Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu.

Rubus chingii Hu is the only species that is used for both edible and medicinal purposes among the 194 species of the genus Rubus in China. It is well known for its sweet and sour fresh fruits that are rich in vitamins and for its dried immature fruits that are used to treat kidney-related ailments. This study aims to evaluate genetic diversity and population structure and build a core germplasm repository of 132 R. chingii accessions from the provinces of Jiangxi and Fujian, using Hyper-seq-derived single-nucleotide polymorphism (SNP) markers. This is the first genetic study of R. chingii based on SNP molecular markers, and a total of 1,303,850 SNPs and 433,159 insertions/deletions (InDels) were identified. Low values for observed heterozygosity, nucleotide diversity (Pi) and fixation indexes (Fis) indicated low genetic diversity within populations, and an analysis of molecular variance (AMOVA) showed that 37.4% and 62.6% of the variations were found between populations and within samples, respectively. Four main clusters were identified by means of neighbor-joining (NJ) trees, the ADMIXTURE program and principal component analysis (PCA). Based on the genetic diversity, we finally constructed 38 representative core collections, representing 50% of the total core germplasm samples and 95.3% of the genotypes. In summary, the results of our study can provide valuable information on the genetic structure of R. chingii germplasm resources, which is helpful for further explorations of potential high-quality genes and for formulating future breeding and conservation strategies.

Production of recombinant HPV11/16 E6/E7-MBP-His6 fusion proteins and their potential to induce cytokine secretion by immune cells in peripheral blood.

Human papillomavirus (HPV) infection poses a significant threat to public health worldwide. Targeting the function of HPV E6 and E7 proteins and activating the host immune response against these proteins represent promising therapeutic strategies for combating HPV-related diseases. Consequently, the efficient production of soluble, high-purity E6 and E7 proteins is crucial for function and host immune response studies. In this context, we selected the pMCSG19 protein expression vector for Escherichia coli to produce soluble MBP-His6 tagged HPV11/16 E6/E7 proteins, achieving relatively high purity and yield. Notably, these proteins exhibited low toxicity to peripheral blood mononuclear cells (PBMCs) and did not compromise their viability. Additionally, the recombinant proteins were capable of inducing the secretion of multiple cytokines by immune cells in peripheral blood, indicating their potential to elicit immune responses. In conclusion, our study offers a novel approach for the production of HPV11/16 E6/E7 fusion proteins with relatively high purity and yield. The fusing HPV11/16 E6/E7 proteins to MBP-His6 tag may serve as a valuable method for large-scale protein production in future research endeavors.

Prognostic value and chemotherapy response prediction of a proliferation essential gene signature in colon cancer.

BACKGROUND: Colon cancer is a common malignant tumor in the digestive tract. Exploring new treatment targets is of great significance for improving the survival rate of colon cancer patients. The present study mainly analyzes the impact of proliferation essential genes (PLEGs) on the prognosis and chemotherapy response of colon cancer patients, as well as identifying the expression and cellular functions of important PLEG. METHODS: The DepMap database was utilized for identification of PLEG in colon cancer cells. Through DEGs screening, WGCNA, univariate cox regression survival analysis, and LASSO, a PLEG signature (PLEGs) model was constructed. The impact of PLEGs on the prognosis of colon cancer patients and their response to chemotherapy was further analyzed. Finally, we conducted a random forest analysis and implemented functional experiments to investigate the prominent PLEG that is linked to the development of colon cancer. RESULTS: Based on the expression and prognosis of PLEG, we constructed a PLEGs prognosis model which can effectively predict the prognosis of colon cancer patients and their response to chemotherapy treatment. Random forest analysis showed that UBA1 is a key PLEG in the progression of colon cancer. Immunohistochemistry results revealed that UBA1 protein is significantly upregulated in colon cancer tissues. Cell functional experiments demonstrated that knocking down UBA1 can inhibit the proliferation, invasion, and migration abilities of colon cancer cells. CONCLUSION: PLEGs have the potential to serve as predictive biomarkers for prognosis and chemotherapy response in colon cancer patients. Among the PLEG, UBA1 plays a prominent role in promoting the malignant progression of colon cancer cells.

A spike-targeting bispecific T cell engager strategy provides dual layer protection against SARS-CoV-2 infection in vivo.

Neutralizing antibodies exert a potent inhibitory effect on viral entry; however, they are less effective in therapeutic models than in prophylactic models, presumably because of their limited efficacy in eliminating virus-producing cells via Fc-mediated cytotoxicity. Herein, we present a SARS-CoV-2 spike-targeting bispecific T-cell engager (S-BiTE) strategy for controlling SARS-CoV-2 infection. This approach blocks the entry of free virus into permissive cells by competing with membrane receptors and eliminates virus-infected cells via powerful T cell-mediated cytotoxicity. S-BiTE is effective against both the original and Delta variant of SARS-CoV2 with similar efficacy, suggesting its potential application against immune-escaping variants. In addition, in humanized mouse model with live SARS-COV-2 infection, S-BiTE treated mice showed significantly less viral load than neutralization only treated group. The S-BiTE strategy may have broad applications in combating other coronavirus infections.

Chromosome-level assemblies of cultivated water chestnut Trapa bicornis and its wild relative Trapa incisa.

Water chestnut (Trapa L.) is a floating-leaved aquatic plant with high edible and medicinal value. In this study, we presented chromosome-level genome assemblies of cultivated large-seed species Trapa bicornis and its wild small-seed relative Trapa incisa by using PacBio HiFi long reads and Hi-C technology. The T. bicornis and T. incisa assemblies consisted of 479.90 Mb and 463.97 Mb contigs with N50 values of 13.52 Mb and 13.77 Mb, respectively, and repeat contents of 62.88% and 62.49%, respectively. A total of 33,306 and 33,315 protein-coding genes were predicted in T. bicornis and T. incisa assemblies, respectively. There were 159,232 structural variants affecting more than 11 thousand genes detected between the two genomes. The phylogenetic analysis indicated that the lineage leading to Trapa was diverged from the lineage to Sonneratia approximately 23 million years ago. These two assemblies provide valuable resources for future evolutionary and functional genomic research and molecular breeding of water chestnut.

Development and Validation of a Risk Scoring Tool for Bronchopulmonary Dysplasia in Preterm Infants Based on a Systematic Review and Meta-Analysis.

Background: Bronchopulmonary dysplasia (BPD) is the most common serious pulmonary morbidity in preterm infants with high disability and mortality rates. Early identification and treatment of BPD is critical. Objective: This study aimed to develop and validate a risk scoring tool for early identification of preterm infants that are at high-risk for developing BPD. Methods: The derivation cohort was derived from a systematic review and meta-analysis of risk factors for BPD. The statistically significant risk factors with their corresponding odds ratios were utilized to construct a logistic regression risk prediction model. By scoring the weights of each risk factor, a risk scoring tool was established and the risk stratification was divided. External verification was carried out by a validation cohort from China. Results: Approximately 83,034 preterm infants with gestational age < 32 weeks and/or birth weight < 1500 g were screened in this meta-analysis, and the cumulative incidence of BPD was about 30.37%. The nine predictors of this model were Chorioamnionitis, Gestational age, Birth weight, Sex, Small for gestational age, 5 min Apgar score, Delivery room intubation, and Surfactant and Respiratory distress syndrome. Based on the weight of each risk factor, we translated it into a simple clinical scoring tool with a total score ranging from 0 to 64. External validation showed that the tool had good discrimination, the area under the curve was 0.907, and that the Hosmer-Lemeshow test showed a good fit (p = 0.3572). In addition, the results of the calibration curve and decision curve analysis suggested that the tool showed significant conformity and net benefit. When the optimal cut-off value was 25.5, the sensitivity and specificity were 0.897 and 0.873, respectively. The resulting risk scoring tool classified the population of preterm infants into low-risk, low-intermediate, high-intermediate, and high-risk groups. This BPD risk scoring tool is suitable for preterm infants with gestational age < 32 weeks and/or birth weight < 1500 g. Conclusions: An effective risk prediction scoring tool based on a systematic review and meta-analysis was developed and validated. This simple tool may play an important role in establishing a screening strategy for BPD in preterm infants and potentially guide early intervention.

Systematic Quality Evaluation of Epimedium wushanense T. S. Ying Based on Two Quality Control Standards: Total Flavonoid Glycosides and Epimedin C.

Two quality control standards, total flavonoid glycosides of Epimedii Folium and epimedin C of Epimedii Wushanensis Folium, were used to systematically evaluate the quality of Epimedium wushanense T. S. Ying, so as to provide reference for its germplasm screening and resource utilization. Seven representative populations of E. wushanense covering its main distribution areas were uniformly sampled during the flowering period. There were significant quality differences among the populations of E. wushanense. According to the quality standard of total flavonoid glycosides, all populations were superior to the quality standard of the Chinese Pharmacopoeia for Epimedii Folium, with more than 1.5 % total flavonoid glycosides. The variation ranges of epimedin A, epimedin B, epimedin C, icariin and total flavonoid glycosides were 0.40-0.76 %, 0.51-0.83 %, 1.70-9.31 %, 0.40-1.23 % and 3.05-10.61 %, respectively. According to the quality standard of epimedin C, all populations were better than the quality standard of the Chinese Pharmacopoeia for Epimedii Wushanensis Folium, with more than 1.0 % epimedin C. The variation range of epimedin C was 2.22-10.06 %. When comparing the results of the two methods, a trend of slightly lower mean values was found for total flavonoid glycosides, except for the HBXW population. The quality of E. wushanense was superior to both the quality standard of Epimedii Folium and Epimedii Wushanense Folium in the Chinese Pharmacopoeia. Epimedin C was the most abundant component. Among the investigated populations, HBXW and HBGK exhibited the highest quality, and may provide excellent genetic resources for standardized cultivation. In addition, the habitat of these populations can also serve a reference for cultivation conditions.

Injectable, Hierarchically Degraded Bioactive Scaffold for Bone Regeneration.

Bioactive materials play vital roles in the repair of critical bone defects. However, bone tissue engineering and regenerative medicine are still challenged by the need to repair bone defects evenly and completely. In this study, we functionally simulated the natural creeping substitution process of autologous bone repair by constructing an injectable, hierarchically degradable bioactive scaffold with a composite hydrogel, decalcified bone matrix (DBM) particles, and bone morphogenetic protein 2. This composite scaffold exhibited superior mechanical properties. The scaffold promoted cell proliferation and osteogenic differentiation through multiple signaling pathways. The hierarchical degradation rates of the crosslinked hydrogel and DBM particles accelerated tissue ingrowth and bone formation with a naturally woven bone-like structure in vivo. In the rat calvarial critical defect repair model, the composite scaffold provided even and complete repair of the entire defect area while also integrating the new and host bone effectively. Our results indicate that this injectable, hierarchically degradable bioactive scaffold promotes bone regeneration and provides a promising strategy for evenly and completely repairing the bone defects.

Ni-MOF composite polypyrrole applied to supercapacitor energy storage.

Electrodes for supercapacitors made from metal-organic frameworks (MOFs) are still hindered by electron transfer properties. Therefore, an electrode composite material Ni-MOF@PPy was synthesized from a Ni-based metal-organic framework (Ni-MOF) doped with poly-pyrrole (PPy) using a simple chemical oxidation method to improve its electron transfer property. After introducing the electrochemically active substance K4Fe(CN)6 into the electrolyte, the composite material had a specific capacitance of 1815.4 F g-1 at a current density of 1 A g-1. Ni-MOF@PPy and active carbon (AC) as the positive and negative electrodes have been used, respectively, to assemble asymmetric supercapacitors (ASCs) in the KOH and K4Fe(CN)6 mixed electrolyte. This novel Ni-MOF@PPy//AC ASC energy storage device can provide 38.5 W h kg-1 energy density, 7001 W kg-1 power density, and 90.2% capacitance retention after 3000 cycles. Therefore, Ni-MOF@PPy//AC ASC is an excellent energy storage device with practical and economic value. The synergistic effect strategy proposed in this work can be easily applied to develop other MOFs with unique crystal structures as well as other redox active additives, providing new avenues and research ideas for exploring novel energy storage devices.

Direct adsorption sampling and ambient mass spectrometry analysis of tobacco smoke with porous paper strips.

Chemical analysis of atmospheric aerosols by conventional analytical methods is usually required to perform complicated and time-consuming sample preparation processes. In recent decades, ambient ionization mass spectrometry (AI-MS) methods have been proven to be simple, rapid, and effective analytical tools for direct analysis of various complex samples. In this work, we applied porous paper filters for direct adsorptive sampling of tobacco smoke, and then the sampled paper filters were performed the emitters of the paper spray ionization (PSI) device. An auto-sampling device was made to control the generation and collection of tobacco smoke. Nicotine, the typical compound of tobacco smoke, was used to optimize the key conditions of auto-sampling. Moreover, different types of tobacco smoke were also compared with multivariate variable analysis, and the makers of tobacco smoke from different sources of tobacco smoke were investigated. By using this method, direct sampling and analysis of a single tobacco sample can be completed within minutes. Overall, our results show that PSI-MS is a powerful tool that integrates collection, extraction, ionization, and identification analytes in smoke.

Spheroid Formation Enhances the Regenerative Capacity of Nucleus Pulposus Cells via Regulating N-CDH and ITGß1 Interaction.

Background: Nucleus pulposus (NP) degeneration is the core pathological change of intervertebral disc (IVD) degenerative diseases, but currently, no effective therapy is available. With the rapid development of biomaterials and tissue engineering in recent years, biomaterial-assisted cell transplantation becomes a promising therapy for IVD degeneration. However, the application is severely limited by the weak biological characteristics of NP cells (NPCs), such as a moderate proliferation ability, weak self-renewal capacity, and minimal extracellular matrix (ECM) synthesis capacity, caused by the current inappropriate cell seeding or grafting methods. Methods: Here, we developed a three-dimensional (3D) spheroidizing culture method to construct NPC spheroids and investigated repair and regeneration potential of these spheroids in vitro and in vivo. The in vitro biological characteristics (including cell viability and proliferation), and in vivo functions (including anti-degeneration potential and ability to induce tissue repair) of NPC spheroids and monolayer-cultured NPCs were compared. Furthermore, an RNA-seq-based transcriptome analysis and a series of function experiments were performed to elucidate the potential mechanisms of their differences that were involved in the tissue regeneration process. Results: NPC spheroids exhibited obviously superior self-renewal and ECM synthesis capacities compared to monolayers of NPCs in vitro. In vivo, NPC spheroids generated more functional ECM components, primarily aggrecan (ACAN) and collagen type II (Col2), and markedly promoted NP regeneration in the disc degeneration model induced by partial NP excision. Additionally, the biological characteristics and functions of NPC spheroids were to some extent regulated by the interaction of N-cadherin (N-CDH) and Integrinß1 (ITGß1), two key mechanosensing ECM-receptors expressed on NPCs. Conclusions: The NPC spheroidizing culture method is beneficial for cell renewal and the generation of functional ECM in NP tissue. The molecular mechanism involved in this regeneration process is closely associated with the regulation of the N-CDH and ITGß1 interaction-mediated ECM homeostesis. Moreover, the strategy of hydrogel-assisted NPC spheroids transplantation may potentially be used in the future treatment of IVD degeneration.

The complete chloroplast genome sequences of two ornamental Epimedium species (Berberidaceae).

Both Epimedium sutchuenense Franch. 1894 and E. fargesii Franch. 1894 are perennial herbs with excellent ornamental values due to their showy flowers. However, little molecular research has been done on these species. Here, the complete chloroplast (cp) genome of E. sutchuenense and E. fargesii was analyzed and reported. The cp genome sizes of E. sutchuenense and E. fargesii were 157, 263 and 157, 133 bp, respectively. Both the two cp genomes contained a pair of inverted repeat regions (IRs) (25,782 and 25,796 bp), separated by the small single-copy (SSC) region (17,106 and 17,071 bp) and a large single-copy (LSC) region (88,593 and 88,470 bp). A total of 113 unique genes were annotated in each of the two cp genomes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis supported a close relationship between E. sutchuenense and E. wushanense, while E. fargesii had no clear clustering branch.

The complete chloroplast genome of Epimedium jinchengshanense Y. J. Zhang & J. Q. Li (Berberidaceae), an ornamental and medicinal species.

Epimedium jinchengshanense Y. J. Zhang & J. Q. Li 2014 is an important ornamental and medicinal herb, but of unclear taxonomy. In this study, the complete chloroplast genome of E. jinchengshanense was sequenced. The genome was 157,169 bp in length, with a large single-copy region of 88, 520 bp, a small single-copy region of 17,075 bp and 2 inverted repeat regions of 25, 787 bp. The genome consisted of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The GC contents were 38.78%. Phylogenetic analysis showed a close relationship between E. jinchengshanense and E. ilicifolium, which was explained by the morphological similarity of flowers and leaves of the two species.

Plastid genome data provide new insights into the phylogeny and evolution of the genus Epimedium.

INTRODUCTION: Epimedium L., the largest herbaceous genus of Berberidaceae, is one of the most taxonomically difficult representatives. The classification and phylogenetic relationships within Epimedium are controversial and unresolved. OBJECTIVES: For the first time, we systematically studied the phylogeny and evolution of Epimedium based on plastid genome (plastome) data for better understanding this enigmatic genus. METHODS: We explored the molecular phylogeny, assessed the infrageneric classification, estimated the divergence times, and inferred the ancestral states for flower traits of Epimedium based on 45 plastomes from 32 species. RESULTS: The Epimedium plastome length ranged from 156,635 bp to 159,956 bp. Four types of plastome organization with different inverted repeat boundary changes were identified. Phylogenetic analysis revealed a strong support for the sister relationship of sect. Macroceras and sect. Diphyllon but did not provide a distinct route for petal evolution in sect. Diphyllon. Disharmony between phylogenetic relationships and traditional classification of sect. Diphyllon was observed. Results from divergence time analysis showed that Epimedium diverged in the early Pleistocene (~2.11 Ma, 95% HPD = 1.88-2.35 Ma). Ancestral character state reconstructions indicated transitions from long spur (large-flowered group) to other petal types (small-flowered group) in Epimedium. CONCLUSION: These findings provide new insights into the relationships among Epimedium species and pave the way for better elucidation of the classification and evolution of this genus.

Muscular injury was identified the risk factor of post-operative stenosis after large area but non-circumferential esophageal endoscopic submucosal dissection.

BACKGROUND: The incidence of post-operative stenosis after esophageal Endoscopic Submucosal Dissection (ESD) ranks high. This study aimed to investigate the association between the degree of muscular injury and the incidence of post-operative stenosis. RESEARCH DESIGN: This was a retrospective study of 133 patients with superficial esophageal lesions treated by non-circumferential ESD enrolled between January 2016 and May 2021 at two endoscopy centers. Demographic and clinical parameters were analyzed. A novel muscular injury classification system was proposed. Stenosis risk factors were identified using multivariate logistic regression. The association between the different degrees of muscular injury and the incidence of post-operative stenosis was investigated further by propensity score matching (PSM). RESULTS: There were 133 cases evaluated in this study, 33 of which developed stenosis. Multivariate analysis suggested lesions located in the upper 1/3 of the esophagus, resections >5/6 of the circumference, and muscular injury (Grade 3 or 4 according to our proposed classification) were risk factors for stenosis. Correlation analysis suggested a positive association between the degree of muscular injury and the incidence of post-operative stenosis (r = 0.408, p < .05). For PSM, 29 stenosis cases were matched and univariate analysis further corroborated that muscular injuries of grade 3 (OR = 6.429, 95%CI = 1.318-31.367, p = .021) or 4 (OR = 7, 95%CI = 1.068-45.901, p = .043) were risk factors for stenosis. CONCLUSION: Grade 3-4 muscular injury was identified as a risk factor of post-operative stenosis.

Chemical Constituents of the Marine Fungus Penicillium sp. MCCC 3A00228.

One new (d-arabinitol-anofinicate, 1) and fourteen known (2-15) compounds were isolated from the marine Penicillium sp. MCCC 3A00228. The structure of the new compound was established mainly by extensive spectroscopic analyses. Compound 1 exhibited weak transcriptional effect on Nur77. While compound 13 showed moderate in vitro anti-proliferative effect against QGY7701, H1299, and HCT116 tumor cells with IC50 values of 21.2 µM, 18.2 µM, and 17.6 µM, respectively.

Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp.

Sarcandra glabra has significant metabolically active bioingredients of pharmaceutical importance. The deficiency of molecular markers for S. glabra is a hindrance in molecular breeding for genetic improvement. In this study, 57.756 million pair-end reads were generated by transcriptome sequencing in S. glabra (Thunb.) Nakai and its subspecies S. glabra ssp. brachystachys. A total of 141,954 unigenes with 646.63 bp average length were assembled. A total of 25,620 simple sequence repeats, 726,476 single nucleotide polymorphisms, and 42,939 insertions and deletions were identified, and the associated unigenes and differentially expressed genes were characterized. This work enhanced the molecular marker resources and will facilitate molecular breeding and gene mining in S. glabra spp.

Engineering mesenchymal stromal cells with neutralizing and anti-inflammatory capability against SARS-CoV-2 infection.

The emergence of the novel human severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to the pandemic of coronavirus disease 2019 (COVID-19), which has markedly affected global health and the economy. Both uncontrolled viral replication and a proinflammatory cytokine storm can cause severe tissue damage in patients with COVID-19. SARS-CoV-2 utilizes angiotensin-converting enzyme 2 (ACE2) as its entry receptor. In this study, we generated ACE2 extracellular domain-Fc and single-chain variable fragment-interleukin 6 (IL-6) single-chain variable fragment against IL-6 receptor (scFv-IL6R)-Fc fusion proteins to differentially neutralize viruses and ameliorate the cytokine storm. The human ACE2 (hACE2)1-740-Fc fusion protein showed a potent inhibitory effect on pseudo-typed SARS-CoV-2 entry and a good safety profile in mice. In addition, scFv-IL6R-Fc strongly blocked IL-6 signal activation. We also established a mesenchymal stromal cell (MSC)-based hACE21-740-Fc and scFv-IL6R-Fc delivery system, which could serve as a potential therapy strategy for urgent clinical needs of patients with COVID-19.