In this study,we isolated starches from non-traditional sources,including quinoa,lentil,arrowhead,gorgon fruit,sorghum,chickpea,proso millet,and purple potato and investigated their morphology,physicochemical,and func...In this study,we isolated starches from non-traditional sources,including quinoa,lentil,arrowhead,gorgon fruit,sorghum,chickpea,proso millet,and purple potato and investigated their morphology,physicochemical,and functional properties.Significant differences in starch particle morphology,swelling power,solubility,syneresis,crystalline pattern,and pasting viscosity were observed among the starches from these nontraditional sources.Further,all these isolated starches had unique properties because of their characteristic distinct granules when seen under scanning electron microscopy(SEM).The amylose content of the isolated starches shown significant difference(P<0.05),and the values ranged between 11.46%and 37.61%.Results demonstrated that the isolated starches contained between 79.82%to 86.56%starch,indicating that the isolated starches had high purity.X-ray diffraction(XRD)patterns of starches isolated from sorghum,proso millet,quinoa,purple potato,and gorgon fruit presented A-type diffraction pattern;while lentil seeds,arrowhead,and chickpea starches presented C-type diffraction pattern.Overall,these results will promote the development of products based on starch isolated from non-traditional starches.展开更多
Fallopia multiflora(Thunb.)Harald,a vine belonging to the Polygonaceae family,is used in traditional medicine.The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging....Fallopia multiflora(Thunb.)Harald,a vine belonging to the Polygonaceae family,is used in traditional medicine.The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging.This study describes the assembly of the F.multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data(with a contig N50 of 1.97 megabases),1.44 gigabases of which was assigned to 11 pseudochromosomes.Comparative genomics confirmed that F.multiflora shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation.Combining genomics,transcriptomics,and metabolomics data to map a network of associated genes and metabolites,we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F.multiflora.These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes.Moreover,the reference genome of F.multiflora is a useful addition to the genomes of the Polygonaceae family.展开更多
Strabismus and amblyopia are common ophthalmologic developmental diseases caused by abnormal visual experiences. However, the underlying pathogenesis and visual defects are still not fully understood. Most studies hav...Strabismus and amblyopia are common ophthalmologic developmental diseases caused by abnormal visual experiences. However, the underlying pathogenesis and visual defects are still not fully understood. Most studies have used experimental interference to establish diseaseassociated animal models, while ignoring the natural pathophysiological mechanisms. This study was designed to investigate whether natural strabismus and amblyopia are associated with abnormal neurological defects. We screened one natural strabismic monkey(Macaca fascicularis) and one natural amblyopic monkey from hundreds of monkeys, and retrospectively analyzed one human strabismus case. Neuroimaging, behavioral,neurophysiological, neurostructural, and genovariation features were systematically evaluated using magnetic resonance imaging(MRI), behavioral tasks, flash visual evoked potentials(FVEP),electroretinogram(ERG), optical coherence tomography(OCT), and whole-genome sequencing(WGS), respectively. Results showed that the strabismic patient and natural strabismic and amblyopic monkeys exhibited similar abnormal asymmetries in brain structure, i.e., ipsilateral impaired right hemisphere. Visual behavior, visual function, retinal structure, and fundus of the monkeys were impaired. Aberrant asymmetry in binocular visual function and structure between the strabismic and amblyopic monkeys was closely related, with greater impairment of the left visual pathway.Several similar known mutant genes for strabismus and amblyopia were also identified. In conclusion,natural strabismus and amblyopia are accompanied by abnormal asymmetries of the visual system,especially visual neurophysiological and neurostructural defects. Our results suggest that future therapeutic and mechanistic studies should consider defects and asymmetries throughout the entire visual system.展开更多
Recurrence is the key factor affecting the prognosis of osteosarcoma.Currently,there is a lack of clinically useful tools to predict osteosarcoma recurrence.The application of pathological images for artificial intell...Recurrence is the key factor affecting the prognosis of osteosarcoma.Currently,there is a lack of clinically useful tools to predict osteosarcoma recurrence.The application of pathological images for artificial intelligence‐assisted accurate prediction of tumour out-comes is increasing.Thus,the present study constructed a quantitative histological image classifier with tumour nuclear features to predict osteosarcoma outcomes using haema-toxylin and eosin(H&E)‐stained whole‐slide images(WSIs)from 150 osteosarcoma patients.We first segmented eight distinct tissues in osteosarcoma H&E‐stained WSIs,with an average accuracy of 90.63%on the testing set.The tumour areas were auto-matically and accurately acquired,facilitating the tumour cell nuclear feature extraction process.Based on six selected tumour nuclear features,we developed an osteosarcoma histological image classifier(OSHIC)to predict the recurrence and survival of osteo-sarcoma following standard treatment.The quantitative OSHIC derived from tumour nuclear features independently predicted the recurrence and survival of osteosarcoma patients,thereby contributing to precision oncology.Moreover,we developed a fully automated workflow to extract quantitative image features,evaluate the diagnostic values of feature sets and build classifiers to predict osteosarcoma outcomes.Thus,the present study provides a novel tool for predicting osteosarcoma outcomes,which has a broad application prospect in clinical practice.展开更多
BACKGROUND Using gas chromatography-mass spectrometry(GC/MS)analysis,we examined the composition of volatile components present in the yellow and green fruits,seeds,and jam of the scrambling shrub Capparis cartilagine...BACKGROUND Using gas chromatography-mass spectrometry(GC/MS)analysis,we examined the composition of volatile components present in the yellow and green fruits,seeds,and jam of the scrambling shrub Capparis cartilaginea(C.cartilaginea).These plant samples were collected from Kibbutz Yotvata in Israel.In all the tested samples,isothiocyanates were identified.Utilizing the PASS program,we ascertained the biological activity of these isothiocyanates present in the Capparis genus.The study results highlighted that all isothiocyanates could potentially act as apoptosis agonists,making them strong candidates for antitumor drugs.This information holds significant value for the fields of medicinal chemistry,pharmacology,and practical medicine.AIM To investigate the volatile components present in the yellow and green fruits,seeds,and jam of the C.cartilaginea shrub using GC/MS analysis,to detect isothiocyanates in all the analyzed plant samples,and to assess the biological activity of these isothiocyanates utilizing the PASS program.METHODS We utilized two primary methods to analyze the volatile compounds present in the yellow and green fruits,seeds,and jams of the C.cartilaginea,native to Israel.We identified biologically active isothiocyanates in these samples.Their anticipated biological activities were determined using the PASS program,with the most dominant activities being apoptosis agonist,anticarcinogenic,and antineoplastic specifically for genitourinary cancer.RESULTS Fruits,seeds,and jams containing isothiocyanates,which exhibit antineoplastic and anticarcinogenic activities,could be suggested for cancer prevention and management.Specific isothiocyanates,with therapeutic potential in this realm,could be recommended as potent anticancer agents in practical medicine following clinical trials.CONCLUSION The discovery that isothiocyanates exhibit potent antineoplastic and anticarcinogenic activities was unexpected.Additionally,certain isothiocyanates demonstrated antifungal,antiviral(specifically against arbovirus),and antiparasitic properties.展开更多
Cauliflower is an important variety of Brassica oleracea and is planted worldwide.Here,the high-quality genome sequence of cauliflower was reported.The assembled cauliflower genome was 584.60 Mb in size,with a contig ...Cauliflower is an important variety of Brassica oleracea and is planted worldwide.Here,the high-quality genome sequence of cauliflower was reported.The assembled cauliflower genome was 584.60 Mb in size,with a contig N50 of 2.11 Mb,and contained 47,772 genes;56.65%of the genome was composed of repetitive sequences.Among these sequences,long terminal repeats(LTRs)were the most abundant(32.71%of the genome),followed by transposable elements(TEs)(12.62%).Comparative genomic analysis confirmed that after an ancient paleohexaploidy(γ)event,cauliflower underwent two whole-genome duplication(WGD)events shared with Arabidopsis and an additional whole-genome triplication(WGT)event shared with other Brassica species.The present cultivated cauliflower diverged from the ancestral B.oleracea species~3.0 million years ago(Mya).The speciation of cauliflower(~2.0 Mya)was later than that of B.oleracea L.var.capitata(approximately 2.6 Mya)and other Brassica species(over 2.0 Mya).Chromosome no.03 of cauliflower shared the most syntenic blocks with the A,B,and C genomes of Brassica species and its eight other chromosomes,implying that chromosome no.03 might be the most ancient one in the cauliflower genome,which was consistent with the chromosome being inherited from the common ancestor of Brassica species.In addition,2,718 specific genes,228 expanded genes,2 contracted genes,and 1,065 positively selected genes in cauliflower were identified and functionally annotated.These findings provide new insights into the genomic diversity of Brassica species and serve as a valuable reference for molecular breeding of cauliflower.展开更多
The aromatic shrub Lavandula angustifolia produces various volatile terpenoids that serve as resources for essential oils and function in plant-insect communication.To better understand the genetic basis of the terpen...The aromatic shrub Lavandula angustifolia produces various volatile terpenoids that serve as resources for essential oils and function in plant-insect communication.To better understand the genetic basis of the terpenoid diversity in lavender,we present a high-quality reference genome for the Chinese lavender cultivar‘Jingxun 2'using PacBio and Hi-C technologies to anchor the 894.50 Mb genome assembly into 27 pseudochromosomes.In addition to the y triplication event,lavender underwent two rounds of whole-genome duplication(WGD)during the Eocene-Oligocene(29.6 MYA)and Miocene-Pliocene(6.9 MYA)transitions.As a result of tandem duplications and lineage-specific WGDs,gene families related to terpenoid biosynthesis in lavender are substantially expanded compared to those of five other species in Lamiaceae.Many terpenoid biosynthesis transcripts are abundant in glandular trichomes.We further integrated the contents of ecologically functional terpenoids and coexpressed terpenoid biosynthetic genes to construct terpenoid-gene networks.Typical gene clusters,including TPS-TPS,TPS-CYP450,and TPS-BAHD,linked with compounds that primarily function as attractants or repellents,were identified by their similar patterns of change during flower development or in response to methyl jasmonate.Comprehensive analysis of the genetic basis of the production of volatiles in lavender could serve as a foundation for future research into lavender evolution,phytochemistry,and ecology.展开更多
Common wheat(Triticum aestiuum L.)is one of the most important crops because it provides about 20%of the total calories for humans.T.aestiuum is an excellent modern species for studying concerted evolution of sub-geno...Common wheat(Triticum aestiuum L.)is one of the most important crops because it provides about 20%of the total calories for humans.T.aestiuum is an excellent modern species for studying concerted evolution of sub-genomes in polyploid species,because of its large chromosome size and three well-known genome donors.Establishment of common wheat genome reference sequence and development of high-density SNP chips provide an excellent foundation to answer questions of wheat evolution and breeding at the genomic level.By genotyping more than 600 accessions of common wheat and their diploid and tetraploid ancestors using a Wheat660 K SNP array,we found dramatic genome changes due to tetraploidization and hexaploidization,in contrast to weaker influences of domestication and breeding on them.Further,since common wheat was introduced in China in 1500 BCE,Chinese landraces formed two subgroups(T.aestiuum-L1 and T.aestiuum-L2)with considerably diverse geographic distributions and agronomic traits.T.aestiuum-L2,mainly distributed in central and east China is found to have more but smaller oval grains with early maturity characteristics.We found that variation and selection in intergenic regions of the A and B sub-genomes dominated this differentiation,in which chromosomes 7 A and 3 B took the leading roles due to the existence of putative genes related to defense responses and environmental adaption in the highly differentiated regions.Large haplotype blocks were detected on 3 B(232.6-398.3 Mb)and 7 A(211.7-272.9 Mb)in the landraces,forming two distinct haplotypes,respectively.We discovered that artificial crosses in breeding promoted recombination in the whole genome,however,this recombination and differentiation was highly asymmetric among the three sub-genomes in homoeologous regions.In addition,we found that the wide use of European and northern American cultivars in breeding at early era,led dramatic changes in Chinese wheat genome,whereas,the recent breeding functioned to optimize it.This study will provide the insight for reconsideration of wheat evolution and breeding,and a new strategy for parent selection in breeding.展开更多
Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen.Here,we reveal the chromosome-scale genome sequence of M.polymorpha using an integrated approach including Illumina...Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen.Here,we reveal the chromosome-scale genome sequence of M.polymorpha using an integrated approach including Illumina,PacBio and Hi-C technologies.We combined PacBio full-length RNA-seq,metabolomic analysis,structural anatomy analysis and related physiological indexes to elucidate the important agronomic traits of M.polymorpha for forage and vegetable usage.The assembled M.polymorpha genome consisted of 457.53Mb with a long scaffold N50 of 57.72Mb,and 92.92%(441.83Mb)of the assembly was assigned to seven pseudochromosomes.Comparative genomic analysis revealed that expansion and contraction of the photosynthesis and lignin biosynthetic gene families,respectively,led to enhancement of nutritious compounds and reduced lignin biosynthesis in M.polymorpha.In addition,we found that several positively selected nitrogen metabolism-related genes were responsible for crude protein biosynthesis.Notably,the metabolomic results revealed that a large number of flavonoids,vitamins,alkaloids,and terpenoids were enriched in M.polymorpha.These results imply that the decreased lignin content but relatively high nutrient content of M.polymorpha enhance its edibility and nutritional value as a forage and vegetable.Our genomic data provide a genetic basis that will accelerate functional genomic and breeding research on M.polymorpha as well as other Medicago and legume plants.展开更多
Jujube(Ziziphus jujuba Mill.)is an important perennial fruit tree with a range of interesting horticultural traits.It was domesticated from wild jujube(Ziziphus acidojujuba),but the genomic variation dynamics and gene...Jujube(Ziziphus jujuba Mill.)is an important perennial fruit tree with a range of interesting horticultural traits.It was domesticated from wild jujube(Ziziphus acidojujuba),but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood.Here,we report a comprehensive genome variation map based on the resequencing of 350 accessions,including wild,semi-wild and cultivated jujube plants,at a>15×depth.Using the combination of a genome-wide association study(GWAS)and selective sweep analysis,we identified several candidate genes potentially involved in regulating seven domestication traits in jujube.For fruit shape and kernel shape,we integrated the GWAS approach with transcriptome profiling data,expression analysis and the transgenic validation of a candidate gene to identify a causal gene,ZjFS3,which encodes an ethyleneresponsive transcription factor.Similarly,we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS.In the selective sweep analysis,we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy fruits.This study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube.展开更多
Centipedegrass[Eremochloa ophiuroides(Munro)Hack.],a member of the Panicoideae subfamily,is one of the most important warm-season turfgrasses originating from China.This grass has an extremely developed prostrate grow...Centipedegrass[Eremochloa ophiuroides(Munro)Hack.],a member of the Panicoideae subfamily,is one of the most important warm-season turfgrasses originating from China.This grass has an extremely developed prostrate growth habit and has been widely used in transitional and warm climatic regions.To better understand the genetic basis of important biological characteristics,such as prostrate growth and seed yield,in warm-season turfgrasses,we present a high-quality reference genome for centipedegrass and use PacBio,BioNano,and Hi-C technologies to anchor the 867.43 Mb genome assembly into nine pseudochromosomes,with a scaffold N50 of 86.05 Mb and 36,572 annotated genes.Centipedegrass was most closely related to sorghum and diverged from their common ancestor~16.8 Mya.We detected a novel chromosome reshuf fling event in centipedegrass,namely,the nest chromosome fusion event in which fusion of chromosomes 8 and 10 of sorghum into chromosome 3 of centipedegrass likely occurred after the divergence of centipedegrass from sorghum.The typical prostrate growth trait in centipedegrass may be linked to the expansion of candidate PROSTRATE GROWTH 1(PROG1)genes on chromosome 2.Two orthologous genes of OsPROGl,EoPROGl,and EoPROG2,were con firmed to increase the stem number and decrease the stem angle in Arabidopsis.Collectively,our assembled reference genome of centipedegrass offers new knowledge and resources to dissect the genome evolution of Panicoideae and accelerate genome-assisted breeding and improvement of plant architecture in turf plants.展开更多
Type 2 diabetes(T2D)mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem.High-throughput sequencing technologies such as whole-genom...Type 2 diabetes(T2D)mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem.High-throughput sequencing technologies such as whole-genome and whole-exome sequencing approaches have provided numerous new insights into the molecular bases of T2D.Recent advances in the application of sequencing technologies to T2D research include,but are not limited to:(1)Fine mapping of causal rare and common genetic variants;(2)Identification of confident genelevel associations;(3)Identification of novel candidate genes by specific scoring approaches;(4)Interrogation of disease-relevant genes and pathways by transcriptional profiling and epigenome mapping techniques;and(5)Investigation of microbial community alterations in patients with T2D.In this work we review these advances in application of next-generation sequencing methods for elucidation of T2D pathogenesis,as well as progress and challenges in implementation of this new knowledge about T2D genetics in diagnosis,prevention,and treatment of the disease.展开更多
Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis hasbeen used as a traditional medicine for more than 2000 years in China and many other Asian countri...Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis hasbeen used as a traditional medicine for more than 2000 years in China and many other Asian countries. Thepharmacological activities of C. chinensis have been validated by research. Here, we present a de novo high-qualitygenome of C. chinensis with a chromosome-level genome of ~958.20 Mb, a contig N50 of 1.58 Mb, and a scaffold N50of 4.53 Mb. We found that the relatively large genome size of C. chinensis was caused by the amplification of longterminal repeat (LTR) retrotransposons. In addition, a whole-genome duplication event in ancestral Ranunculales wasdiscovered. Comparative genomic analysis revealed that the tyrosine decarboxylase (TYDC) and (S)-norcoclaurinesynthase (NCS) genes were expanded and that the aspartate aminotransferase gene (ASP5) was positively selected inthe berberine metabolic pathway. Expression level and HPLC analyses showed that the berberine content was highestin the roots of C. chinensis in the third and fourth years. The chromosome-level reference genome of C. chinensisprovides important genomic data for molecular-assisted breeding and active ingredient biosynthesis.展开更多
Pitaya(Hylocereus)is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide,and it has attracted significant attention because of its betalain-abundant fruits.Nonetheless,t...Pitaya(Hylocereus)is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide,and it has attracted significant attention because of its betalain-abundant fruits.Nonetheless,the lack of a pitaya reference genome significantly hinders studies focused on its evolution,as well as the potential for genetic improvement of this crop.Herein,we employed various sequencing approaches,namely,PacBio-SMRT,Illumina HiSeq paired-end,10×Genomics,and Hi-C(high-throughput chromosome conformation capture)to provide a chromosome-level genomic assembly of‘GHB’pitaya(H.undatus,2n=2x=22 chromosomes).The size of the assembled pitaya genome was 1.41 Gb,with a scaffold N50 of~127.15 Mb.In total,27,753 protein-coding genes and 896.31Mb of repetitive sequences in the H.undatus genome were annotated.Pitaya has undergone a WGT(whole-genome triplication),and a recent WGD(whole-genome duplication)occurred after the gamma event,which is common to the other species in Cactaceae.A total of 29,328 intact LTR-RTs(~696.45Mb)were obtained in H.undatus,of which two significantly expanded lineages,Ty1/copia and Ty3/gypsy,were the main drivers of the expanded genome.A high-density genetic map of F1 hybrid populations of‘GHB’בDahong’pitayas(H.monacanthus)and their parents were constructed,and a total of 20,872 bin markers were identified(56,380 SNPs)for 11 linkage groups.More importantly,through transcriptomic and WGCNA(weighted gene coexpression network analysis),a global view of the gene regulatory network,including structural genes and the transcription factors involved in pitaya fruit betalain biosynthesis,was presented.Our data present a valuable resource for facilitating molecular breeding programs of pitaya and shed novel light on its genomic evolution,as well as the modulation of betalain biosynthesis in edible fruits.展开更多
Opium poppy(Papaver somniferum)is a source of morphine,codeine,and semisynthetic derivatives,including oxycodone and naltrexone.Here,we report the de novo assembly and genomic analysis of P.somniferum traditional land...Opium poppy(Papaver somniferum)is a source of morphine,codeine,and semisynthetic derivatives,including oxycodone and naltrexone.Here,we report the de novo assembly and genomic analysis of P.somniferum traditional landrace‘Chinese Herbal Medicine’.Variations between the 2.62 Gb CHM genome and that of the previously sequenced high noscapine 1(HN1)variety were also explored.Among 79,668 protein-coding genes,we functionally annotated 88.9%,compared to 68.8%reported in the HN1 genome.Gene family and 4DTv comparative analyses with three other Papaveraceae species revealed that opium poppy underwent two whole-genome duplication(WGD)events.The first of these,in ancestral Ranunculales,expanded gene families related to characteristic secondary metabolite production and disease resistance.The more recent species-specific WGD mediated by transposable elements resulted in massive genome expansion.Genes carrying structural variations and large-effect variants associated with agronomically different phenotypes between CHM and HN1 that were identified through our transcriptomic comparison of multiple organs and developmental stages can enable the development of new varieties.These genomic and transcriptomic analyses will provide a valuable resource that informs future basic and agricultural studies of the opium poppy.展开更多
Mesenchymal stromal cells (MSCs) can be obtained from several sources and the significant differences in their properties make it crucial to investigate the differentiation potential of MSCs from different sources to ...Mesenchymal stromal cells (MSCs) can be obtained from several sources and the significant differences in their properties make it crucial to investigate the differentiation potential of MSCs from different sources to determine the optimal source of MSCs. We investigated if this biological heterogeneity in MSCs from different sources results in different mechanisms for their differentiation. In this study, we compared the gene expression patterns of phenotypically defined MSCs derived from three ontogenically different sources: Embryonic stem cells (hES-MSCs), Fetal limb (Flb-MSCs) and Bone Marrow (BM-MSCs). Differentially expressed genes between differentiated cells and undifferentiated controls were compared across the three MSC sources. We found minimal overlap (5% - 16%) in differentially expressed gene sets among the three sources. Flb-MSCs were similar to BM-MSCs based on differential gene expression patterns. Pathway analysis of the differentially expressed genes using Ingenuity Pathway Analysis (IPA) revealed a large variation in the canonical pathways leading to MSC differentiation. The similar canonical pathways among the three sources were lineage specific. The Flb-MSCs showed maximum overlap of canonical pathways with the BM-MSCs, indicating that the Flb-MSCs are an intermediate source between the less specialised hES-MSC source and the more specialised BM-MSC source. The source specific pathways prove that MSCs from the three ontogenically different sources use different biological pathways to obtain similar differentiation outcomes. Thus our study advocates the understanding of biological pathways to obtain optimal sources of MSCs for various clinical applications.展开更多
Breast cancer is one of the leading causes of cancer-related deaths in women worldwide.It is a cancer that originates from the mammary ducts and involves mutations in multiple genes.Recently,the treatment of breast ca...Breast cancer is one of the leading causes of cancer-related deaths in women worldwide.It is a cancer that originates from the mammary ducts and involves mutations in multiple genes.Recently,the treatment of breast cancer has become increasingly challenging owing to the increase in tumor heterogeneity and aggressiveness,which gives rise to therapeutic resistance.Epidemiological,populationbased,and hospital-based case-control studies have demonstrated an association between high intake of certain Allium vegetables and a reduced risk in the development of breast cancer.Diallyl disulfide(DADS)and diallyl trisulfide(DATS)are the main allyl sulfur compounds present in garlic,and are known to exhibit anticancer activity as they interfere with breast cancer cell proliferation,tumor metastasis,and angiogenesis.The present review highlights multidrug resistance mechanisms and their signaling pathways in breast cancer.This review discusses the potential anticancer activities of DADS and DATS,with emphasis on drug resistance in triple-negative breast cancer(TNBC).Understanding the anticancer activities of DADS and DATS provides insights into their potential in targeting drug resistance mechanisms of TNBC,especially in clinical studies.展开更多
Background: Posttraumatic stress disorder (PTSD) is an anxiety disease influenced by both environmental and genetic factors, which affects a patient’s quality of life and social stability. Recent studies have shown t...Background: Posttraumatic stress disorder (PTSD) is an anxiety disease influenced by both environmental and genetic factors, which affects a patient’s quality of life and social stability. Recent studies have shown that the pathogenesis of PTSD is associated with apoptosis;however, the molecular mechanisms that cause such damage are not well-understood. Also it is unclear whether these pathologic alterations are genetically determined or caused by other factors. The aim of this study was to investigate the genetic association of functional polymorphisms in genes coding for apoptosis-related Bcl-2 and Bax proteins with PTSD as well as proteins levels in the blood of affected subjects. Methods: The study groups consisted of 200 combat veterans with PTSD and an equal number of healthy subjects with no family- or past-history of any psychiatric disorders. Bax and Bcl-2 proteins levels in blood were measured by ELISA. DNA samples were genotyped for SNPs using PCR-SSP. Results: According to our results, PTSD patients are characterized by increased levels of apoptotic proteins and the imbalance in the Bax/Bcl-2 ratio compared to healthy subjects. Our results also demonstrate that rs956572*A minor allele of the BCL2 gene was overrepresented in patients with PTSD compared to healthy subjects. Conclusions: The results implicate Bcl-2 and Bax in pathogenesis of PTSD on genetic and protein levels, though further studies on enlarged cohort and in different populations are required.展开更多
Background: Posttraumatic stress disorder (PTSD) is a complex severe polygenic psychiatric disease, influenced by environmental and genetic factors. PTSD development and progression is characterized by cognitive impai...Background: Posttraumatic stress disorder (PTSD) is a complex severe polygenic psychiatric disease, influenced by environmental and genetic factors. PTSD development and progression is characterized by cognitive impairment, which may result in altered processes of nervous system development and synaptic plasticity, where a number of growth factors and their receptors were shown to play important role. Since neurotrophins play an essential role in the development of central nervous system, it is widely implicated in psychiatric disorders. The aim of this study is to investigate the potential association functional polymorphisms of genes encoding netrin G1 (NTNG1), brain-derived neurotrophic factor (BDNF), nerve growth factor (NGF) and its receptor (NGFR) with PTSD. Methods: Study groups consisted of 200 combat veterans with PTSD and an equal number of controls with no family or past history of any psychiatric disorders. The DNA samples were genotyped for NTNG1 rs62811;BDNF rs6265;NGF rs6330, rs4839435;NGFR rs11466155, rs734194 SNPs using polymerase chain reaction with sequence specific primers. Results: According to the results, NGF rs6330 was overrepresented in patients with PTSD compared to controls. Furthermore, negative association for BDNF rs6265, NGF rs4839435 and NGFR rs734194 was observed in PTSD patients. Conclusions: In summary, BDNF rs6265, NGF rs6330, rs4839435 and NGFR rs734194 are implicated in PTSD in Armenian population. However, further research is required to provide the definitive evidence of selected polymorphism association with gene expression.展开更多
基金jointly supported by two research grants(R202016 and R202017)from Beijing Normal University-Hong Kong Baptist University United International College,China。
文摘In this study,we isolated starches from non-traditional sources,including quinoa,lentil,arrowhead,gorgon fruit,sorghum,chickpea,proso millet,and purple potato and investigated their morphology,physicochemical,and functional properties.Significant differences in starch particle morphology,swelling power,solubility,syneresis,crystalline pattern,and pasting viscosity were observed among the starches from these nontraditional sources.Further,all these isolated starches had unique properties because of their characteristic distinct granules when seen under scanning electron microscopy(SEM).The amylose content of the isolated starches shown significant difference(P<0.05),and the values ranged between 11.46%and 37.61%.Results demonstrated that the isolated starches contained between 79.82%to 86.56%starch,indicating that the isolated starches had high purity.X-ray diffraction(XRD)patterns of starches isolated from sorghum,proso millet,quinoa,purple potato,and gorgon fruit presented A-type diffraction pattern;while lentil seeds,arrowhead,and chickpea starches presented C-type diffraction pattern.Overall,these results will promote the development of products based on starch isolated from non-traditional starches.
基金This study was funded by the National Natural Science Foundation of China(No.81973432)the Major Increase and Reduction Project at the Central Level(No.2060302)+1 种基金Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine(ZYYCXTD-D-202005)CAMS Innovation Fund for Medical Sciences(2019-I2M-5-065).
文摘Fallopia multiflora(Thunb.)Harald,a vine belonging to the Polygonaceae family,is used in traditional medicine.The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging.This study describes the assembly of the F.multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data(with a contig N50 of 1.97 megabases),1.44 gigabases of which was assigned to 11 pseudochromosomes.Comparative genomics confirmed that F.multiflora shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation.Combining genomics,transcriptomics,and metabolomics data to map a network of associated genes and metabolites,we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F.multiflora.These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes.Moreover,the reference genome of F.multiflora is a useful addition to the genomes of the Polygonaceae family.
基金supported by the National Natural Science Foundation of China(81870682,81961128021,81670885)National Key R&D Program of China(2022YEF0203200,2021ZD0200103,2018YFA0108300)+2 种基金Guangdong Provincial Key R&D Programs(2018B030335001,2018B030337001)Local Innovative and Research Teams Project of Guangdong(2017BT01S138)Science and Technology Program of Guangzhou(202007030011,202007030010)。
文摘Strabismus and amblyopia are common ophthalmologic developmental diseases caused by abnormal visual experiences. However, the underlying pathogenesis and visual defects are still not fully understood. Most studies have used experimental interference to establish diseaseassociated animal models, while ignoring the natural pathophysiological mechanisms. This study was designed to investigate whether natural strabismus and amblyopia are associated with abnormal neurological defects. We screened one natural strabismic monkey(Macaca fascicularis) and one natural amblyopic monkey from hundreds of monkeys, and retrospectively analyzed one human strabismus case. Neuroimaging, behavioral,neurophysiological, neurostructural, and genovariation features were systematically evaluated using magnetic resonance imaging(MRI), behavioral tasks, flash visual evoked potentials(FVEP),electroretinogram(ERG), optical coherence tomography(OCT), and whole-genome sequencing(WGS), respectively. Results showed that the strabismic patient and natural strabismic and amblyopic monkeys exhibited similar abnormal asymmetries in brain structure, i.e., ipsilateral impaired right hemisphere. Visual behavior, visual function, retinal structure, and fundus of the monkeys were impaired. Aberrant asymmetry in binocular visual function and structure between the strabismic and amblyopic monkeys was closely related, with greater impairment of the left visual pathway.Several similar known mutant genes for strabismus and amblyopia were also identified. In conclusion,natural strabismus and amblyopia are accompanied by abnormal asymmetries of the visual system,especially visual neurophysiological and neurostructural defects. Our results suggest that future therapeutic and mechanistic studies should consider defects and asymmetries throughout the entire visual system.
基金supported by the China Postdoctoral Science Foundation(2021M692792)National Natural Science Foun-dation of China(82103499,81872173,82072959,U1809205,61771249,91959207,81871352)+2 种基金Natural Science Foundation of Jiangsu Province of China(BK20181411)Natural Science Foundation of Zhejiang Province(LD21H160002)Med-ical and Health Science and Technology Plan of Department of Health of Zhejiang Province(WKJ‐ZJ‐1821).
文摘Recurrence is the key factor affecting the prognosis of osteosarcoma.Currently,there is a lack of clinically useful tools to predict osteosarcoma recurrence.The application of pathological images for artificial intelligence‐assisted accurate prediction of tumour out-comes is increasing.Thus,the present study constructed a quantitative histological image classifier with tumour nuclear features to predict osteosarcoma outcomes using haema-toxylin and eosin(H&E)‐stained whole‐slide images(WSIs)from 150 osteosarcoma patients.We first segmented eight distinct tissues in osteosarcoma H&E‐stained WSIs,with an average accuracy of 90.63%on the testing set.The tumour areas were auto-matically and accurately acquired,facilitating the tumour cell nuclear feature extraction process.Based on six selected tumour nuclear features,we developed an osteosarcoma histological image classifier(OSHIC)to predict the recurrence and survival of osteo-sarcoma following standard treatment.The quantitative OSHIC derived from tumour nuclear features independently predicted the recurrence and survival of osteosarcoma patients,thereby contributing to precision oncology.Moreover,we developed a fully automated workflow to extract quantitative image features,evaluate the diagnostic values of feature sets and build classifiers to predict osteosarcoma outcomes.Thus,the present study provides a novel tool for predicting osteosarcoma outcomes,which has a broad application prospect in clinical practice.
文摘BACKGROUND Using gas chromatography-mass spectrometry(GC/MS)analysis,we examined the composition of volatile components present in the yellow and green fruits,seeds,and jam of the scrambling shrub Capparis cartilaginea(C.cartilaginea).These plant samples were collected from Kibbutz Yotvata in Israel.In all the tested samples,isothiocyanates were identified.Utilizing the PASS program,we ascertained the biological activity of these isothiocyanates present in the Capparis genus.The study results highlighted that all isothiocyanates could potentially act as apoptosis agonists,making them strong candidates for antitumor drugs.This information holds significant value for the fields of medicinal chemistry,pharmacology,and practical medicine.AIM To investigate the volatile components present in the yellow and green fruits,seeds,and jam of the C.cartilaginea shrub using GC/MS analysis,to detect isothiocyanates in all the analyzed plant samples,and to assess the biological activity of these isothiocyanates utilizing the PASS program.METHODS We utilized two primary methods to analyze the volatile compounds present in the yellow and green fruits,seeds,and jams of the C.cartilaginea,native to Israel.We identified biologically active isothiocyanates in these samples.Their anticipated biological activities were determined using the PASS program,with the most dominant activities being apoptosis agonist,anticarcinogenic,and antineoplastic specifically for genitourinary cancer.RESULTS Fruits,seeds,and jams containing isothiocyanates,which exhibit antineoplastic and anticarcinogenic activities,could be suggested for cancer prevention and management.Specific isothiocyanates,with therapeutic potential in this realm,could be recommended as potent anticancer agents in practical medicine following clinical trials.CONCLUSION The discovery that isothiocyanates exhibit potent antineoplastic and anticarcinogenic activities was unexpected.Additionally,certain isothiocyanates demonstrated antifungal,antiviral(specifically against arbovirus),and antiparasitic properties.
基金supported by grants from the National Key Research and Development Program of China(2017YFD0101805)the Modern Agro-Industry Technology Research System,China(CARS-23-A-07)+1 种基金the Vegetable Modern Agro-Industry Technology Research System,Tianjin(ITTVRS2017004)the Natural Science Foundation of China(No.31872115).
文摘Cauliflower is an important variety of Brassica oleracea and is planted worldwide.Here,the high-quality genome sequence of cauliflower was reported.The assembled cauliflower genome was 584.60 Mb in size,with a contig N50 of 2.11 Mb,and contained 47,772 genes;56.65%of the genome was composed of repetitive sequences.Among these sequences,long terminal repeats(LTRs)were the most abundant(32.71%of the genome),followed by transposable elements(TEs)(12.62%).Comparative genomic analysis confirmed that after an ancient paleohexaploidy(γ)event,cauliflower underwent two whole-genome duplication(WGD)events shared with Arabidopsis and an additional whole-genome triplication(WGT)event shared with other Brassica species.The present cultivated cauliflower diverged from the ancestral B.oleracea species~3.0 million years ago(Mya).The speciation of cauliflower(~2.0 Mya)was later than that of B.oleracea L.var.capitata(approximately 2.6 Mya)and other Brassica species(over 2.0 Mya).Chromosome no.03 of cauliflower shared the most syntenic blocks with the A,B,and C genomes of Brassica species and its eight other chromosomes,implying that chromosome no.03 might be the most ancient one in the cauliflower genome,which was consistent with the chromosome being inherited from the common ancestor of Brassica species.In addition,2,718 specific genes,228 expanded genes,2 contracted genes,and 1,065 positively selected genes in cauliflower were identified and functionally annotated.These findings provide new insights into the genomic diversity of Brassica species and serve as a valuable reference for molecular breeding of cauliflower.
基金the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA23080603)the National Natural Science Foundation of China(Grant No.31701956)。
文摘The aromatic shrub Lavandula angustifolia produces various volatile terpenoids that serve as resources for essential oils and function in plant-insect communication.To better understand the genetic basis of the terpenoid diversity in lavender,we present a high-quality reference genome for the Chinese lavender cultivar‘Jingxun 2'using PacBio and Hi-C technologies to anchor the 894.50 Mb genome assembly into 27 pseudochromosomes.In addition to the y triplication event,lavender underwent two rounds of whole-genome duplication(WGD)during the Eocene-Oligocene(29.6 MYA)and Miocene-Pliocene(6.9 MYA)transitions.As a result of tandem duplications and lineage-specific WGDs,gene families related to terpenoid biosynthesis in lavender are substantially expanded compared to those of five other species in Lamiaceae.Many terpenoid biosynthesis transcripts are abundant in glandular trichomes.We further integrated the contents of ecologically functional terpenoids and coexpressed terpenoid biosynthetic genes to construct terpenoid-gene networks.Typical gene clusters,including TPS-TPS,TPS-CYP450,and TPS-BAHD,linked with compounds that primarily function as attractants or repellents,were identified by their similar patterns of change during flower development or in response to methyl jasmonate.Comprehensive analysis of the genetic basis of the production of volatiles in lavender could serve as a foundation for future research into lavender evolution,phytochemistry,and ecology.
基金supported by the National Key Research and Development Program of China(2016YFD0100302)the CAAS Program(Y2017PT39)Jiangsu Collaborative Innovation Center for Modern Crop Production。
文摘Common wheat(Triticum aestiuum L.)is one of the most important crops because it provides about 20%of the total calories for humans.T.aestiuum is an excellent modern species for studying concerted evolution of sub-genomes in polyploid species,because of its large chromosome size and three well-known genome donors.Establishment of common wheat genome reference sequence and development of high-density SNP chips provide an excellent foundation to answer questions of wheat evolution and breeding at the genomic level.By genotyping more than 600 accessions of common wheat and their diploid and tetraploid ancestors using a Wheat660 K SNP array,we found dramatic genome changes due to tetraploidization and hexaploidization,in contrast to weaker influences of domestication and breeding on them.Further,since common wheat was introduced in China in 1500 BCE,Chinese landraces formed two subgroups(T.aestiuum-L1 and T.aestiuum-L2)with considerably diverse geographic distributions and agronomic traits.T.aestiuum-L2,mainly distributed in central and east China is found to have more but smaller oval grains with early maturity characteristics.We found that variation and selection in intergenic regions of the A and B sub-genomes dominated this differentiation,in which chromosomes 7 A and 3 B took the leading roles due to the existence of putative genes related to defense responses and environmental adaption in the highly differentiated regions.Large haplotype blocks were detected on 3 B(232.6-398.3 Mb)and 7 A(211.7-272.9 Mb)in the landraces,forming two distinct haplotypes,respectively.We discovered that artificial crosses in breeding promoted recombination in the whole genome,however,this recombination and differentiation was highly asymmetric among the three sub-genomes in homoeologous regions.In addition,we found that the wide use of European and northern American cultivars in breeding at early era,led dramatic changes in Chinese wheat genome,whereas,the recent breeding functioned to optimize it.This study will provide the insight for reconsideration of wheat evolution and breeding,and a new strategy for parent selection in breeding.
基金the Graduate Student Innovation Foundation of Jiangsu Province(No.KYCX20_2992).
文摘Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen.Here,we reveal the chromosome-scale genome sequence of M.polymorpha using an integrated approach including Illumina,PacBio and Hi-C technologies.We combined PacBio full-length RNA-seq,metabolomic analysis,structural anatomy analysis and related physiological indexes to elucidate the important agronomic traits of M.polymorpha for forage and vegetable usage.The assembled M.polymorpha genome consisted of 457.53Mb with a long scaffold N50 of 57.72Mb,and 92.92%(441.83Mb)of the assembly was assigned to seven pseudochromosomes.Comparative genomic analysis revealed that expansion and contraction of the photosynthesis and lignin biosynthetic gene families,respectively,led to enhancement of nutritious compounds and reduced lignin biosynthesis in M.polymorpha.In addition,we found that several positively selected nitrogen metabolism-related genes were responsible for crude protein biosynthesis.Notably,the metabolomic results revealed that a large number of flavonoids,vitamins,alkaloids,and terpenoids were enriched in M.polymorpha.These results imply that the decreased lignin content but relatively high nutrient content of M.polymorpha enhance its edibility and nutritional value as a forage and vegetable.Our genomic data provide a genetic basis that will accelerate functional genomic and breeding research on M.polymorpha as well as other Medicago and legume plants.
基金supported by the Key Science and Technology Program of Henan Province(192102110058 and 202102110046)the Key Research Projects of Henan Higher Education Institutions(17A180030).
文摘Jujube(Ziziphus jujuba Mill.)is an important perennial fruit tree with a range of interesting horticultural traits.It was domesticated from wild jujube(Ziziphus acidojujuba),but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood.Here,we report a comprehensive genome variation map based on the resequencing of 350 accessions,including wild,semi-wild and cultivated jujube plants,at a>15×depth.Using the combination of a genome-wide association study(GWAS)and selective sweep analysis,we identified several candidate genes potentially involved in regulating seven domestication traits in jujube.For fruit shape and kernel shape,we integrated the GWAS approach with transcriptome profiling data,expression analysis and the transgenic validation of a candidate gene to identify a causal gene,ZjFS3,which encodes an ethyleneresponsive transcription factor.Similarly,we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS.In the selective sweep analysis,we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy fruits.This study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube.
基金This work was funded by the National Natural Science Foundation of China[Grant No.31902060,31771870,31902046,32072608]the Natural Science Foundation of Jiangsu Province,China[Grant No.BK20180315,BK20200288]+1 种基金the Jiangsu Agricultural Science and Tech no logy Inno vatio n Fund[Grant No.CX(20)3141]the Open Fund of Jia ngsu Provin cial Key Lab oratory for the Resea rch and Utilizati on of Pla nt Resource,China[Grant No.JSPKLB201840,JSPKLB201817,JSPKLB201927].
文摘Centipedegrass[Eremochloa ophiuroides(Munro)Hack.],a member of the Panicoideae subfamily,is one of the most important warm-season turfgrasses originating from China.This grass has an extremely developed prostrate growth habit and has been widely used in transitional and warm climatic regions.To better understand the genetic basis of important biological characteristics,such as prostrate growth and seed yield,in warm-season turfgrasses,we present a high-quality reference genome for centipedegrass and use PacBio,BioNano,and Hi-C technologies to anchor the 867.43 Mb genome assembly into nine pseudochromosomes,with a scaffold N50 of 86.05 Mb and 36,572 annotated genes.Centipedegrass was most closely related to sorghum and diverged from their common ancestor~16.8 Mya.We detected a novel chromosome reshuf fling event in centipedegrass,namely,the nest chromosome fusion event in which fusion of chromosomes 8 and 10 of sorghum into chromosome 3 of centipedegrass likely occurred after the divergence of centipedegrass from sorghum.The typical prostrate growth trait in centipedegrass may be linked to the expansion of candidate PROSTRATE GROWTH 1(PROG1)genes on chromosome 2.Two orthologous genes of OsPROGl,EoPROGl,and EoPROG2,were con firmed to increase the stem number and decrease the stem angle in Arabidopsis.Collectively,our assembled reference genome of centipedegrass offers new knowledge and resources to dissect the genome evolution of Panicoideae and accelerate genome-assisted breeding and improvement of plant architecture in turf plants.
基金Supported by D.O.Ott Research Institute of Obstetrics,Gynaecology and Reproductology,project 558-2019-0012(АААА-А19-119021290033-1)of FSBSI
文摘Type 2 diabetes(T2D)mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem.High-throughput sequencing technologies such as whole-genome and whole-exome sequencing approaches have provided numerous new insights into the molecular bases of T2D.Recent advances in the application of sequencing technologies to T2D research include,but are not limited to:(1)Fine mapping of causal rare and common genetic variants;(2)Identification of confident genelevel associations;(3)Identification of novel candidate genes by specific scoring approaches;(4)Interrogation of disease-relevant genes and pathways by transcriptional profiling and epigenome mapping techniques;and(5)Investigation of microbial community alterations in patients with T2D.In this work we review these advances in application of next-generation sequencing methods for elucidation of T2D pathogenesis,as well as progress and challenges in implementation of this new knowledge about T2D genetics in diagnosis,prevention,and treatment of the disease.
基金the Basic Research Projects of Chongqing Province(No.cstc2017jxjl-jbky-120013)China National Science and Technology Project of the 12th 5-Year Plan(2011BAI13B02-1)Chongqing Platform and Base Construction Project(cstc2014ptjd10001).
文摘Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis hasbeen used as a traditional medicine for more than 2000 years in China and many other Asian countries. Thepharmacological activities of C. chinensis have been validated by research. Here, we present a de novo high-qualitygenome of C. chinensis with a chromosome-level genome of ~958.20 Mb, a contig N50 of 1.58 Mb, and a scaffold N50of 4.53 Mb. We found that the relatively large genome size of C. chinensis was caused by the amplification of longterminal repeat (LTR) retrotransposons. In addition, a whole-genome duplication event in ancestral Ranunculales wasdiscovered. Comparative genomic analysis revealed that the tyrosine decarboxylase (TYDC) and (S)-norcoclaurinesynthase (NCS) genes were expanded and that the aspartate aminotransferase gene (ASP5) was positively selected inthe berberine metabolic pathway. Expression level and HPLC analyses showed that the berberine content was highestin the roots of C. chinensis in the third and fourth years. The chromosome-level reference genome of C. chinensisprovides important genomic data for molecular-assisted breeding and active ingredient biosynthesis.
基金This work was supported by the National Natural Science Foundation of China(grant nos.31972367 and 31960578)Key Science and Technology Planning Project of Guangzhou(grant no.201904020015)+2 种基金Science and Technology Program of Zhanjiang(grant no.2019A01003)Science and Technology Program of Guangzhou(grant nos.202002020060,201704020003 and 2014Y2-00164)Key Realm R&D Program of Guangdong Province(grant no.2018B020202011).
文摘Pitaya(Hylocereus)is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide,and it has attracted significant attention because of its betalain-abundant fruits.Nonetheless,the lack of a pitaya reference genome significantly hinders studies focused on its evolution,as well as the potential for genetic improvement of this crop.Herein,we employed various sequencing approaches,namely,PacBio-SMRT,Illumina HiSeq paired-end,10×Genomics,and Hi-C(high-throughput chromosome conformation capture)to provide a chromosome-level genomic assembly of‘GHB’pitaya(H.undatus,2n=2x=22 chromosomes).The size of the assembled pitaya genome was 1.41 Gb,with a scaffold N50 of~127.15 Mb.In total,27,753 protein-coding genes and 896.31Mb of repetitive sequences in the H.undatus genome were annotated.Pitaya has undergone a WGT(whole-genome triplication),and a recent WGD(whole-genome duplication)occurred after the gamma event,which is common to the other species in Cactaceae.A total of 29,328 intact LTR-RTs(~696.45Mb)were obtained in H.undatus,of which two significantly expanded lineages,Ty1/copia and Ty3/gypsy,were the main drivers of the expanded genome.A high-density genetic map of F1 hybrid populations of‘GHB’בDahong’pitayas(H.monacanthus)and their parents were constructed,and a total of 20,872 bin markers were identified(56,380 SNPs)for 11 linkage groups.More importantly,through transcriptomic and WGCNA(weighted gene coexpression network analysis),a global view of the gene regulatory network,including structural genes and the transcription factors involved in pitaya fruit betalain biosynthesis,was presented.Our data present a valuable resource for facilitating molecular breeding programs of pitaya and shed novel light on its genomic evolution,as well as the modulation of betalain biosynthesis in edible fruits.
基金the National Science Foundation of China(Grant 81671876)the Fundamental Research Funds for the Central Public Welfare Research Institutes(Grant 2016JB024)。
文摘Opium poppy(Papaver somniferum)is a source of morphine,codeine,and semisynthetic derivatives,including oxycodone and naltrexone.Here,we report the de novo assembly and genomic analysis of P.somniferum traditional landrace‘Chinese Herbal Medicine’.Variations between the 2.62 Gb CHM genome and that of the previously sequenced high noscapine 1(HN1)variety were also explored.Among 79,668 protein-coding genes,we functionally annotated 88.9%,compared to 68.8%reported in the HN1 genome.Gene family and 4DTv comparative analyses with three other Papaveraceae species revealed that opium poppy underwent two whole-genome duplication(WGD)events.The first of these,in ancestral Ranunculales,expanded gene families related to characteristic secondary metabolite production and disease resistance.The more recent species-specific WGD mediated by transposable elements resulted in massive genome expansion.Genes carrying structural variations and large-effect variants associated with agronomically different phenotypes between CHM and HN1 that were identified through our transcriptomic comparison of multiple organs and developmental stages can enable the development of new varieties.These genomic and transcriptomic analyses will provide a valuable resource that informs future basic and agricultural studies of the opium poppy.
文摘Mesenchymal stromal cells (MSCs) can be obtained from several sources and the significant differences in their properties make it crucial to investigate the differentiation potential of MSCs from different sources to determine the optimal source of MSCs. We investigated if this biological heterogeneity in MSCs from different sources results in different mechanisms for their differentiation. In this study, we compared the gene expression patterns of phenotypically defined MSCs derived from three ontogenically different sources: Embryonic stem cells (hES-MSCs), Fetal limb (Flb-MSCs) and Bone Marrow (BM-MSCs). Differentially expressed genes between differentiated cells and undifferentiated controls were compared across the three MSC sources. We found minimal overlap (5% - 16%) in differentially expressed gene sets among the three sources. Flb-MSCs were similar to BM-MSCs based on differential gene expression patterns. Pathway analysis of the differentially expressed genes using Ingenuity Pathway Analysis (IPA) revealed a large variation in the canonical pathways leading to MSC differentiation. The similar canonical pathways among the three sources were lineage specific. The Flb-MSCs showed maximum overlap of canonical pathways with the BM-MSCs, indicating that the Flb-MSCs are an intermediate source between the less specialised hES-MSC source and the more specialised BM-MSC source. The source specific pathways prove that MSCs from the three ontogenically different sources use different biological pathways to obtain similar differentiation outcomes. Thus our study advocates the understanding of biological pathways to obtain optimal sources of MSCs for various clinical applications.
基金supported by UGC-DAE-CSR,Kolkata(Grant No.:KC/CRS/19/RB-04/1047).
文摘Breast cancer is one of the leading causes of cancer-related deaths in women worldwide.It is a cancer that originates from the mammary ducts and involves mutations in multiple genes.Recently,the treatment of breast cancer has become increasingly challenging owing to the increase in tumor heterogeneity and aggressiveness,which gives rise to therapeutic resistance.Epidemiological,populationbased,and hospital-based case-control studies have demonstrated an association between high intake of certain Allium vegetables and a reduced risk in the development of breast cancer.Diallyl disulfide(DADS)and diallyl trisulfide(DATS)are the main allyl sulfur compounds present in garlic,and are known to exhibit anticancer activity as they interfere with breast cancer cell proliferation,tumor metastasis,and angiogenesis.The present review highlights multidrug resistance mechanisms and their signaling pathways in breast cancer.This review discusses the potential anticancer activities of DADS and DATS,with emphasis on drug resistance in triple-negative breast cancer(TNBC).Understanding the anticancer activities of DADS and DATS provides insights into their potential in targeting drug resistance mechanisms of TNBC,especially in clinical studies.
文摘Background: Posttraumatic stress disorder (PTSD) is an anxiety disease influenced by both environmental and genetic factors, which affects a patient’s quality of life and social stability. Recent studies have shown that the pathogenesis of PTSD is associated with apoptosis;however, the molecular mechanisms that cause such damage are not well-understood. Also it is unclear whether these pathologic alterations are genetically determined or caused by other factors. The aim of this study was to investigate the genetic association of functional polymorphisms in genes coding for apoptosis-related Bcl-2 and Bax proteins with PTSD as well as proteins levels in the blood of affected subjects. Methods: The study groups consisted of 200 combat veterans with PTSD and an equal number of healthy subjects with no family- or past-history of any psychiatric disorders. Bax and Bcl-2 proteins levels in blood were measured by ELISA. DNA samples were genotyped for SNPs using PCR-SSP. Results: According to our results, PTSD patients are characterized by increased levels of apoptotic proteins and the imbalance in the Bax/Bcl-2 ratio compared to healthy subjects. Our results also demonstrate that rs956572*A minor allele of the BCL2 gene was overrepresented in patients with PTSD compared to healthy subjects. Conclusions: The results implicate Bcl-2 and Bax in pathogenesis of PTSD on genetic and protein levels, though further studies on enlarged cohort and in different populations are required.
文摘Background: Posttraumatic stress disorder (PTSD) is a complex severe polygenic psychiatric disease, influenced by environmental and genetic factors. PTSD development and progression is characterized by cognitive impairment, which may result in altered processes of nervous system development and synaptic plasticity, where a number of growth factors and their receptors were shown to play important role. Since neurotrophins play an essential role in the development of central nervous system, it is widely implicated in psychiatric disorders. The aim of this study is to investigate the potential association functional polymorphisms of genes encoding netrin G1 (NTNG1), brain-derived neurotrophic factor (BDNF), nerve growth factor (NGF) and its receptor (NGFR) with PTSD. Methods: Study groups consisted of 200 combat veterans with PTSD and an equal number of controls with no family or past history of any psychiatric disorders. The DNA samples were genotyped for NTNG1 rs62811;BDNF rs6265;NGF rs6330, rs4839435;NGFR rs11466155, rs734194 SNPs using polymerase chain reaction with sequence specific primers. Results: According to the results, NGF rs6330 was overrepresented in patients with PTSD compared to controls. Furthermore, negative association for BDNF rs6265, NGF rs4839435 and NGFR rs734194 was observed in PTSD patients. Conclusions: In summary, BDNF rs6265, NGF rs6330, rs4839435 and NGFR rs734194 are implicated in PTSD in Armenian population. However, further research is required to provide the definitive evidence of selected polymorphism association with gene expression.
