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
Identifying genetic variants that contribute to phenotypic variation is expected to provide insights into the etiology of complex traits. Here we show how combining genetic mapping in an outbred population of rats wit...Identifying genetic variants that contribute to phenotypic variation is expected to provide insights into the etiology of complex traits. Here we show how combining genetic mapping in an outbred population of rats with sequence data from the progenitors of the population made it possible to identify causal variants and genes for a large number of phenotypes. We identified 355 genomic loci contributing to 122 measures relevant to six models of disease, including fear-related behaviors and experimental autoimmune encephalomyelitis. At 35 of those loci we identified the responsible gene, and in some cases, the responsible variant.展开更多
Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signa...Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka ×Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL colocating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley.展开更多
Biological databases serve as a global fundamental infrastructure for the worldwide scientific community,which dramatically aid the transformation of big data into knowledge discovery and drive significant innovations...Biological databases serve as a global fundamental infrastructure for the worldwide scientific community,which dramatically aid the transformation of big data into knowledge discovery and drive significant innovations in a wide range of research fields.Given the rapid data production,biological databases continue to increase in size and importance.To build a catalog of worldwide biological databases,we curate a total of 5825 biological databases from 8931 publications,which are geographically distributed in 72 countries/regions and developed by 1975 institutions(as of September 20,2022).We further devise a z-index,a novel index to characterize the scientific impact of a database,and rank all these biological databases as well as their hosting institutions and countries in terms of citation and z-index.Consequently,we present a series of statistics and trends of worldwide biological databases,yielding a global perspective to better understand their status and impact for life and health sciences.An up-to-date catalog of worldwide biological databases,as well as their curated meta-information and derived statistics,is publicly available at Database Commons(https://ngdc.cncb.ac.cn/databasecommons/).展开更多
The FAIR principles describe characteristics intended to support access to and reuse of digital artifacts in the scientific research ecosystem.Persistent,globally unique identifiers,resolvable on the Web,and associate...The FAIR principles describe characteristics intended to support access to and reuse of digital artifacts in the scientific research ecosystem.Persistent,globally unique identifiers,resolvable on the Web,and associated with a set of additional descriptive metadata,are foundational to FAIR data.Here we describe some basic principles and exemplars for their design,use and orchestration with other system elements to achieve FAIRness for digital research objects.展开更多
RNA in situ hybridization (ISH), including chromogenic ISH (CISH) and fluorescent ISH (FISH), has become a powerful tool for revealing the spatial distribution ofgene transcripts in model organisms. Previously, ...RNA in situ hybridization (ISH), including chromogenic ISH (CISH) and fluorescent ISH (FISH), has become a powerful tool for revealing the spatial distribution ofgene transcripts in model organisms. Previously, we developed a robust protocol for wholemount RNA CISH in the pea aphid Acyrthosiphon pisum, an emerging insect genomicmodel. In order to improve the resolving capacity of gene detection, we comprehensively surveyed current protocols of whole-mount RNA-FISH and developed protocols that allow,using confocal microscopy, clearer visualization of target messenger RNAs (mRNAs) - including those subcellularly localized and those with spatially overlapping expression. Wefind that Fast dye-based substrate fluorescence (SF), tyramide signal amplification (TSA), and TSA Plus all enable identifying gene expression thanks to multiplex amplificationof fluorescent signals. By contrast, methods of direct fluorescence (DF) do not allow visualizing signals. Detection of a single gene target was achieved with SF and TSA Plusfor most mRNAs, whereas TSA only allowed visualization of abundant transcripts such as Apvasl andAppiwi2 in the germ cells. For detection of multiple gene targets using doubleFISH, we recommend: (i) TSA/TSA, rather than TSA Plus/TSA Plus for colocalized mRNAs abundantly expressed in germ ceils, as proteinase K treatment can be omitted;and (ii) SF/TSA Plus for other gene targets such as Apenl and Apen2 as inactivation of enzyme conjugates is not required. SF/SF is not ideal for double FISH experiments due tosignal blurring. Based on these new conditions for RNA-FISH, we have obtained a better understanding of germline specification and embryonic segmentation in the pea aphid.We anticipate that the RNA-FISH protocols for the pea aphid may also be used for other aphids and possibly other insect species, thus expanding the range of species from whichuseful insights into development and evolution may be obtained.展开更多
Introduction Biological databases represent an extraordinary collective volume of work.Diligently built up over decades and comprising many millions of contributions from the biomedical research community,biological d...Introduction Biological databases represent an extraordinary collective volume of work.Diligently built up over decades and comprising many millions of contributions from the biomedical research community,biological databases provide worldwide access to a massive number of records(also known as entries)[1].Starting from individual laboratories,genomes are sequenced.展开更多
We introduce the concept of Canonical Workflow Building Blocks(CWBB),a methodology of describing and wrapping computational tools,in order for them to be utilised in a reproducible manner from multiple workflow langua...We introduce the concept of Canonical Workflow Building Blocks(CWBB),a methodology of describing and wrapping computational tools,in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms.The concept is implemented and demonstrated with the BioExcel Building Blocks library(BioBB),a collection of tool wrappers in the field of computational biomolecular simulation.Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow,built using this library and run with 5 different Workflow Manager Systems(WfMS).We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research(CWFR)in order to improve widespread adoption and reuse of computational methods across workflow language barriers.展开更多
The FAIR principles have been widely cited,endorsed and adopted by a broad range of stakeholders since their publication in 2016.By intention,the 15 FAIR guiding principles do not dictate specific technological implem...The FAIR principles have been widely cited,endorsed and adopted by a broad range of stakeholders since their publication in 2016.By intention,the 15 FAIR guiding principles do not dictate specific technological implementations,but provide guidance for improving Findability,Accessibility,Interoperability and Reusability of digital resources.This has likely contributed to the broad adoption of the FAIR principles,because individual stakeholder communities can implement their own FAIR solutions.However,it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations.Thus,while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways,for true interoperability we need to support convergence in implementation choices that are widely accessible and(re)-usable.We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible,robust,widespread and consistent FAIR implementations.Any self-identified stakeholder community may either choose to reuse solutions from existing implementations,or when they spot a gap,accept the challenge to create the needed solution,which,ideally,can be used again by other communities in the future.Here,we provide interpretations and implementation considerations(choices and challenges)for each FAIR principle.展开更多
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.
文摘Identifying genetic variants that contribute to phenotypic variation is expected to provide insights into the etiology of complex traits. Here we show how combining genetic mapping in an outbred population of rats with sequence data from the progenitors of the population made it possible to identify causal variants and genes for a large number of phenotypes. We identified 355 genomic loci contributing to 122 measures relevant to six models of disease, including fear-related behaviors and experimental autoimmune encephalomyelitis. At 35 of those loci we identified the responsible gene, and in some cases, the responsible variant.
基金supported by the Spanish Ministry of Economy and Competitiveness(grant numbers AGL2010-21929 and AGL2013-48756-R)the Spanish Ministry of Economy and Competitiveness,the Agencia Estatal de Investigación,and the European Regional Development Fund(grant number AGL2016–80967-R)Government of Aragon(Research Group A08_20R)。
文摘Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka ×Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL colocating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant Nos.XDA19090116 and XDA19050302)the National Natural Science Foundation of China(Grant Nos.31871328 and 32030021)+2 种基金the Professional Association of the Alliance of International Science Organizations(Grant No.ANSO-PA-2020-07)the Youth Innovation Promotion Association of Chinese Academy of Sciences(Grant No.2019104)the International Partnership Program of the Chinese Academy of Sciences(Grant No.153F11KYSB20160008).
文摘Biological databases serve as a global fundamental infrastructure for the worldwide scientific community,which dramatically aid the transformation of big data into knowledge discovery and drive significant innovations in a wide range of research fields.Given the rapid data production,biological databases continue to increase in size and importance.To build a catalog of worldwide biological databases,we curate a total of 5825 biological databases from 8931 publications,which are geographically distributed in 72 countries/regions and developed by 1975 institutions(as of September 20,2022).We further devise a z-index,a novel index to characterize the scientific impact of a database,and rank all these biological databases as well as their hosting institutions and countries in terms of citation and z-index.Consequently,we present a series of statistics and trends of worldwide biological databases,yielding a global perspective to better understand their status and impact for life and health sciences.An up-to-date catalog of worldwide biological databases,as well as their curated meta-information and derived statistics,is publicly available at Database Commons(https://ngdc.cncb.ac.cn/databasecommons/).
基金This work was supported in part by the European Union’s Horizon 2020 program under grant agreements 777523,FREYA“Connected Open Identifiers for Discovery,Access and Use of Research Resources”,654248,CORBEL+1 种基金“Coordinated Research Infrastructures Building Enduring Life-science services”,and 823830Bioexcel2,"BioExcel-2 Centre of Excellence for Computational Biomolecular Research".Many thanks to Paul Groth for his helpful comments on the manuscript.
文摘The FAIR principles describe characteristics intended to support access to and reuse of digital artifacts in the scientific research ecosystem.Persistent,globally unique identifiers,resolvable on the Web,and associated with a set of additional descriptive metadata,are foundational to FAIR data.Here we describe some basic principles and exemplars for their design,use and orchestration with other system elements to achieve FAIRness for digital research objects.
文摘RNA in situ hybridization (ISH), including chromogenic ISH (CISH) and fluorescent ISH (FISH), has become a powerful tool for revealing the spatial distribution ofgene transcripts in model organisms. Previously, we developed a robust protocol for wholemount RNA CISH in the pea aphid Acyrthosiphon pisum, an emerging insect genomicmodel. In order to improve the resolving capacity of gene detection, we comprehensively surveyed current protocols of whole-mount RNA-FISH and developed protocols that allow,using confocal microscopy, clearer visualization of target messenger RNAs (mRNAs) - including those subcellularly localized and those with spatially overlapping expression. Wefind that Fast dye-based substrate fluorescence (SF), tyramide signal amplification (TSA), and TSA Plus all enable identifying gene expression thanks to multiplex amplificationof fluorescent signals. By contrast, methods of direct fluorescence (DF) do not allow visualizing signals. Detection of a single gene target was achieved with SF and TSA Plusfor most mRNAs, whereas TSA only allowed visualization of abundant transcripts such as Apvasl andAppiwi2 in the germ cells. For detection of multiple gene targets using doubleFISH, we recommend: (i) TSA/TSA, rather than TSA Plus/TSA Plus for colocalized mRNAs abundantly expressed in germ ceils, as proteinase K treatment can be omitted;and (ii) SF/TSA Plus for other gene targets such as Apenl and Apen2 as inactivation of enzyme conjugates is not required. SF/SF is not ideal for double FISH experiments due tosignal blurring. Based on these new conditions for RNA-FISH, we have obtained a better understanding of germline specification and embryonic segmentation in the pea aphid.We anticipate that the RNA-FISH protocols for the pea aphid may also be used for other aphids and possibly other insect species, thus expanding the range of species from whichuseful insights into development and evolution may be obtained.
基金funding from the Australian Research Council through a Discovery Project(Grant No.DP150101550)
文摘Introduction Biological databases represent an extraordinary collective volume of work.Diligently built up over decades and comprising many millions of contributions from the biomedical research community,biological databases provide worldwide access to a massive number of records(also known as entries)[1].Starting from individual laboratories,genomes are sequenced.
基金a project funded by the European Union contracts H2020-INFRAEDI-02-2018823830,and H2020-EINFRA-2015-1675728funded through EOSC-Life(https://www.eosc-life.eu)contract H2020-INFRAEOSC-2018-2824087ELIXIR-CONVERGE(https://elixir-europe.org)contract H2020-INFRADEV-2019-2871075.
文摘We introduce the concept of Canonical Workflow Building Blocks(CWBB),a methodology of describing and wrapping computational tools,in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms.The concept is implemented and demonstrated with the BioExcel Building Blocks library(BioBB),a collection of tool wrappers in the field of computational biomolecular simulation.Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow,built using this library and run with 5 different Workflow Manager Systems(WfMS).We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research(CWFR)in order to improve widespread adoption and reuse of computational methods across workflow language barriers.
基金The work of A.Jacobsen,C.Evelo,M.Thompson,R.Cornet,R.Kaliyaperuma and M.Roos is supported by funding from the European Union’s Horizon 2020 research and innovation program under the EJP RD COFUND-EJP N°825575.The work of A.Jacobsen,C.Evelo,C.Goble,M.Thompson,N.Juty,R.Hooft,M.Roos,S-A.Sansone,P.McQuilton,P.Rocca-Serra and D.Batista is supported by funding from ELIXIR EXCELERATE,H2020 grant agreement number 676559.R.Hooft was further funded by NL NWO NRGWI.obrug.2018.009.N.Juty and C.Goble were funded by CORBEL(H2020 grant agreement 654248)N.Juty,C.Goble,S-A.Sansone,P.McQuilton,P.Rocca-Serra and D.Batista were funded by FAIRplus(IMI grant agreement 802750)+13 种基金N.Juty,C.Goble,M.Thompson,M.Roos,S-A.Sansone,P.McQuilton,P.Rocca-Serra and D.Batista were funded by EOSClife H2020-EU(grant agreement number 824087)C.Goble was funded by DMMCore(BBSRC BB/M013189/)M.Thompson,M.Roos received funding from NWO(VWData 400.17.605)S-A.Sansone,P.McQuilton,P.Rocca-Serra and D.Batista have been funded by grants awarded to S-A.Sansone from the UK BBSRC and Research Councils(BB/L024101/1,BB/L005069/1)EU(H2020-EU 634107H2020-EU 654241,IMI(IMPRiND 116060)NIH Data Common Fund,and from the Wellcome Trust(ISA-InterMine 212930/Z/18/ZFAIRsharing 208381/A/17/Z)The work of A.Waagmeester has been funded by grant award number GM089820 from the National Institutes of Health.M.Kersloot was funded by the European Regional Development Fund(KVW-00163).The work of N.Meyers was funded by the National Science Foundation(OAC 1839030)The work of M.D.Wilkinson is funded by Isaac Peral/Marie Curie cofund with the Universidad Politecnica de Madrid and the Ministerio de Economia y Competitividad grant number TIN2014-55993-RMThe work of B.Magagna,E.Schultes,L.da Silva Santos and K.Jeffery is funded by the H2020-EU 824068The work of B.Magagna,E.Schultes and L.da Silva Santos is funded by the GO FAIR ISCO grant of the Dutch Ministry of Science and CultureThe work of G.Guizzardi is supported by the OCEAN Project(FUB).M.Courtot received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No.802750.R.Cornet was further funded by FAIR4Health(H2020-EU grant agreement number 824666)K.Jeffery received funding from EPOS-IP H2020-EU agreement 676564 and ENVRIplus H2020-EU agreement 654182.
文摘The FAIR principles have been widely cited,endorsed and adopted by a broad range of stakeholders since their publication in 2016.By intention,the 15 FAIR guiding principles do not dictate specific technological implementations,but provide guidance for improving Findability,Accessibility,Interoperability and Reusability of digital resources.This has likely contributed to the broad adoption of the FAIR principles,because individual stakeholder communities can implement their own FAIR solutions.However,it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations.Thus,while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways,for true interoperability we need to support convergence in implementation choices that are widely accessible and(re)-usable.We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible,robust,widespread and consistent FAIR implementations.Any self-identified stakeholder community may either choose to reuse solutions from existing implementations,or when they spot a gap,accept the challenge to create the needed solution,which,ideally,can be used again by other communities in the future.Here,we provide interpretations and implementation considerations(choices and challenges)for each FAIR principle.