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Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape
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作者 Hainan Liu Maosong Pei +5 位作者 Charles Ampomah-Dwamena Yaxin Shang Yihe Yu Tonglu Wei Qiaofang Shi Dalong Guo 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2024年第3期863-875,共13页
The firmness of table grape berries is a crucial quality parameter. Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive. To enhance our comprehension of the under... The firmness of table grape berries is a crucial quality parameter. Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive. To enhance our comprehension of the underlying molecular factors, we initially identified differentially expressed genes(DEGs) by comparing the transcriptomes of folic acid(FA)-treated and water-treated(CK) berries at different time points. We then analyzed the sequences to detect alternatively spliced(AS) genes associated with postharvest softening. A total of 2,559 DEGs were identified and categorized into four subclusters based on their expression patterns, with subcluster-4 genes exhibiting higher expression in the CK group compared with the FA treatment group. There were 1,045 AS-associated genes specific to FA-treated berries and 1,042 in the CK-treated berries, respectively. Gene Ontology(GO) annotation indicated that the AS-associated genes in CK-treated berries were predominantly enriched in cell wall metabolic processes,particularly cell wall degradation processes. Through a comparison between treatment-associated AS genes and subcluster-4 DEGs, we identified eight genes, including Pectinesterase 2(VvPE2, Vitvi15g00704), which encodes a cell wall-degrading enzyme and was predicted to undergo an A3SS event. The reverse transcription polymerase chain reaction further confirmed the presence of a truncated transcript variant of VvPE2 in the FA-treated berries.Our study provides a comprehensive analysis of AS events in postharvest grape berries using transcriptome sequencing and underscores the pivotal role of VvPE2 during the postharvest storage of grape berries. 展开更多
关键词 GRAPE postharvest softening folic acid alternative splicing Pectinesterase 2 alternative 3'splice site(A3SS)
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A Neural-network-based Alternative Scheme to Include Nonhydrostatic Processes in an Atmospheric Dynamical Core
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作者 Yang XIA Bin WANG +13 位作者 Lijuan LI Li LIU Jianghao LI Li DONG Shiming XU Yiyuan LI Wenwen XIA Wenyu HUANG Juanjuan LIU Yong WANG Hongbo LIU Ye PU Yujun HE Kun XIA 《Advances in Atmospheric Sciences》 SCIE CAS CSCD 2024年第6期1083-1099,I0002,I0003,共19页
Here,a nonhydrostatic alternative scheme(NAS)is proposed for the grey zone where the nonhydrostatic impact on the atmosphere is evident but not large enough to justify the necessity to include an implicit nonhydrostat... Here,a nonhydrostatic alternative scheme(NAS)is proposed for the grey zone where the nonhydrostatic impact on the atmosphere is evident but not large enough to justify the necessity to include an implicit nonhydrostatic solver in an atmospheric dynamical core.The NAS is designed to replace this solver,which can be incorporated into any hydrostatic models so that existing well-developed hydrostatic models can effectively serve for a longer time.Recent advances in machine learning(ML)provide a potential tool for capturing the main complicated nonlinear-nonhydrostatic relationship.In this study,an ML approach called a neural network(NN)was adopted to select leading input features and develop the NAS.The NNs were trained and evaluated with 12-day simulation results of dry baroclinic-wave tests by the Weather Research and Forecasting(WRF)model.The forward time difference of the nonhydrostatic tendency was used as the target variable,and the five selected features were the nonhydrostatic tendency at the last time step,and four hydrostatic variables at the current step including geopotential height,pressure in two different forms,and potential temperature,respectively.Finally,a practical NAS was developed with these features and trained layer by layer at a 20-km horizontal resolution,which can accurately reproduce the temporal variation and vertical distribution of the nonhydrostatic tendency.Corrected by the NN-based NAS,the improved hydrostatic solver at different horizontal resolutions can run stably for at least one month and effectively reduce most of the nonhydrostatic errors in terms of system bias,anomaly root-mean-square error,and the error of the wave spatial pattern,which proves the feasibility and superiority of this scheme. 展开更多
关键词 neural network nonhydrostatic alternative scheme atmospheric model dynamical core
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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing
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作者 Yinqing Yang Lei Zhang +7 位作者 Qi Tang Lingkui Zhang Xing Li Shumin Chen Kang Zhang Ying Li Xilin Hou Feng Cheng 《Horticultural Plant Journal》 SCIE CAS CSCD 2024年第4期961-970,共10页
Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so on.The genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of B.oleracea,ha... Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so on.The genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of B.oleracea,has been widely used as a common reference in biological research.Although its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 transcripts.Additionally,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold stress.Meanwhile,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS analysis.Overall,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms. 展开更多
关键词 Brassica oleracea Oxford nanopore technologies Gene annotation alternative splicing
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2,3,5,4’-Tetrahydroxystilbene-2-O-b-D-Glucoside modulates CHEK2 and CCND1 alternative splicing to inhibit MCF-7 cells proliferation
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作者 Hui Shen You-Zhi Zhang +5 位作者 Peng-Yu Wang Shuo Zhang Huan Pan Bei-Bei Liu Long-Sheng Xu Jian-Fen Shen 《Traditional Medicine Research》 2024年第1期33-46,共14页
Background:In our previous study,we observed a synergistic effect of 2,3,5,4’-Tetrahydroxystilbene-2-O-b-D-glucoside combined with adriamycin to induce apoptosis in MCF-7 breast cancer cells.However,the underlying me... Background:In our previous study,we observed a synergistic effect of 2,3,5,4’-Tetrahydroxystilbene-2-O-b-D-glucoside combined with adriamycin to induce apoptosis in MCF-7 breast cancer cells.However,the underlying mechanisms of epigenetic modifications,such as alternative splicing,have not been explored.In this study,we aimed to investigate the mechanism by which THSG inhibits MCF-7 cell proliferation using full-length transcriptome sequencing.Methods:First,cell viability was examined using the methyl thiazolyl tetrazolium method and full-length transcriptome sequencing was performed to identify genes and pathways.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used to identify the principal pathways and targets of THSG.Flow cytometry analysis of cell cycle distribution was performed.Meanwhile,the analysis of alternative splicing and domains of the key proteins was conducted.Quantitative polymerase chain reaction and western blotting were performed for verification.Results:THSG showed significant cytotoxic activity in MCF-7 cells.Full-length transcriptome sequencing revealed differential alternative splicing with 173 upregulated and 263 downregulated genes.Further analysis identified distinct differential expression of genes(CHEK2-211 and CCND1-201)involved in the cell cycle in the THSG-treated group.Subsequently,alternative splicing types of CHEK2(mutually exclusive exon)and CCND1(intron retention).We found that THSG downregulated mRNA expression,as confirmed by quantitative polymerase chain reaction analysis.Interestingly,protein structural analysis revealed that THSG treatment led to the generation of CHK2-211,which was the result of a mutation in the amino acid residues(GLU-150,ASN-151)of the CHEK2 domain(VAL-150,GLY-151).and CyclinD1-201 were obtained when an amino acid(ASP-267)in the domain was lost in CyclinD1.Moreover,molecular docking analysis demonstrated that the domains of key proteins could bind THSG more effectively,with no difference in affinity.Western blotting confirmed that THSG inhibited the expression of CHK2 and CyclinD1.Conclusion:THSG modulated the alternative splicing of CHEK2 and CCND1 by inducing G0/G1 cell cycle arrest,consequently suppressing MCF-7 cell proliferation. 展开更多
关键词 THSG breast cancer full-length transcriptome sequencing alternative splicing
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Workshop “Navigating the Transition: Standards Powering the Journey of Alternative Fuel Infrastructure”
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《China Standardization》 2024年第2期67-67,共1页
April 18, Brussels, Belgium In light of recent significant regulatory changes within the European Union impacting the transport sector, such as the Alternative Fuels Infrastructure Regulation(AFIR), Re Fuel EU and Fue... April 18, Brussels, Belgium In light of recent significant regulatory changes within the European Union impacting the transport sector, such as the Alternative Fuels Infrastructure Regulation(AFIR), Re Fuel EU and Fuel EU Maritime, the role of European standardization becomes increasingly critical in facilitating the transition towards the deployment of alternative fuels. 展开更多
关键词 TRANSITION alternative MARITIME
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Use of Topical Complementary and Alternative Medicines (CAM) in Diabetic Septic Foot Disease in Makkah Region, Western of Saudi Arabia, an Exploratory Study
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作者 Mohamed Elamin Salih Hatim Alrizqi +5 位作者 Mohammed Hussain Abdullah Alshumrani Ismail Alhasani Ali Alkhamisi Hamzah Alsayed Fahad Alqarni 《Journal of Biosciences and Medicines》 2024年第3期245-258,共14页
Diabetes is a chronic condition that is significantly impacted daily by environment. At least one in five Saudis, suffer from diabetes. “Diabetes is a pandemic of unprecedented magnitude spiraling out of control” (B... Diabetes is a chronic condition that is significantly impacted daily by environment. At least one in five Saudis, suffer from diabetes. “Diabetes is a pandemic of unprecedented magnitude spiraling out of control” (Boulton). Saudi Arabia ranks the second highest in the Middle East, and is the seventh in the world for the prevalence of diabetes (WHO). Diabetes mellitus (DM) has been found to be related to high mortality, morbidity accompanied by poor general health and lower quality of life. Current Saudi diabetes patients’ behaviors, practices, and beliefs regarding foot health problems such as ulcers, are not well investigated. Diabetic patients frequently utilize natural remedies and Herbs for self-medication as a part of complementary and alternative Medicine. Aim of study: To explore the widespread use of the alternative remedies in the local communities of the Western Saudi Arabia, the drives behind using and to focus on the potential adverse effects following their usage. Method: A descriptive, cross-sectional study of 386 diabetic patients with feet problems in Makkah Region, West of Saudi Arabia during the period April - June 2023. Results: Out of the 531 participants, only 386 participants reported diabetic foot disorder (DFD). Most of the participant were above 65 years of age group (24.61 %). Male (52.08%) more than female (47.92%) in the research group. All of the participants had diabetic foot disorders at least once. The prevalence of complementary and alternative medicines (CAM) use among them was 67.88%, as solitary or in combination with hospital medicines. Honey headed the list followed by myrrh and black seeds. Acquaintances advice (59.54%) was the most reason for using the alternative medicine. 60.30% of Diabetic foot patient complained of adverse effects during CAM remedies use. Conclusion: Consumption of CAM remedies among diabetic patients for Diabetic Foot Disorder (DFD) is common. Honey headed the list followed by myrrh and black seeds. Additional wide-scale research is required to establish their actual efficacy, safety and potential adverse out-comes and to generalize the outcomes. 展开更多
关键词 Diabetic Foot Ulcer Diabetes Complementary and alternative Medicine CAM West of Saudi Arabia
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Molecular targets and mechanisms of different aberrant alternative splicing in metastatic liver cancer
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作者 De-Yi Geng Qing-Shan Chen +7 位作者 Wan-Xian Chen Lin-Sa Zhou Xiao-Sha Han Qi-Hu Xie Geng-Hong Guo Xue-Fen Chen Jia-Sheng Chen Xiao-Ping Zhong 《World Journal of Clinical Oncology》 2024年第4期531-539,共9页
Metastasis remains a major challenge in the successful management of malignant diseases.The liver is a major site of metastatic disease and a leading cause of death from gastrointestinal malignancies such as colon,sto... Metastasis remains a major challenge in the successful management of malignant diseases.The liver is a major site of metastatic disease and a leading cause of death from gastrointestinal malignancies such as colon,stomach,and pancreatic cancers,as well as melanoma,breast cancer,and sarcoma.As an important factor that influences the development of metastatic liver cancer,alternative splicing drives the diversity of RNA transcripts and protein subtypes,which may provide potential to broaden the target space.In particular,the dysfunction of splicing factors and abnormal expression of splicing variants are associated with the occurrence,progression,aggressiveness,and drug resistance of cancers caused by the selective splicing of specific genes.This review is the first to provide a detailed summary of the normal splicing process and alterations that occur during metastatic liver cancer.It will cover the role of alternative splicing in the mechanisms of metastatic liver cancer by examining splicing factor changes,abnormal splicing,and the contribution of hypoxia to these changes during metastasis. 展开更多
关键词 alternative splicing CARCINOMA HEPATOCELLULAR Metastasic Liver neoplasms PROGNOSIS
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Progression of Corneal Astigmatism after Phaco-Alternative at the University Hospital Center of the Oueme-Plateau Department in Porto-Novo
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作者 Chakiratou Olaïdé Adoukê Abouki Edjrokinto Ahomadegbe Djrodéhou Espérancia Neuilly +4 位作者 Issifou Amadou Alfa Bio Nestor Aïgbè Soulé Alamou Lisette Odoulami Ignace Sounouvou 《Open Journal of Ophthalmology》 2024年第3期313-323,共11页
Objective: To study the postoperative evolution of corneal astigmatism following phaco-alternative at the University Hospital Center of Ouémé-Plateau (UHC-OP) in Porto-Novo. Method: This was a prospective, c... Objective: To study the postoperative evolution of corneal astigmatism following phaco-alternative at the University Hospital Center of Ouémé-Plateau (UHC-OP) in Porto-Novo. Method: This was a prospective, cross-sectional study with a descriptive and analytical purpose conducted from April 19 to September 20, 2021;a period of 6 months. The study included all patients presenting with senile or non-senile cataracts without a history of corneal trauma and who underwent phaco-alternative during the study period. Results: A total of 62 eyes underwent phaco-alternative. The average age was 63 ± 12 years with a male predominance of 59.7%. Phaco-alternative was performed with 74.2% linear incision and 25.8% smile incision. Perioperative incidents were mainly capsular ruptures with vitreous loss occurring in 8.1% of cases. The mean preoperative astigmatism was 1.29 ± 1.5 D with an axis of 180˚ ± 20˚, indicating with-the-rule astigmatism. The mean postoperative astigmatism was 2.2 ± 1.5 D with an axis of 90˚ ± 20˚, indicating against-the-rule astigmatism. The mean induced astigmatism at Day 30 was 1.4 ± 1.2 D for smile incision and 1.8 ± 1.2 D for linear incision. Conclusion: Phaco-alternative yields good results with few complications but remains astigmatogenic. The smile incision appears to be less astigmatogenic. 展开更多
关键词 Cataract Phaco-alternative Smile Incision ASTIGMATISM
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Magnesium alloys as extremely promising alternatives for temporary orthopedic implants-A review 被引量:2
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作者 C.A.Niranjan T.Raghavendra +4 位作者 Madhuri P.Rao C.Siddaraju M.Gupta Vikram Kumar S.Jain R.Aishwarya 《Journal of Magnesium and Alloys》 SCIE EI CAS CSCD 2023年第8期2688-2718,共31页
Mg alloys are emerging as potential and very promising alternatives for replacing permanent metallic implant materials such as steels and titanium in applications where the implants need to be removed following healin... Mg alloys are emerging as potential and very promising alternatives for replacing permanent metallic implant materials such as steels and titanium in applications where the implants need to be removed following healing through revision surgery.Use of Mg alloys for implant application is seen as a game changer and Mg alloys are almost perfect materials for the future in both engineering and biomedical applications.Present review therefore focuses on highlighting significance of Mg alloys in biomedical field and risks of using permanent metallic implants particularly when the implants are no longer required after the injury is healed.In this review,importance of orthopedic implants in present scenario,serious concern related to accidents that are causing permanent disabilities,demand in orthopedic implant market worldwide,potential applications of Mg based materials and their compatibility in biological environment is presented and discussed.In addition,degradation rate,major reactions associated with Mg based materials and effect of alloying elements on implant performance are also discussed based on in-vivo results.Recent advances in development of Mg alloys through various techniques and their performance in in-vitro conditions are also outlined.Possible ways to eliminate the limitations of Mg alloys include alloying,melt purification,surface alterations,surface modifications,chemical treatment,secondary processing etc.are discussed.Challenges and opportunities for Mg alloys to become ideal implant material is also addressed. 展开更多
关键词 Accidents FRACTURES Burden of fracture Magnesium Ultimate alternative Degradation rate ALLOYING Melt purification Coating
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Attitudes and understanding of complementary and alternative medicine in cancer care:An exploratory study of patients’perspectives in Karachi,Pakistan 被引量:1
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作者 Shahlla Imam Muneeba Aijaz +7 位作者 Wajiha Iffat Shazia Qasim Jamshed Nahlah Elkudssiah Ismail Ganesh Sritheran Paneerselvam Khang Wen Goh Long Chiau Ming Halima Sadia Iqbal Azhar 《Asian Pacific Journal of Tropical Medicine》 SCIE CAS 2023年第9期400-408,共9页
Objective:To evaluate the prevalence and types of complementary and alternative medicine(CAM)modalities among patients with cancer in Karachi,Pakistan.Methods:This descriptive cross-sectional study was conducted from ... Objective:To evaluate the prevalence and types of complementary and alternative medicine(CAM)modalities among patients with cancer in Karachi,Pakistan.Methods:This descriptive cross-sectional study was conducted from March 2021 to December 2021.Five hundred patients with cancer were invited to participate in the study.Electronic databases,namely,Google scholar,Publons,EMBASE,PubMed,Chinese National Knowledge Infrastructure Database,and ResearchGate was used for questionnaire designed.The self-administered survey included questions on demographic characteristics,education level,socio-economic conditions and information about CAM therapies,prevalence,effectiveness,and common CAM modalities.Statistical analysis was conducted using SPSS software version 22.Results:Out of the 500 invited patients,433(86.6%)successfully completed and returned the questionnaires.In contrast to patients who were with younger,highly educated,professionally active,higher income,and had advanced cancer,time since diagnosis,type of treatment,cancer types and family history are significantly associated with CAM use.The results showed that 59.8%of the participants were acquainted with complementary and/or alternative medicine and considered safe owing to its natural ingredients.The prevalence of CAM usage among cancer patients was 40.9%and the most widely used CAM modality was herbal medicine(27.7%)and dietary supplements(28.8%).Patients used CAM as a complementary therapy to improve the morphological parameter(28.2%),strengthen the immune system(6.8%),and to decrease the side effects of conventional treatment(18.1%).Most of the respondents get the information regarding CAM therapy from the electronic media(43.2%)and the family members(48%)rather than healthcare personnel.Conclusions:Participants used CAM modalities along with the conventional health care practices.Further multicentre studies should be conducted to provide information regarding the usage of CAM therapies and their eventual benefits in patients with cancer. 展开更多
关键词 alternative medicine Cancer patients Complementary medicine Cross-sectional study
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Essential Oils as an Alternative to Antibiotics to Reduce the Incidence and Severity of Necrotic Enteritis in Broiler Chickens: A Short Review
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作者 Makenly E. Coles Brittany D. Graham +8 位作者 Juan D. Latorre Victor M. Petrone-Garcia Xochitl Hernandez-Velasco Inkar Castellanos-Huerta Xiaolun Sun Billy M. Hargis Saeed El-Ashram Awad A. Shehata Guillermo Tellez-Isaias 《Food and Nutrition Sciences》 CAS 2023年第3期233-257,共25页
Due to the removal of antibiotic growth promoters (AGPs) and consumer pressure for antibiotic-free (ABF) or no antibiotics ever (NAE) poultry production, there is a need for sustainable alternatives to prevent disease... Due to the removal of antibiotic growth promoters (AGPs) and consumer pressure for antibiotic-free (ABF) or no antibiotics ever (NAE) poultry production, there is a need for sustainable alternatives to prevent disease in commercial poultry operations. Without AGPs, there has been a rise in diseases that were traditionally controlled by subtherapeutic levels of antibiotics in the diet. This has impacted the health of commercial poultry and has been a significant cost to poultry producers. To mitigate this, the industry has started to investigate alternatives to antibiotics to treat these forthcoming health issues, such as necrotic enteritis (NE). NE is an enteric disease caused by an over proliferation of toxigenic Clostridium perfringens (CP) in the gastrointestinal tract. Although CP is a commensal in the avian intestinal tract, dysbiosis caused by inflammation and impaired intestinal integrity facilitates uncontrolled replication of CP. Infectious agents, such as Eimeria maxima, appear to be a predominant predisposing factor that promotes NE. However, non-infectious stressors, including dietary changes, have also been associated with NE to some degree. As a result of increased pressure to restrict the use of antibiotics, there is a need for research evaluating the efficacy of alternatives, such as plant-derived essential oils, as potential tools to mitigate NE in commercial poultry flocks. The aim of this study is to review the effects of essential oils as an alternative to antibiotics to reduce the incidence and severity of necrotic enteritis in broiler chickens. 展开更多
关键词 Necrotic Enteritis Essential Oils CHICKENS Clostridium perfringens alternatives to Antibiotics
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The Alternative Therapeutic in Pediatric Cancer: What We Know?
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作者 Kaoutar Danaoui Meriem El Baz Jamila El Houdzi 《Open Journal of Pediatrics》 CAS 2023年第3期368-378,共11页
Scientific research has brought about enormous national advancements in cancer management. Currently, Morocco provides several therapeutic tools for cancer, among them chemotherapy, surgery and radiotherapy. In Morocc... Scientific research has brought about enormous national advancements in cancer management. Currently, Morocco provides several therapeutic tools for cancer, among them chemotherapy, surgery and radiotherapy. In Morocco, there is not enough published data on the use of alternative medicine in pediatric oncology. Owing to the increased interest and lack of data on this practice, we conducted this study. It aims to evaluate the uptake, the types of therapies used, the factors influencing, the reasons for this choice and the cost of AM used by patients. An investigation through a questionnaire was carried out on thirty-four children following for cancer within the pediatric hematology and oncology department (PHO) of Marrakech. The survey was conducted over a period of one month and a half between July 25 and September 5, 2022. Data were collected through a questionnaire. From the medical files, we collected data regarding type of cancer, date of admission to PHO department and the treatment received. We asked about the type of AM used: herbs, honey, spiritual AM, zamzam water (water from a “sacred” source in Mecca). Using alternative therapies is a common practice in pediatric oncology with various reasons, among them, the declining socioeconomic level, the diversity, the cultural background, the psychological and the functional status of patients and sometimes the dissatisfaction with conventional medicine. 展开更多
关键词 alternative Therapeutic Cancer Chronic Disease Treatment Morocco Herbs Medicines PEDIATRIC Chemotherapy
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Alternative polyadenylation events in epithelial cells sense endometritis progression in dairy cows
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作者 Meagan J.STOTTS Yangzi ZHANG +5 位作者 Shuwen ZHANG Jennifer J.MICHAL Juan VELEZ Bothe HANS Martin MAQUIVAR Zhihua JIANG 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2023年第6期1820-1832,共13页
Endometritis(inflammation of the endometrial lining) is one of the most devastating reproductive diseases in dairy cattle, resulting in substantial production loss and causing more than $650 million in lost revenue an... Endometritis(inflammation of the endometrial lining) is one of the most devastating reproductive diseases in dairy cattle, resulting in substantial production loss and causing more than $650 million in lost revenue annually in the USA.We hypothesize that alternative polyadenylation(APA) sites serve as decisive sensors for endometrium health and disease in dairy cows. Endometrial cells collected from 18 cows with purulent vaginal discharge scored 0 to 2 were used for APA profiling with our whole transcriptome termini site sequencing(WTTS-seq) method. Overall, pathogens trigger hosts to use more differentially expressed APA(DE-APA), more intronic DE-APA, more DE-APA sites per gene and more DE-genes associated with inflammation. Host CD59 molecule(CD59), Fc fragment of IgG receptor IIa(FCGR2A), lymphocyte antigen 75(LY75) and plasminogen(PLG) may serve as initial contacts or combats with pathogens on cell surface, followed by activation of nuclear receptor subfamily 1 group H member 4(NR1H4) to regulate AXL receptor tyrosine kinase(AXL), FGR proto-oncogene, Src family tyrosine kinase(FGR), HCK protooncogene, Src family tyrosine kinase(HCK) and integrin subunit beta 2(ITGB2) for anti-inflammation. This study is the first to show significance of cilium pathways in endometrium health and animal reproduction. MIR21 and MIR30A would be perfect antagonistic biomarkers for diagnosis of either inflammation or anti-inflammation. These novel findings will set precedent for future genomic studies to aid the dairy industry develop new strategies to reduce endometritis incidence and improve fertility. 展开更多
关键词 organic dairy ENDOMETRITIS alternative polyadenylation infection progression antagonistic biomarkers
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Comprehensive analysis of the full-length transcripts and alternative splicing involved in clubroot resistance in Chinese cabbage
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作者 SU He-nan YUAN Yu-xiang +8 位作者 YANG Shuang-juan WEI Xiao-chun ZHAO Yan-yan WANG Zhi-yong QIN Liu-yue YANG Zhi-yuan NIU Liu-jing LI Lin ZHANG Xiao-wei 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2023年第11期3284-3295,共12页
Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soilborne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassic... Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soilborne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassica crops. Previous studies on the gene transcripts related to Chinese cabbage resistance to clubroot mainly employed RNA-seq technology,although it cannot provide accurate transcript assembly and structural information. In this study, PacBio RS II SMRT sequencing was used to generate full-length transcriptomes of mixed roots at 0, 2, 5, 8, 13, and 22 days after P. brassicae infection in the clubroot-resistant line DH40R. Overall, 39 376 high-quality isoforms and 26 270 open reading frames(ORFs) were identified from the SMRT sequencing data. Additionally, 426 annotated long noncoding RNAs(lncRNAs),56 transcription factor(TF) families, 1 883 genes with poly(A) sites and 1 691 alternative splicing(AS) events were identified. Furthermore, 1 201 of the genes had at least one AS event in DH40R. A comparison with RNA-seq data revealed six differentially expressed AS genes(one for disease resistance and five for defensive response) that are potentially involved in P. brassicae resistance. The results of this study provide valuable resources for basic research on clubroot resistance in Chinese cabbage. 展开更多
关键词 Chinese cabbage CLUBROOT full-length transcriptome SMRT sequencing alternative splicing
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Alternative polyadenylation-related genetic variants contribute to bladder cancer risk
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作者 Ting Liu Jingjing Gu +8 位作者 Chuning Li Mengfan Guo Lin Yuan Qiang Lv Chao Qin Mulong Du Haiyan Chu Hanting Liu Zhengdong Zhang 《The Journal of Biomedical Research》 CAS CSCD 2023年第6期405-417,共13页
Aberrant alternative polyadenylation(APA)events play an important role in cancers,but little is known about whether APA-related genetic variants contribute to the susceptibility to bladder cancer.Previous genome-wide ... Aberrant alternative polyadenylation(APA)events play an important role in cancers,but little is known about whether APA-related genetic variants contribute to the susceptibility to bladder cancer.Previous genome-wide association study performed APA quantitative trait loci(apaQTL)analyses in bladder cancer,and identified 17955 single nucleotide polymorphisms(SNPs).We found that gene symbols of APA affected by apaQTL-associated SNPs were closely correlated with cancer signaling pathways,high mutational burden,and immune infiltration.Association analysis showed that apaQTL-associated SNPs rs34402449 C>A,rs2683524 C>T,and rs11540872 C>G were significantly associated with susceptibility to bladder cancer(rs34402449:OR=1.355,95%confidence interval[CI]:1.159-1.583,P=1.33×10^(−4);rs2683524:OR=1.378,95%CI:1.164-1.632,P=2.03×10^(−4);rs11540872:OR=1.472,95%CI:1.193-1.815,P=3.06×10^(−4)).Cumulative effect analysis showed that the number of risk genotypes and smoking status were significantly associated with an increased risk of bladder cancer(P_(trend)=2.87×10^(−12)).We found that PRR13,being demonstrated the most significant effect on cell proliferation in bladder cancer cell lines,was more highly expressed in bladder cancer tissues than in adjacent normal tissues.Moreover,the rs2683524 T allele was correlated with shorter 3′untranslated regions of PRR13 and increased PRR13 expression levels.Collectively,our findings have provided informative apaQTL resources and insights into the regulatory mechanisms linking apaQTL-associated variants to bladder cancer risk. 展开更多
关键词 alternative polyadenylation genetic variant bladder cancer PRR13 apaQTL
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Do alternative stable states exist in large shallow Taihu Lake,China?
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作者 Yan LI Yu MA +7 位作者 Haijun WANG Hongzhu WANG Yongde CUI Shijun BIAN Miao ZHANG Mengmei LIU Yexin YU Marc SCHALLENBERG 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2023年第3期959-971,共13页
Regime shifts from submersed macrophyte dominance to phytoplankton dominance have been widely reported in small-to medium-sized shallow lakes.However,alternative stable states in large shallow lakes(surface area>50... Regime shifts from submersed macrophyte dominance to phytoplankton dominance have been widely reported in small-to medium-sized shallow lakes.However,alternative stable states in large shallow lakes(surface area>500 km^(2))remain unconfirmed.To understand the alternative stable states and the main influencing factors of submersed macrophytes in large lakes,the ecosystem states from monitoring data from 1959 to 2019 in large shallow Taihu Lake(2338 km^(2)in average depth of 2.12 m)in China were examined.Changes in submersed macrophyte coverage(C_(Mac))and phytoplankton chlorophyll a(Chl a)in the time series and their relationships with environmental factors were analyzed.During the field investigation from August 2018 to May 2019,nutrients and Chl a showed obvious heterogeneity across the lake,being generally higher in the western and northern areas and lower in the southeast area,while C_(Mac)was only observed in the eastern areas,e.g.,East Taihu Lake,Xukou Bay,and Gonghu Bay.During the long-term monitoring from 1959 to 2019 in the Central Region,Meiliang Bay,and East Taihu Lake,Chl a increased significantly in the time series.C_(Mac)varied slightly among different subareas,always at low levels(<10%)in the Central Region and Meiliang Bay but at relatively high levels in East Taihu Lake(10%–90%).Frequency distributions of response variables had no multimodality except for C_(Mac)in East Taihu Lake,with two peaks between 15%and 20%and between 55%and 60%.A dual relationship was found between Chl a and total phosphorus(TP)in the areas with and without macrophytes,while C_(Mac)showed no relationship with TP,and submersed macrophytes did not flourish in the Central Region and Meiliang Bay even when TP was at very low levels(≈10 mg/m3).Taihu Lake had similar algal turbidity(TurbAlg)as small-to mediumsized lakes but generally presented with higher values of nonalgal turbidity(TurbNonAlg),as did their contribution to total turbidity as a percentage.This study suggested that large shallow Taihu Lake may have no alternative stable states,but more evidence is needed for East Taihu Lake,which was dominated by macrophytes,as it remains unknown whether hysteresis occurs between the processes of eutrophication and oligotrophication.Unfavorable conditions caused by wind might be the main reason due to the absence of submersed macrophytes in Taihu Lake.These results demonstrate that stricter nutrient control is needed to maintain a healthy state or to recover from a decayed state for large lakes. 展开更多
关键词 alternative stable state submersed macrophyte PHYTOPLANKTON Taihu Lake large shallow lake
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Encapsulated peracetic acid as a valid broad‑spectrum antimicrobial alternative,leading to beneficial microbiota compositional changes and enhanced performance in broiler chickens
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作者 Salvatore Galgano Leah Conway +2 位作者 Nikki Dalby Adrian Fellows Jos G.MHoudijk 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2023年第5期2128-2142,共15页
Background Antimicrobial alternatives are urgently needed,including for poultry production systems.In this study,we tested the potential broad-range antimicrobial alternative peracetic acid,delivered in feed via the h... Background Antimicrobial alternatives are urgently needed,including for poultry production systems.In this study,we tested the potential broad-range antimicrobial alternative peracetic acid,delivered in feed via the hydrolysis of encapsulated precursors through a 28-day study using 375 Ross 308 broiler chickens.We tested two peracetic acid concentrations,30 and 80 mg/kg on birds housed on re-used litter,and we evaluated the impact of both levels on gut microbial communities,bacterial concentration,antimicrobial resistance genes relative abundance and growth performance when compared to control birds housed on either clean or re-used litter.Results Body weight gain and feed conversion ratio improved in peracetic acid fed birds.At d 28,birds given 30 mg/kg of peracetic acid had a decreased Firmicutes and an increased Proteobacteria abundance in the jejunum,accompanied by an increase in Bacillus,Flavonifractor and Rombustia in the caeca,and a decreased abundance of tetracycline resistance genes.Chicken given 80 mg/kg of peracetic acid had greater caecal abundance of macrolides lincosamides and streptogramins resistance genes.Growth performance on clean litter was reduced compared to reused litter,which concurred with increased caecal abundance of Blautia,decreased caecal abundance of Escherichia/Shigella,Anaerostipes and Jeotgalicoccus,and greater gene abundance of vancomycin,tetracycline,and macrolides resistance genes.Conclusions Peracetic acid could be used as a safe broad-spectrum antimicrobial alternative in broilers.Encapsulated precursors were able to reduce the bacterial concentration in the jejunum whilst promoting the proliferation of probiotic genera in the caeca,especially at the low peracetic acid concentrations tested,and improve growth performance.Moreover,our findings offer further insights on potential benefits of rearing birds on re-used litter,suggesting that the latter could be associated with better performance and reduced antimicrobial resistance risk compared to clean litter rearing. 展开更多
关键词 Antimicrobial alternative Antimicrobial resistance Broiler chicken MICROBIOTA Peracetic acid Performance 16S rRNA gene
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Non-Cooperative Behavior Management in Large-Scale Group Decision-Making Considering the Altruistic Behaviors of Experts and Its Application in Emergency Alternative Selection
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作者 Mingjun Jiang 《Computer Modeling in Engineering & Sciences》 SCIE EI 2023年第7期487-515,共29页
Emergency decision-making problems usually involve many experts with different professional backgrounds and concerns,leading to non-cooperative behaviors during the consensus-reaching process.Many studies on noncooper... Emergency decision-making problems usually involve many experts with different professional backgrounds and concerns,leading to non-cooperative behaviors during the consensus-reaching process.Many studies on noncooperative behavior management assumed that the maximumdegree of cooperation of experts is to totally accept the revisions suggested by the moderator,which restricted individuals with altruistic behaviors to make more contributions in the agreement-reaching process.In addition,when grouping a large group into subgroups by clustering methods,existing studies were based on the similarity of evaluation values or trust relationships among experts separately but did not consider them simultaneously.In this study,we introduce a clustering method considering the similarity of evaluation values and the trust relations of experts and then develop a consensusmodel taking into account the altruistic behaviors of experts.First,we cluster experts into subgroups by a constrained Kmeans clustering algorithm according to the opinion similarity and trust relationship of experts.Then,we calculate the weights of experts and clusters based on the centrality degrees of experts.Next,to enhance the quality of consensus reaching,we identify three kinds of non-cooperative behaviors and propose corresponding feedback mechanisms relying on the altruistic behaviors of experts.A numerical example is given to show the effectiveness and practicality of the proposed method in emergency decision-making.The study finds that integrating altruistic behavior analysis in group decision-making can safeguard the interests of experts and ensure the integrity of decision-making information. 展开更多
关键词 Large-scale group decision making altruistic behavior non-cooperative behaviors consensus reaching emergency alternative selection
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A review of complementary and alternative medicine used in cancer care:challenges and prospects
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作者 Samson Seyi Enitan Godwin Avwioro +4 位作者 Esther Ngozi Adejumo Oluwakemi Anike Ladipo Chinenye Alaezi Okorochi Gideon Taiwo Oluwaloye Damilola Christianah Ademola-Kemiki 《TMR Integrative Medicine》 2023年第21期1-7,共7页
Cancer is a leading cause of death globally,and most patients with cancers frequently seek for complementary and alternative medicine(CAM)to ameliorate their condition.Some of the available CAM care include:acupunctur... Cancer is a leading cause of death globally,and most patients with cancers frequently seek for complementary and alternative medicine(CAM)to ameliorate their condition.Some of the available CAM care include:acupuncture,aromatherapy,Ayurvedic medicinal drug,cannabis,chelation remedy,homeopathy,hypnotherapy,massage therapy,naturopathic medication,and conventional Chinese remedy amongst others.Despite the growing use of CAM,the evidence-base for its efficacy and safety is limited.Major challenges confronting the efficient deployment of CAM is lack of standardization and regulation;as well as the demand for more extensive studies to validate their safety and efficacy.Integrative oncology which is the combination of CAM and conventional cancer care is likewise complicated through the potential adverse interactions between CAM options and most cancers drugs.The article serves as a guide for healthcare providers and patients to determine how CAM can be safely integrated into the cancer care paradigm.Taking into account safety concerns,however,more studies need to be conducted to properly evaluate its efficacy.Ultimately,CAM can help cancer patients in achieving greater health and well-being. 展开更多
关键词 alternative medicine CANCER CARE CHALLENGES PROSPECTS
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Pitfalls and promises of bile duct alternatives:There is plenty of room in the regenerative surgery
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作者 Ilya D Klabukov Denis S Baranovskii +1 位作者 Peter V Shegay Andrey D Kaprin 《World Journal of Gastroenterology》 SCIE CAS 2023年第30期4701-4705,共5页
Current abdominal surgery has several approaches for biliary reconstruction.However,the creation of functional and clinically applicable bile duct substitutes still represents an unmet need.In the paper by Miyazawa an... Current abdominal surgery has several approaches for biliary reconstruction.However,the creation of functional and clinically applicable bile duct substitutes still represents an unmet need.In the paper by Miyazawa and colleagues,approaches to the creation of bile duct alternatives were summarized,and the reasons for the lack of development in this area were explained.The history of bile duct surgery since the nineteenth century was also traced,leading to the conclusion that the use of bioabsorbable materials holds promise for the creation of bile duct substitutes in the future.We suggest three ideas that may stimulate progress in the field of bile duct substitute creation.First,a systematic analysis of the causative factors leading to failure or success in the creation of bile duct substitutes may help to develop more effective approaches.Second,the regeneration of a bile duct is delicately balanced between epithelialization and subsequent submucosal maturation within limited time frames,which may be more apparent when using quantitative models to estimate outcomes.Third,the utilization of the organism’s endogenous regeneration abilities may enhance the creation of bile duct substitutes.We are convinced that an interdisciplinary approach,including quantitative methods,machine learning,and deep retrospective analysis of the causes that led to success and failure in studies on the creation of bile duct substitutes,holds great value.Additionally,more attention should be directed towards the balance of epithelialization and submucosal maturation rates,as well as induced angiogenesis.These ideas deserve further investigation to pave the way for bile duct restoration with physiologically relevant outcomes. 展开更多
关键词 Bile duct alternative Bile duct substitute Regenerative medicine Regene rative surgery Theoretical surgery Quantitative human physiology
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