In this study,we searched for dispersed repeats(DRs)in the rice(Oryza sativa)genome using the iterative procedure(IP)method.The results revealed that the O.sativa genome contained 79 DR families,comprising 992739 DNA ...In this study,we searched for dispersed repeats(DRs)in the rice(Oryza sativa)genome using the iterative procedure(IP)method.The results revealed that the O.sativa genome contained 79 DR families,comprising 992739 DNA repeats,of which 496762 and 495977 were identified on the forward and reverse DNA strands,respectively.The detected DRs were,on average,374 bp in length and occupied 66.4%of the O.sativa genome.Totally 61%of DRs,identified by the IP method,overlapped with previously annotated dispersed repeats(ADRs)detected using the Extensive De Novo TE Annotator(EDTA)pipeline.展开更多
Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression...Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.展开更多
Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastom...Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastome structural variation,which is induced by one pair of small inverted repeats,can also result in leaf variegation.Here we show a complex plastome structural variation caused by intermolecular and intramolecular recombination across three pairs of small inverted repeats accounts for leaf variegation in a widely cultivated shrub Heptapleurum ellipticum(Araliaceae).This plastome structural variation contains two deletions and two duplications,resulting in dramatic expansion of IRs,substantial contraction of LSC and loss of 11 genes that essential for photosynthesis.Plastome heteroplasmy was detected in both green and albino sectors of variegated leaves.Relative to green sectors,albino sectors in the variegated leaves exhibit significantly reduced expression for the 11 genes lost in the mutated plastome as well as 26 other genes,but significantly increased expression for one gene related to translation apparatus.Optical and transmission electron microscopy observations showed that mesophyll cells of albino sectors possess plastids lacking grana lamellae,which likely carry the mutated plastome and contribute to albinism.In both sectors,the first layer of spongy mesophyll cells beneath the lower epidermis contains normal chloroplasts,suggesting periclinal division of the lower epidermis during development.Our study demonstrates that multiple small repeats can collectively mediate intra-and inter-molecular recombination in plastome and offers a new mechanism accounting for leaf variegation in plants.展开更多
Background:Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms,like human diseases and microbial productivities of target bioproducts.Methods:Here,we develop...Background:Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms,like human diseases and microbial productivities of target bioproducts.Methods:Here,we developed a bacterial type-II toxin-antitoxin-mediated method to manipulate genomic integration of tandem gene repeats in Saccharomyces cerevisiae and further visualised the evolutionary trajectories of gene repeats.We designed a tri-vector system to introduce toxin-antitoxin-driven gene amplification modules.Results:This system delivered multi-copy gene integration in the form of tandem gene repeats spontaneously and independently from toxin-antitoxin-mediated selection.Inducing the toxin(RelE)expressing via a copper(II)-inducible CUP1 promoter successfully drove the in-situ gene amplification of the antitoxin(RelB)module,resulting in~40 copies of a green fluorescence reporter gene per copy of genome.Copy-number changes,copy-number increase and copy-number decrease,and stable maintenance were visualised using the green fluorescence protein and blue chromoprotein AeBlue as reporters.Copy-number increases happened spontaneously and independent on a selection pressure.Increased copy number was quickly enriched through toxin-antitoxin-mediated selection.Conclusion:In summary,the bacterial toxin-antitoxin systems provide a flexible mechanism to manipulate gene copy number in eukaryotic cells and can be exploited for synthetic biology and metabolic engineering applications.展开更多
BACKGROUND The previous studies have primarily focused on the influence of botulinum toxin A(BoNT-A)injection on emotions during the period of peak motor symptom improvement in blepharospasm patients,based on facial f...BACKGROUND The previous studies have primarily focused on the influence of botulinum toxin A(BoNT-A)injection on emotions during the period of peak motor symptom improvement in blepharospasm patients,based on facial feedback hypothesis.AIM To evaluate the sustained anxiolytic and antidepressant effects of BoNT-A in blepharospasm patients beyond motor symptom control.METHODS We recruited benign essential blepharospasm patients with BoNT-A treatment and collected their data to compare scale scores of Jankovic Rating Scale,Blepharospasm Disability Index,Self-rating Anxiety Scale(SAS),Self-rating Depression Scale(SDS),Hamilton Anxiety Scale and Hamilton Depression Scale between pretreatment(baseline)and pre-reinjection(treatment),to further assess the effects of repeated treatments with BoNT by using sub-group analyses in the certain special states.RESULTS A total of 21 eligible blepharospasm patients were with the mean age of 58.4 years and a male-to-female ratio of 1:6.Significantly decreases in the subscale scores of SDS and SAS,including SDS well-being index,decreased capacity and hard to decide,SAS inability to sit still and headache were showed at post-a single BoNT-A injection when scale scores of Jankovic Rating Scale and Blepharospasm Disability Index were matched between baseline and posttreatment.With each additional BoNT-A injection,the odds ratio of patients with the moderate depressive symptoms decreased by 92.6%.Moreover,BoNT treatment remained a decrease in the subscale scores of SDS and SAS in patients with repeated injections.CONCLUSION This study is to demonstrate that repeated BoNT-A injection have a long-lasting relief for anxiety and depressive symptoms in blepharospasm even after its motor symptom-modulating effects have diminished.展开更多
This study investigates the genetic variability and environmental adaptability of Acacia hybrid clones across three distinct ecological regions,providing insights into growth characteristics and stem quality for futur...This study investigates the genetic variability and environmental adaptability of Acacia hybrid clones across three distinct ecological regions,providing insights into growth characteristics and stem quality for future breeding strategies.42 natural hybrid clones were evaluated over a five-year period in three clonal trials in northern,central and southern Vietnam for height(HT),diameter at breast height(DBH),volume(VOL),trunk straightness(STR),branch size(BRA)and survival.Significant clonal differences were found in all traits across all three regions.From age 2-5,the clone repeatability(H_(C)^(2))for growth traits improved from 0.19 to 0.59,indicating substantial genetic control.Genotypic coefficients of variation(CVG)for volume ranged from 21%to 34%,suggesting significant potential for genetic improvement.Site-to-site genotypic correlations ranged from 0.53 to 0.78,pointing to the existence of genotype-environment interactions.Clones derived from Acacia mangium material demonstrated enhanced growth,while the hybrid clones exhibited superior stem quality,particularly in terms of straightness.The findings emphasize the importance of selecting clones that are adapted to specific environmental conditions,with both growth and quality traits considered in breeding programs.展开更多
Objective This study aimed to determine the temporal trends in sleep duration among Chinese adults.Methods In this series of repeated nationally representative cross-sectional surveys(China Chronic Disease and Risk Fa...Objective This study aimed to determine the temporal trends in sleep duration among Chinese adults.Methods In this series of repeated nationally representative cross-sectional surveys(China Chronic Disease and Risk Factors Surveillance)conducted between 2010 and 2018,a total of 645,420 adult participants(97,741 in 2010;175,749 in 2013;187,777 in 2015;and 184,153 in 2018)were included in the trend analysis.Linear and logistic regression models were utilized to assess trends in sleep duration.Results In 2018,the estimated overall mean sleep duration among the Chinese adult population was7.58(SD,1.45)hours per day,with no significant trend from 2010.A significant increase in short sleep duration(≤6 hours)was observed in the total population,from 15.3%(95%CI:14.1%–16.5%)in 2010 to18.5%(95%CI:17.7%–19.3%)in 2018(P<0.001).Similarly,the trend in long sleep duration(>9 hours)was also significant,increasing in weighted prevalence from 7.2%(95%CI:6.3%–8.1%)in 2010 to 9.0%(95%CI:8.2%–9.9%)in 2018(P<0.001).Conclusion The prevalence of both short and long sleep durations significantly increased among Chinese adults from 2010 to 2018,highlighting the urgency of health initiatives to promote optimal sleep duration in China.展开更多
Objective:To investigate the potential link between chromosomal polymorphisms in couples who had a medical history of idiopathic recurrent pregnancy loss.Methods:Cytogenetic investigation was conducted with mitogen(Ph...Objective:To investigate the potential link between chromosomal polymorphisms in couples who had a medical history of idiopathic recurrent pregnancy loss.Methods:Cytogenetic investigation was conducted with mitogen(Phytohemagglutinin-M,Gibco)stimulated blood T lymphocytes by Giemsa trypsin Giemsa banding and Ag-NOR banding on 580 couples with a history of idiopathic recurrent pregnancy loss and 240 couples from the general population.Thirty good chromosomal spreads were captured,karyotyped,and analyzed.The karyotypes were designated using the International System for Human Cytogenomic Nomenclature 2024.Pearson Chi-square test was used to compare the frequency of chromosomal polymorphism variations in the idiopathic recurrent pregnancy loss group with the general population group.Results:A conventional cytogenetic investigation revealed that 45.43%of couples experiencing idiopathic recurrent pregnancy loss presented with various types of chromosomal polymorphic variants,compared to 11.88%in the general population.The overall frequency of these chromosomal polymorphic variants was significantly higher in the idiopathic recurrent pregnancy loss group compared to the general population group(OR 9.97,95%CI 6.99-14.21;P<0.05).Additionally,the prevalence of polymorphic variants was higher among males(49.14%)than females(41.72%)(P=0.01).Conclusions:Chromosomal polymorphic analysis may play a crucial role in the assessment and careful clinical management of cases with idiopathic recurrent pregnancy loss,especially when no other conclusive reasons are identified during the initial evaluation.Therefore,heteromorphism should not be overlooked while investigating the causes of idiopathic recurrent pregnancy loss.展开更多
At present,there is currently a lack of unified standard methods for the determination of antimony content in groundwater in China.The precision and trueness of related detection technologies have not yet been systema...At present,there is currently a lack of unified standard methods for the determination of antimony content in groundwater in China.The precision and trueness of related detection technologies have not yet been systematically and quantitatively evaluated,which limits the effective implementation of environmental monitoring.In response to this key technical gap,this study aimed to establish a standardized method for determining antimony in groundwater using Hydride Generation–Atomic Fluorescence Spectrometry(HG-AFS).Ten laboratories participated in inter-laboratory collaborative tests,and the statistical analysis of the test data was carried out in strict accordance with the technical specifications of GB/T 6379.2—2004 and GB/T 6379.4—2006.The consistency and outliers of the data were tested by Mandel's h and k statistics,the Grubbs test and the Cochran test,and the outliers were removed to optimize the data,thereby significantly improving the reliability and accuracy.Based on the optimized data,parameters such as the repeatability limit(r),reproducibility limit(R),and method bias value(δ)were determined,and the trueness of the method was statistically evaluated.At the same time,precision-function relationships were established,and all results met the requirements.The results show that the lower the antimony content,the lower the repeatability limit(r)and reproducibility limit(R),indicating that the measurement error mainly originates from the detection limit of the method and instrument sensitivity.Therefore,improving the instrument sensitivity and reducing the detection limit are the keys to controlling the analytical error and improving precision.This study provides reliable data support and a solid technical foundation for the establishment and evaluation of standardized methods for the determination of antimony content in groundwater.展开更多
BACKGROUND Repeated application of the Pringle maneuver is a key obstacle to safe minimally invasive repeat liver resection(MISRLR).However,limited technical guidance is available.AIM To study the utility of newly dev...BACKGROUND Repeated application of the Pringle maneuver is a key obstacle to safe minimally invasive repeat liver resection(MISRLR).However,limited technical guidance is available.AIM To study the utility of newly developed Pringle taping method guided by liver surface in MISRLR.METHODS We retrospectively reviewed 72 cases of MISRLR performed by a single surgeon at two centers from August 2015 to July 2024.Beginning in October 2019,a liver surface-guided encirclement of hepatoduodenal ligament(LSEH)was used for repeat Pringle taping.Perioperative outcomes including Pringle taping success,operative time,blood loss,conversion rate,morbidity,and mortality were assessed.RESULTS Laparoscopic and robotic approaches were used in 63 patients and 9 patients,respectively.The median operative time,blood loss,and hospital stay were 331.5 minutes,70 mL,and 8 days,respectively.Open conversion occurred in two cases(2.8%)due to severe adhesions and right renal vein injury.Clavien-Dindo grade≥III complications occurred in 5.6%of cases with no mortality.Anti-adhesion barriers were used in 54 patients(75.0%).LSEH was attempted in 57 cases,improving Pringle taping success from 33.0%to 91.4%(P<0.001).LSEH succeeded in all patients with prior open liver resection(n=11).Among 6 patients in whom LSEH failed,3 patients(50.0%)had undergone a third liver resection,and 1 patient had a history of distal gastrectomy with choledochoduodenostomy.CONCLUSION The newly developed LSEH technique for Pringle taping in MISRLR was feasible,enhancing safety and reproducibility even in patients with a history of open liver resection.展开更多
Objective\ To understand the transcription of BamHI L DNA fragment from genome of strong virulent GA strain of Marek′s disease herpesvirus (MDV) in lymphoblastoid tumor tissue induced by oncogenic strain Beijing 1 ...Objective\ To understand the transcription of BamHI L DNA fragment from genome of strong virulent GA strain of Marek′s disease herpesvirus (MDV) in lymphoblastoid tumor tissue induced by oncogenic strain Beijing 1 (a specific local strain in China) of MDV. Methods\ Two oligonucleotide primers were synthesized according to the reported sequence of \%meq\% gene an ideal oncogenic candidate and our previously determined sequence of BamHI L fragment of Marek′s disease herpesvirus (MDV), respectively. Reverse transcriptase PCR(RT PCR) assay was performed by using these primers and the mRNA as a template which was isolated from visceral lymphoblastoid tumors obtained from chickens artificially infected with strain Beijing 1 of oncogenic MDV. Southern blot molecular hybridization was further carried out to detect the product of RT PCR with digoxigenin labeled nucleotide probe from BamHI I2 and L fragment in the gene library of MDV strain GA, respectively. Results\ Two probes could simultaneously hybridize this cDNA amplified by RT PCR with a length of about 730 bp. Conclusion\ It is suggested that \%meq\% transcription could extend from the right hand end of BamHI I2 to the adjacent BamHI L, and the BamHI L region was likely to be transcribed in MDV induced lymphoblastoid tumors.展开更多
AIM:To evaluate the influence of MUC1 mucin variable number of tandem repeats (VNTR) variability on H pylori adhesion to gastric cells. METHODS: Enzyme linked immunosorbent assay (ELISA)-based adhesion assays were per...AIM:To evaluate the influence of MUC1 mucin variable number of tandem repeats (VNTR) variability on H pylori adhesion to gastric cells. METHODS: Enzyme linked immunosorbent assay (ELISA)-based adhesion assays were performed to measure the adhesion of different H pylori strains (HP26695 and HPTx30a) to gastric carcinoma cell lines (GP202 and MKN45) and GP202 clones expressing recombinant MUC1 with different VNTR lengths. RESULTS: Evaluation of adhesion results shows that H pylori pathogenic strain HP26695 has a significantly higher (P < 0.05) adhesion to all the cell lines and clones tested, when compared to the non-pathogenic strain HPTx30a. Bacteria showed a significantly higher (P < 0.05) adhesion to the GP202 cell line, when compared to the MKN45 cell line. Furthermore, both strains showed a significantly higher (P < 0.05) adhesion to GP202 clones with larger MUC1 VNTR domains. CONCLUSION: This work shows that MUC1 mucin variability conditions H pylori binding to gastric cells. The extent of bacterial adhesion depends on the size of theMUC1 VNTR domain. The adhesion is further dependent on bacterial pathogenicity and the gastric cell line. MUC1 mucin variability may contribute to determine H pylori colonization of the gastric mucosa.展开更多
We have compared genetic diversity of 24 Chinese weak-winter, Swedish winter and spring B. napus accessions by inter-simple sequence repeats (ISSRs). By cluster analysis (UPGMA) based on 125 polymorphism bands amplifi...We have compared genetic diversity of 24 Chinese weak-winter, Swedish winter and spring B. napus accessions by inter-simple sequence repeats (ISSRs). By cluster analysis (UPGMA) based on 125 polymorphism bands amplified with 20 primers, the 24 accessions were divided into three groups. Six Swedish winter lines and eight Chinese weak-winter lines were in the group I and the groupⅡwere two Chinese weak-winter lines XiangyoulS and Bao81. The third group contained eight Swedish spring lines. Principal co-ordinates analysis (PCO) showed similar groupings to cluster analysis. Results from cluster analysis and PCO analysis showed very clearly that Chinese weak-winter, Swedish spring and winter accessions were distinguished from each other and Chinese weak-winter accessions in this study were genetically closer to Swedish winter accessions than to Swedish spring accessions. The Chinese weak-winter accessions had larger diversity than Swedish spring or winter accessions did. This study indicated that ISSR is a suitable and effective tool to evaluate genetic diversity among rapeseed germplasm.展开更多
Interspecific hybridization is an important approach to improve cultivated peanut varieties. Cytological markers such as tandem repeats will facilitate alien gene introgression in peanut. Telomeric repeats have also b...Interspecific hybridization is an important approach to improve cultivated peanut varieties. Cytological markers such as tandem repeats will facilitate alien gene introgression in peanut. Telomeric repeats have also been frequently used in chromosome research. Most plant telomeric repeats are（TTTAGGG）n that are mainly distributed at the chromosome ends, although interstitial telomeric repeats（ITRs） are also commonly identified. In this study, the telomeric repeat was chromosomally localized in 10 Arachis species through sequential GISH（genomic in situ hybridization） and FISH（fluorescence in situ hybridization） combined with 4＇,6-diamidino-2-phenylindole（DAPI） staining. Six ITRs were identified such as in the centromeric region of chromosome Bi5 in Arachis ipa？nsis, pericentromeric regions of chromosomes As5 in A. stenosperma, Bho7 in A. hoehnei and Av5 in A. villosa, nucleolar organizer regions of chromosomes As3 in A. stenosperma and Adi3 in A. diogoi, subtelomeric regions of chromosomes Bho9 in A. hoehnei and Adu7 in A. duranensis, and telomeric region of chromosome Es7 in A. stenophylla. The distributions of the telomeric repeat, 5S r DNA, 45 S r DNA and DAPI staining pattern provided not only ways of distinguishing different chromosomes, but also karyotypes with a higher resolution that could be used in evolutionary genome research. The distribution of telomeric repeats, 5S r DNA and 45 S r DNA sites in this study, along with inversions detected on the long arms of chromosomes Kb10 and Bho10, indicated frequent chromosomal rearrangements during evolution of Arachis species.展开更多
Perciformes,the largest order of vertebrates with 20 suborders,is the most diverse fish order that dominates vertebrate ocean life.The complete mitochondrial control region(CR) of Trichiurus japonicus(Trichiuridae,Sco...Perciformes,the largest order of vertebrates with 20 suborders,is the most diverse fish order that dominates vertebrate ocean life.The complete mitochondrial control region(CR) of Trichiurus japonicus(Trichiuridae,Scombroidei) and Pampus sp.(Stromateidae,Stromateoidei) were amplified and sequenced.Together with data from GenBank,the tandem repeats in the mitochondrial CR from 48 species,which covered nine suborders of Perciformes,are reported in this study.The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei.The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence.Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks,which was first reported in Perciformes and vertebrates.This might have resulted from interruption of the polymerase activity during the H-strand synthesis.The four broader patterns presented here for the tandem repeats,including those in both the 5' and 3' ends,only in the either 5' or 3' end,and in the central conserved domain of the control region,will be useful for understanding the evolution of species.展开更多
Aim： To investigate the role of CAG and GGN repeats as genetic background affecting androgen insensitivity syndrome （AIS） phenotype. Methods： We analyzed lengths of androgen receptor （AR）-CAG and GGN repeats in ...Aim： To investigate the role of CAG and GGN repeats as genetic background affecting androgen insensitivity syndrome （AIS） phenotype. Methods： We analyzed lengths of androgen receptor （AR）-CAG and GGN repeats in 69 AIS cases, along with 136 unrelated normal male individuals. The lengths of repeats were analyzed using polymerase chain reaction （PCR） amplification followed by allelic genotyping to determine allele length. Results： Our study revealed significantly shorter mean lengths of CAG repeats in patients （mean 18.25 repeats, range 14-26 repeats） in comparison to the controls （mean 22.57 repeats, range 12-39 repeats） （two-tailed P 〈 0.0001）. GGN repeats, however, did not differ significantly between patients （mean 21.48 repeats） and controls （mean 21.21 repeats） （two- tailed P = 0.474）. Among patients＇ groups, the mean number of CAG repeats in partial androgen insensitivity cases （mean 15.83 repeats） was significantly less than in complete androgen insensitivity cases （mean 19.46 repeats） （two- tailed P 〈 0.0001）. Conclusion： The findings suggest that shorter lengths of repeats in the AR gene might act as low penetrance genetic background in varying manifestation of androgen insensitivity.展开更多
Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study...Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.展开更多
Interferon-induced protein with tetratricopeptide repeats 1(IFIT1), also known as interferon-induced protein 56(IFI56) or Interferon-stimulated protein 56(ISG56), was originally identified as a protein induced upon tr...Interferon-induced protein with tetratricopeptide repeats 1(IFIT1), also known as interferon-induced protein 56(IFI56) or Interferon-stimulated protein 56(ISG56), was originally identified as a protein induced upon treatment with interferon and inhibited by viral replication and translational initiation. In this study, Epinephelus lanceolatus IFIT1(ELIFIT1) gene was cloned for the first time. The complete cDNA of El IFIT1 gene includes 2921 nucleotides, and encodes a 437-amino acid(AA) protein. The putative ELIFIT1 protein has 9 TRP domains and is highly similar with IFIT1 proteins in other teleosts. In healthy fish, ELIFIT1 gene was highly expressed in the blood, which indicate its specific function in the peripheral immune system. Its expression was also observed in various immunity-related tissues including spleen, intestine, and kidney, Inducted with spotted knifejaw iridovirus(SKIV), ELIFIT1 gene expression was upregulated in the spleen, kidney, and liver 24 h after induction and reached its peak at 72 h, indicating that ELIFIT1 may play an important role in antivirus. These findings contribute to the understanding of the antiviral regulation of ELIFIT1 gene in teleost.展开更多
The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the t...The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.展开更多
基金supported by the Russian Science Foundation,Russia(Grant No.24-24-00031).
文摘In this study,we searched for dispersed repeats(DRs)in the rice(Oryza sativa)genome using the iterative procedure(IP)method.The results revealed that the O.sativa genome contained 79 DR families,comprising 992739 DNA repeats,of which 496762 and 495977 were identified on the forward and reverse DNA strands,respectively.The detected DRs were,on average,374 bp in length and occupied 66.4%of the O.sativa genome.Totally 61%of DRs,identified by the IP method,overlapped with previously annotated dispersed repeats(ADRs)detected using the Extensive De Novo TE Annotator(EDTA)pipeline.
基金supported by the National Natural Science Foundation of China(32172010)the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006).
文摘Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.
基金supported financially by the National Natural Science Foundation of China(31811530297 and 32170217).
文摘Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastome structural variation,which is induced by one pair of small inverted repeats,can also result in leaf variegation.Here we show a complex plastome structural variation caused by intermolecular and intramolecular recombination across three pairs of small inverted repeats accounts for leaf variegation in a widely cultivated shrub Heptapleurum ellipticum(Araliaceae).This plastome structural variation contains two deletions and two duplications,resulting in dramatic expansion of IRs,substantial contraction of LSC and loss of 11 genes that essential for photosynthesis.Plastome heteroplasmy was detected in both green and albino sectors of variegated leaves.Relative to green sectors,albino sectors in the variegated leaves exhibit significantly reduced expression for the 11 genes lost in the mutated plastome as well as 26 other genes,but significantly increased expression for one gene related to translation apparatus.Optical and transmission electron microscopy observations showed that mesophyll cells of albino sectors possess plastids lacking grana lamellae,which likely carry the mutated plastome and contribute to albinism.In both sectors,the first layer of spongy mesophyll cells beneath the lower epidermis contains normal chloroplasts,suggesting periclinal division of the lower epidermis during development.Our study demonstrates that multiple small repeats can collectively mediate intra-and inter-molecular recombination in plastome and offers a new mechanism accounting for leaf variegation in plants.
基金supported partially by the Australian Government through the Australian Research Council Centres of Excellence funding scheme(project CE200100029)。
文摘Background:Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms,like human diseases and microbial productivities of target bioproducts.Methods:Here,we developed a bacterial type-II toxin-antitoxin-mediated method to manipulate genomic integration of tandem gene repeats in Saccharomyces cerevisiae and further visualised the evolutionary trajectories of gene repeats.We designed a tri-vector system to introduce toxin-antitoxin-driven gene amplification modules.Results:This system delivered multi-copy gene integration in the form of tandem gene repeats spontaneously and independently from toxin-antitoxin-mediated selection.Inducing the toxin(RelE)expressing via a copper(II)-inducible CUP1 promoter successfully drove the in-situ gene amplification of the antitoxin(RelB)module,resulting in~40 copies of a green fluorescence reporter gene per copy of genome.Copy-number changes,copy-number increase and copy-number decrease,and stable maintenance were visualised using the green fluorescence protein and blue chromoprotein AeBlue as reporters.Copy-number increases happened spontaneously and independent on a selection pressure.Increased copy number was quickly enriched through toxin-antitoxin-mediated selection.Conclusion:In summary,the bacterial toxin-antitoxin systems provide a flexible mechanism to manipulate gene copy number in eukaryotic cells and can be exploited for synthetic biology and metabolic engineering applications.
基金Supported by the Special Funds of Jiangsu Provincial Key Research and Development Projects,No.BE2019612Scientific Research Project Cooperated by Lanzhou Biotechnology Development Co.,Ltd.+3 种基金the Key R&D Program of Jiangsu Science and Technology Project,No.BE2022049 and No.BE2022049-1National Natural Science Foundation of China,No.82171249Nanjing Rehabilitation Medicine Center ProjectJiangsu Provincial Health Commission Special Fund for Aging and Health.
文摘BACKGROUND The previous studies have primarily focused on the influence of botulinum toxin A(BoNT-A)injection on emotions during the period of peak motor symptom improvement in blepharospasm patients,based on facial feedback hypothesis.AIM To evaluate the sustained anxiolytic and antidepressant effects of BoNT-A in blepharospasm patients beyond motor symptom control.METHODS We recruited benign essential blepharospasm patients with BoNT-A treatment and collected their data to compare scale scores of Jankovic Rating Scale,Blepharospasm Disability Index,Self-rating Anxiety Scale(SAS),Self-rating Depression Scale(SDS),Hamilton Anxiety Scale and Hamilton Depression Scale between pretreatment(baseline)and pre-reinjection(treatment),to further assess the effects of repeated treatments with BoNT by using sub-group analyses in the certain special states.RESULTS A total of 21 eligible blepharospasm patients were with the mean age of 58.4 years and a male-to-female ratio of 1:6.Significantly decreases in the subscale scores of SDS and SAS,including SDS well-being index,decreased capacity and hard to decide,SAS inability to sit still and headache were showed at post-a single BoNT-A injection when scale scores of Jankovic Rating Scale and Blepharospasm Disability Index were matched between baseline and posttreatment.With each additional BoNT-A injection,the odds ratio of patients with the moderate depressive symptoms decreased by 92.6%.Moreover,BoNT treatment remained a decrease in the subscale scores of SDS and SAS in patients with repeated injections.CONCLUSION This study is to demonstrate that repeated BoNT-A injection have a long-lasting relief for anxiety and depressive symptoms in blepharospasm even after its motor symptom-modulating effects have diminished.
基金funded by the project:Breeding and selection of Acacia hybrids and Acacia auriculiformis for large-timber plantation establishment in major ecological zones(000.00.16.G06-230504-0003).
文摘This study investigates the genetic variability and environmental adaptability of Acacia hybrid clones across three distinct ecological regions,providing insights into growth characteristics and stem quality for future breeding strategies.42 natural hybrid clones were evaluated over a five-year period in three clonal trials in northern,central and southern Vietnam for height(HT),diameter at breast height(DBH),volume(VOL),trunk straightness(STR),branch size(BRA)and survival.Significant clonal differences were found in all traits across all three regions.From age 2-5,the clone repeatability(H_(C)^(2))for growth traits improved from 0.19 to 0.59,indicating substantial genetic control.Genotypic coefficients of variation(CVG)for volume ranged from 21%to 34%,suggesting significant potential for genetic improvement.Site-to-site genotypic correlations ranged from 0.53 to 0.78,pointing to the existence of genotype-environment interactions.Clones derived from Acacia mangium material demonstrated enhanced growth,while the hybrid clones exhibited superior stem quality,particularly in terms of straightness.The findings emphasize the importance of selecting clones that are adapted to specific environmental conditions,with both growth and quality traits considered in breeding programs.
基金supported by the National Natural Science Foundation of China(82341245,82371491)the Chinese Central Government(Key Project of Public Health Program)the National Key Research and Development Program of China(2018YFC1311706,2018YFC1311702)。
文摘Objective This study aimed to determine the temporal trends in sleep duration among Chinese adults.Methods In this series of repeated nationally representative cross-sectional surveys(China Chronic Disease and Risk Factors Surveillance)conducted between 2010 and 2018,a total of 645,420 adult participants(97,741 in 2010;175,749 in 2013;187,777 in 2015;and 184,153 in 2018)were included in the trend analysis.Linear and logistic regression models were utilized to assess trends in sleep duration.Results In 2018,the estimated overall mean sleep duration among the Chinese adult population was7.58(SD,1.45)hours per day,with no significant trend from 2010.A significant increase in short sleep duration(≤6 hours)was observed in the total population,from 15.3%(95%CI:14.1%–16.5%)in 2010 to18.5%(95%CI:17.7%–19.3%)in 2018(P<0.001).Similarly,the trend in long sleep duration(>9 hours)was also significant,increasing in weighted prevalence from 7.2%(95%CI:6.3%–8.1%)in 2010 to 9.0%(95%CI:8.2%–9.9%)in 2018(P<0.001).Conclusion The prevalence of both short and long sleep durations significantly increased among Chinese adults from 2010 to 2018,highlighting the urgency of health initiatives to promote optimal sleep duration in China.
基金funded by the Technology Development Board(TDB)of India's Ministry of Science and Technology(TDB/M-25/2018-19).
文摘Objective:To investigate the potential link between chromosomal polymorphisms in couples who had a medical history of idiopathic recurrent pregnancy loss.Methods:Cytogenetic investigation was conducted with mitogen(Phytohemagglutinin-M,Gibco)stimulated blood T lymphocytes by Giemsa trypsin Giemsa banding and Ag-NOR banding on 580 couples with a history of idiopathic recurrent pregnancy loss and 240 couples from the general population.Thirty good chromosomal spreads were captured,karyotyped,and analyzed.The karyotypes were designated using the International System for Human Cytogenomic Nomenclature 2024.Pearson Chi-square test was used to compare the frequency of chromosomal polymorphism variations in the idiopathic recurrent pregnancy loss group with the general population group.Results:A conventional cytogenetic investigation revealed that 45.43%of couples experiencing idiopathic recurrent pregnancy loss presented with various types of chromosomal polymorphic variants,compared to 11.88%in the general population.The overall frequency of these chromosomal polymorphic variants was significantly higher in the idiopathic recurrent pregnancy loss group compared to the general population group(OR 9.97,95%CI 6.99-14.21;P<0.05).Additionally,the prevalence of polymorphic variants was higher among males(49.14%)than females(41.72%)(P=0.01).Conclusions:Chromosomal polymorphic analysis may play a crucial role in the assessment and careful clinical management of cases with idiopathic recurrent pregnancy loss,especially when no other conclusive reasons are identified during the initial evaluation.Therefore,heteromorphism should not be overlooked while investigating the causes of idiopathic recurrent pregnancy loss.
基金supported by the National Natural Science Foundation of China(Project No.42307555).
文摘At present,there is currently a lack of unified standard methods for the determination of antimony content in groundwater in China.The precision and trueness of related detection technologies have not yet been systematically and quantitatively evaluated,which limits the effective implementation of environmental monitoring.In response to this key technical gap,this study aimed to establish a standardized method for determining antimony in groundwater using Hydride Generation–Atomic Fluorescence Spectrometry(HG-AFS).Ten laboratories participated in inter-laboratory collaborative tests,and the statistical analysis of the test data was carried out in strict accordance with the technical specifications of GB/T 6379.2—2004 and GB/T 6379.4—2006.The consistency and outliers of the data were tested by Mandel's h and k statistics,the Grubbs test and the Cochran test,and the outliers were removed to optimize the data,thereby significantly improving the reliability and accuracy.Based on the optimized data,parameters such as the repeatability limit(r),reproducibility limit(R),and method bias value(δ)were determined,and the trueness of the method was statistically evaluated.At the same time,precision-function relationships were established,and all results met the requirements.The results show that the lower the antimony content,the lower the repeatability limit(r)and reproducibility limit(R),indicating that the measurement error mainly originates from the detection limit of the method and instrument sensitivity.Therefore,improving the instrument sensitivity and reducing the detection limit are the keys to controlling the analytical error and improving precision.This study provides reliable data support and a solid technical foundation for the establishment and evaluation of standardized methods for the determination of antimony content in groundwater.
文摘BACKGROUND Repeated application of the Pringle maneuver is a key obstacle to safe minimally invasive repeat liver resection(MISRLR).However,limited technical guidance is available.AIM To study the utility of newly developed Pringle taping method guided by liver surface in MISRLR.METHODS We retrospectively reviewed 72 cases of MISRLR performed by a single surgeon at two centers from August 2015 to July 2024.Beginning in October 2019,a liver surface-guided encirclement of hepatoduodenal ligament(LSEH)was used for repeat Pringle taping.Perioperative outcomes including Pringle taping success,operative time,blood loss,conversion rate,morbidity,and mortality were assessed.RESULTS Laparoscopic and robotic approaches were used in 63 patients and 9 patients,respectively.The median operative time,blood loss,and hospital stay were 331.5 minutes,70 mL,and 8 days,respectively.Open conversion occurred in two cases(2.8%)due to severe adhesions and right renal vein injury.Clavien-Dindo grade≥III complications occurred in 5.6%of cases with no mortality.Anti-adhesion barriers were used in 54 patients(75.0%).LSEH was attempted in 57 cases,improving Pringle taping success from 33.0%to 91.4%(P<0.001).LSEH succeeded in all patients with prior open liver resection(n=11).Among 6 patients in whom LSEH failed,3 patients(50.0%)had undergone a third liver resection,and 1 patient had a history of distal gastrectomy with choledochoduodenostomy.CONCLUSION The newly developed LSEH technique for Pringle taping in MISRLR was feasible,enhancing safety and reproducibility even in patients with a history of open liver resection.
文摘Objective\ To understand the transcription of BamHI L DNA fragment from genome of strong virulent GA strain of Marek′s disease herpesvirus (MDV) in lymphoblastoid tumor tissue induced by oncogenic strain Beijing 1 (a specific local strain in China) of MDV. Methods\ Two oligonucleotide primers were synthesized according to the reported sequence of \%meq\% gene an ideal oncogenic candidate and our previously determined sequence of BamHI L fragment of Marek′s disease herpesvirus (MDV), respectively. Reverse transcriptase PCR(RT PCR) assay was performed by using these primers and the mRNA as a template which was isolated from visceral lymphoblastoid tumors obtained from chickens artificially infected with strain Beijing 1 of oncogenic MDV. Southern blot molecular hybridization was further carried out to detect the product of RT PCR with digoxigenin labeled nucleotide probe from BamHI I2 and L fragment in the gene library of MDV strain GA, respectively. Results\ Two probes could simultaneously hybridize this cDNA amplified by RT PCR with a length of about 730 bp. Conclusion\ It is suggested that \%meq\% transcription could extend from the right hand end of BamHI I2 to the adjacent BamHI L, and the BamHI L region was likely to be transcribed in MDV induced lymphoblastoid tumors.
基金Portuguese Foundation for Science and Technology(FCT)Project POCTI/CBO/44812/2002+1 种基金Project POCTI/SAU-IMI/56895/2004 National Institutes of Health, R01-CA57362
文摘AIM:To evaluate the influence of MUC1 mucin variable number of tandem repeats (VNTR) variability on H pylori adhesion to gastric cells. METHODS: Enzyme linked immunosorbent assay (ELISA)-based adhesion assays were performed to measure the adhesion of different H pylori strains (HP26695 and HPTx30a) to gastric carcinoma cell lines (GP202 and MKN45) and GP202 clones expressing recombinant MUC1 with different VNTR lengths. RESULTS: Evaluation of adhesion results shows that H pylori pathogenic strain HP26695 has a significantly higher (P < 0.05) adhesion to all the cell lines and clones tested, when compared to the non-pathogenic strain HPTx30a. Bacteria showed a significantly higher (P < 0.05) adhesion to the GP202 cell line, when compared to the MKN45 cell line. Furthermore, both strains showed a significantly higher (P < 0.05) adhesion to GP202 clones with larger MUC1 VNTR domains. CONCLUSION: This work shows that MUC1 mucin variability conditions H pylori binding to gastric cells. The extent of bacterial adhesion depends on the size of theMUC1 VNTR domain. The adhesion is further dependent on bacterial pathogenicity and the gastric cell line. MUC1 mucin variability may contribute to determine H pylori colonization of the gastric mucosa.
文摘We have compared genetic diversity of 24 Chinese weak-winter, Swedish winter and spring B. napus accessions by inter-simple sequence repeats (ISSRs). By cluster analysis (UPGMA) based on 125 polymorphism bands amplified with 20 primers, the 24 accessions were divided into three groups. Six Swedish winter lines and eight Chinese weak-winter lines were in the group I and the groupⅡwere two Chinese weak-winter lines XiangyoulS and Bao81. The third group contained eight Swedish spring lines. Principal co-ordinates analysis (PCO) showed similar groupings to cluster analysis. Results from cluster analysis and PCO analysis showed very clearly that Chinese weak-winter, Swedish spring and winter accessions were distinguished from each other and Chinese weak-winter accessions in this study were genetically closer to Swedish winter accessions than to Swedish spring accessions. The Chinese weak-winter accessions had larger diversity than Swedish spring or winter accessions did. This study indicated that ISSR is a suitable and effective tool to evaluate genetic diversity among rapeseed germplasm.
基金supported by the China Agriculture Research System(CARS-14)the Henan Provincial Agriculture Research System,China(S2012-05)the Major Technology Research and Development Program of Henan Province,China(141100110600)
文摘Interspecific hybridization is an important approach to improve cultivated peanut varieties. Cytological markers such as tandem repeats will facilitate alien gene introgression in peanut. Telomeric repeats have also been frequently used in chromosome research. Most plant telomeric repeats are（TTTAGGG）n that are mainly distributed at the chromosome ends, although interstitial telomeric repeats（ITRs） are also commonly identified. In this study, the telomeric repeat was chromosomally localized in 10 Arachis species through sequential GISH（genomic in situ hybridization） and FISH（fluorescence in situ hybridization） combined with 4＇,6-diamidino-2-phenylindole（DAPI） staining. Six ITRs were identified such as in the centromeric region of chromosome Bi5 in Arachis ipa？nsis, pericentromeric regions of chromosomes As5 in A. stenosperma, Bho7 in A. hoehnei and Av5 in A. villosa, nucleolar organizer regions of chromosomes As3 in A. stenosperma and Adi3 in A. diogoi, subtelomeric regions of chromosomes Bho9 in A. hoehnei and Adu7 in A. duranensis, and telomeric region of chromosome Es7 in A. stenophylla. The distributions of the telomeric repeat, 5S r DNA, 45 S r DNA and DAPI staining pattern provided not only ways of distinguishing different chromosomes, but also karyotypes with a higher resolution that could be used in evolutionary genome research. The distribution of telomeric repeats, 5S r DNA and 45 S r DNA sites in this study, along with inversions detected on the long arms of chromosomes Kb10 and Bho10, indicated frequent chromosomal rearrangements during evolution of Arachis species.
基金Supported by the National Natural Science Foundation of China(No.40676085)
文摘Perciformes,the largest order of vertebrates with 20 suborders,is the most diverse fish order that dominates vertebrate ocean life.The complete mitochondrial control region(CR) of Trichiurus japonicus(Trichiuridae,Scombroidei) and Pampus sp.(Stromateidae,Stromateoidei) were amplified and sequenced.Together with data from GenBank,the tandem repeats in the mitochondrial CR from 48 species,which covered nine suborders of Perciformes,are reported in this study.The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei.The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence.Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks,which was first reported in Perciformes and vertebrates.This might have resulted from interruption of the polymerase activity during the H-strand synthesis.The four broader patterns presented here for the tandem repeats,including those in both the 5' and 3' ends,only in the either 5' or 3' end,and in the central conserved domain of the control region,will be useful for understanding the evolution of species.
文摘Aim： To investigate the role of CAG and GGN repeats as genetic background affecting androgen insensitivity syndrome （AIS） phenotype. Methods： We analyzed lengths of androgen receptor （AR）-CAG and GGN repeats in 69 AIS cases, along with 136 unrelated normal male individuals. The lengths of repeats were analyzed using polymerase chain reaction （PCR） amplification followed by allelic genotyping to determine allele length. Results： Our study revealed significantly shorter mean lengths of CAG repeats in patients （mean 18.25 repeats, range 14-26 repeats） in comparison to the controls （mean 22.57 repeats, range 12-39 repeats） （two-tailed P 〈 0.0001）. GGN repeats, however, did not differ significantly between patients （mean 21.48 repeats） and controls （mean 21.21 repeats） （two- tailed P = 0.474）. Among patients＇ groups, the mean number of CAG repeats in partial androgen insensitivity cases （mean 15.83 repeats） was significantly less than in complete androgen insensitivity cases （mean 19.46 repeats） （two- tailed P 〈 0.0001）. Conclusion： The findings suggest that shorter lengths of repeats in the AR gene might act as low penetrance genetic background in varying manifestation of androgen insensitivity.
基金supported by National Natural Science Foundation of China(31790413)supported by National Natural Science Foundation of China(31760657)。
文摘Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.
基金supported by the Shandong Breeding Project (No. 2016LZGC009)the Projects from Laboratory for Marine Fisheries Science and Food Production Processes+2 种基金Pilot National Laboratory for Marine Science and Technology (Qingdao)(Nos. 2018-MFS-T08, 2017A STCP-OS15)the Central Public-interest Scientific Institution Basal Research Fund,CAFS (No. 2020TD20)the Central Public-Interest Scientific Institution Basal Re-search Fund,YSFRI,CAFS (No. 20603022018026)。
文摘Interferon-induced protein with tetratricopeptide repeats 1(IFIT1), also known as interferon-induced protein 56(IFI56) or Interferon-stimulated protein 56(ISG56), was originally identified as a protein induced upon treatment with interferon and inhibited by viral replication and translational initiation. In this study, Epinephelus lanceolatus IFIT1(ELIFIT1) gene was cloned for the first time. The complete cDNA of El IFIT1 gene includes 2921 nucleotides, and encodes a 437-amino acid(AA) protein. The putative ELIFIT1 protein has 9 TRP domains and is highly similar with IFIT1 proteins in other teleosts. In healthy fish, ELIFIT1 gene was highly expressed in the blood, which indicate its specific function in the peripheral immune system. Its expression was also observed in various immunity-related tissues including spleen, intestine, and kidney, Inducted with spotted knifejaw iridovirus(SKIV), ELIFIT1 gene expression was upregulated in the spleen, kidney, and liver 24 h after induction and reached its peak at 72 h, indicating that ELIFIT1 may play an important role in antivirus. These findings contribute to the understanding of the antiviral regulation of ELIFIT1 gene in teleost.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)Science and Technology Basic Resources Investigation Program of China(2021FY100200)+1 种基金Yunnan Revitalization Talent Support Program“Young Talent”and"Innovation Team"Projectsthe 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy of Science(XTBG-1450101)。
文摘The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.
