From January 2001 to January 2002, 50 patients of candidal vaginitis were treated by Kushen powder (KSP,苦参散) combined with Canesten as the treatment group, and controlled by a control group including another 50 pat...From January 2001 to January 2002, 50 patients of candidal vaginitis were treated by Kushen powder (KSP,苦参散) combined with Canesten as the treatment group, and controlled by a control group including another 50 patients treated with Canesten alone. The therapeutic results were satisfactory and reported as follows.展开更多
Mostly candida resides as an opportunistic organism on epithelial surfaces of human being. However, under auspicious conditions can cause infections including serious life threatening invasive candidiasis with subsequ...Mostly candida resides as an opportunistic organism on epithelial surfaces of human being. However, under auspicious conditions can cause infections including serious life threatening invasive candidiasis with subsequent mortality particularly in immune deficit and hospitalized patients having co-morbids. Limited data are published on the prevalence of candidiasis, based on the researches conducted at few tertiary care settings which are not representing the overall disease burden in our country, Pakistan. Therefore, this study was conducted to evaluate the frequency and sensitivity patterns of candidiasis in our community. Methods: Out of total 1020 specimens, 130 clinical samples were identified as candidal positive, obtained from March to May 2018. These samples were isolated from vagina, oropharynx, urine, tracheal aspirates, pus, blood, tips of the intubations, wounds and fluids of the body cavities. Identification of candida, its species and antifungal sensitivity screening was done by Kirby Bauer’s disk diffusion method according to CLSI guide lines’ (M - 44 A2 series, 2009). Results: A significant majority, 80 (61.5%) of candidal strains were isolated from females with female to male ratio 8:5 and most of these isolates were obtained from high vaginal swabs (43.75%). Four candidal species (Candida albicans 80%, Candida tropicalis 10%, Candida glabrata 9.2% and Candida ciferrii 0.8%) were isolated from all positive specimens. Maximum number of the positive samples 52 (40%) were obtained from ICU patients. Sensitivity test of candidal positive samples revealed that commonly used azole antifungal drugs, fluconazole and voriconazole were highly resistant, with respective 57.7% and 70.8% resistance. Conclusion: Candidiasis is highly prevalent in our clinical set up and more frequently infecting females in comparison to males as most of the positive isolates were retrieved from HVS (high vaginal swabs). Still, C. albicans was found to be the most prevalent specie isolated among all candida samples. Our study also demonstrated that the resistance of most commonly prescribed antifungals, azoles have shown a rapid rise. Therefore, it is recommended that before prescription of antifungal drugs the clinicians should routinely recommend culture and sensitivity testing of samples taken from candida infected individuals.展开更多
Background Candidal balanoposthJtis （CB） is a common male genital infection. Autoimmune mechanisms may play an important role in the pathOgenesis of CB. Interleukin-2 （IL-2） is an important molecule in cell-mediat...Background Candidal balanoposthJtis （CB） is a common male genital infection. Autoimmune mechanisms may play an important role in the pathOgenesis of CB. Interleukin-2 （IL-2） is an important molecule in cell-mediated immunity. Methods One hundred and one patients were diagnosed with CB using mycology culture in the dermatology and urology clinics in our hospital. Ninety-four healthy males were randomly selected as controls. We studied serum levels of IL-2 of patients with CB using ELISA and analyzed the correlations between serum IL-2 and clinical data. Results Serum IL-2 concentrations in CB patients were significantly lower than that in the control group （（7.80±4.78） vs. （15.44±7.90） rig/L; t=2.27, P 〈0.05）. The incidence of CB in the low-level group was significantly higher than that in the high-level group （70% （71/101） vs. 36% （30/84）, P 〈0.05）. Low levels of serum IL-2, comorbidity with other sexually transmitted diseases （STDs）, and sexual partners with vulvovaginal candidiasis （VVC） increased the risk of CB. Conclusion The pathogenesis of CB is a complex procedure that includes internal autoimmune factors.展开更多
Background Candidal esophagitis is the primary infection among all digestive tract opportunistic ones in acquired immunodeficiency syndrome （AIDS） cases. X-ray manifestation reports of it are still rare. This study ...Background Candidal esophagitis is the primary infection among all digestive tract opportunistic ones in acquired immunodeficiency syndrome （AIDS） cases. X-ray manifestation reports of it are still rare. This study aimed to conduct a retrospective analysis on the X-ray data of 6 AIDS cases complicated with candidal esophagitis, and to study the X-ray characteristics of it combined with the findings from gastroscopy.展开更多
Lung cancer is the most common but fatal malignant tumor worldwide.Patients with lung cancer experienced a relatively low 5-year overall survival rate,and issues such as metastasis and drug resistance remain prominent...Lung cancer is the most common but fatal malignant tumor worldwide.Patients with lung cancer experienced a relatively low 5-year overall survival rate,and issues such as metastasis and drug resistance remain prominent challenges in its clinical management.Neddylation,a novel type of post-translational modification,was overactivated in lung cancer and was closely associated with its occurrence,development,metastasis,and drug resistance.This review systematically summarizes the biological process of neddylation and deeply explores the latest research progress on how neddylation affects lung cancer cell proliferation,metastasis,and drug resistance mechanisms,with a focus on its regulation of key molecules such as Cullin-RING E3 ligases and the SCCRO family.Meanwhile,it concludes the current advances in potential therapeutic agents targeting neddylation-related targets,including small-molecule compounds(such as Pevonedistat)and natural extracts(such as arctigenin).Finally,the review prospectively evaluates the application potential and questions requiring further exploration of neddylation in lung cancer treatment.In conclusion,we aim to systematically summarize the biological process of neddylation,critically explore its roles in lung cancer proliferation,metastasis,and drug resistance,and evaluate the therapeutic potential of neddylation-targeting agents.展开更多
Chinese abbreviations improve communicative efficiency by extracting key components from longer expressions.They are widely used in both daily communication and professional domains.However,existing abbreviation gener...Chinese abbreviations improve communicative efficiency by extracting key components from longer expressions.They are widely used in both daily communication and professional domains.However,existing abbreviation generation methods still face two major challenges.First,sequence-labeling-based approaches often neglect contextual meaning by making binary decisions at the character level,leading to abbreviations that fail to capture semantic completeness.Second,generation-basedmethods rely heavily on a single decoding process,which frequently produces correct abbreviations but ranks them lower due to inadequate semantic evaluation.To address these limitations,we propose a novel two-stage frameworkwithGeneration–Iterative Optimization forAbbreviation(GIOA).In the first stage,we design aChain-of-Thought prompting strategy and incorporate definitional and situational contexts to generate multiple abbreviation candidates.In the second stage,we introduce a Semantic Preservation Dynamic Adjustment mechanism that alternates between character-level importance estimation and semantic restoration to optimize candidate ranking.Experiments on two public benchmark datasets show that our method outperforms existing state-of-the-art approaches,achieving Hit@1 improvements of 15.15%and 13.01%,respectively,while maintaining consistent results in Hit@3.展开更多
Colorectal cancer(CRC)is a prevalent malignancy worldwide,posing a significant public health concern.Mounting evidence has confirmed that timely early screening facilitates the detection of incipient CRC,thereby enhan...Colorectal cancer(CRC)is a prevalent malignancy worldwide,posing a significant public health concern.Mounting evidence has confirmed that timely early screening facilitates the detection of incipient CRC,thereby enhancing patient prognosis.Obviously,non-participation of asymptomatic individuals in screening programs hampers early diagnosis and may adversely affect long-term outcomes for CRC patients.In this letter,we provide a comprehensive overview of the current status of early screening practices,while also thoroughly examine the dilemmas and potential solutions associated with early screening for CRC.In response to these issues,we proffer a set of recommendations directed at governmental authorities and the general public,which focus on augmenting financial investment,establishing standardized screening protocols,advancing technological capabilities,and bolstering public awareness campaigns.The importance of collaborative efforts from various stakeholders cannot be overstated in the quest to enhance early detection rates and alleviate the societal burden of CRC.展开更多
Plant height(PH),primary lateral branch length(PBL),and branch number(BN)are architectural components impacting peanut pod yield,biomass production,and adaptivity to mechanical harvesting.In this study,a recombinant i...Plant height(PH),primary lateral branch length(PBL),and branch number(BN)are architectural components impacting peanut pod yield,biomass production,and adaptivity to mechanical harvesting.In this study,a recombinant inbred population consisting of 181 individual lines was used to determine genetic controls of PH,PBL,and BN across three environments.Phenotypic data collected from the population demonstrated continuous distributions and transgressive segregation patterns.Broad-sense heritability of PH,PBL,and BN was found to be 0.87,0.88,and 0.92,respectively.Unconditional individual environmental analysis revealed 35 additive QTLs with phenotypic variation explained(PVE)ranging from 4.57 to 21.68%.A two-round meta-analysis resulted in 24consensus and 19 unique QTLs.Five unique QTLs exhibited pleiotropic effects and their genetic bases(pleiotropy or tight linkage)were evaluated.A joint analysis was performed to estimate the QTL by environment interaction(QEI)effects on PH,PBL,and BN,collectively explaining phenotypic variations of 10.80,11.02,and 7.89%,respectively.We identified 3 major and stable QTL regions(uq9-3,uq10-2,and uq16-1)on chromosomes 9,10,and 16,spanning1.43-1.53 Mb genomic regions.Candidate genes involved in phytohormones biosynthesis,signaling,and cell wall development were proposed to regulate these morphological traits.These results provide valuable information for further genetic studies and the development of molecular markers applicable to peanut architecture improvement.展开更多
As artificial intelligence(AI)technology has continued to develop,its efficient data processing and pattern recognition capabilities have significantly improved the precision and speed of decision-making processes,and...As artificial intelligence(AI)technology has continued to develop,its efficient data processing and pattern recognition capabilities have significantly improved the precision and speed of decision-making processes,and it has been widely applied across various fields.In the field of astronomy,AI techniques have demonstrated unique advantages,particularly in the identification of pulsars and their candidates.AI is able to address the challenges of pulsar celestial body identification and classification because of its accuracy and efficiency.This paper systematically surveys commonly used AI models for pulsar candidate identification,analyzing and discussing the typical applications of machine learning,artificial neural networks,convolutional neural networks,and generative adversarial networks in candidate identification.Furthermore,it explores how th.e introduction of AI techniques not only enhances the efficiency and accuracy of pulsar identification but also provides new perspectives and tools for pulsar survey data processing,thus playing a significant role in advancing pulsar research and the field of astronomy.展开更多
Productive tiller number(PTN)is a pivotal trait that significantly influences wheat grain yield.To date,there have been limited reports on the cloning of genes that regulate PTN in wheat.The quantitative trait locus(Q...Productive tiller number(PTN)is a pivotal trait that significantly influences wheat grain yield.To date,there have been limited reports on the cloning of genes that regulate PTN in wheat.The quantitative trait locus(QTL)QPtn.sau-4B,associated with PTN,was previously mapped between the markers KASP-1 and KASP-3 on the chromosome 4B.Here,utilizing 12 newly developed markers and phenotypic data of PTN from recombinants identified within this interval,QPtn.sau-4B was further fine-mapped to a 2.58 Mb interval on wheat chromosome arm 4BS.Within this interval,we identified 14 genes with high-confidence and 32 genes with low-confidence.A 0.17 Mb deletion fragment contained TraesCS4B03G0092600 and TraesCS4B03G0093100,which were assigned as candidate genes for QPtn.sau-4B.Additionally,QPtn.sau-4B had potential to enhance both PTN and grain yield in wheat.Cloning this locus would support the development of wheat cultivars with increased grain yield.展开更多
Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in...Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in cucumber have been identified.Here,the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments,with naturally occurring high temperatures over two years.Seventeen of the 88 accessions were identified as highly heat-tolerant.Using a genome-wide association study,five loci(gHII3.1,gHII3.2,gHII3.3,gHII4.1 and gHII6.1)on three chromosomes associated with heat tolerance were detected.Pairwise linkage disequilibrium correlation,sequence polymorphisms,and qRT-PCR analyses at these loci,identified five candidate genes predicted to be casual for heat stress response in cucumber.CsaV3_3G04883,CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs,and were significantly up-regulated by heat stress in the heat-tolerant genotypes.CsaV3_3G031890 was also induced by heat stress,but in the heatsensitive genotypes,and sequence polymorphism was only found in the promoter region.Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms.Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge.It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.展开更多
Degenerative cervical myelopathy is a common cause of spinal cord injury,with longer symptom duration and higher myelopathy severity indicating a worse prognosis.While numerous studies have investigated serological bi...Degenerative cervical myelopathy is a common cause of spinal cord injury,with longer symptom duration and higher myelopathy severity indicating a worse prognosis.While numerous studies have investigated serological biomarkers for acute spinal cord injury,few studies have explored such biomarkers for diagnosing degenerative cervical myelopathy.This study involved 30 patients with degenerative cervical myelopathy(51.3±7.3 years old,12 women and 18 men),seven healthy controls(25.7±1.7 years old,one woman and six men),and nine patients with cervical spondylotic radiculopathy(51.9±8.6 years old,three women and six men).Analysis of blood samples from the three groups showed clear differences in transcriptomic characteristics.Enrichment analysis identified 128 differentially expressed genes that were enriched in patients with neurological disabilities.Using least absolute shrinkage and selection operator analysis,we constructed a five-gene model(TBCD,TPM2,PNKD,EIF4G2,and AP5Z1)to diagnose degenerative cervical myelopathy with an accuracy of 93.5%.One-gene models(TCAP and SDHA)identified mild and severe degenerative cervical myelopathy with accuracies of 83.3%and 76.7%,respectively.Signatures of two immune cell types(memory B cells and memory-activated CD4^(+)T cells)predicted levels of lesions in degenerative cervical myelopathy with 80%accuracy.Our results suggest that peripheral blood RNA biomarkers could be used to predict lesion severity in degenerative cervical myelopathy.展开更多
Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid b...Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity,especially as we are facing important climate and agriculture challenges.To this aim the genomic architecture of 480 goats belonging to five breeds(i.e.,Saanen[SAA],Camosciata delle Alpi[CAM],Murciano-Granadina[MUR],Maltese[MAL],Sarda[SAR])reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits.Inbreeding,runs of homozygosity(ROH)and runs of heterozygosity(ROHet)were identified.Finally,candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.Results In total,we detected 10,341 ROH in the SAA genome,11,063 ROH in the CAM genome,12,250 ROH in the MUR genome,8,939 ROH in the MAL genome,and 18,441 ROH in the SAR genome.Moreover,we identified 4,087 ROHet for SAA,3,360 for CAM,2,927 for MUR,3,701 for MAL,and 3,576 for SAR,with SAR having the highest heterozygosity coefficient.Interestingly,when computing the inbreeding coefficient using homozygous segment(FROH),SAA showed the lowest value while MAL the highest one,suggesting the need to improve selecting strategies to preserve genetic diversity within the population.Among the most significant candidate genes,we identified several ones linked to different physiological functions,such as milk production(e.g.,DGAT1,B4GALT1),immunity(GABARAP,GPS2)and adaptation to environment(e.g.,GJA3,GJB2 and GJB6).Conclusions This study highlighted the genetic diversity within and among five goat breeds.The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation,which might negatively impact the animal population.Conversely,high levels of ROHet might indicate regions of the genetic diversity,beneficial for breed health and resilience.Therefore,these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.展开更多
Maize root system plays a crucial role in the development of the aboveground plant and determines the yield through the uptake of water and nutrients in the field.However,the genetic architecture of the maize root sys...Maize root system plays a crucial role in the development of the aboveground plant and determines the yield through the uptake of water and nutrients in the field.However,the genetic architecture of the maize root system is largely unknown mainly due to its complexity and the interactions between genotype and environment.Using a high-throughput semi-automatic hydroponic platform with stable conditions,we comprehensively characterized the root system in a core population of 518 diverse inbred lines of maize.Population structure analysis revealed that the panel has stratification and a linkage disequilibrium decay distance of less than 50 kb.Based on genotyping with the high-density 600 K SNPs,we conducted a genome wide association analysis(GWAS)and identified nine SNPs and seven candidate genes significantly associated with 24 traits.One candidate gene,GRMZM2G400533,is located at the upstream 5 kb region from the leading SNP(AX-91771718)and was significantly associated with primary root length and preferentially expressed in the primary root and crown root.Expression of GRMZM2G400533 increased as the primary root developed but was negatively correlated with primary root elongation.An analysis of candidate gene GRMZM2G400533 identified three functional variants and eight allelic haplotypes.This study will broaden our understanding of maize root development and provide a theoretical basis for maize improvement through optimization of the root system.展开更多
Sesame is a multi-purpose high-value oilseed crop,which can beused in the food,feed,and cosmetics applica-tions.The low yield of sesame is due to the lack of high-yielding and locally adapted varieties,which have the ...Sesame is a multi-purpose high-value oilseed crop,which can beused in the food,feed,and cosmetics applica-tions.The low yield of sesame is due to the lack of high-yielding and locally adapted varieties,which have the susceptibility to capsule shattering and biotic and abiotic stresses.The breeding gains in sesame are low and stagnant compared to other oilseed crops such as canola,groundnut and sunflower.Breeding for enhanced yieldrelated,oil quantity and quality,biotic and abiotic stresses tolerant varieties is vital to the adaptation of the climate change.Several genes and quantitative trait loci(QTLs)related to yield-related,oil quantity and quality,biotic and abiotic stresses tolerant have been identified through modern plant breeding tools in sesame.The depth understanding of the genetic basis,molecular mechanisms and regulatory genes involved in yield-related,oil quantity and quality,biotic and abiotic stresses tolerant in sesame is important for the improvement of sesame breeding programs.This article reviews and documents these achievements will provide fundamental data and references for practical applications of sesam research.展开更多
Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and...Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield components.In this study,a natural population of 201 maize inbred lines was used for genome-wide association analysis,which identified nine SNPs on chromosomes 2,5,8,9,and 10 that were significantly associated with ear leaf type structure.Further verification through qRT-PCR confirmed the association of five candidate genes with these SNPs,with the Zm00001d008651 gene showing significant differential expression in the compact and flat maize inbred lines.Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)databasessuggested that this gene is involved in the glycolysis process.An analysis of the basic properties of this gene revealed that it encodes a stable,basic protein consisting of 593 amino acids with some hydrophobic properties.The promoter region contains stress and hormone(abscisic acid(ABA))related elements.The mutant of this gene increased the first ear leaf angle(eLA)and leaf angle of the first leaf below the first ear(bLA)by 4.96 and 0.97°,respectively,compared with normal inbred lines.Overall,this research sheds light on the regulatory mechanism of ear and leaf structures that influence density tolerance and provides solid foundational work for the development of new varieties.展开更多
Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.展开更多
Crude fat is an important nutritional component of maize kernels.However,the genetic mechanisms underlying crude fat content in maize kernels remain elusive.Previous studies used single-model genome-wide association s...Crude fat is an important nutritional component of maize kernels.However,the genetic mechanisms underlying crude fat content in maize kernels remain elusive.Previous studies used single-model genome-wide association studies(GWAS)with limited population sizes,which can result in false loci positives and hinder functional gene identification.Therefore,this study used a population consisting of 495 maize inbred lines,combined with 1.25 million single nucleotide polymorphisms(SNPs),and implemented GWAS using six models to identify quantitative trait nucleotides(QTNs)controlling crude fat content and to mine key genes.The results revealed a wide variation in crude fat content(0.62-16.03%)and broad-sense heritability(H^(2))(96.23%).In total,744 significant QTNs were detected,with 147 co-located across different models,environments,and methods.Based on the 147 colocated QTNs,candidate genes were searched at 50 kb up-and down-stream intervals of each QTN.We finally screened eight candidate genes(GRMZM2G169089,GRMZM2G117935,GRMZM2G002075,GRMZM2G368838,GRMZM2G058496,GRMZM2G090669,GRMZM2G001241,and GRMZM2G333454)related to crude fat content that exhibited high expression levels during kernel development in maize inbred line B73.Notably,GRMZM2G169089,GRMZM2G117935,GRMZM2G002075,and GRMZM2G368838 are involved in the linoleic acid metabolic pathway,oil metabolism,kernel growth,and development in maize.Furthermore,co-expression network analysis revealed that the eight candidate genes strongly correlated with 30 known genes.Proteins encoded by candidate genes interact with other proteins and play an important role in oil content and oleic acid metabolism in maize kernels.The best haplotypes of candidate genes might increase crude fat content without decreasing maize yield.These results broaden the understanding of the genetic mechanism of crude fat content and facilitate marker-assisted selection for high-crude fat breeding programs for maize.展开更多
Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet ful...Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet fully understood.Therefore,determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands.The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development.Specifically,to mine a greater number of candidate genes related to grape seed traits,this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study(GWAS)to mine candidate genes.In the two-year analysis using principal component analysis(PCA),we extracted five principal components with a cumulative contribution rate of 96.586%.The cumulative contribution rate for component 1 reached 87.352%.Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits.The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits.These SNP loci were distributed on 18 chromosomes,except for chromosome 4,with most SNP loci distributed on chromosome 18.Based on the physical location of single nucleotide polymorphism(SNP)markers significantly associated with seed-related traits in the grape reference genome,candidate genes are screened within the range of linkage disequilibrium(LD)attenuation distance,both upstream and downstream of the significant SNP loci.These candidate genes were mainly transcription factor-related genes(VvMADS4 and VvMADS5),ubiquitin ligase-related genes(E3 ubiquitin ligase BIG BROTHER),serine/threonine protein kinase-related genes,and carbohydrate metabolism-related genes(Sucrose Synthase 2)and simultaneously controlled multiple(at least two or more)seed traits.These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation.In this work,we identified new gene loci related to grape seed traits.Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.展开更多
Maternal health during pregnancy has a direct impact on the risk and severity of neurodevelopmental disorders(NDDs)in the offspring,especially in the case of drug exposure.However,little progress has been made to asse...Maternal health during pregnancy has a direct impact on the risk and severity of neurodevelopmental disorders(NDDs)in the offspring,especially in the case of drug exposure.However,little progress has been made to assess the risk of drug exposure during pregnancy due to ethical constraints and drug use factors.We collected and manually curated sub-pathways and pathways(sub-/pathways)and drug information to propose an analytical framework for predicting drug candidates.This framework linked sub-/pathway activity and drug response scores derived from gene transcription data and was applied to human fetal brain development and six NDDs.Further,specific and pleiotropic sub-/pathways/drugs were identified using entropy,and sex bias was analyzed in conjunction with logistic regression and random forest models.We identified 19 disorder-associated and 256 regionally pleiotropic and specific candidate drugs that targeted risk sub-/pathways in NDDs,showing temporal or spatial changes across fetal development.Moreover,5443 differential drug-sub-/pathways exhibited sex-biased differences after filling in the gender labels.A user-friendly NDDP visualization website(https://ndd-lab.shinyapps.io/NDDP)was developed to allow researchers and clinicians to access and retrieve data easily.Our framework overcame data gaps and identified numerous pleiotropic and specific candidates across six disorders and fetal developmental trajectories.This could significantly contribute to drug discovery during pregnancy and can be applied to a wide range of traits.展开更多
文摘From January 2001 to January 2002, 50 patients of candidal vaginitis were treated by Kushen powder (KSP,苦参散) combined with Canesten as the treatment group, and controlled by a control group including another 50 patients treated with Canesten alone. The therapeutic results were satisfactory and reported as follows.
文摘Mostly candida resides as an opportunistic organism on epithelial surfaces of human being. However, under auspicious conditions can cause infections including serious life threatening invasive candidiasis with subsequent mortality particularly in immune deficit and hospitalized patients having co-morbids. Limited data are published on the prevalence of candidiasis, based on the researches conducted at few tertiary care settings which are not representing the overall disease burden in our country, Pakistan. Therefore, this study was conducted to evaluate the frequency and sensitivity patterns of candidiasis in our community. Methods: Out of total 1020 specimens, 130 clinical samples were identified as candidal positive, obtained from March to May 2018. These samples were isolated from vagina, oropharynx, urine, tracheal aspirates, pus, blood, tips of the intubations, wounds and fluids of the body cavities. Identification of candida, its species and antifungal sensitivity screening was done by Kirby Bauer’s disk diffusion method according to CLSI guide lines’ (M - 44 A2 series, 2009). Results: A significant majority, 80 (61.5%) of candidal strains were isolated from females with female to male ratio 8:5 and most of these isolates were obtained from high vaginal swabs (43.75%). Four candidal species (Candida albicans 80%, Candida tropicalis 10%, Candida glabrata 9.2% and Candida ciferrii 0.8%) were isolated from all positive specimens. Maximum number of the positive samples 52 (40%) were obtained from ICU patients. Sensitivity test of candidal positive samples revealed that commonly used azole antifungal drugs, fluconazole and voriconazole were highly resistant, with respective 57.7% and 70.8% resistance. Conclusion: Candidiasis is highly prevalent in our clinical set up and more frequently infecting females in comparison to males as most of the positive isolates were retrieved from HVS (high vaginal swabs). Still, C. albicans was found to be the most prevalent specie isolated among all candida samples. Our study also demonstrated that the resistance of most commonly prescribed antifungals, azoles have shown a rapid rise. Therefore, it is recommended that before prescription of antifungal drugs the clinicians should routinely recommend culture and sensitivity testing of samples taken from candida infected individuals.
文摘Background Candidal balanoposthJtis （CB） is a common male genital infection. Autoimmune mechanisms may play an important role in the pathOgenesis of CB. Interleukin-2 （IL-2） is an important molecule in cell-mediated immunity. Methods One hundred and one patients were diagnosed with CB using mycology culture in the dermatology and urology clinics in our hospital. Ninety-four healthy males were randomly selected as controls. We studied serum levels of IL-2 of patients with CB using ELISA and analyzed the correlations between serum IL-2 and clinical data. Results Serum IL-2 concentrations in CB patients were significantly lower than that in the control group （（7.80±4.78） vs. （15.44±7.90） rig/L; t=2.27, P 〈0.05）. The incidence of CB in the low-level group was significantly higher than that in the high-level group （70% （71/101） vs. 36% （30/84）, P 〈0.05）. Low levels of serum IL-2, comorbidity with other sexually transmitted diseases （STDs）, and sexual partners with vulvovaginal candidiasis （VVC） increased the risk of CB. Conclusion The pathogenesis of CB is a complex procedure that includes internal autoimmune factors.
文摘Background Candidal esophagitis is the primary infection among all digestive tract opportunistic ones in acquired immunodeficiency syndrome （AIDS） cases. X-ray manifestation reports of it are still rare. This study aimed to conduct a retrospective analysis on the X-ray data of 6 AIDS cases complicated with candidal esophagitis, and to study the X-ray characteristics of it combined with the findings from gastroscopy.
基金supported by the National Natural Science Foundation of China(No.82574683)the National Natural Science Foundation of Science and Technology Department of Sichuan Province(Nos.2023NSFSC1928 and 2023NSFSC1992)+2 种基金Project of State Administration of Traditional Chinese Medicine of China(No.ZYYCXTD-D-202209)Project of Sichuan Provincial Administration of Traditional Chinese Medicine(No.2022C001)Fundamental Research Funds for the Central Universities(No.YJ201880).
文摘Lung cancer is the most common but fatal malignant tumor worldwide.Patients with lung cancer experienced a relatively low 5-year overall survival rate,and issues such as metastasis and drug resistance remain prominent challenges in its clinical management.Neddylation,a novel type of post-translational modification,was overactivated in lung cancer and was closely associated with its occurrence,development,metastasis,and drug resistance.This review systematically summarizes the biological process of neddylation and deeply explores the latest research progress on how neddylation affects lung cancer cell proliferation,metastasis,and drug resistance mechanisms,with a focus on its regulation of key molecules such as Cullin-RING E3 ligases and the SCCRO family.Meanwhile,it concludes the current advances in potential therapeutic agents targeting neddylation-related targets,including small-molecule compounds(such as Pevonedistat)and natural extracts(such as arctigenin).Finally,the review prospectively evaluates the application potential and questions requiring further exploration of neddylation in lung cancer treatment.In conclusion,we aim to systematically summarize the biological process of neddylation,critically explore its roles in lung cancer proliferation,metastasis,and drug resistance,and evaluate the therapeutic potential of neddylation-targeting agents.
基金supported by the National Key Research and Development Program of China(2020AAA0109300)the Shanghai Collaborative Innovation Center of data intelligence technology(No.0232-A1-8900-24-13).
文摘Chinese abbreviations improve communicative efficiency by extracting key components from longer expressions.They are widely used in both daily communication and professional domains.However,existing abbreviation generation methods still face two major challenges.First,sequence-labeling-based approaches often neglect contextual meaning by making binary decisions at the character level,leading to abbreviations that fail to capture semantic completeness.Second,generation-basedmethods rely heavily on a single decoding process,which frequently produces correct abbreviations but ranks them lower due to inadequate semantic evaluation.To address these limitations,we propose a novel two-stage frameworkwithGeneration–Iterative Optimization forAbbreviation(GIOA).In the first stage,we design aChain-of-Thought prompting strategy and incorporate definitional and situational contexts to generate multiple abbreviation candidates.In the second stage,we introduce a Semantic Preservation Dynamic Adjustment mechanism that alternates between character-level importance estimation and semantic restoration to optimize candidate ranking.Experiments on two public benchmark datasets show that our method outperforms existing state-of-the-art approaches,achieving Hit@1 improvements of 15.15%and 13.01%,respectively,while maintaining consistent results in Hit@3.
文摘Colorectal cancer(CRC)is a prevalent malignancy worldwide,posing a significant public health concern.Mounting evidence has confirmed that timely early screening facilitates the detection of incipient CRC,thereby enhancing patient prognosis.Obviously,non-participation of asymptomatic individuals in screening programs hampers early diagnosis and may adversely affect long-term outcomes for CRC patients.In this letter,we provide a comprehensive overview of the current status of early screening practices,while also thoroughly examine the dilemmas and potential solutions associated with early screening for CRC.In response to these issues,we proffer a set of recommendations directed at governmental authorities and the general public,which focus on augmenting financial investment,establishing standardized screening protocols,advancing technological capabilities,and bolstering public awareness campaigns.The importance of collaborative efforts from various stakeholders cannot be overstated in the quest to enhance early detection rates and alleviate the societal burden of CRC.
基金supported by the Natural Science Foundation of Shandong Province,China(ZR2022MC045)the National Natural Science Foundation of China(32001584,32201876)+2 种基金the Major Science and Technology Program of Xinjiang Uygur Autonomous Region,China(2022A02008-3)the Breeding Project from Department of Science&Technology of Shandong Province,China(2022LZGC007)the Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences,China(CXGC2023A06,CXGC2023A39 and CXGC2023A46),and the Major Scientific and Technological Achievements Cultivation Program of Shandong Academy of Agricultural Sciences,China(CXGC2025E02)。
文摘Plant height(PH),primary lateral branch length(PBL),and branch number(BN)are architectural components impacting peanut pod yield,biomass production,and adaptivity to mechanical harvesting.In this study,a recombinant inbred population consisting of 181 individual lines was used to determine genetic controls of PH,PBL,and BN across three environments.Phenotypic data collected from the population demonstrated continuous distributions and transgressive segregation patterns.Broad-sense heritability of PH,PBL,and BN was found to be 0.87,0.88,and 0.92,respectively.Unconditional individual environmental analysis revealed 35 additive QTLs with phenotypic variation explained(PVE)ranging from 4.57 to 21.68%.A two-round meta-analysis resulted in 24consensus and 19 unique QTLs.Five unique QTLs exhibited pleiotropic effects and their genetic bases(pleiotropy or tight linkage)were evaluated.A joint analysis was performed to estimate the QTL by environment interaction(QEI)effects on PH,PBL,and BN,collectively explaining phenotypic variations of 10.80,11.02,and 7.89%,respectively.We identified 3 major and stable QTL regions(uq9-3,uq10-2,and uq16-1)on chromosomes 9,10,and 16,spanning1.43-1.53 Mb genomic regions.Candidate genes involved in phytohormones biosynthesis,signaling,and cell wall development were proposed to regulate these morphological traits.These results provide valuable information for further genetic studies and the development of molecular markers applicable to peanut architecture improvement.
基金supported by the National Key R&D Program of China(2021YFC2203502 and 2022YFF0711502)the National Natural Science Foundation of China(NSFC)(12173077)+4 种基金the Tianshan Talent Project of Xinjiang Uygur Autonomous Region(2022TSYCCX0095 and 2023TSYCCX0112)the Scientific Instrument Developing Project of the Chinese Academy of Sciences(PTYQ2022YZZD01)China National Astronomical Data Center(NADC)the Operation,Maintenance and Upgrading Fund for Astronomical Telescopes and Facility Instruments,budgeted from the Ministry of Finance of China(MOF)and administrated by the Chinese Academy of Sciences(CAS)Natural Science Foundation of Xinjiang Uygur Autonomous Region(2022D01A360)。
文摘As artificial intelligence(AI)technology has continued to develop,its efficient data processing and pattern recognition capabilities have significantly improved the precision and speed of decision-making processes,and it has been widely applied across various fields.In the field of astronomy,AI techniques have demonstrated unique advantages,particularly in the identification of pulsars and their candidates.AI is able to address the challenges of pulsar celestial body identification and classification because of its accuracy and efficiency.This paper systematically surveys commonly used AI models for pulsar candidate identification,analyzing and discussing the typical applications of machine learning,artificial neural networks,convolutional neural networks,and generative adversarial networks in candidate identification.Furthermore,it explores how th.e introduction of AI techniques not only enhances the efficiency and accuracy of pulsar identification but also provides new perspectives and tools for pulsar survey data processing,thus playing a significant role in advancing pulsar research and the field of astronomy.
基金supported by National Key Research and Development Program of China(2023YFD1201900)National Nat-ural Science Foundation of China(32472078,31971937)+2 种基金Natural Science Foundation of Sichuan Province(2024NSFSC0312)Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province(myzdsys24-01)the Key Laboratory of Exploitation and Study of Distinctive Plants in Education Department of Sichuan Province(TSZW2023ZB-10).
文摘Productive tiller number(PTN)is a pivotal trait that significantly influences wheat grain yield.To date,there have been limited reports on the cloning of genes that regulate PTN in wheat.The quantitative trait locus(QTL)QPtn.sau-4B,associated with PTN,was previously mapped between the markers KASP-1 and KASP-3 on the chromosome 4B.Here,utilizing 12 newly developed markers and phenotypic data of PTN from recombinants identified within this interval,QPtn.sau-4B was further fine-mapped to a 2.58 Mb interval on wheat chromosome arm 4BS.Within this interval,we identified 14 genes with high-confidence and 32 genes with low-confidence.A 0.17 Mb deletion fragment contained TraesCS4B03G0092600 and TraesCS4B03G0093100,which were assigned as candidate genes for QPtn.sau-4B.Additionally,QPtn.sau-4B had potential to enhance both PTN and grain yield in wheat.Cloning this locus would support the development of wheat cultivars with increased grain yield.
基金supported by Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(Grant No.G20220628003-03)Chongqing Municipal People's Government and Chinese Academy of Agricultural Sciences strategic cooperation project,Key-Area Research and Development Program of Guangdong Province(Grant No.2020B020220001)+3 种基金the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.CARS-23)Science and Technology Innovation Program of the Chinese Academy of Agricultural Science(Grant No.CAAS-ASTIP-IVFCAAS)Central public-interest Scientific Institution Basal Research Fund(Grant No.Y2017PT52)the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture,P.R.China。
文摘Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in cucumber have been identified.Here,the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments,with naturally occurring high temperatures over two years.Seventeen of the 88 accessions were identified as highly heat-tolerant.Using a genome-wide association study,five loci(gHII3.1,gHII3.2,gHII3.3,gHII4.1 and gHII6.1)on three chromosomes associated with heat tolerance were detected.Pairwise linkage disequilibrium correlation,sequence polymorphisms,and qRT-PCR analyses at these loci,identified five candidate genes predicted to be casual for heat stress response in cucumber.CsaV3_3G04883,CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs,and were significantly up-regulated by heat stress in the heat-tolerant genotypes.CsaV3_3G031890 was also induced by heat stress,but in the heatsensitive genotypes,and sequence polymorphism was only found in the promoter region.Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms.Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge.It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.
基金supported by Hunan Provincial Key Research and Development Program,No.2021SK2002(to BW)the Natural Science Foundation of Hunan Province of China(General Program),No.2021JJ30938(to YL)。
文摘Degenerative cervical myelopathy is a common cause of spinal cord injury,with longer symptom duration and higher myelopathy severity indicating a worse prognosis.While numerous studies have investigated serological biomarkers for acute spinal cord injury,few studies have explored such biomarkers for diagnosing degenerative cervical myelopathy.This study involved 30 patients with degenerative cervical myelopathy(51.3±7.3 years old,12 women and 18 men),seven healthy controls(25.7±1.7 years old,one woman and six men),and nine patients with cervical spondylotic radiculopathy(51.9±8.6 years old,three women and six men).Analysis of blood samples from the three groups showed clear differences in transcriptomic characteristics.Enrichment analysis identified 128 differentially expressed genes that were enriched in patients with neurological disabilities.Using least absolute shrinkage and selection operator analysis,we constructed a five-gene model(TBCD,TPM2,PNKD,EIF4G2,and AP5Z1)to diagnose degenerative cervical myelopathy with an accuracy of 93.5%.One-gene models(TCAP and SDHA)identified mild and severe degenerative cervical myelopathy with accuracies of 83.3%and 76.7%,respectively.Signatures of two immune cell types(memory B cells and memory-activated CD4^(+)T cells)predicted levels of lesions in degenerative cervical myelopathy with 80%accuracy.Our results suggest that peripheral blood RNA biomarkers could be used to predict lesion severity in degenerative cervical myelopathy.
基金supported by the Italian Ministry of Agriculture,Food Sovereignty and Forests(project GOOD-MILK,D.M.9367185—09/12/2020,CUP C29C20000450001,Roma,Italy)the Regional Government of Sardinia(Progetto Strategico Sulcis,CUP J73C17000070007,Cagliari,Italy).
文摘Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity,especially as we are facing important climate and agriculture challenges.To this aim the genomic architecture of 480 goats belonging to five breeds(i.e.,Saanen[SAA],Camosciata delle Alpi[CAM],Murciano-Granadina[MUR],Maltese[MAL],Sarda[SAR])reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits.Inbreeding,runs of homozygosity(ROH)and runs of heterozygosity(ROHet)were identified.Finally,candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.Results In total,we detected 10,341 ROH in the SAA genome,11,063 ROH in the CAM genome,12,250 ROH in the MUR genome,8,939 ROH in the MAL genome,and 18,441 ROH in the SAR genome.Moreover,we identified 4,087 ROHet for SAA,3,360 for CAM,2,927 for MUR,3,701 for MAL,and 3,576 for SAR,with SAR having the highest heterozygosity coefficient.Interestingly,when computing the inbreeding coefficient using homozygous segment(FROH),SAA showed the lowest value while MAL the highest one,suggesting the need to improve selecting strategies to preserve genetic diversity within the population.Among the most significant candidate genes,we identified several ones linked to different physiological functions,such as milk production(e.g.,DGAT1,B4GALT1),immunity(GABARAP,GPS2)and adaptation to environment(e.g.,GJA3,GJB2 and GJB6).Conclusions This study highlighted the genetic diversity within and among five goat breeds.The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation,which might negatively impact the animal population.Conversely,high levels of ROHet might indicate regions of the genetic diversity,beneficial for breed health and resilience.Therefore,these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.
基金supported by the National Natural Science Foundation of China(32160440)the Manas County National Hybrid Corn Seed Production Base Construction Project,China(MNSZZDX-2021-01)the National Key Research and Development Programs of China(2022YFF1003304)。
文摘Maize root system plays a crucial role in the development of the aboveground plant and determines the yield through the uptake of water and nutrients in the field.However,the genetic architecture of the maize root system is largely unknown mainly due to its complexity and the interactions between genotype and environment.Using a high-throughput semi-automatic hydroponic platform with stable conditions,we comprehensively characterized the root system in a core population of 518 diverse inbred lines of maize.Population structure analysis revealed that the panel has stratification and a linkage disequilibrium decay distance of less than 50 kb.Based on genotyping with the high-density 600 K SNPs,we conducted a genome wide association analysis(GWAS)and identified nine SNPs and seven candidate genes significantly associated with 24 traits.One candidate gene,GRMZM2G400533,is located at the upstream 5 kb region from the leading SNP(AX-91771718)and was significantly associated with primary root length and preferentially expressed in the primary root and crown root.Expression of GRMZM2G400533 increased as the primary root developed but was negatively correlated with primary root elongation.An analysis of candidate gene GRMZM2G400533 identified three functional variants and eight allelic haplotypes.This study will broaden our understanding of maize root development and provide a theoretical basis for maize improvement through optimization of the root system.
基金supported by the National Key Research and Devel-opment Program of China(2024YFD1600100)the Talented Young Scientist Program(TYSP)+5 种基金the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2024-OCRI)China Agriculture Research System(CARS-14)Hubei International Science and Technology Cooperation Project(2022EHB034,2024EHA055)Science and Technology Innovation Project of Hubei province(2024-620-000-001-031)Fundamental Research Funds for Central Non-profit Scientific Institution(1610172023003)the National Center for Crops Germplasm Re-sources(NCCGR-2024-016).
文摘Sesame is a multi-purpose high-value oilseed crop,which can beused in the food,feed,and cosmetics applica-tions.The low yield of sesame is due to the lack of high-yielding and locally adapted varieties,which have the susceptibility to capsule shattering and biotic and abiotic stresses.The breeding gains in sesame are low and stagnant compared to other oilseed crops such as canola,groundnut and sunflower.Breeding for enhanced yieldrelated,oil quantity and quality,biotic and abiotic stresses tolerant varieties is vital to the adaptation of the climate change.Several genes and quantitative trait loci(QTLs)related to yield-related,oil quantity and quality,biotic and abiotic stresses tolerant have been identified through modern plant breeding tools in sesame.The depth understanding of the genetic basis,molecular mechanisms and regulatory genes involved in yield-related,oil quantity and quality,biotic and abiotic stresses tolerant in sesame is important for the improvement of sesame breeding programs.This article reviews and documents these achievements will provide fundamental data and references for practical applications of sesam research.
基金supported by the Key Research and Development Project of Heilongjiang Province,China(2022ZX02B01)。
文摘Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield components.In this study,a natural population of 201 maize inbred lines was used for genome-wide association analysis,which identified nine SNPs on chromosomes 2,5,8,9,and 10 that were significantly associated with ear leaf type structure.Further verification through qRT-PCR confirmed the association of five candidate genes with these SNPs,with the Zm00001d008651 gene showing significant differential expression in the compact and flat maize inbred lines.Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)databasessuggested that this gene is involved in the glycolysis process.An analysis of the basic properties of this gene revealed that it encodes a stable,basic protein consisting of 593 amino acids with some hydrophobic properties.The promoter region contains stress and hormone(abscisic acid(ABA))related elements.The mutant of this gene increased the first ear leaf angle(eLA)and leaf angle of the first leaf below the first ear(bLA)by 4.96 and 0.97°,respectively,compared with normal inbred lines.Overall,this research sheds light on the regulatory mechanism of ear and leaf structures that influence density tolerance and provides solid foundational work for the development of new varieties.
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金supported by the National Natural Science Foundation of China(32101700)the China Postdoctoral Science Foundation(2022M7111220)+1 种基金the Science and Technology Innovation Program of Hunan Province,China(2021RC2082)and the Postgraduate Scientific Research Innovation Project of Hunan Province,China(CX20230697)。
文摘Crude fat is an important nutritional component of maize kernels.However,the genetic mechanisms underlying crude fat content in maize kernels remain elusive.Previous studies used single-model genome-wide association studies(GWAS)with limited population sizes,which can result in false loci positives and hinder functional gene identification.Therefore,this study used a population consisting of 495 maize inbred lines,combined with 1.25 million single nucleotide polymorphisms(SNPs),and implemented GWAS using six models to identify quantitative trait nucleotides(QTNs)controlling crude fat content and to mine key genes.The results revealed a wide variation in crude fat content(0.62-16.03%)and broad-sense heritability(H^(2))(96.23%).In total,744 significant QTNs were detected,with 147 co-located across different models,environments,and methods.Based on the 147 colocated QTNs,candidate genes were searched at 50 kb up-and down-stream intervals of each QTN.We finally screened eight candidate genes(GRMZM2G169089,GRMZM2G117935,GRMZM2G002075,GRMZM2G368838,GRMZM2G058496,GRMZM2G090669,GRMZM2G001241,and GRMZM2G333454)related to crude fat content that exhibited high expression levels during kernel development in maize inbred line B73.Notably,GRMZM2G169089,GRMZM2G117935,GRMZM2G002075,and GRMZM2G368838 are involved in the linoleic acid metabolic pathway,oil metabolism,kernel growth,and development in maize.Furthermore,co-expression network analysis revealed that the eight candidate genes strongly correlated with 30 known genes.Proteins encoded by candidate genes interact with other proteins and play an important role in oil content and oleic acid metabolism in maize kernels.The best haplotypes of candidate genes might increase crude fat content without decreasing maize yield.These results broaden the understanding of the genetic mechanism of crude fat content and facilitate marker-assisted selection for high-crude fat breeding programs for maize.
基金supported by grants from the Basic Research Business Fees for Public Welfare in Xinjiang Autonomous Region(Mining candidate genes related to grape seed traits based on GWAS,KY2023028)the Xinjiang Uygur Autonomous Region Tianchi Talent-Young Doctor for Chuan Zhang(Revealing the domestication history of Xinjiang native grape varieties and genetic analysis of important agronomic traits)the Xinjiang Academy of Agricultural Sciences Youth Science and Technology Backbone Innovation Ability Training Project(xjnkq-2023006).
文摘Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet fully understood.Therefore,determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands.The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development.Specifically,to mine a greater number of candidate genes related to grape seed traits,this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study(GWAS)to mine candidate genes.In the two-year analysis using principal component analysis(PCA),we extracted five principal components with a cumulative contribution rate of 96.586%.The cumulative contribution rate for component 1 reached 87.352%.Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits.The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits.These SNP loci were distributed on 18 chromosomes,except for chromosome 4,with most SNP loci distributed on chromosome 18.Based on the physical location of single nucleotide polymorphism(SNP)markers significantly associated with seed-related traits in the grape reference genome,candidate genes are screened within the range of linkage disequilibrium(LD)attenuation distance,both upstream and downstream of the significant SNP loci.These candidate genes were mainly transcription factor-related genes(VvMADS4 and VvMADS5),ubiquitin ligase-related genes(E3 ubiquitin ligase BIG BROTHER),serine/threonine protein kinase-related genes,and carbohydrate metabolism-related genes(Sucrose Synthase 2)and simultaneously controlled multiple(at least two or more)seed traits.These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation.In this work,we identified new gene loci related to grape seed traits.Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.
基金supported by the National Natural Science Foundation of China[81701350 and 31671252]the Health Technology Plan of Zhejiang Province[2023RC205].
文摘Maternal health during pregnancy has a direct impact on the risk and severity of neurodevelopmental disorders(NDDs)in the offspring,especially in the case of drug exposure.However,little progress has been made to assess the risk of drug exposure during pregnancy due to ethical constraints and drug use factors.We collected and manually curated sub-pathways and pathways(sub-/pathways)and drug information to propose an analytical framework for predicting drug candidates.This framework linked sub-/pathway activity and drug response scores derived from gene transcription data and was applied to human fetal brain development and six NDDs.Further,specific and pleiotropic sub-/pathways/drugs were identified using entropy,and sex bias was analyzed in conjunction with logistic regression and random forest models.We identified 19 disorder-associated and 256 regionally pleiotropic and specific candidate drugs that targeted risk sub-/pathways in NDDs,showing temporal or spatial changes across fetal development.Moreover,5443 differential drug-sub-/pathways exhibited sex-biased differences after filling in the gender labels.A user-friendly NDDP visualization website(https://ndd-lab.shinyapps.io/NDDP)was developed to allow researchers and clinicians to access and retrieve data easily.Our framework overcame data gaps and identified numerous pleiotropic and specific candidates across six disorders and fetal developmental trajectories.This could significantly contribute to drug discovery during pregnancy and can be applied to a wide range of traits.
