Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships betwe...Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships between the genomic variabilities and the current organ-or system-based definition and classification of disease in Western medi⁃cine.The major challenges in the effort to establish and develop precision medicine are how diseases should be defined and classified in an integrated systemic or omic scale and also on an individualized basis.The phenomics approach to the understanding of diseases will allow the transition from focused phenotype/genotype studies to a systemic largescale phenome and genome,proteome,metabolome approach and the identification of a systemically integrated setof biomarkers for diagnosis and prognosis of disease phenome(or Zhenghou).Phenome-wide associated study(PheWAS)may soon lead the field of medical research and provide insightful and novel clues for redefinition of the disease phenome and its clinical classifications and personalized treatment and ultimately precision medicine.Pharma⁃cophenomics is to characterize the phenomes of drug response and also to identify the corresponding therapeutic targets at the level of systems biology.As a complement of pharmacogenomics/proteomics/metabolomics,pharmacoph⁃enomics offers a suite of new technologies and platforms for the transition from focused phenotype-genotype study to a systematic phenome-genome approach and refine drug research with systematically-defined drug response and thera⁃peutic targets.Therefore,pharmacophenomics will provide a new paradigm for the study of drug response including effects and toxicities at the level of systems biology and will identify the corresponding therapeutic targets and principles for combination treatment and prevention of disease using Fangji or Fufang that takes into account individual variability in genes,environment,and lifestyle for each person.展开更多
Objective: This study aimed to explore the experiences of women in the process of formula feeding their infants. The World Health Organization has emphasized the importance of breastfeeding for infant health. After de...Objective: This study aimed to explore the experiences of women in the process of formula feeding their infants. The World Health Organization has emphasized the importance of breastfeeding for infant health. After decades of breastfeeding promotions,breastfeeding rates in Hong Kong have been rising consistently; however, the low continuation rate is alarming. This study explores women's experiences with formula feeding their infants, including factors affecting their decision to do so.Methods: A qualitative approach using an interpretative phenomenological analysis(IPA) was adopted as the study design. Data were collected from 2014 to 2015 through individual in-depth unstructured interviews with 16 women, conducted between 3 and 12 months after the birth of their infant. Data were analyzed using IPA.Results: Three main themes emerged as follows:(1) self-struggle, with the subthemes of feeling like a milk cow and feeling trapped;(2) family conflict, with the subtheme of sharing the spotlight; and(3) interpersonal tensions, with the subthemes of embarrassment,staring, and innocence. Many mothers suffered various stressors and frustrations during breastfeeding. These findings suggest a number of pertinent areas that need to be considered in preparing an infant feeding campaign.Conclusions: The findings of this study reinforce our knowledge of women's struggles with multiple sources of pressure, such as career demands, childcare demands, and family life after giving birth. All mothers should be given assistance in making informed decisions about the optimal approach to feeding their babies given their individual situation and be provided with support to pursue their chosen feeding method.展开更多
An emerging area of interest in understanding disease phenotypes is systems genomics.Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations.A wide num...An emerging area of interest in understanding disease phenotypes is systems genomics.Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations.A wide number of methods have been employed and strategies such as polygenic risk score and allele frequencies have been useful,but understanding the candidate genes harboring those mutations is an unmet goal.In this perspective,using systems genomic approaches,we highlight the application of phenome-interactome networks in diabetes and provide deep insights.LINC01128,which we previously described as candidate for diabetes,is shown as an example to discuss the approach.展开更多
Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional measurements.Most mod...Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional measurements.Most modern crop phenomics use different sensors to collect reflective,emitted,and fluorescence signals,etc.,from plant organs at different spatial and temporal resolutions.Such multi-modal,high-dimensional data not only accelerates basic research on crop physiology,genetics,and whole plant systems modeling,but also supports the optimization of field agronomic practices,internal environments of plant factories,and ultimately crop breeding.Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection,management,sharing,and processing,developing capabilities to measure physiological parameters,and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.展开更多
The rapid development of such research field as multi-omics and artificial intelligence(AI)has made it possible to acquire and analyze the multi-dimensional big data of human phenomes.Increasing evidence has indicated...The rapid development of such research field as multi-omics and artificial intelligence(AI)has made it possible to acquire and analyze the multi-dimensional big data of human phenomes.Increasing evidence has indicated that phenomics can pro-vide a revolutionary strategy and approach for discovering new risk factors,diagnostic biomarkers and precision therapies of diseases,which holds profound advantages over conventional approaches for realizing precision medicine:first,the big data of patients'phenomes can provide remarkably richer information than that of the genomes;second,phenomic studies on diseases may expose the correlations among cross-scale and multi-dimensional phenomic parameters as well as the mecha-nisms underlying the correlations;and third,phenomics-based studies are big data-driven studies,which can significantly enhance the possibility and efficiency for generating novel discoveries.However,phenomic studies on human diseases are still in early developmental stage,which are facing multiple major challenges and tasks:first,there is significant deficiency in analytical and modeling approaches for analyzing the multi-dimensional data of human phenomes;second,it is crucial to establish universal standards for acquirement and management of phenomic data of patients;third,new methods and devices for acquirement of phenomic data of patients under clinical settings should be developed;fourth,it is of significance to establish the regulatory and ethical guidelines for phenomic studies on diseases;and fifth,it is important to develop effective international cooperation.It is expected that phenomic studies on diseases would profoundly and comprehensively enhance our capacity in prevention,diagnosis and treatment of diseases.展开更多
Due to the limitations of existing approaches,a rapid,sensitive,accurate,comprehensive,and generally applicable strategy to diagnose and treat bacterial and fungal infections remains a major challenge.Here,based on th...Due to the limitations of existing approaches,a rapid,sensitive,accurate,comprehensive,and generally applicable strategy to diagnose and treat bacterial and fungal infections remains a major challenge.Here,based on the ramanome technology platform,we propose a culture‐free,one cell resolution,phenome‐genome‐combined strategy called single‐cell identification,viability and vitality tests and source tracking(SCIVVS).For each cell directly extracted from a clinical specimen,the fingerprint region of the D2O‐probed single cell Raman spectrum(SCRS)enables species‐level identification based on a reference SCRS database of pathogen species,whereas the C‐D band accurately quantifies viability,metabolic vitality,phenotypic susceptibility to antimicrobials,and their intercellular heterogeneity.Moreover,to source track a cell,Raman‐activated cell sorting followed by sequencing or cultivation proceeds,producinging an indexed,high coverage genome assembly or a pure culture from precisely one pathogenic cell.Finally,an integrated SCIVVS workflow that features automated profiling and sorting of metabolic and morphological phenomes can complete the entire process in only a few hours.Because it resolves heterogeneity for both the metabolic phenome and genome,targets functions,can be automated,and is orders‐of‐magnitude faster while cost‐effective,SCIVVS is a new technological and data framework to diagnose and treat bacterial and fungal infections in various clinical and disease control settings.展开更多
Human phenomics is defned as the comprehensive collection of observable phenotypes and characteristics infuenced by a complex interplay among factors at multiple scales.These factors include genes,epigenetics at the m...Human phenomics is defned as the comprehensive collection of observable phenotypes and characteristics infuenced by a complex interplay among factors at multiple scales.These factors include genes,epigenetics at the microscopic level,organs,microbiome at the mesoscopic level,and diet and environmental exposures at the macroscopic level.“Phenomic imaging”utilizes various imaging techniques to visualize and measure anatomical structures,biological functions,metabolic processes,and biochemical activities across diferent scales,both in vivo and ex vivo.Unlike conventional medical imaging focused on disease diagnosis,phenomic imaging captures both normal and abnormal traits,facilitating detailed correlations between macro-and micro-phenotypes.This approach plays a crucial role in deciphering phenomes.This review provides an overview of diferent phenomic imaging modalities and their applications in human phenomics.Additionally,it explores the associations between phenomic imaging and other omics disciplines,including genomics,transcriptomics,proteomics,immunomics,and metabolomics.By integrating phenomic imaging with other omics data,such as genomics and metabolomics,a comprehensive understanding of biological systems can be achieved.This integration paves the way for the development of new therapeutic approaches and diagnostic tools.展开更多
The bacterial family Mycobacteriaceae includes pathogenic and nonpathogenic bacteria,and systematic research on their genome and phenome can give comprehensive perspectives for exploring their disease mechanism.In thi...The bacterial family Mycobacteriaceae includes pathogenic and nonpathogenic bacteria,and systematic research on their genome and phenome can give comprehensive perspectives for exploring their disease mechanism.In this study,the pheno-types of Mycobacteriaceae were inferred from available phenomic data,and 82 microbial phenotypic traits were recruited as data elements of the microbial phenome.This Mycobacteriaceae phenome contains five categories and 20 subcategories of polyphasic phenotypes,and three categories and eight subcategories of functional phenotypes,all of which are complemen-tary to the existing data standards of microbial phenotypes.The phenomic data of Mycobacteriaceae strains were compiled by literature mining,third-party database integration,and bioinformatics annotation.The phenotypes were searchable and comparable from the website of the Mycobacteriaceae Phenome Atlas(MPA,https://www.biosi no.org/mpa/).A topological data analysis of MPA revealed the co-evolution between Mycobacterium tuberculosis and virulence factors,and uncovered potential pathogenicity-associated phenotypes.Two hundred and sixty potential pathogen-enriched pathways were found by Fisher's exact test.The application of MPA may provide novel insights into the pathogenicity mechanism and antimicrobial targets of Mycobacteriaceae.展开更多
The tree shrew(Tupaia belangeri)has long been proposed as a suitable alternative to non-human primates(NHPs)in biomedical and laboratory research due to its close evolutionary relationship with primates.In recent year...The tree shrew(Tupaia belangeri)has long been proposed as a suitable alternative to non-human primates(NHPs)in biomedical and laboratory research due to its close evolutionary relationship with primates.In recent years,significant advances have facilitated tree shrew studies,including the determination of the tree shrew genome,genetic manipulation using spermatogonial stem cells,viral vector-mediated gene delivery,and mapping of the tree shrew brain atlas.However,the limited availability of tree shrews globally remains a substantial challenge in the field.Additionally,determining the key questions best answered using tree shrews constitutes another difficulty.Tree shrew models have historically been used to study hepatitis B virus(HBV)and hepatitis C virus(HCV)infection,myopia,and psychosocial stress-induced depression,with more recent studies focusing on developing animal models for infectious and neurodegenerative diseases.Despite these efforts,the impact of tree shrew models has not yet matched that of rodent or NHP models in biomedical research.This review summarizes the prominent advancements in tree shrew research and reflects on the key biological questions addressed using this model.We emphasize that intensive dedication and robust international collaboration are essential for achieving breakthroughs in tree shrew studies.The use of tree shrews as a unique resource is expected to gain considerable attention with the application of advanced techniques and the development of viable animal models,meeting the increasing demands of life science and biomedical research.展开更多
Since whole-genome sequencing of many crops has been achieved,crop functional genomics studies have stepped into the big-data and high-throughput era.However,acquisition of large-scale phenotypic data has become one o...Since whole-genome sequencing of many crops has been achieved,crop functional genomics studies have stepped into the big-data and high-throughput era.However,acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies.Nevertheless,recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years.In this article,we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades.We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies.Finally,we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap.It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.展开更多
Genome sequencing opened the flood gate of ＂-omics＂ studies, among which the research about correlations between genomic and phenomic variables is an important part. With the development of functional genomics and s...Genome sequencing opened the flood gate of ＂-omics＂ studies, among which the research about correlations between genomic and phenomic variables is an important part. With the development of functional genomics and systems biology, genome-wide investigation of the correlations between many genomic and phenomic variables became possible. In this review, five genomic variables, such as evolution rate （or ＂age＂ of the gene）, the length of intron and ORF （protein length） in one gene, the biases of amino acid composition and codon usage, along with the phenomic variables related to expression patterns （level and breadth） are focused on. In most cases, genes with higher mRNA/protein expression level tend to evolve slowly, have less intronic DNA, code for smaller proteins, and have higher biases of amino acid composition and codon usage. In addition, broadly expressed proteins evolve more slowly and are shorter than tissue-specific proteins. Studies in this field are helpful for deeper understanding the signatures of selection mediated by the features of gene expression and are of great significance to enrich the evolution theory.展开更多
Plant phenomics(PP)has been recognized as a bottleneck in studying the interactions of genomics and environment on plants,limiting the progress of smart breeding and precise cultivation.High-throughput plant phenotypi...Plant phenomics(PP)has been recognized as a bottleneck in studying the interactions of genomics and environment on plants,limiting the progress of smart breeding and precise cultivation.High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits.Proximal and remote sensing(PRS)techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis.Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications.This progress covers most aspects of PRS application in PP,including patterns of global spatial distribution and temporal dynamics,specific PRS technologies,phenotypic research fields,working environments,species,and traits.Subsequently,we demonstrate how to link PRS to multi-omics studies,including how to achieve multi-dimensional PRS data acquisition and processing,how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance,and how to link PP to multi-omics association analysis.Finally,we identify three future perspectives for PRS-based PP:(1)strengthening the spatial and temporal consistency of PRS data,(2)exploring novel phenotypic traits,and(3)facilitating multi-omics communication.展开更多
The systematicness of phenomics and Traditional Chinese Medicine(TCM)enable these two disciplines to interlink with each other.This article discussed the similarity in theory and application between TCM and phenomics ...The systematicness of phenomics and Traditional Chinese Medicine(TCM)enable these two disciplines to interlink with each other.This article discussed the similarity in theory and application between TCM and phenomics and illustrates their respective advantages in diagnosis and treatment of diseases,forming a new discipline eventually.Chinese medicine phe-nomics(Chinmedphenomics)is built on classic TCM,combined with phenomics technology,and the development of which needs the mega cohort with TCM syndrome and the characteristics of precision medicine as well as multi-disciplinary coop-eration,which is personalized,precise and promising,providing unique scientific insights into understanding human health.展开更多
Skin is a complex ecosystem colonized by millions of microorganisms,including bacteria,fungi,and viruses.Skin microbiota is believed to exert critical functions in maintaining host skin health.Profiling the structure ...Skin is a complex ecosystem colonized by millions of microorganisms,including bacteria,fungi,and viruses.Skin microbiota is believed to exert critical functions in maintaining host skin health.Profiling the structure of skin microbial community is the first step to overview the ecosystem.However,the community composition is highly individualized and extremely complex.To explore the fundamental factors driving the complexity of the ecosystem,namely the selection pressures,we review the present studies on skin microbiome from the perspectives of ecology.This review summarizes the following:(1)the composition of substances/nutrients in the cutaneous ecological environment that are derived from the host and the environment,highlighting their proposed function on skin microbiota;(2)the features of dominant skin commensals to occupy ecological niches,through self-adaptation and microbe–microbe interactions;(3)how skin microbes,by their structures or bioactive molecules,reshape host skin phenotypes,including skin immunity,maintenance of skin physiology such as pH and hydration,ultraviolet(UV)protection,odor production,and wound healing.This review aims to re-examine the host–microbe interactions from the ecological perspectives and hopefully to give new inspiration to this field.展开更多
The spin echo (SE) phenomenon discovered in the pulse nuclear magnetic resonance (PNMR) exerts significant influence on the field of magnetic resonance. It was first reported by E. L. Hahn in 1950. The discovery of SE...The spin echo (SE) phenomenon discovered in the pulse nuclear magnetic resonance (PNMR) exerts significant influence on the field of magnetic resonance. It was first reported by E. L. Hahn in 1950. The discovery of SE provided a new method for a better understanding of NMR phenomenon. For example, it solved the difficul-展开更多
Linking natural genetic variation to trait variation can help determine the functional roles ofdifferent genes.Variations of one or several traits are often assessed separately.High-throughput phenotyping and data min...Linking natural genetic variation to trait variation can help determine the functional roles ofdifferent genes.Variations of one or several traits are often assessed separately.High-throughput phenotyping and data mining can capture dozens or hundreds of traits from the same individuals.Here,we test the association between markers within a gene and many traits simultaneously.This genome–phenome wide association study(GPWAS)is both a multi-marker and multi-trait test.Genes identified using GPWAS with 260 phenotypic traits in maize were enriched for genes independently linked to phenotypic variation.Traits associated with classical mutants were consistent with reported phenotypes for mutant alleles.Genes linked to phenomic variation in maize using GPWAS shared molecular,population genetic,and evolutionary features with classical mutants in maize.Genes linked to phenomic variation in Arabidopsis using GPWAS are significantly enriched in genes with known loss-of-function phenotypes.GPWAS may be an effective strategy to identify genes in which loss-of-function alleles produce mutant phenotypes.The shared signatures present in classical mutants and genes identified using GPWAS may be markers for genes with a role in specifying plant phenotypes generally or pleiotropy specifically.展开更多
文摘Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships between the genomic variabilities and the current organ-or system-based definition and classification of disease in Western medi⁃cine.The major challenges in the effort to establish and develop precision medicine are how diseases should be defined and classified in an integrated systemic or omic scale and also on an individualized basis.The phenomics approach to the understanding of diseases will allow the transition from focused phenotype/genotype studies to a systemic largescale phenome and genome,proteome,metabolome approach and the identification of a systemically integrated setof biomarkers for diagnosis and prognosis of disease phenome(or Zhenghou).Phenome-wide associated study(PheWAS)may soon lead the field of medical research and provide insightful and novel clues for redefinition of the disease phenome and its clinical classifications and personalized treatment and ultimately precision medicine.Pharma⁃cophenomics is to characterize the phenomes of drug response and also to identify the corresponding therapeutic targets at the level of systems biology.As a complement of pharmacogenomics/proteomics/metabolomics,pharmacoph⁃enomics offers a suite of new technologies and platforms for the transition from focused phenotype-genotype study to a systematic phenome-genome approach and refine drug research with systematically-defined drug response and thera⁃peutic targets.Therefore,pharmacophenomics will provide a new paradigm for the study of drug response including effects and toxicities at the level of systems biology and will identify the corresponding therapeutic targets and principles for combination treatment and prevention of disease using Fangji or Fufang that takes into account individual variability in genes,environment,and lifestyle for each person.
文摘Objective: This study aimed to explore the experiences of women in the process of formula feeding their infants. The World Health Organization has emphasized the importance of breastfeeding for infant health. After decades of breastfeeding promotions,breastfeeding rates in Hong Kong have been rising consistently; however, the low continuation rate is alarming. This study explores women's experiences with formula feeding their infants, including factors affecting their decision to do so.Methods: A qualitative approach using an interpretative phenomenological analysis(IPA) was adopted as the study design. Data were collected from 2014 to 2015 through individual in-depth unstructured interviews with 16 women, conducted between 3 and 12 months after the birth of their infant. Data were analyzed using IPA.Results: Three main themes emerged as follows:(1) self-struggle, with the subthemes of feeling like a milk cow and feeling trapped;(2) family conflict, with the subtheme of sharing the spotlight; and(3) interpersonal tensions, with the subthemes of embarrassment,staring, and innocence. Many mothers suffered various stressors and frustrations during breastfeeding. These findings suggest a number of pertinent areas that need to be considered in preparing an infant feeding campaign.Conclusions: The findings of this study reinforce our knowledge of women's struggles with multiple sources of pressure, such as career demands, childcare demands, and family life after giving birth. All mothers should be given assistance in making informed decisions about the optimal approach to feeding their babies given their individual situation and be provided with support to pursue their chosen feeding method.
文摘An emerging area of interest in understanding disease phenotypes is systems genomics.Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations.A wide number of methods have been employed and strategies such as polygenic risk score and allele frequencies have been useful,but understanding the candidate genes harboring those mutations is an unmet goal.In this perspective,using systems genomic approaches,we highlight the application of phenome-interactome networks in diabetes and provide deep insights.LINC01128,which we previously described as candidate for diabetes,is shown as an example to discuss the approach.
基金supported by National Research and Development Program of Ministry of Science and Technology of China(2020YFA0907600,2018YFA0900600,2019YFA09004600)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27020105,XDB37020104,XDA24010203,XDA0450202)+2 种基金National Science Foundation of China(31870214)the National Key Research and Development Program of China(2023YFF1000100)STI2030eMajor Projects(2023ZD04076).
文摘Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional measurements.Most modern crop phenomics use different sensors to collect reflective,emitted,and fluorescence signals,etc.,from plant organs at different spatial and temporal resolutions.Such multi-modal,high-dimensional data not only accelerates basic research on crop physiology,genetics,and whole plant systems modeling,but also supports the optimization of field agronomic practices,internal environments of plant factories,and ultimately crop breeding.Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection,management,sharing,and processing,developing capabilities to measure physiological parameters,and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.
基金the financial support by two research grants from Shanghai Municipal Science and Technology Major Project(No.2017SHZDZX01)(to W.Y.).
文摘The rapid development of such research field as multi-omics and artificial intelligence(AI)has made it possible to acquire and analyze the multi-dimensional big data of human phenomes.Increasing evidence has indicated that phenomics can pro-vide a revolutionary strategy and approach for discovering new risk factors,diagnostic biomarkers and precision therapies of diseases,which holds profound advantages over conventional approaches for realizing precision medicine:first,the big data of patients'phenomes can provide remarkably richer information than that of the genomes;second,phenomic studies on diseases may expose the correlations among cross-scale and multi-dimensional phenomic parameters as well as the mecha-nisms underlying the correlations;and third,phenomics-based studies are big data-driven studies,which can significantly enhance the possibility and efficiency for generating novel discoveries.However,phenomic studies on human diseases are still in early developmental stage,which are facing multiple major challenges and tasks:first,there is significant deficiency in analytical and modeling approaches for analyzing the multi-dimensional data of human phenomes;second,it is crucial to establish universal standards for acquirement and management of phenomic data of patients;third,new methods and devices for acquirement of phenomic data of patients under clinical settings should be developed;fourth,it is of significance to establish the regulatory and ethical guidelines for phenomic studies on diseases;and fifth,it is important to develop effective international cooperation.It is expected that phenomic studies on diseases would profoundly and comprehensively enhance our capacity in prevention,diagnosis and treatment of diseases.
基金National Key R&D Program of China,Grant/Award Number:2022YFA1304101CAS,Grant/Award Number:XDB29050400+1 种基金National Natural Science Foundation of China,Grant/Award Number:32030003Shenzhen‐Hong Kong Innovation Circle Plan,Grant/Award Number:SGDX2019081623060946。
文摘Due to the limitations of existing approaches,a rapid,sensitive,accurate,comprehensive,and generally applicable strategy to diagnose and treat bacterial and fungal infections remains a major challenge.Here,based on the ramanome technology platform,we propose a culture‐free,one cell resolution,phenome‐genome‐combined strategy called single‐cell identification,viability and vitality tests and source tracking(SCIVVS).For each cell directly extracted from a clinical specimen,the fingerprint region of the D2O‐probed single cell Raman spectrum(SCRS)enables species‐level identification based on a reference SCRS database of pathogen species,whereas the C‐D band accurately quantifies viability,metabolic vitality,phenotypic susceptibility to antimicrobials,and their intercellular heterogeneity.Moreover,to source track a cell,Raman‐activated cell sorting followed by sequencing or cultivation proceeds,producinging an indexed,high coverage genome assembly or a pure culture from precisely one pathogenic cell.Finally,an integrated SCIVVS workflow that features automated profiling and sorting of metabolic and morphological phenomes can complete the entire process in only a few hours.Because it resolves heterogeneity for both the metabolic phenome and genome,targets functions,can be automated,and is orders‐of‐magnitude faster while cost‐effective,SCIVVS is a new technological and data framework to diagnose and treat bacterial and fungal infections in various clinical and disease control settings.
基金Shanghai Municipal Science and Technology Major Project(2017SHZDZX01).
文摘Human phenomics is defned as the comprehensive collection of observable phenotypes and characteristics infuenced by a complex interplay among factors at multiple scales.These factors include genes,epigenetics at the microscopic level,organs,microbiome at the mesoscopic level,and diet and environmental exposures at the macroscopic level.“Phenomic imaging”utilizes various imaging techniques to visualize and measure anatomical structures,biological functions,metabolic processes,and biochemical activities across diferent scales,both in vivo and ex vivo.Unlike conventional medical imaging focused on disease diagnosis,phenomic imaging captures both normal and abnormal traits,facilitating detailed correlations between macro-and micro-phenotypes.This approach plays a crucial role in deciphering phenomes.This review provides an overview of diferent phenomic imaging modalities and their applications in human phenomics.Additionally,it explores the associations between phenomic imaging and other omics disciplines,including genomics,transcriptomics,proteomics,immunomics,and metabolomics.By integrating phenomic imaging with other omics data,such as genomics and metabolomics,a comprehensive understanding of biological systems can be achieved.This integration paves the way for the development of new therapeutic approaches and diagnostic tools.
基金supported by the National Key R&D Program of China(2021YFF0703702,2021YFC2301502,and 2018YFA0900704)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB38030100)+1 种基金Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)the Biological Resources Programme,Chinese Academy of Sciences(KFJ-BRP-017-79 and KFJ-BRP-009-001).
文摘The bacterial family Mycobacteriaceae includes pathogenic and nonpathogenic bacteria,and systematic research on their genome and phenome can give comprehensive perspectives for exploring their disease mechanism.In this study,the pheno-types of Mycobacteriaceae were inferred from available phenomic data,and 82 microbial phenotypic traits were recruited as data elements of the microbial phenome.This Mycobacteriaceae phenome contains five categories and 20 subcategories of polyphasic phenotypes,and three categories and eight subcategories of functional phenotypes,all of which are complemen-tary to the existing data standards of microbial phenotypes.The phenomic data of Mycobacteriaceae strains were compiled by literature mining,third-party database integration,and bioinformatics annotation.The phenotypes were searchable and comparable from the website of the Mycobacteriaceae Phenome Atlas(MPA,https://www.biosi no.org/mpa/).A topological data analysis of MPA revealed the co-evolution between Mycobacterium tuberculosis and virulence factors,and uncovered potential pathogenicity-associated phenotypes.Two hundred and sixty potential pathogen-enriched pathways were found by Fisher's exact test.The application of MPA may provide novel insights into the pathogenicity mechanism and antimicrobial targets of Mycobacteriaceae.
基金supported by the STI2030-Major Projects(2021ZD0200900 to Y.G.Y.)"Light of West China" Program of the Chinese Academy of Sciences(xbzg-zdsys-202302 to Y.G.Y.)
文摘The tree shrew(Tupaia belangeri)has long been proposed as a suitable alternative to non-human primates(NHPs)in biomedical and laboratory research due to its close evolutionary relationship with primates.In recent years,significant advances have facilitated tree shrew studies,including the determination of the tree shrew genome,genetic manipulation using spermatogonial stem cells,viral vector-mediated gene delivery,and mapping of the tree shrew brain atlas.However,the limited availability of tree shrews globally remains a substantial challenge in the field.Additionally,determining the key questions best answered using tree shrews constitutes another difficulty.Tree shrew models have historically been used to study hepatitis B virus(HBV)and hepatitis C virus(HCV)infection,myopia,and psychosocial stress-induced depression,with more recent studies focusing on developing animal models for infectious and neurodegenerative diseases.Despite these efforts,the impact of tree shrew models has not yet matched that of rodent or NHP models in biomedical research.This review summarizes the prominent advancements in tree shrew research and reflects on the key biological questions addressed using this model.We emphasize that intensive dedication and robust international collaboration are essential for achieving breakthroughs in tree shrew studies.The use of tree shrews as a unique resource is expected to gain considerable attention with the application of advanced techniques and the development of viable animal models,meeting the increasing demands of life science and biomedical research.
基金the National Key Research and Development Program of China(2016YFD0100101-18,2016YFD0100103)the National Natural Science Foundation of China(31770397,21800305)+2 种基金the Fundamental Research Funds for the Central Universities(2662017PY058,2662017QD044)UK-China grant BBSRC(grant no.BB/R02118X/1)the National Institute of Food and Agriculture,U.S.Department of Agriculture,Hatch project(ALA014-1-16016).
文摘Since whole-genome sequencing of many crops has been achieved,crop functional genomics studies have stepped into the big-data and high-throughput era.However,acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies.Nevertheless,recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years.In this article,we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades.We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies.Finally,we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap.It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.
基金supported by the National Hightech R&D Program (863 Program) (No. 2006AA02A308)the National Basic Research Program of China (973 Program) (No. 2006CB910401, 2006CB910801 and 2006CB910600)+3 种基金the National Natural Science Foundation of China (No. 30700988 and 30700356)the National Natural Science Foundation of China for Creative Research Groups (No. 30621063)the Chinese State Key Project Specialized for Infectious Diseases (No. 2008ZX10002-016, 2009ZX10004-103 and 2009ZX09301002)supported by the State Key Laboratory of Proteomics (No. SKLP-Y200801)
文摘Genome sequencing opened the flood gate of ＂-omics＂ studies, among which the research about correlations between genomic and phenomic variables is an important part. With the development of functional genomics and systems biology, genome-wide investigation of the correlations between many genomic and phenomic variables became possible. In this review, five genomic variables, such as evolution rate （or ＂age＂ of the gene）, the length of intron and ORF （protein length） in one gene, the biases of amino acid composition and codon usage, along with the phenomic variables related to expression patterns （level and breadth） are focused on. In most cases, genes with higher mRNA/protein expression level tend to evolve slowly, have less intronic DNA, code for smaller proteins, and have higher biases of amino acid composition and codon usage. In addition, broadly expressed proteins evolve more slowly and are shorter than tissue-specific proteins. Studies in this field are helpful for deeper understanding the signatures of selection mediated by the features of gene expression and are of great significance to enrich the evolution theory.
基金supported by the Hainan Yazhou Bay Seed Lab(no.B21HJ1005)the Fundamental Research Funds for the Central Universities(no.KYCYXT2022017)+5 种基金the Open Project of Key Laboratory of Oasis Eco-agriculture,Xinjiang Production and Construction Corps(no.202101)the Jiangsu Association for Science and Technology Independent Innovation Fund Project(no.CX(21)3107)the High Level Personnel Project of Jiangsu Province(no.JSSCBS20210271)the China Postdoctoral Science Foundation(no.2021M691490)the Jiangsu Planned Projects for Postdoctoral Research Funds(no.2021K520C)the JBGS Project of Seed Industry Revitalization in Jiangsu Province(no.JBGS[2021]007).
文摘Plant phenomics(PP)has been recognized as a bottleneck in studying the interactions of genomics and environment on plants,limiting the progress of smart breeding and precise cultivation.High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits.Proximal and remote sensing(PRS)techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis.Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications.This progress covers most aspects of PRS application in PP,including patterns of global spatial distribution and temporal dynamics,specific PRS technologies,phenotypic research fields,working environments,species,and traits.Subsequently,we demonstrate how to link PRS to multi-omics studies,including how to achieve multi-dimensional PRS data acquisition and processing,how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance,and how to link PP to multi-omics association analysis.Finally,we identify three future perspectives for PRS-based PP:(1)strengthening the spatial and temporal consistency of PRS data,(2)exploring novel phenotypic traits,and(3)facilitating multi-omics communication.
基金supported by National Key R&D Program of China(2018YFC1704300)National Natural Science Foundation of China(81730107,81973883)+6 种基金Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)Shanghai Scientific Research Project(17401971100)Shanghai TCM Medical Center of Chronic Disease(2017ZZ01010)Three Years Action to Accelerate the Development of Traditional Chinese Medicine Plan(ZY(2018-2020)-CCCX-3003)the Program for Innovative Research Team of Ministry of Education of China(IRT1270)the Program for Innovative Research Team of Ministry of Science and Technology of China(2015RA4002)Sanming Project of Medicine in Shenzhen(SZSM201808072).
文摘The systematicness of phenomics and Traditional Chinese Medicine(TCM)enable these two disciplines to interlink with each other.This article discussed the similarity in theory and application between TCM and phenomics and illustrates their respective advantages in diagnosis and treatment of diseases,forming a new discipline eventually.Chinese medicine phe-nomics(Chinmedphenomics)is built on classic TCM,combined with phenomics technology,and the development of which needs the mega cohort with TCM syndrome and the characteristics of precision medicine as well as multi-disciplinary coop-eration,which is personalized,precise and promising,providing unique scientific insights into understanding human health.
基金This work was supported by the Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)the CAMS Innovation Fund for Medical Sciences(2019-I2M-5-066)+1 种基金the 111 Project(B13016)a startup grant from the Greater Bay Area Institute of Precision Medicine(Guangzhou),Fudan University to JX.
文摘Skin is a complex ecosystem colonized by millions of microorganisms,including bacteria,fungi,and viruses.Skin microbiota is believed to exert critical functions in maintaining host skin health.Profiling the structure of skin microbial community is the first step to overview the ecosystem.However,the community composition is highly individualized and extremely complex.To explore the fundamental factors driving the complexity of the ecosystem,namely the selection pressures,we review the present studies on skin microbiome from the perspectives of ecology.This review summarizes the following:(1)the composition of substances/nutrients in the cutaneous ecological environment that are derived from the host and the environment,highlighting their proposed function on skin microbiota;(2)the features of dominant skin commensals to occupy ecological niches,through self-adaptation and microbe–microbe interactions;(3)how skin microbes,by their structures or bioactive molecules,reshape host skin phenotypes,including skin immunity,maintenance of skin physiology such as pH and hydration,ultraviolet(UV)protection,odor production,and wound healing.This review aims to re-examine the host–microbe interactions from the ecological perspectives and hopefully to give new inspiration to this field.
文摘The spin echo (SE) phenomenon discovered in the pulse nuclear magnetic resonance (PNMR) exerts significant influence on the field of magnetic resonance. It was first reported by E. L. Hahn in 1950. The discovery of SE provided a new method for a better understanding of NMR phenomenon. For example, it solved the difficul-
基金This work is supported by National Science Foundation Awards MCB-1838307 and OIA-1826781 to J.C.S.In additionwe received support from the Quantitative Life Sciences Initiative at the University of Nebraska-Lincoln+1 种基金which in turn received support from the University of Nebraska Program of ExcellenceThis work was completed utilizing the Holla nd Computi ng Center of the University of Nebraska,which receives support from the Nebraska Research Initiative.
文摘Linking natural genetic variation to trait variation can help determine the functional roles ofdifferent genes.Variations of one or several traits are often assessed separately.High-throughput phenotyping and data mining can capture dozens or hundreds of traits from the same individuals.Here,we test the association between markers within a gene and many traits simultaneously.This genome–phenome wide association study(GPWAS)is both a multi-marker and multi-trait test.Genes identified using GPWAS with 260 phenotypic traits in maize were enriched for genes independently linked to phenotypic variation.Traits associated with classical mutants were consistent with reported phenotypes for mutant alleles.Genes linked to phenomic variation in maize using GPWAS shared molecular,population genetic,and evolutionary features with classical mutants in maize.Genes linked to phenomic variation in Arabidopsis using GPWAS are significantly enriched in genes with known loss-of-function phenotypes.GPWAS may be an effective strategy to identify genes in which loss-of-function alleles produce mutant phenotypes.The shared signatures present in classical mutants and genes identified using GPWAS may be markers for genes with a role in specifying plant phenotypes generally or pleiotropy specifically.
