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
Viticulture,like other fields of agriculture,is currently facing important challenges that will be addressed only through sustained,dedicated and coordinated research.Although the methods used in biology have evolved ...Viticulture,like other fields of agriculture,is currently facing important challenges that will be addressed only through sustained,dedicated and coordinated research.Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature,in many domains of study,including grapevine research,there is a need to improve the findability,accessibility,interoperability and reusability(FAIR-ness)of these data.Considering the heterogeneous nature of the data produced,the transnational nature of the scientific community and the experience gained elsewhere,we have formed an open working group,in the framework of the International Grapevine Genome Program(www.vitaceae.org),to construct a coordinated federation of information systems holding grapevine data distributed around the world,providing an integrated set of interfaces supporting advanced data modeling,rich semantic integration and the next generation of data mining tools.To achieve this goal,it will be critical to develop,implement and adopt appropriate standards for data annotation and formatting.The development of this system,the GrapeIS,linking genotypes to phenotypes,and scientific research to agronomical and oeneological data,should provide new insights into grape biology,and allow the development of new varieties to meet the challenges of biotic and abiotic stress,environmental change,and consumer demand.展开更多
MINFLUX has achieved extraordinary resolution in superresolution imaging and single fluorophore tracking.It is based on localizing single fluorophores by rapid probing with a patterned beam that features a local inten...MINFLUX has achieved extraordinary resolution in superresolution imaging and single fluorophore tracking.It is based on localizing single fluorophores by rapid probing with a patterned beam that features a local intensity minimum.Current implementations,however,are complex and expensive and are limited in speed and robustness.Here,we show that a combination of an electro-optical modulator with a segmented birefringent element such as a spatial light modulator produces a variable phase plate for which the phase can be scanned on the MHz timescale.Bisected or top-hat phase patterns generate high-contrast compact excitation point-spread functions for MINFLUX localization in the x,y,and z-direction,respectively,which can be scanned across a fluorophore within a microsecond,switched within 60 microseconds and alternated among different excitation wavelengths.We discuss how to compensate for non-optimal performance of the components and present a robust 3D and multi-color MINFLUX excitation module,which we envision as an integral component of a high-performance and cost-effective open-source MINFLUX.展开更多
In a recent study published in Nature,Zepeda-Rivera et al.1 discovered that one distinct clade of Fusobacterium nucleatum animalis(Fna)dominates the colorectal cancer(CRC)tumor niche.The work unravels a more precise u...In a recent study published in Nature,Zepeda-Rivera et al.1 discovered that one distinct clade of Fusobacterium nucleatum animalis(Fna)dominates the colorectal cancer(CRC)tumor niche.The work unravels a more precise understanding of a major bacterial species associated with CRC progression,thereby establishing a new focus for future studies,which may aid to develop improved microbiome-based diagnostics and treatments(Fig.1).展开更多
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the...The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes.This was first demonstrated on biological samples a decade ago on the giant mimivirus.Since then,a large collaboration has been pushing the limit of the smallest sample that can be imaged.The ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of macromolecules.Here we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single proteins.From the pattern,it is possible to determine the approximate orientation of the protein.Our experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.展开更多
The prevalence of metabolic-dysfunction-associated steatotic liver disease(MASLD)is alarmingly high;it is estimated to affect up to a quarter of the global population,making it the most common liver disorder worldwide...The prevalence of metabolic-dysfunction-associated steatotic liver disease(MASLD)is alarmingly high;it is estimated to affect up to a quarter of the global population,making it the most common liver disorder worldwide.MASLD is characterized by excessive hepatic fat accumulation and is commonly associated with comorbidities such as obesity,dyslipidemia,and insulin resistance;however,it can also manifest in lean individuals.Therefore,it is crucial to develop effective therapies for this complex condition.Currently,there are no approved medications for MASLD treatment,so there is a pressing need to investigate alternative approaches.Extensive research has characterized MASLD as a multifaceted disease,frequently linked to metabolic disorders that stem from dietary habits.Evidence suggests that changes in the gut microbiome play a fundamental role in the development and progression of MASLD from simple steatosis to steatohepatitis and even hepatocellular carcinoma(HCC).In this review,we critically examine the literature on the emerging field of gut-microbiota-based therapies for MASLD and metabolicdysfunction-associated steatohepatitis(MASH),including interventions such as fecal microbiota transplantation(FMT),probiotics,prebiotics,short-chain fatty acids,antibiotics,metabolic pathway targeting,and immune checkpoint kinase blockade.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
In a recent paper published in Science,Wei et al.report that long-interspersed element-1(LINE1)RNA is a key target of the N6-methyladenosine(m6A)‘eraser’fat mass and obesity-associated protein(FTO).The FTO-LINE1 RNA...In a recent paper published in Science,Wei et al.report that long-interspersed element-1(LINE1)RNA is a key target of the N6-methyladenosine(m6A)‘eraser’fat mass and obesity-associated protein(FTO).The FTO-LINE1 RNA axis is involved in chromatin regulation and is essential for mammalian development.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
Light sheet fluorescence microscopy(LSFM)is rapidly becoming an essential technology for mesoscopic imaging of samples such as embryos and adult mouse organs.However,LSFM can suffer from optical artifacts for which th...Light sheet fluorescence microscopy(LSFM)is rapidly becoming an essential technology for mesoscopic imaging of samples such as embryos and adult mouse organs.However,LSFM can suffer from optical artifacts for which there is no intrinsic solution.The attenuation of light due to absorbing material causes“shadow”artifacts along both the illumination and detection paths.Several approaches have been introduced to reduce this problem,including scanning illumination and multi-view imaging.However,neither of these approaches completely eliminates the problem.If the distribution of the absorbing material is complex,shadows cannot be avoided.We introduce a new approach that relies on multi-modal integration of two very different mesoscopic techniques.Unlike LSFM,optical projection tomography(OPT)can operate in transmission mode to create a voxel map of the 3D distribution of the sample’s optical attenuation.Here,we demonstrate a hybrid instrument(OPTiSPIM)that can quantify this attenuation and use the information to correct the shadow artifacts of LSFM.展开更多
During free exploration,the emergence of patterned and sequential behavioral responses to an unknown environment reflects exploration traits and adaptation.However,the behavioral dynamics and neural substrates underly...During free exploration,the emergence of patterned and sequential behavioral responses to an unknown environment reflects exploration traits and adaptation.However,the behavioral dynamics and neural substrates underlying the exploratory behavior remain poorly understood.We developed computational tools to quantify the exploratory behavior and performed in vivo electrophysiological recordings in a large arena in which mice made sequential excursions into unknown territory.Occupancy entropy was calculated to characterize the cumulative and moment-to-moment behavioral dynamics in explored and unexplored territories.Local field potential analysis revealed that the theta activity in the dorsal hippocampus(d HPC)was highly correlated with the occupancy entropy.Individual d HPC and prefrontal cortex(PFC)oscillatory activities could classify various aspects of free exploration.Initiation of exploration was accompanied by a coordinated decrease and increase in theta activity in PFC and d HPC,respectively.Our results indicate that d HPC and PFC work synergistically in shaping free exploration by modulating exploratory traits during emergence and visits to an unknown environment.展开更多
Dear Editor, Deleted in colorectal cancer （DCC） is a single pass transmembrane glycoprotein that was originally identified in humans as a candidate tumor suppressor （Fearon et al., 1990）. DCC belongs to the immuno...Dear Editor, Deleted in colorectal cancer （DCC） is a single pass transmembrane glycoprotein that was originally identified in humans as a candidate tumor suppressor （Fearon et al., 1990）. DCC belongs to the immunoglobulin superfamily, and the extracellular fragment is composed of four immunoglobu- lin-like （Ig-like） domains followed by six fibronectin type III （FN） domains. DCC plays a pivotal role in axon guidance by mediating a combination of attractive and repulsive effects through interactions with the diffusible guidance cue,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.
基金The foundations and the first draft of this paper were set up during a workshop organized in Bordeaux,France in February 2015 with the financial support of the Gallo Wine Company,INRA and of the Institut des Sciences de la Vigne et du Vin.
文摘Viticulture,like other fields of agriculture,is currently facing important challenges that will be addressed only through sustained,dedicated and coordinated research.Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature,in many domains of study,including grapevine research,there is a need to improve the findability,accessibility,interoperability and reusability(FAIR-ness)of these data.Considering the heterogeneous nature of the data produced,the transnational nature of the scientific community and the experience gained elsewhere,we have formed an open working group,in the framework of the International Grapevine Genome Program(www.vitaceae.org),to construct a coordinated federation of information systems holding grapevine data distributed around the world,providing an integrated set of interfaces supporting advanced data modeling,rich semantic integration and the next generation of data mining tools.To achieve this goal,it will be critical to develop,implement and adopt appropriate standards for data annotation and formatting.The development of this system,the GrapeIS,linking genotypes to phenotypes,and scientific research to agronomical and oeneological data,should provide new insights into grape biology,and allow the development of new varieties to meet the challenges of biotic and abiotic stress,environmental change,and consumer demand.
基金H2020 Marie Skłodowska-Curie Actions(RobMin grant no.101031734 to T.D.)the European Research Council(grant no.ERC CoG-724489 to J.R.)the European Molecular Biology Laboratory(T.D.and J.R.).
文摘MINFLUX has achieved extraordinary resolution in superresolution imaging and single fluorophore tracking.It is based on localizing single fluorophores by rapid probing with a patterned beam that features a local intensity minimum.Current implementations,however,are complex and expensive and are limited in speed and robustness.Here,we show that a combination of an electro-optical modulator with a segmented birefringent element such as a spatial light modulator produces a variable phase plate for which the phase can be scanned on the MHz timescale.Bisected or top-hat phase patterns generate high-contrast compact excitation point-spread functions for MINFLUX localization in the x,y,and z-direction,respectively,which can be scanned across a fluorophore within a microsecond,switched within 60 microseconds and alternated among different excitation wavelengths.We discuss how to compensate for non-optimal performance of the components and present a robust 3D and multi-color MINFLUX excitation module,which we envision as an integral component of a high-performance and cost-effective open-source MINFLUX.
文摘In a recent study published in Nature,Zepeda-Rivera et al.1 discovered that one distinct clade of Fusobacterium nucleatum animalis(Fna)dominates the colorectal cancer(CRC)tumor niche.The work unravels a more precise understanding of a major bacterial species associated with CRC progression,thereby establishing a new focus for future studies,which may aid to develop improved microbiome-based diagnostics and treatments(Fig.1).
基金supported by the Universität Hamburg and DFG grant numbers(INST 152/772-1|152/774-1|152/775-1|152/776-1|152/777-1 FUGG)We acknowledge the support of funding from:Cluster of Excellence‘CUI:Advanced Imaging of Matter’of the Deutsche Forschungsgemeinschaft(DFG)-EXC 2056-project ID 390715994+7 种基金ERC-2013-CoG COMOTION 614507NFR 240770Fellowship from the Joachim Herz Stiftung(P.L.X.)P.L.X.and H.N.C.acknowledge support from the Human Frontiers Science Program(RGP0010/2017)J.H.acknowledges support from the European Development Fund:Structural dynamics of biomolecular systems(ELIBIO)(CZ.02.1.01/0.0/0.0/15_003/0000447)EMBO long-term fellowship(ALTF 356-2018)awarded to L.E.F.the Röntgen-Ångström Cluster(2015-06107 and 2019-06092)the Swedish Research Council(2017-05336,2018-00234 and 2019-03935)the Swedish Foundation for Strategic Research(ITM17-0455).
文摘The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes.This was first demonstrated on biological samples a decade ago on the giant mimivirus.Since then,a large collaboration has been pushing the limit of the smallest sample that can be imaged.The ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of macromolecules.Here we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single proteins.From the pattern,it is possible to determine the approximate orientation of the protein.Our experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.
基金Federal Ministry of Education and Research(Q-HCC,01KD2214)the Sino-German Center for Research Promotion(GZ-1546 and C-0012)+5 种基金the State Ministry of Baden-Wuerttemberg for Sciences,Research and Arts supporting the Clinical Cooperation Unit Healthy Metabolism at the Center for Preventive Medicine and Digital Health(CCU Healthy Metabolism)the Baden-Wuerttemberg Center for Digital Early Disease Detection and Prevention(BW-ZDFP)the Foundation for Biomedical Alcohol Research,Schriesheim,Germanyfunded by the Federal Ministry of Education and Research(BMBF)the Ministry of Culture and Science of the German State of North Rhine-Westphalia(MKW)(NRW Rueckkehrprogramm)under the Excellence Strategy of the Federal Government and the Länderthe German Research Foundation(DFG,403224013-SFB1382,gut-liver axis).
文摘The prevalence of metabolic-dysfunction-associated steatotic liver disease(MASLD)is alarmingly high;it is estimated to affect up to a quarter of the global population,making it the most common liver disorder worldwide.MASLD is characterized by excessive hepatic fat accumulation and is commonly associated with comorbidities such as obesity,dyslipidemia,and insulin resistance;however,it can also manifest in lean individuals.Therefore,it is crucial to develop effective therapies for this complex condition.Currently,there are no approved medications for MASLD treatment,so there is a pressing need to investigate alternative approaches.Extensive research has characterized MASLD as a multifaceted disease,frequently linked to metabolic disorders that stem from dietary habits.Evidence suggests that changes in the gut microbiome play a fundamental role in the development and progression of MASLD from simple steatosis to steatohepatitis and even hepatocellular carcinoma(HCC).In this review,we critically examine the literature on the emerging field of gut-microbiota-based therapies for MASLD and metabolicdysfunction-associated steatohepatitis(MASH),including interventions such as fecal microbiota transplantation(FMT),probiotics,prebiotics,short-chain fatty acids,antibiotics,metabolic pathway targeting,and immune checkpoint kinase blockade.
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P.S.acknowledges funding from the Peter und Traudl Engelhorn StiftungOpen Access funding enabled and organized by Projekt DEAL.
文摘In a recent paper published in Science,Wei et al.report that long-interspersed element-1(LINE1)RNA is a key target of the N6-methyladenosine(m6A)‘eraser’fat mass and obesity-associated protein(FTO).The FTO-LINE1 RNA axis is involved in chromatin regulation and is essential for mammalian development.
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the European Union’s 7th Framework VIBRANT project(No.228933 of the FP7-NMP)the Sinergia project(CRII3_125477)of the Swiss National Science Foundation(SNSF)+1 种基金support from the Spanish Ministry of Economy and Competitiveness,“Centro de Excelencia Severo Ochoa 2013–2017”from the CERCA Programme/Generalitat de Catalunya.
文摘Light sheet fluorescence microscopy(LSFM)is rapidly becoming an essential technology for mesoscopic imaging of samples such as embryos and adult mouse organs.However,LSFM can suffer from optical artifacts for which there is no intrinsic solution.The attenuation of light due to absorbing material causes“shadow”artifacts along both the illumination and detection paths.Several approaches have been introduced to reduce this problem,including scanning illumination and multi-view imaging.However,neither of these approaches completely eliminates the problem.If the distribution of the absorbing material is complex,shadows cannot be avoided.We introduce a new approach that relies on multi-modal integration of two very different mesoscopic techniques.Unlike LSFM,optical projection tomography(OPT)can operate in transmission mode to create a voxel map of the 3D distribution of the sample’s optical attenuation.Here,we demonstrate a hybrid instrument(OPTiSPIM)that can quantify this attenuation and use the information to correct the shadow artifacts of LSFM.
基金the National Natural Science Foundation of China(32070985)Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions(NYKFKT20190018)Shenzhen Key Laboratory of Translational Research for Brain Diseases(ZDSYS20200828154800001)。
文摘During free exploration,the emergence of patterned and sequential behavioral responses to an unknown environment reflects exploration traits and adaptation.However,the behavioral dynamics and neural substrates underlying the exploratory behavior remain poorly understood.We developed computational tools to quantify the exploratory behavior and performed in vivo electrophysiological recordings in a large arena in which mice made sequential excursions into unknown territory.Occupancy entropy was calculated to characterize the cumulative and moment-to-moment behavioral dynamics in explored and unexplored territories.Local field potential analysis revealed that the theta activity in the dorsal hippocampus(d HPC)was highly correlated with the occupancy entropy.Individual d HPC and prefrontal cortex(PFC)oscillatory activities could classify various aspects of free exploration.Initiation of exploration was accompanied by a coordinated decrease and increase in theta activity in PFC and d HPC,respectively.Our results indicate that d HPC and PFC work synergistically in shaping free exploration by modulating exploratory traits during emergence and visits to an unknown environment.
文摘Dear Editor, Deleted in colorectal cancer （DCC） is a single pass transmembrane glycoprotein that was originally identified in humans as a candidate tumor suppressor （Fearon et al., 1990）. DCC belongs to the immunoglobulin superfamily, and the extracellular fragment is composed of four immunoglobu- lin-like （Ig-like） domains followed by six fibronectin type III （FN） domains. DCC plays a pivotal role in axon guidance by mediating a combination of attractive and repulsive effects through interactions with the diffusible guidance cue,
