the peak. Finally, we observed that the number of days between R1 and harvest was consistently identified as a key factor driving edamame quality by both stepwise regression and neural network analysis. These research results will help define a planting and harvest strategy for edamame production in Arkansas and the United States Mid-South.

Alternative splicing of pre-mRNA is a key mechanism for increasing the complexity of proteins in humans, causing a diversity of expression of transcriptomes and proteomes in a tissue-specific manner. Alternative splicing is regulated by a variety of splicing factors. However, the changes and errors of splicing regulation caused by splicing factors are strongly related to many diseases, something which represents one of this study’s main interests. Further understanding of alternative splicing regulation mediated by cellular factors is also a prospective choice to develop specific drugs for targeting the dynamic RNA splicing process. In this review, we firstly concluded the basic principle of alternative splicing. Afterwards, we showed how splicing isoforms affect physiological activities through specific disease examples. Finally, the available treatment methods relative to adjusting splicing activities have been summarized.

Three near-infrared emitters (2TPA-QBT, 2MeTPA-BT and TPA-QBT-MeTPA) were rationally designed and synthesized. Density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations showed that the introduction of mono- or di-methyl groups between the donors and acceptor could result in the spatial configuration changing greatly for 2MeTPA-QBT and TPA-QBT-MeTPA compared to their parent compound 2TPA-QBT. The emission of TPA-QBT-MeTPA had a more obvious hybridized local and charge transfer feature (HLCT) based on the influence of the steric hindrance of the methyl substituent. Attributed to their different spatial configurations and luminescence mechanisms, different emission wavelengths with photoluminescent quantum yields of 26%, 38% and 34% in toluene, as well as 24%, 27% and 31% in 4,4′-bis(N-carbazolyl)-1,1′-biphenyl (CBP) doped film, were observed for 2TPA-QBT, 2MeTPA-QBT and TPA-QBT-MeTPA, respectively. The constructed organic light-emitting devices (OLEDs) displayed electroluminescence with emission peaks at 728, 693 and 710 nm, with maximum external quantum efficiencies of 1.58%, 1.33% and 3.02% for the 2TPA-QBT, 2MeTPA-QBT and TPA-QBT-MeTPA-doped OLEDs, respectively. This work illustrated the effect of spatial configuration changes on the luminescence properties of donor-acceptor-type organic emitters.

Human papillomaviruses (HPVs) have evolved to use the DNA repair machinery to replicate its DNA genome in differentiated cells. HPV activates the DNA damage response (DDR) in infected cells. Cellular DDR factors are recruited to the HPV DNA genome and position the cellular DNA polymerase on the HPV DNA and progeny genomes are synthesized. Following HPV DNA replication, HPV late gene expression is activated. Recent research has shown that the DDR factors also interact with RNA binding proteins and affects RNA processing. DDR factors activated by DNA damage and that associate with HPV DNA can recruit splicing factors and RNA binding proteins to the HPV DNA and induce HPV late gene expression. This induction is the result of altered alternative polyadenylation and splicing of HPV messenger RNA (mRNA). HPV uses the DDR machinery to replicate its DNA genome and to activate HPV late gene expression at the level of RNA processing.

The particle damping technology is a passive vibration control technique. The particle dampers (PDs) as one of the passive damping devices has found wide use in the field of aeronautical engineering, mechanical engineering, and civil engineering because it has several advantages compared with the forms of viscous damping, for example, structure simplicity, low cost, robust properties, and being effective over a wide range of frequencies. In this paper, a novelty simulation method based on multiphase flow theory (MFT) is developed to evaluate the particle damping characteristics using FEM combining DEM with COMSOL Multiphysics. First, the effects of the collisions and friction between the particles are interpreted as an equivalent nonlinear viscous damping based on MFT of gas particle. Next, the contribution of PDs is estimated as equivalent spring-damper system. Then a cantilever rectangular plate treated with PDs is introduced in a finite element model of structure system. Finally frequency response functions (FRFs) of the plate without and with particle dampers are predicted to study characteristics of the particle damping plates under forced vibration. Meanwhile, an experimental verification is performed. Simulation results are in good agreement with experiment date. It is concluded that the simulation method in this paper is valid.

The human papillomavirus type 16 (HPV16) life cycle can be divided into an early stage in which the HPV16 genomic DNA is replicated, and a late stage in which the HPV16 structural proteins are synthesized and virions are produced. A strong coupling between the viral life cycle and the differentiation state of the infected cell is highly characteristic of all HPVs. The switch from the HPV16 early gene expression program to the late requires a promoter switch, a polyadenylation signal switch and a shift in alternative splicing. A number of cis-acting RNA elements on the HPV16 mRNAs and cellular and viral factors interacting with these elements are involved in the control of HPV16 gene expression. This review summarizes our knowledge of HPV16 cis-acting RNA elements and cellular and viral trans-acting factors that regulate HPV16 gene expression at the level of splicing and polyadenylation.

Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were analyzed in wheat callus cells co-cultured with Agrobacterium by using RNA sequencing (RNA-seq) and two-dimensional electrophoresis (2-DE) in conjunction with mass spectrometry (MS). A set of 4,889 DEGs and 90 DEPs were identified, respectively. Most of them are related to metabolism, chromatin assembly or disassembly and immune defense. After comparative analysis, 24 of the 90 DEPs were detected in RNA-seq and proteomics datasets simultaneously. In addition, real-time RT-PCR experiments were performed to check the differential expression of the 24 genes, and the results were consistent with the RNA-seq data. According to gene ontology (GO) analysis, we found that a big part of these differentially expressed genes were related to the process of stress or immunity response. Several putative determinants and candidate effectors responsive to Agrobacterium mediated transformation of wheat cells were discussed. We speculate that some of these genes are possibly related to Agrobacterium infection. Our results will help to understand the interaction between Agrobacterium and host cells, and may facilitate developing efficient transformation strategies in cereal crops.

BACKGROUND: Human adenoviruses (HAdVs) have been implicated as important agents in a wide range of human illnesses. To date, 58 distinct HAdV serotypes have been identified and can be grouped into six species. For the immunological diagnosis of adenoviruses, the hexon protein, a structural protein, has been used. The potential of other HAdV proteins has not been fully addressed. METHODOLOGY/PRINCIPAL FINDINGS: In this study, a nonstructural antigenic protein, the DNA binding protein (DBP) of human adenovirus 5 and 35 (Ad5, Ad35) - was identified using immunoproteomic technology. The expression of Ad5 and Ad35 DBP in insect cells could be detected by rhesus monkey serum antibodies and healthy adult human serum positive for Ad5 and Ad35. Recombinant DBPs elicited high titer antibodies in mice. Their conserved domain displayed immunological cross-reactions with heterologous DBP antibodies in Western blot assays. DBP-IgM ELISA showed higher sensitivity adenovirus IgM detection than the commercial Adenovirus IgM Human ELISA Kit. A Western blot method developed based on Ad5 DBP was highly consistent with (χ(2) = 44.9, P

A series of bedaquiline analogs containing H-bond donors were designed as anti-Mycobacterium tuberculosis drugs. A pair of diastereoisomers (R/S- and S/S-isomers) was selected from these designed compounds for synthetic and stereochemical research. The title compounds were synthesized from chiral precursors for the first time and the absolute configurations (ACs) were determined by electronic circular dichroism (ECD) with quantum chemical calculations. Moreover, a single crystal of the S/S compound was obtained for X-ray diffraction analysis, and the crystal structure showed high consistency with the geometry, confirming the reliability of ACs obtained by ECD analyses and theoretical simulation. Furthermore, the effect of stereochemistry on the anti-tuberculosis activity was investigated. The MICs of the R/S- and S/S-isomers against Mycobacterium phlei 1180 are 9.6 and 32.1 μg·mL−1, respectively. Finally, molecular docking was carried out to evaluate the inhibitory nature and binding mode differences between diastereoisomers.

Salt is a severe abiotic stress that reduces soybean [Glycine max (L.) Merr.] yield by >20% in saline soils and irrigated fields. Marker-assisted selection (MAS) is an efficient method to identify salt-tolerant soybean lines. 'Osage' is a salt-tolerant and high-yielding cultivar in the Mid-South of the United States and is a distant progeny tracing five generations back to 'S-100'. The objective of this study was to determine the inheritance of salt tolerance in Osage soybean by identifying the quantitative trait loci (QTL) controlling the trait. A chloride (Cl-) includer, 'RA-452', was crossed with Cl- excluder, Osage, to develop an F4:6 mapping population. The F4:6 lines were genotyped by 5403 single nucleotide polymorphism (SNP) markers spanning 20 chromosomes (Chr.), of which, 1269 were polymorphic. The salt stress response of F4:6 lines, along with parental genotypes, was evaluated in the greenhouse in April and June 2013. Three different treatments (120 mM NaCl, 120 mM KCl, and water) were initiated at V1 stage and continued for ~18 to 21 d. The leaf Cl- contents were quantified by inductively coupled plasma optical emission spectroscopy. Composite interval mapping analysis indicated that a major Cl--tolerant QTL was confirmed and narrowed down on Chr. 3 in both NaCl and KCl treatments, a novel Cl--tolerant QTL on Chr. 15 was identified in NaCl treatment, and a novel Cl--tolerant QTL on Chr. 13 was identified in the KCl treatment. Two annotated genes, Glyma.13G161800 and Glyma.15G091600, were proposed to be the candidate gene conferring the Cl- tolerance within QTL region on Chr. 13 and 15, respectively. A total of 27 SNP markers were significantly associated with Cl- tolerance, which could be used for MAS in breeding salt-tolerant soybean lines. [ABSTRACT FROM AUTHOR]

Soybean mosaic virus (SMV), a member of the Potyviridae family, is the most common virus negatively affecting yield and seed quality in soybean [Glycine max (L.) Merr.]. Seven SMV strains, G1 through G7, and three independent SMV resistance genes (R-genes), Rsv1, Rsv3, and Rsv4, have been previously identified. The Rsv1 locus contains at least 10 alleles conferring differential plant reactions to SMV strains, and it was mapped at very complex resistancegene-rich region. In this study, two alleles of the Rsv1 locus were analyzed by crossing PI 96983 (Rsv1) and cultivar York (Rsv1-y) soybean to evaluate whether Rsv1 and Rsv1-y belong to the same or different but closely linked loci. To break possible linkage, 3000 F2:3 lines were developed and investigated using infections of the SMVG1 strain in a greenhouse. The occurrence of segregating and susceptible lines indicated tight linkage between two genes. The recombination frequency (RF) was estimated using the maximum likelihood (ML) formula concluding that Rsv1 and Rsv1-y are two tightly linked loci located apart with genetic distance of 2.2 cM on chromosome 13. A new symbol of Rsv5 has been assigned for the resistance gene in York to replace the original Rsv1-y allele assignment. This research provided the first evidence for existence of two R-genes on chromosome 13, conferring resistance to different SMV strains. Both loci, Rsv1 and Rsv5, can be easily transferred into susceptible cultivars in a breeding program to provide broad and durable protection against SMV strains. [ABSTRACT FROM AUTHOR]

The aim of the present study was to investigate the radiosensitizing effects of homeobox (HOX) transcript antisense RNA (HOTAIR) long non-coding RNA on breast cancer tumor cells and examine the underlying mechanisms. Recombinant plasmid vectors containing HOTAIR gene were constructed and MDA-MB231 cells were transfected with these plasmids using liposomes. The cells were treated with radiation and cell apoptosis, proliferation, and double-stranded DNA breaks were examined. HOXD10, phosphorylated AKT (p-AKT) and p-BAD expression levels were measured using western blot analysis. The results showed a higher expression of HOTAIR in advanced tumor cells. HOTAIR efficiently enhanced radioresistance in MDA-MB231 breast cancer cells and accelerated proliferation through the Akt pathway by targeting HOXD10. In conclusion, the findings demonstrated that HOTAIR gene is a valid therapeutic target for the reversal of radiotherapy resistance in breast cancer. [ABSTRACT FROM AUTHOR]

Information on biomass yield and forage nutritive value of grain- and forage-type soybean [Glycine max (L.) Merr.] cultivars is of interest to livestock and row-crop farmers. We studied grain and forage genotypes for biomass, forage nutritive value, and seed yield across two Arkansas locations over 2 yr. Results revealed that stem and total biomass at the R1 (beginning bloom) reproductive growth stage were significantly greater in forage genotypes than in grain genotypes. Forage genotypes had a greater amount of stem biomass (208.7 and 484.0 g m-2) at both R1 and R6 stages and leaf biomass (246.2 g m-2) at R1 than grain genotypes (140.4, 309.2, and 243.8 g m-2, respectively). At R6, grain genotypes had greater amounts of leaf (388.3 g m-2) and pod biomass (350.5 g m-2) than forage genotypes (350.4 and 272.5 g m-2, respectively). There were no differences in leaf and total biomass between forage and grain genotypes at R6. Grain genotypes showed significantly greater seed yield than the forage genotypes (2662.3 vs. 1320.2 kg ha-1), but no differences in seed protein and oil. Forage genotypes had less crude protein and greater acid detergent fiber than grain genotypes, while their neutral detergent fiber concentrations varied among growth stages. Forage soybeans had lower forage nutritive value than grain soybeans overall. For the southern latitude of Arkansas and southern states, we recommend the late-maturing forage genotypes 'Tyrone' and 'SG13-53' and grain genotypes 'Arksoy' and 'Centennial' for planting as forage crops. Our results provide valuable information to growers of these distinctly different soybean types. [ABSTRACT FROM AUTHOR]

Particle damping is a kind of passive and strongly nonlinear damping for energy dissipation. Many researchers have expended huge amounts of effort and time to study internal mechanism of particle damping. However, there is not a systematic and feasible approach for estimating damping performance of non-obstructive particle damping (NOPD). In this paper, we performed studies to mathematically evaluate the damping effect of particle damping based on principles of gas-solid flows. In consideration of the structural characteristics of NOPD which granular materials should be filled into sealed cavity of vibrating structure and the damping act on lateral and bottom of holes in NOPD technology, the gross damping is divided into lateral damping and bottom damping by Janson's theory of stress change direction. And the damping coefficients are compiled into a plug-in by MATLAB and are invoked in FEM software by enterprise integration kits of COMSOL. Meanwhile the frequency domain and time domain analysis of the experiment are used to verify the prediction accuracy of dynamic vibration response of an aluminium cantilever beam which ONPD is imposed at the free end with different packing rate and granular material, the result indicate that the mathematical model has excellent performance to predict the dynamic vibration response of NOPD. Then, the relationship damping effect with the particle filling ratio, particle density and length-diameter ratio of the hole is also researched using co-simulation, it should be noted that larger packing rate and particle density, smaller length-diameter ratio of the hole can play excellent damping effects in NOPD. [ABSTRACT FROM AUTHOR]

Low-noise, energy-saving and improved sound quality has been the major concern for the eco-design of household appliance product. In this paper, taking off from vibro-acoustic coupling, a composite noise control scheme (CNCS) combined with dynamic vibration absorbing technology, the sound absorption technique, controlling noise in the outlet, and particle damping technique is developed to control the sound radiation from an outdoor unit of a split air-conditioner based on sound sources identification. With the help of developed experiment platform, application effect of each technology and CNCS are measured, experimental evaluation shows that the developed CNCS can reduce the sound pressure level (SPL) more than 10 dB. To clarify the application effect of CNCS in sound quality further, it should be evaluated subjectively by using experiments. Experimental result shows that the stability and smoothness of the unit's noise have been greatly improved in time domain signal of sound pressure, the fluctuation strength is greatly improved for the controlled unit, the value at the left ear is reduced from 0.0195 vacil to 0.0146 vacil, and the right ear value is 0.0141 vacil instead of 0.0251 vacil. In addition, the sharpness has also been significantly reduced after CNCS, the value at the left ear decreases from 2.11 acum to 1.97 acum, and 2.01 acum to 1.86 acum for the right ear. So, CNCS is a pragmatic technique to control noise, vibration and improving sound quality. [ABSTRACT FROM AUTHOR]

The particle damper as a passive means for vibration suppression, is preferred due to its simplicity and easy to implement and control, with no need for any auxiliary power equipment. The bottleneck of the design for the particle damper is that damping performance is influenced by many parameters including particle material and size, packing ratio and cavity dimensions of enclosure such as length, width and diameter. In fact, the overall damping effect of particle damper is closely related to the primary structure system parameters. However, the influences of the excitation point, dampers arrangements, excitation force amplitude, and excitation force type for overall damping effect are scarce reported in the open literatures. How to exert particle damper on the structure and how many particles filled within the cavity, which are needed to face the problem in the engineering practice. In the face of doubt above-mentioned, the above questions will be clarified in this paper. At the same time, an optimization algorithm by the application of genetic algorithms of BP neural network is carried out in order to get most excellent damping effect. These will offer significance guidance to design and conduct particle dampers implement in the specific engineering practice with reference significance. [ABSTRACT FROM AUTHOR]

Ethylene response factors (ERFs) comprise a large family of transcription factors that regulate numerous biological processes including growth, development, and response to environmental stresses. Here, we report that Pti5, an ERF in tomato [Solanum lycopersicum (Linnaeus)] was transcriptionally upregulated in response to the potato aphid Macrosiphum euphorbiae (Thomas), and contributed to plant defences that limited the population growth of this phloem-feeding insect. Virus-induced gene silencing of Pti5 enhanced aphid population growth on tomato, both on an aphid-susceptible cultivar and on a near-isogenic genotype that carried the Mi-1.2 resistance (R) gene. These results indicate that Pti5 contributes to basal resistance in susceptible plants and also can synergize with other R gene-mediated defences to limit aphid survival and reproduction. Although Pti5 contains the ERF motif, induction of this gene by aphids was independent of ethylene, since the ACC deaminase (ACD) transgene, which inhibits ethylene synthesis, did not diminish the responsiveness of Pti5 to aphid infestation. Furthermore, experiments with inhibitors of ethylene synthesis revealed that Pti5 and ethylene have distinctly different roles in plant responses to aphids. Whereas Pti5 contributed to antibiotic plant defences that limited aphid survival and reproduction on both resistant (Mi-1.2+) and susceptible (Mi-1.2-) genotypes, ethylene signalling promoted aphid infestation on susceptible plants but contributed to antixenotic defences that deterred the early stages of aphid host selection on resistant plants. These findings suggest that the antixenotic defences that inhibit aphid settling and the antibiotic defences that depress fecundity and promote mortality are regulated through different signalling pathways. [ABSTRACT FROM AUTHOR]

The simple gaseous compound ethylene (ET) has long been recognized as a common component of plant responses to insect feeding and pathogen attack. However, it is presently uncertain whether it plays a role in host–plant resistance to piercing–sucking insects such as aphids. In these experiments, we investigated the expression of key ET-associated genes in resistant and susceptible interactions in two model systems: the tomato- Mi- Macrosiphum euphorbiae (Thomas) (Hemiptera: Aphididae: Macrosiphini) system and the melon-virus aphid transmission gene ( Vat)- Aphis gossypii Glover (Hemiptera: Aphididiae: Aphidini) system. We examined expression patterns of genes associated with ET synthesis, perception, signal transduction, and downstream response. When compared with control plants, plants infested with aphids showed marked differences in gene expression. In particular, ET signaling pathway genes and downstream response genes were highly upregulated in the resistant interaction between A. gossypii and Vat +, indicating ET may play a role in Vat-mediated host–plant resistance. A key integrator between the ET and jasmonic acid pathways ( Cm-ERF1) showed the strongest response. [ABSTRACT FROM AUTHOR]

Flowering represents a crucial transition from a vegetative to a reproductive phase of the plant life cycle. Despite extensive studies, the molecular mechanisms controlling flowering remain elusive. Although the enzymes involved are unknown, methylation of histone H3 K9 and K27 correlates with repression of FLOWERING LOCUS C (FLC), an essential transcriptional repressor involved in flowering time control in Arabidopsis thaliana; in contrast, methylation of H3K4 correlates with FLC activation. Here we show that loss-of-function of SET DOMAIN GROUP 8 (SDG 8), which encodes a homologue of the yeast SET2 histone methyltransferase, results in reduced dimethylation of histone H3K36, particularly in chromatin associated with the FLC promoter and the first intron, regions that contain essential cis-elements for transcription. sdg8 mutants display reduced FLC expression and flower early, establishing SDG8-mediated H3K36 methylation as a novel epigenetic memory code required for FLC expression in preventing early flowering. This is the first demonstrated role of H3K36 methylation in eukaryote development. [ABSTRACT FROM AUTHOR]