BACKGROUND Mycosis fungoides is the most common primary cutaneous T-cell lymphoma,whereas generalized erythroderma is rare.In this report,we describe a case of mycosis fungoides with generalized erythroderma using com...BACKGROUND Mycosis fungoides is the most common primary cutaneous T-cell lymphoma,whereas generalized erythroderma is rare.In this report,we describe a case of mycosis fungoides with generalized erythroderma using complete clinical data and[18F]fluoroDglucose positron emission tomography/computed tomography(18F-FDG PET/CT)images.CASE SUMMARY Systemic skin redness with desquamation for three years confirmed mycosis fungoides within one month.The patient underwent left axillary lymphadenectomy biopsy;pathological biopsy suggested abnormal T-cell lesions consistent with mycosis fungoides involving lymph nodes.The patient received methotrexate,5 mg twice weekly,as part of their chemotherapy regimen.Patients January half after discharge,no obvious cause of high fever,left axillary lymph nodes with red heat pain,and rupture entered our hospital for treatment.CONCLUSION The 18F-FDG PET/CT is essential for early diagnosis and timely treatment.展开更多
The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and Eas...The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.展开更多
Effective conservation of threatened biota relies on accurate assessments and scientific guidance.As an unfortunate example,Chinese giant salamanders(Andrias,CGS)remain critically endangered in nature.Misguided conser...Effective conservation of threatened biota relies on accurate assessments and scientific guidance.As an unfortunate example,Chinese giant salamanders(Andrias,CGS)remain critically endangered in nature.Misguided conservation efforts,e.g.,commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids,have further compromised conservation initiatives.Limited information on wild populations of CGS poses a significant conservation challenge.Following 18-month long field monitoring,we now report the discovery of a wild population of CGS in a closed nature reserve in Jiangxi Province,China.Genomic assessments reveal its genetic distinctiveness and do not detect genetic admixture with other species.Based on morphological and molecular evidences,we describe this CGS as a new species Andrias jiangxiensis sp.nov.This is the only known species of CGS today with a genetically pure,reproducing,in situ population.This discovery emphasizes the important role that closed nature reserves play in protecting species,and the necessity of integrating long-term field monitoring and genetic assessments.It sets a new pathway for discovering and conserving endangered species,especially for those biotas that are similarly being extirpated by anthropogenic translocations and overexploitation.展开更多
BACKGROUND As one of the most common tumors,gastric cancer(GC)has a high mortality rate,since current examination approaches cannot achieve early diagnosis.Fusobacterium nucleatum(Fn)primarily colonized in the oral ca...BACKGROUND As one of the most common tumors,gastric cancer(GC)has a high mortality rate,since current examination approaches cannot achieve early diagnosis.Fusobacterium nucleatum(Fn)primarily colonized in the oral cavity,has been reported to be involved in the development of gastrointestinal tumor.Until now,little is known about the relationship between salivary Fn and GC.AIM To determine whether salivary Fn could be a biomarker to diagnose GC and explore the influence of Fn on GC cells.METHODS The abundance of Fn in saliva was quantified by droplet digital polymerase chain reaction in 120 GC patients,31 atrophic gastritis(AG)patients,35 non-AG(NAG)patients,26 gastric polyp(GP)patients,and 20 normal controls(NC)from Qilu Hospital of Shandong University from January 2019 to December 2020.Receiver operating characteristic(ROC)curve analysis was performed to evaluate the diagnostic value of Fn as well as traditional serum tumor markers,including carcinoembryonic antigen(CEA),carbohydrate antigen(CA)19-9,and CA72-4.Transwell assay and wound-healing assay were conducted to assess the influence of Fn infection on GC cells.The expression of epithelial-mesenchymal transition(EMT)markers was detected using western blot assay.RESULTS We found that the level of salivary Fn in GC patients was significantly increased compared with those in AG,NAG,and GP patients and NC(P<0.001).ROC curve analysis showed a favorable capability of Fn(73.33% sensitivity;82.14%specificity;area under the curve:0.813)in GC diagnosis,which was superior to that of CEA,CA19-9,CA72-4,ferritin,and sialic acid.The Fn level in saliva of GC patients was increased as the TNM stage increased.GC patients with lymph node metastasis had higher Fn levels than those without metastasis.Both transwell and wound-healing assays indicated that Fn infection promoted the migration and invasion of GC cells.Western blot analysis showed that Fn infection decreased the expression of E-cadherin and increased the expressions of N-cadherin,vimentin,and snail.CONCLUSION Fn abundance in saliva could be used as a promising biomarker to diagnose GC,and Fn infection could promote GC metastasis by accelerating the EMT process.展开更多
Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reser...Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses(SC2r-CoVs).Here,we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species,and detected positive signals in muscles of four Manis javanica and,for the first time,one M.pentadactyla.Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia.Using in-solution hybridization capture sequencing,we assembled a partial pangolin SC2r-CoV(pangolin-CoV)genome sequence of 22895 bp(MP20)from the M.pentadactyla sample.Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M.javanica seized by Guangxi Customs.A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated.Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated.Given the potential infectivity of pangolin-CoVs,the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.展开更多
A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition....A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition.In the past several decades,the primate clade has been a research focus in genome sequencing due to its unique phylogenetic position and key importance.展开更多
DEAR EDITOR,Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles and plays an essential role in mammalian development and growth.Mammalia...DEAR EDITOR,Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles and plays an essential role in mammalian development and growth.Mammalian genomic imprinting has primarily been studied in mice and humans,with only limited information available for pigs.To systematically characterize this phenomenon and evaluate imprinting status between different species,we investigated imprinted genes on a genome-wide scale in pig brain tissues.展开更多
Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in domestication.However,domestication histories of these two lineages remain enigmatic.We therefore com...Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in domestication.However,domestication histories of these two lineages remain enigmatic.We therefore compared several population characteristics between these two lineages based on global sampling,which included 171 sequences obtained in this study(including Middle Asian,East Asian,and African samples)plus 536 published sequences(including European,Asian,and African samples).The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop(D-loop)sequences,respectively.The Clade I lineage experienced an increase in population size more than 8000 years ago and shows a complex haplotype network.In contrast,the population size of the Clade II lineage has remained relatively constant,with a simpler haplotype network.Although the distribution of the two lineages was almost equal across the Eurasian mainland,they still presented discernible but complex geographic bias in most parts of Africa,which are known as their domestication sites.Donkeys from sub-Saharan Africa tended to descend from the Clade I lineage,whereas the Clade II lineage was dominant along the East and North coasts of Africa.Furthermore,the migration routes inferred from diversity decay suggested different expansion across China between the two lineages.Altogether,these differences indicated non-simultaneous domestication of the two lineages,which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa,respectively.展开更多
Evolutionary biologists are always interested in deciphering the geographic context of diversification,therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms tha...Evolutionary biologists are always interested in deciphering the geographic context of diversification,therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same region.Here, we used multi-locus genetic data along with environmental data to investigate shared phylogeographic patterns among three Asianendemic newt genera, Cynops, Paramesotriton and Pachytriton, which occurred in montane/submontane streams or ponds in southern China. Our 222samples from 78 localities covered the entire range of the three genera and represented the largest dataset of this group to date. We reconstructed matrilineal genealogies from two protein-coding,mitochondrial genes, and gene network from two nuclear genes. We also estimated divergence times of major cladogenetic events and used occurrence data to evaluate niche difference and similarity between lineages. Our results revealed a common basal split in all three genera that corresponds to the separation of two geographic terrains of southern China.Those ancient divergence occurred during middle to late Miocene and likely correlate with paleoclimatic fluctuations caused by the uplift of the Qinghai-Xizang (Tibet) Plateau (QTP).Particularly,the strengthening and weakening of Asian summer monsoons during the Miocene may have profoundly impacted southern China and led to repeatedly vicariance in those newts.However,despite differences in realized niches between lineages,there is no evidence for divergence of fundamental niches.Preservation of old newt matriline lineages in mountains of southern China suggests that the region acts as both museums and cradles of speciation.Based on those results,we advocate a multi-pronged protection strategy for newts in the three genera.展开更多
For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bron...For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.展开更多
The grey wolf （Canis lupus） is one of the most widely distributed terrestrial mammals, and its distribution and ecology in Europe and North America are largely well described. However, the distribution of grey wolve...The grey wolf （Canis lupus） is one of the most widely distributed terrestrial mammals, and its distribution and ecology in Europe and North America are largely well described. However, the distribution of grey wolves in southern China is still highly controversial. Several well-known western literatures stated that there were no grey wolves in southern China, while the presence of grey wolves across China has been indicated in A Guide to the Mammals of China, published by Princeton University Press. It is essential to solve this discrepancy since dogs may have originated from grey wolves in southern China. Therefore, we systematically investigated Chinese literatures about wild animal surveys and identified more than 100 articles and books that included information of the distribution of grey wolves in China. We also surveyed the collections of three Chinese natural museums and found 26 grey wolf skins specimens collected across China. Moreover, we investigated the fossil records in China and identified 25 archaeological sites with wolf remains including south China. In conclusion, with the comprehensive summary of Chinese literatures, museum specimens and fossil records, we demonstrate that grey wolves do distribute across all parts of the Chinese mainland, including the most southern parts.展开更多
DEAR EDITOR,Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding,making it difficult for scientists to reveal...DEAR EDITOR,Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding,making it difficult for scientists to reveal the genetic regulatory mechanisms.Capture Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic regions.It can identify interactions among target loci and all other loci in a genome with low cost and high resolution.Here,we developed CaptureProbe,a user-friendly,graphical Java tool for the design of capture probes across a range of target sites or regions.Numerous parameters helped to achieve and optimize the designed probes.Design testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe specificity.Hence,this program will help scientists conduct genome spatial interaction research.展开更多
Objective Increasing evidence has indicated that there is a correlation between Fusobacterium nucleatum(F.nucleatum)abundance and poor prognosis of colorectal cancer(CRC).Furthermore,tumor metastasis plays a decisive ...Objective Increasing evidence has indicated that there is a correlation between Fusobacterium nucleatum(F.nucleatum)abundance and poor prognosis of colorectal cancer(CRC).Furthermore,tumor metastasis plays a decisive role in the prognosis of CRC patients.Therefore,it was hypothesized that the abundance of F.nucleatum in CRC tissues affects the tumor metastasis.Methods In the present study,F.nucleatum DNA obtained from 141 resected CRC samples was quantified by qPCR to determine whether there were differences in F.nucleatum abundance between groups with and without CRC metastasis.Results The results revealed that F.nucleatum was more abundant in CRC patients with metastasis,and CRC tissues enriched with F.nucleatum had a higher risk of lymph node metastasis and distant metastasis.The receiver operating characteristic curve indicated that F.nucleatum in CRC tissues could be used as an indicator for CRC metastasis,to some extent.Furthermore,the in vitro experiments(electron microscopy,and migration and invasion trials)revealed that F.nucleatum was a highly invasive bacterial strain,and could significantly enhance the invasion and migration capacity of SW480 and SW620 cells.In addition,a meta-analysis comprehensively indicated a slight correlation between F.nucleatum abundance and advanced CRC stage(RR=1.17,95%CI:1.00–1.37,P=0.04,random effect).Conclusion There is a correlation between F.nucleatum abundance and CRC metastasis,and F.nucleatum may serve as a metastasis biomarker for CRC patients.展开更多
The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize th...The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.展开更多
Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demon...Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.展开更多
Quality deficiencies in single nucleotide polymorphism （SNP） analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 21...Quality deficiencies in single nucleotide polymorphism （SNP） analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was -43.8%, with 980 （18.1%）individuals completely missing mitochondrial SNP genotyping （missingness rate=l）. In males, the genotype missingness rate was -28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping （locus missingness rate=0）, whereas 5.9% of autosomal SNPs had a locus missingness rate=l. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.展开更多
Comparative genomics is a powerful approach that comprehensively interprets the genome. Herein, we performed whole genome comparative analysis of 16 Diptera genomes, including four mosquitoes and 12 Drosophilae. We fo...Comparative genomics is a powerful approach that comprehensively interprets the genome. Herein, we performed whole genome comparative analysis of 16 Diptera genomes, including four mosquitoes and 12 Drosophilae. We found more than 540 000 constraint elements （CEs） in the Diptera genome, with the majority found in the intergenic, coding and intronic regions. Accelerated elements （AEs） identified in mosquitoes were mostly in the proteincoding regions （〉93%）, which differs from vertebrates in genomic distribution. Some genes functionally enriched in blood digestion, body temperature regulation and insecticide resistance showed rapid evolution not only in the lineage of the recent common ancestor of mosquitoes （RCAM）, but also in some mosquito lineages. This may be associated with lineage-specific traits and/or adaptations in comparison with other insects. Our findings revealed that although universally fast evolution acted on biological systems in RCAM, such as hematophagy, same adaptations also appear to have occurred through distinct degrees of evolution in different mosquito species, enabling them to be successful blood feeders in different environments.展开更多
DEAR EDITOR,Cis-regulatory elements play an important role in the development of traits and disease in organisms(Ma et al.,2020;Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclope...DEAR EDITOR,Cis-regulatory elements play an important role in the development of traits and disease in organisms(Ma et al.,2020;Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements(ENCODE)(Davis et al., 2018) and Functional Annotation of Animal Genomes(FAANG)(FAANG Consortium et al., 2015)offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms.展开更多
文摘BACKGROUND Mycosis fungoides is the most common primary cutaneous T-cell lymphoma,whereas generalized erythroderma is rare.In this report,we describe a case of mycosis fungoides with generalized erythroderma using complete clinical data and[18F]fluoroDglucose positron emission tomography/computed tomography(18F-FDG PET/CT)images.CASE SUMMARY Systemic skin redness with desquamation for three years confirmed mycosis fungoides within one month.The patient underwent left axillary lymphadenectomy biopsy;pathological biopsy suggested abnormal T-cell lesions consistent with mycosis fungoides involving lymph nodes.The patient received methotrexate,5 mg twice weekly,as part of their chemotherapy regimen.Patients January half after discharge,no obvious cause of high fever,left axillary lymph nodes with red heat pain,and rupture entered our hospital for treatment.CONCLUSION The 18F-FDG PET/CT is essential for early diagnosis and timely treatment.
基金supported by grants from the National Natural Science Foundation of China(31472000)National 973 Program of China(2013CB835203)Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)
文摘The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.
基金equally supported by the STS Program of Chinese Academy of Sciencesand the Strategic Priority Research Program of Chinese Academy of Sciences(XDB31000000)+1 种基金The Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)Jiangxi Academy of Sciences(2021YSBG50008)partially supported it。
文摘Effective conservation of threatened biota relies on accurate assessments and scientific guidance.As an unfortunate example,Chinese giant salamanders(Andrias,CGS)remain critically endangered in nature.Misguided conservation efforts,e.g.,commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids,have further compromised conservation initiatives.Limited information on wild populations of CGS poses a significant conservation challenge.Following 18-month long field monitoring,we now report the discovery of a wild population of CGS in a closed nature reserve in Jiangxi Province,China.Genomic assessments reveal its genetic distinctiveness and do not detect genetic admixture with other species.Based on morphological and molecular evidences,we describe this CGS as a new species Andrias jiangxiensis sp.nov.This is the only known species of CGS today with a genetically pure,reproducing,in situ population.This discovery emphasizes the important role that closed nature reserves play in protecting species,and the necessity of integrating long-term field monitoring and genetic assessments.It sets a new pathway for discovering and conserving endangered species,especially for those biotas that are similarly being extirpated by anthropogenic translocations and overexploitation.
基金Supported by the National Natural Science Foundation of China,No.81972005 and 82172339the Natural Science Foundation of Shandong Province,No.ZR2020MH238Shandong Medical and Health Technology Development Project,No.2018WS327.
文摘BACKGROUND As one of the most common tumors,gastric cancer(GC)has a high mortality rate,since current examination approaches cannot achieve early diagnosis.Fusobacterium nucleatum(Fn)primarily colonized in the oral cavity,has been reported to be involved in the development of gastrointestinal tumor.Until now,little is known about the relationship between salivary Fn and GC.AIM To determine whether salivary Fn could be a biomarker to diagnose GC and explore the influence of Fn on GC cells.METHODS The abundance of Fn in saliva was quantified by droplet digital polymerase chain reaction in 120 GC patients,31 atrophic gastritis(AG)patients,35 non-AG(NAG)patients,26 gastric polyp(GP)patients,and 20 normal controls(NC)from Qilu Hospital of Shandong University from January 2019 to December 2020.Receiver operating characteristic(ROC)curve analysis was performed to evaluate the diagnostic value of Fn as well as traditional serum tumor markers,including carcinoembryonic antigen(CEA),carbohydrate antigen(CA)19-9,and CA72-4.Transwell assay and wound-healing assay were conducted to assess the influence of Fn infection on GC cells.The expression of epithelial-mesenchymal transition(EMT)markers was detected using western blot assay.RESULTS We found that the level of salivary Fn in GC patients was significantly increased compared with those in AG,NAG,and GP patients and NC(P<0.001).ROC curve analysis showed a favorable capability of Fn(73.33% sensitivity;82.14%specificity;area under the curve:0.813)in GC diagnosis,which was superior to that of CEA,CA19-9,CA72-4,ferritin,and sialic acid.The Fn level in saliva of GC patients was increased as the TNM stage increased.GC patients with lymph node metastasis had higher Fn levels than those without metastasis.Both transwell and wound-healing assays indicated that Fn infection promoted the migration and invasion of GC cells.Western blot analysis showed that Fn infection decreased the expression of E-cadherin and increased the expressions of N-cadherin,vimentin,and snail.CONCLUSION Fn abundance in saliva could be used as a promising biomarker to diagnose GC,and Fn infection could promote GC metastasis by accelerating the EMT process.
基金This work was supported by the National Key Research and Development Projects of the Ministry of Science and Technology of China,National Key Research and Development Program of China(2021YFC0863300)Ministry of Agriculture of China(2016ZX08009003-006)+1 种基金Key Program of Chinese Academy of Sciences(KJZD-SW-L11)Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(the Large Research Infrastructure Funding)。
文摘Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses(SC2r-CoVs).Here,we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species,and detected positive signals in muscles of four Manis javanica and,for the first time,one M.pentadactyla.Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia.Using in-solution hybridization capture sequencing,we assembled a partial pangolin SC2r-CoV(pangolin-CoV)genome sequence of 22895 bp(MP20)from the M.pentadactyla sample.Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M.javanica seized by Guangxi Customs.A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated.Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated.Given the potential infectivity of pangolin-CoVs,the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.
基金supported by the National Natural Science Foundation of China(31822048)Strategic Priority Research Program of the Chinese Academy of Sciences(XDPB17)。
文摘A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition.In the past several decades,the primate clade has been a research focus in genome sequencing due to its unique phylogenetic position and key importance.
基金supported by the Ministry of Agriculture of China(2016ZX08009003-006)National Key R&D Program of China(2019YFA0110700)+1 种基金Science&Technology Department of Yunnan Province(2019HA003)Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)。
文摘DEAR EDITOR,Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles and plays an essential role in mammalian development and growth.Mammalian genomic imprinting has primarily been studied in mice and humans,with only limited information available for pigs.To systematically characterize this phenomenon and evaluate imprinting status between different species,we investigated imprinted genes on a genome-wide scale in pig brain tissues.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA2004010302)Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK0501)+3 种基金National Natural Science Foundation of China(31860305)Sino-Africa Joint Research Center,Chinese Academy of Sciences(SAJC201611)Research Center for Ecology and Environment of Central Asia,Chinese Academy of Sciences.Y.L.was supported by the Young Academic and Technical Leader Raising Foundation of Yunnan ProvinceSamples used in this study were provided by the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)
文摘Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in domestication.However,domestication histories of these two lineages remain enigmatic.We therefore compared several population characteristics between these two lineages based on global sampling,which included 171 sequences obtained in this study(including Middle Asian,East Asian,and African samples)plus 536 published sequences(including European,Asian,and African samples).The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop(D-loop)sequences,respectively.The Clade I lineage experienced an increase in population size more than 8000 years ago and shows a complex haplotype network.In contrast,the population size of the Clade II lineage has remained relatively constant,with a simpler haplotype network.Although the distribution of the two lineages was almost equal across the Eurasian mainland,they still presented discernible but complex geographic bias in most parts of Africa,which are known as their domestication sites.Donkeys from sub-Saharan Africa tended to descend from the Clade I lineage,whereas the Clade II lineage was dominant along the East and North coasts of Africa.Furthermore,the migration routes inferred from diversity decay suggested different expansion across China between the two lineages.Altogether,these differences indicated non-simultaneous domestication of the two lineages,which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa,respectively.
基金supported by the Strategic Priority Research Program,CAS (XDB31040202,XDA19050303)China’s Biodiversity Observation Network (Sino-BON),Digitalization,Development and Application of Biotic Resource (202002AA100007)+5 种基金Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences (Large Research Infrastructure Funding)National Natural Science Foundation of China (32170478)Yunnan FundamentalResearchProject(202001AW070016,202005AC160046)Young Talent Project of China Association for Science and Technology (2019-2021QNRC001)Second Tibetan Plateau Scientific Expedition and Research Program(2019QZKK0501)supported by the CAS President’s International Fellowship Initiative (PIFI) to R.W.M.
文摘Evolutionary biologists are always interested in deciphering the geographic context of diversification,therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same region.Here, we used multi-locus genetic data along with environmental data to investigate shared phylogeographic patterns among three Asianendemic newt genera, Cynops, Paramesotriton and Pachytriton, which occurred in montane/submontane streams or ponds in southern China. Our 222samples from 78 localities covered the entire range of the three genera and represented the largest dataset of this group to date. We reconstructed matrilineal genealogies from two protein-coding,mitochondrial genes, and gene network from two nuclear genes. We also estimated divergence times of major cladogenetic events and used occurrence data to evaluate niche difference and similarity between lineages. Our results revealed a common basal split in all three genera that corresponds to the separation of two geographic terrains of southern China.Those ancient divergence occurred during middle to late Miocene and likely correlate with paleoclimatic fluctuations caused by the uplift of the Qinghai-Xizang (Tibet) Plateau (QTP).Particularly,the strengthening and weakening of Asian summer monsoons during the Miocene may have profoundly impacted southern China and led to repeatedly vicariance in those newts.However,despite differences in realized niches between lineages,there is no evidence for divergence of fundamental niches.Preservation of old newt matriline lineages in mountains of southern China suggests that the region acts as both museums and cradles of speciation.Based on those results,we advocate a multi-pronged protection strategy for newts in the three genera.
文摘For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.
基金supported by grants from the National Natural Science Foundation of China(91531303)the 973 program(2013CB835200 and 2013CB835202)+3 种基金the Breakthrough Project of Strategic Priority Program of the Chinese Academy of Sciences(XDB13000000)grants from the Carl Trygger Foundationthe Agria and Swedish Kennel Club research foundationsupported by the Youth Innovation Promotion Association,Chinese Academy of Sciences
文摘The grey wolf （Canis lupus） is one of the most widely distributed terrestrial mammals, and its distribution and ecology in Europe and North America are largely well described. However, the distribution of grey wolves in southern China is still highly controversial. Several well-known western literatures stated that there were no grey wolves in southern China, while the presence of grey wolves across China has been indicated in A Guide to the Mammals of China, published by Princeton University Press. It is essential to solve this discrepancy since dogs may have originated from grey wolves in southern China. Therefore, we systematically investigated Chinese literatures about wild animal surveys and identified more than 100 articles and books that included information of the distribution of grey wolves in China. We also surveyed the collections of three Chinese natural museums and found 26 grey wolf skins specimens collected across China. Moreover, we investigated the fossil records in China and identified 25 archaeological sites with wolf remains including south China. In conclusion, with the comprehensive summary of Chinese literatures, museum specimens and fossil records, we demonstrate that grey wolves do distribute across all parts of the Chinese mainland, including the most southern parts.
基金supported by the Ministry of Agriculture of China(2016ZX08009003-006)Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)
文摘DEAR EDITOR,Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding,making it difficult for scientists to reveal the genetic regulatory mechanisms.Capture Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic regions.It can identify interactions among target loci and all other loci in a genome with low cost and high resolution.Here,we developed CaptureProbe,a user-friendly,graphical Java tool for the design of capture probes across a range of target sites or regions.Numerous parameters helped to achieve and optimize the designed probes.Design testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe specificity.Hence,this program will help scientists conduct genome spatial interaction research.
基金the National Natural Science Foundation of China(No.81972005 and No.82172339)the Natural Science Foundation of Shandong Province(No.ZR2020MH238 and No.ZR2020MH257)the Shandong Medical and Health Technology Development Project(No.2018WSB20002).
文摘Objective Increasing evidence has indicated that there is a correlation between Fusobacterium nucleatum(F.nucleatum)abundance and poor prognosis of colorectal cancer(CRC).Furthermore,tumor metastasis plays a decisive role in the prognosis of CRC patients.Therefore,it was hypothesized that the abundance of F.nucleatum in CRC tissues affects the tumor metastasis.Methods In the present study,F.nucleatum DNA obtained from 141 resected CRC samples was quantified by qPCR to determine whether there were differences in F.nucleatum abundance between groups with and without CRC metastasis.Results The results revealed that F.nucleatum was more abundant in CRC patients with metastasis,and CRC tissues enriched with F.nucleatum had a higher risk of lymph node metastasis and distant metastasis.The receiver operating characteristic curve indicated that F.nucleatum in CRC tissues could be used as an indicator for CRC metastasis,to some extent.Furthermore,the in vitro experiments(electron microscopy,and migration and invasion trials)revealed that F.nucleatum was a highly invasive bacterial strain,and could significantly enhance the invasion and migration capacity of SW480 and SW620 cells.In addition,a meta-analysis comprehensively indicated a slight correlation between F.nucleatum abundance and advanced CRC stage(RR=1.17,95%CI:1.00–1.37,P=0.04,random effect).Conclusion There is a correlation between F.nucleatum abundance and CRC metastasis,and F.nucleatum may serve as a metastasis biomarker for CRC patients.
基金supported by the National Natural Science Foundation of China(32100342,U1902204,31771415,31801054)Bureau of Science and Technology of Yunnan Province(2015FA026)+1 种基金Youth Innovation Promotion AssociationWest Light Foundation of CAS(Y902401081)。
文摘The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.
基金supported by the National Natural Science Foundation of China (31621062)Strategic Priority Research Program of the Chinese Academy of Sciences (XDA2004010302)+4 种基金Second Tibetan Plateau Scientific Expedition and Research (STEP)Program (2019QZKK05010703)supported by the National Natural Science Foundation of China (91731304, 31822048)Strategic Priority Research Program of the Chinese Academy of Sciences (XDB13020600)Qinghai Department of Science and Technology Major ProjectState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan,Yunnan University(2018KF001)supported by the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences (Large Research Infrastructure Funding)
文摘Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
基金supported by grants from the NSFC(91531303)the 973 programs(2013CB8352002013CB835202)
文摘Quality deficiencies in single nucleotide polymorphism （SNP） analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was -43.8%, with 980 （18.1%）individuals completely missing mitochondrial SNP genotyping （missingness rate=l）. In males, the genotype missingness rate was -28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping （locus missingness rate=0）, whereas 5.9% of autosomal SNPs had a locus missingness rate=l. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.
基金Foundation item： This work was supported by grants from the National Natural Science Foundation of China （31271339）
文摘Comparative genomics is a powerful approach that comprehensively interprets the genome. Herein, we performed whole genome comparative analysis of 16 Diptera genomes, including four mosquitoes and 12 Drosophilae. We found more than 540 000 constraint elements （CEs） in the Diptera genome, with the majority found in the intergenic, coding and intronic regions. Accelerated elements （AEs） identified in mosquitoes were mostly in the proteincoding regions （〉93%）, which differs from vertebrates in genomic distribution. Some genes functionally enriched in blood digestion, body temperature regulation and insecticide resistance showed rapid evolution not only in the lineage of the recent common ancestor of mosquitoes （RCAM）, but also in some mosquito lineages. This may be associated with lineage-specific traits and/or adaptations in comparison with other insects. Our findings revealed that although universally fast evolution acted on biological systems in RCAM, such as hematophagy, same adaptations also appear to have occurred through distinct degrees of evolution in different mosquito species, enabling them to be successful blood feeders in different environments.
基金This work was supported by the Chinese Academy of Sciences(XDA24010107)Ministry of Agriculture of China(2016ZX08009003-006)+2 种基金National Natural Science Foundation of China(31621062)Funding for Open Access Charge:Ministry of Agriculture of China(2016ZX08009003-006)Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)。
文摘DEAR EDITOR,Cis-regulatory elements play an important role in the development of traits and disease in organisms(Ma et al.,2020;Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements(ENCODE)(Davis et al., 2018) and Functional Annotation of Animal Genomes(FAANG)(FAANG Consortium et al., 2015)offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms.
