The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow.The AD-genome species Gossypium barbadense,G.tomentosum,and G.mustelinum are part of
Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.aru...Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.arundinaceus has impeded the development of required molecular tools.Dissecting complex genomes into single chromosomes can simplify analyses.The flow-cytometric sorting of a single chromosome of E.arundinaceus in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 E.arundinaceus chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio technologies.The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the chromosome.Of these genes,1877(70.9%)genes were functionally annotated.The phylogenetic relationship of E.arundinaceus with other species using the chromosome1 sequence revealed that E.arundinaceus was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to S.spontaneum and Saccharum spp.hybrids.This study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.展开更多
Multiple BAC-FISH is a powerful tool for modern cytogenetic researching in both animals and plants.But in cotton,this technique is unavailable due to the high percentage of repetitive sequences.
Background:The goal of the assisted reproductive treatment is to transfer one euploid blastocyst and to help infertile women giving birth one healthy neonate.Some algorithms have been used to assess the ploidy status ...Background:The goal of the assisted reproductive treatment is to transfer one euploid blastocyst and to help infertile women giving birth one healthy neonate.Some algorithms have been used to assess the ploidy status of embryos derived from couples with normal chromosome,who subjected to preimplantation genetic testing for aneuploidy(PGT-A)treatment.However,it is currently unknown whether artificial intelligence model can be used to assess the euploidy status of blastocyst derived from populations with chromosomal rearrangement.Methods:From February 2020 to May 2021,we collected the whole raw time-lapse videos at multiple focal planes from in vitro cultured embryos,the clinical information of couples,and the comprehensive chromosome screening results of those blastocysts that had received PGT treatment.Initially,we developed a novel deep learning model called the Attentive Multi-Focus Selection Network(AMSNet)to analyze time-lapse videos in real time and predict blastocyst formation.Building upon AMSNet,we integrated additional clinically predictive variables and created a second deep learning model,the Attentive Multi-Focus Video and Clinical Information Fusion Network(AMCFNet),to assess the euploidy status of embryos.The efficacy of the AMCFNet was further tested in embryos with parental chromosomal rearrangements.The receiver operating characteristic curve(ROC)was used to evaluate the superiority of the model.Results:A total of 4112 embryos with complete time-lapse videos were enrolled for the blastocyst formation prediction task,and 1422 qualified blastocysts received PGT-A(n=589)or PGT for chromosomal structural rearrangement(PGT-SR,n=833)were enrolled for the euploidy assessment task in this study.The AMSNet model using seven focal raw time-lapse videos has the best real-time accuracy.The real-time accuracy for AMSNet to predict blastocyst formation reached above 70%on the day 2 of embryo culture,and then increased to 80%on the day 4 of embryo culture.Combing with 4 clinical features of couples,the AUC of AMCFNet with 7 focal points increased to 0.729 in blastocysts derived from couples with chromosomal rearrangement.Conclusion:Integrating seven focal raw time-lapse images of embryos and parental clinical information,AMCFNet model have the capability of assessing euploidy status in blastocysts derived from couples with chromosomal rearrangement.展开更多
Objective： The progression of human cancer is characterized by the accumulation of genetic instability. An increasing number of experimental genetic molecular techniques have been used to detect chromosome aberration...Objective： The progression of human cancer is characterized by the accumulation of genetic instability. An increasing number of experimental genetic molecular techniques have been used to detect chromosome aberrations. Previous studies on chromosome abnormalities often focused on identifying the frequent loci of chromosome alterations, but rarely addressed the issue of interrelationship of chromosomal abnormalities. In the last few years, several mathematical models have been employed to construct models of carcinogenesis, in an attempt to identify the time order and cause-and-effect relationship of chromosome aberrations. The principles and applications of these models are reviewed and compared in this paper. Mathematical modeling of carcinogenesis can contribute to our understanding of the molecular genetics of tumor development, and identification of cancer related genes, thus leading to improved clinical practice of cancer.展开更多
In order to explore researches about the chromosome karyotype analysis and fluorescence in situ hybridization(FISH) technology in China,using the bibliometric method,taking " fluorescence in situ hybridization(FI...In order to explore researches about the chromosome karyotype analysis and fluorescence in situ hybridization(FISH) technology in China,using the bibliometric method,taking " fluorescence in situ hybridization(FISH) " and " chromosome" as key words,this paper made a statistical analysis on the literature published in China National Knowledge Infrastructure(CNKI) during 2002-2016.The results indicated that the number of papers published in 2002 was the smallest(37),while the number of papers published in 2012 was the largest(125).In terms of the distribution of organizations of authors,in 1201 papers,11 organizations published papers ≥15,accounting for 21.65%.In terms of distribution of papers published by different periodicals,11 periodicals published papers ≥10,accounting for 17.65%.In terms of the papers supported by foundation projects,in all papers searched,377 papers were supported by foundation projects,accounting for 31.39%.In terms of the distribution of doctoral and master's dissertations,259 papers were master's dissertations,accounting for 21.57%;92 papers were doctoral dissertations,accounting for 7.66%.展开更多
文摘The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow.The AD-genome species Gossypium barbadense,G.tomentosum,and G.mustelinum are part of
基金funded by the National Natural Science Foundation of China(31771863)Science and Technology Major Project of the Fujian Province of China(2015NZ0002-2)+3 种基金Special Fund for Scientific and Technological Innovation of the Fujian Agriculture and Forestry University(KFA17168A)Doctoral Students of Fujian Agriculture and Forestry University Going Abroad to Cooperative Research(324-112110082)Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources(SKLCUSA-a201912)supported by ERDF Project“Plants as a tool for sustainable global development”(CZ.02.1.01/0.0/0.0/16_019/0000827)。
文摘Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.arundinaceus has impeded the development of required molecular tools.Dissecting complex genomes into single chromosomes can simplify analyses.The flow-cytometric sorting of a single chromosome of E.arundinaceus in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 E.arundinaceus chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio technologies.The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the chromosome.Of these genes,1877(70.9%)genes were functionally annotated.The phylogenetic relationship of E.arundinaceus with other species using the chromosome1 sequence revealed that E.arundinaceus was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to S.spontaneum and Saccharum spp.hybrids.This study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.
文摘Multiple BAC-FISH is a powerful tool for modern cytogenetic researching in both animals and plants.But in cotton,this technique is unavailable due to the high percentage of repetitive sequences.
基金supported by grants from the National Natural Science Found of China(No.81270750)Natural Science Found of Guangdong China(No.2019A1515011845)+1 种基金Stem Cell Research Founding from Chinese Medical Association(No.19020010780)Sun Yat-sen University 5010 Clinical Research Project(No.2023003).
文摘Background:The goal of the assisted reproductive treatment is to transfer one euploid blastocyst and to help infertile women giving birth one healthy neonate.Some algorithms have been used to assess the ploidy status of embryos derived from couples with normal chromosome,who subjected to preimplantation genetic testing for aneuploidy(PGT-A)treatment.However,it is currently unknown whether artificial intelligence model can be used to assess the euploidy status of blastocyst derived from populations with chromosomal rearrangement.Methods:From February 2020 to May 2021,we collected the whole raw time-lapse videos at multiple focal planes from in vitro cultured embryos,the clinical information of couples,and the comprehensive chromosome screening results of those blastocysts that had received PGT treatment.Initially,we developed a novel deep learning model called the Attentive Multi-Focus Selection Network(AMSNet)to analyze time-lapse videos in real time and predict blastocyst formation.Building upon AMSNet,we integrated additional clinically predictive variables and created a second deep learning model,the Attentive Multi-Focus Video and Clinical Information Fusion Network(AMCFNet),to assess the euploidy status of embryos.The efficacy of the AMCFNet was further tested in embryos with parental chromosomal rearrangements.The receiver operating characteristic curve(ROC)was used to evaluate the superiority of the model.Results:A total of 4112 embryos with complete time-lapse videos were enrolled for the blastocyst formation prediction task,and 1422 qualified blastocysts received PGT-A(n=589)or PGT for chromosomal structural rearrangement(PGT-SR,n=833)were enrolled for the euploidy assessment task in this study.The AMSNet model using seven focal raw time-lapse videos has the best real-time accuracy.The real-time accuracy for AMSNet to predict blastocyst formation reached above 70%on the day 2 of embryo culture,and then increased to 80%on the day 4 of embryo culture.Combing with 4 clinical features of couples,the AUC of AMCFNet with 7 focal points increased to 0.729 in blastocysts derived from couples with chromosomal rearrangement.Conclusion:Integrating seven focal raw time-lapse images of embryos and parental clinical information,AMCFNet model have the capability of assessing euploidy status in blastocysts derived from couples with chromosomal rearrangement.
基金supported by a grant from the Education Department of Zhejiang Province (No.Y200803235)
文摘Objective： The progression of human cancer is characterized by the accumulation of genetic instability. An increasing number of experimental genetic molecular techniques have been used to detect chromosome aberrations. Previous studies on chromosome abnormalities often focused on identifying the frequent loci of chromosome alterations, but rarely addressed the issue of interrelationship of chromosomal abnormalities. In the last few years, several mathematical models have been employed to construct models of carcinogenesis, in an attempt to identify the time order and cause-and-effect relationship of chromosome aberrations. The principles and applications of these models are reviewed and compared in this paper. Mathematical modeling of carcinogenesis can contribute to our understanding of the molecular genetics of tumor development, and identification of cancer related genes, thus leading to improved clinical practice of cancer.
基金Supported by Project of National Natural Science Foundation(31160292)Crop Discipline Construction Project of Tibet Agricultural and Animal Husbandry College(2015ZWXKJS&2016ZWXKJS)
文摘In order to explore researches about the chromosome karyotype analysis and fluorescence in situ hybridization(FISH) technology in China,using the bibliometric method,taking " fluorescence in situ hybridization(FISH) " and " chromosome" as key words,this paper made a statistical analysis on the literature published in China National Knowledge Infrastructure(CNKI) during 2002-2016.The results indicated that the number of papers published in 2002 was the smallest(37),while the number of papers published in 2012 was the largest(125).In terms of the distribution of organizations of authors,in 1201 papers,11 organizations published papers ≥15,accounting for 21.65%.In terms of distribution of papers published by different periodicals,11 periodicals published papers ≥10,accounting for 17.65%.In terms of the papers supported by foundation projects,in all papers searched,377 papers were supported by foundation projects,accounting for 31.39%.In terms of the distribution of doctoral and master's dissertations,259 papers were master's dissertations,accounting for 21.57%;92 papers were doctoral dissertations,accounting for 7.66%.
