In short photoperiods, plants accumulate starch more rapidly in the light and degrade it more slowly at night, ensuring that their starch reserves last until dawn. To investigate the accompanying changes in the timing...In short photoperiods, plants accumulate starch more rapidly in the light and degrade it more slowly at night, ensuring that their starch reserves last until dawn. To investigate the accompanying changes in the timing of growth, Arabidopsis was grown in a range of photoperiods and analyzed for rosette biomass, photosynthesis, respiration, ribosome abundance, polysome loading, starch, and over 40 metabolites at dawn and dusk. The data set was used to model growth rates in the daytime and night, and to identify metabolites that correlate with growth. Modeled growth rates and polysome loading were high in the daytime and at night in long photoperiods, but decreased at night in short photoperiods. Ribosome abundance was similar in all photoperiods. It is discussed how the amount of starch accumulated in the light period, the length of the night, and maintenance costs interact to constrain growth at night in short photoperiods, and alter the strategy for optimizing ribosome use. Significant correlations were found in the day- time and the night between growth rates and the levels of the sugar-signal trehalose 6-phosphate and the amino acid biosynthesis intermediate shikimate, identifying these metabolites as hubs in a network that coordinates growth with diurnal changes in the carbon supply.展开更多
Background The Inspiration4(I4)mission,the first all-civilian orbital flight mission,investigated the physiological effects of short-duration spaceflight through a multi-omic approach.Despite advances,there remains mu...Background The Inspiration4(I4)mission,the first all-civilian orbital flight mission,investigated the physiological effects of short-duration spaceflight through a multi-omic approach.Despite advances,there remains much to learn about human adaptation to spaceflight's unique challenges,including microgravity,immune system perturbations,and radiation exposure.Methods To provide a detailed genetics analysis of the mission,we collected dried blood spots pre-,during,and post-flight for DNA extraction.Telomere length was measured by quantitative PCR,while whole genome and cfDNA sequencing provided insight into genomic stability and immune adaptations.A robust bioinformatic pipeline was used for data analysis,including variant calling to assess mutational burden.Result Telomere elongation occurred during spaceflight and shortened after return to Earth.Cell-free DNA analysis revealed increased immune cell signatures post-flight.No significant clonal hematopoiesis of indeterminate potential(CHIP)or whole-genome instability was observed.The long-term gene expression changes across immune cells suggested cellular adaptations to the space environment persisting months post-flight.Conclusion Our findings provide valuable insights into the physiological consequences of short-duration spaceflight,with telomere dynamics and immune cell gene expression adapting to spaceflight and persisting after return to Earth.CHIP sequencing data will serve as a reference point for studying the early development of CHIP in astronauts,an understudied phenomenon as previous studies have focused on career astronauts.This study will serve as a reference point for future commercial and non-commercial spaceflight,low Earth orbit(LEO)missions,and deep-space exploration.展开更多
Hematopoiesis represents a meticulously regulated and dynamic biological process.Genetic aberrations affecting blood cells,induced by various factors,frequently give rise to hematological tumors.These instances are of...Hematopoiesis represents a meticulously regulated and dynamic biological process.Genetic aberrations affecting blood cells,induced by various factors,frequently give rise to hematological tumors.These instances are often accompanied by a multitude of abnormal post-transcriptional regulatory events,including RNA alternative splicing,RNA localization,RNA degradation,and storage.Notably,post-transcriptional regulation plays a pivotal role in preserving hematopoietic homeostasis.The DEAD-Box RNA helicase genes emerge as crucial post-transcriptional regulatory factors,intricately involved in sustaining normal hematopoiesis through diverse mechanisms such as RNA alternative splicing,RNA modification,and ribosome assembly.This review consolidates the existing knowledge on the role of DEAD-box RNA helicases in regulating normal hematopoiesis and underscores the pathogenicity of mutant DEADBox RNA helicases in malignant hematopoiesis.Emphasis is placed on elucidating both the positive and negative contributions of DEAD-box RNA helicases within the hematopoietic system.展开更多
In the present experiments the changes in levels of ribosome,polysome and 3H-leucine incorporation rate in liver post-mitochondrial supernatant (PM-supernatant) were investigated in Sedericient and Se-supplented rats....In the present experiments the changes in levels of ribosome,polysome and 3H-leucine incorporation rate in liver post-mitochondrial supernatant (PM-supernatant) were investigated in Sedericient and Se-supplented rats.The results demonstrated that the amounts of ribosome and polysome as well as the ratio of polysome to ribosome in liver PM-supernatant from the Se-deficient rats were all remarkahly decreased.In the meantime,the rate of protein synthesis expressed as radioactivity or 3H-leucine incorporated into protein in the PM-supernatant system also decreased significantly.The results suggest that the decreases of ribosomes and proportion of ribosomal aggregates in PM-supernatant may be responsible for the decrease of the protein synthesis activity in liver of the Se-deficient animals.展开更多
Conformational dynamics contribute importantly to enzyme catalysis,such that targeted conformational constraint may affect catalysis.Firefly luciferases undergo extensive structural change during catalysis;key residue...Conformational dynamics contribute importantly to enzyme catalysis,such that targeted conformational constraint may affect catalysis.Firefly luciferases undergo extensive structural change during catalysis;key residues form a hydrophobic pocket,excluding water and enabling maximally energetic light production.Point mutants almost always luminesce at longer wavelengths(lower energy)than the wild type.Conformational constraint,using dipeptide analogue 3 at a position critical for optimized excited state structure,produced luciferase emission at a shorter wavelength by∼10 nm.Incomparison,introduction of conformationally constrained analogues 4,5,or 7 afforded luciferases emitting at longer wavelengths,while a related unconstrained luciferase(analogue 6)exhibited wild-type emission.The constrained luciferases tested were more stable than the wild type.Protein modeling demonstrated that the“inside”or“outside”orientation of the conformationally constrained dipeptide led to the shorter or longer emission wavelength,respectively.More broadly,these results suggest that local conformational constraint can control specific elements of enzyme behavior,both in vitro and in vivo.This represents the first example of studying enzyme function by introducing conformationally constrained dipeptides at a specific protein position.The principles discovered here in luciferase modification will enable studies to control the wavelength emission and photophysical properties of modified luciferases.展开更多
目的构建库容量大、多样性好的核糖体展示单链抗体库,为进一步筛选单链抗体奠定基础。方法对2006年10月1日至11月31日收集于中山大学附属第二医院的人外周血(健康成人2名,胃癌3例,肠癌3例,胰腺癌1例,每例各5mL,新生儿2名各2mL)分离淋巴...目的构建库容量大、多样性好的核糖体展示单链抗体库,为进一步筛选单链抗体奠定基础。方法对2006年10月1日至11月31日收集于中山大学附属第二医院的人外周血(健康成人2名,胃癌3例,肠癌3例,胰腺癌1例,每例各5mL,新生儿2名各2mL)分离淋巴细胞,提取RNA;利用RT-PCR克隆出全套重链可变区基因(variable region of heavy chain,VH)、轻链可变区基因(variable region of light chain,VL);然后利用重叠延伸PCR技术连接构建VH-VL单链抗体库。并通过连接T-Vector转化E.coli JM109大肠埃希菌,经蓝白筛选,挑取阳性克隆测序以鉴定单链抗体组装。结果试验成功构建了单链抗体核糖体展示模板,其库容达1.1×1013。结论大容量核糖体展示单链抗体库的构建为筛选多种人源性单链抗体奠定了基础。展开更多
The structure and function of BNS(bionanosystems)such as macromolecules,viruses and ribosomes are strongly affected by electrostatic interactions.Yet their supra-million atom size makes them difficult to simulate via ...The structure and function of BNS(bionanosystems)such as macromolecules,viruses and ribosomes are strongly affected by electrostatic interactions.Yet their supra-million atom size makes them difficult to simulate via a straightforward PoissonBoltzmann(PB)approach.Here we explore a multiscale approach that results in a coarse-grained PB equation that follows rigorously from the all-atom PB equation.The derivation of the coarse-grained equation follows from an ansatz on the dependence of the electrical potential in two distinct ways,i.e.one reflecting atomic-scale variations and the other capturing nanometer-scale features.With this ansatz and a series expansion of the potential in a length-scale ratio,the coarse-grained PB equation is obtained.This multiscale methodology and an efficient computational methodology provide a way to efficiently simulate BNS electrostatics with atomic-scale resolution for the first time,avoiding the need for excessive supercomputer resources.The coarse-grained PB equation contains a tensorial dielectric constant that mediates the channeling of the electric field along macromolecules in an aqueous medium.The multiscale approach and novel salinity connections to the PB equation presented here should enhance the accuracy and wider applicability of PB modeling。展开更多
文摘In short photoperiods, plants accumulate starch more rapidly in the light and degrade it more slowly at night, ensuring that their starch reserves last until dawn. To investigate the accompanying changes in the timing of growth, Arabidopsis was grown in a range of photoperiods and analyzed for rosette biomass, photosynthesis, respiration, ribosome abundance, polysome loading, starch, and over 40 metabolites at dawn and dusk. The data set was used to model growth rates in the daytime and night, and to identify metabolites that correlate with growth. Modeled growth rates and polysome loading were high in the daytime and at night in long photoperiods, but decreased at night in short photoperiods. Ribosome abundance was similar in all photoperiods. It is discussed how the amount of starch accumulated in the light period, the length of the night, and maintenance costs interact to constrain growth at night in short photoperiods, and alter the strategy for optimizing ribosome use. Significant correlations were found in the day- time and the night between growth rates and the levels of the sugar-signal trehalose 6-phosphate and the amino acid biosynthesis intermediate shikimate, identifying these metabolites as hubs in a network that coordinates growth with diurnal changes in the carbon supply.
基金supported by the Leukemia and Lymphoma Society (Grants No.LLS 9238-16 and MCL7001-18)the National Institutes of Health (Grants No.P01CA214274,R01CA249054 and R01MH117406)the WorldQuant Foundation,NASA (Grants No.80NSSC19K0432,80NSSC22K0254,NNH18ZTT001N-FG2,NNX13AE45G,NNX14AH50G,NNX17AB26G).
文摘Background The Inspiration4(I4)mission,the first all-civilian orbital flight mission,investigated the physiological effects of short-duration spaceflight through a multi-omic approach.Despite advances,there remains much to learn about human adaptation to spaceflight's unique challenges,including microgravity,immune system perturbations,and radiation exposure.Methods To provide a detailed genetics analysis of the mission,we collected dried blood spots pre-,during,and post-flight for DNA extraction.Telomere length was measured by quantitative PCR,while whole genome and cfDNA sequencing provided insight into genomic stability and immune adaptations.A robust bioinformatic pipeline was used for data analysis,including variant calling to assess mutational burden.Result Telomere elongation occurred during spaceflight and shortened after return to Earth.Cell-free DNA analysis revealed increased immune cell signatures post-flight.No significant clonal hematopoiesis of indeterminate potential(CHIP)or whole-genome instability was observed.The long-term gene expression changes across immune cells suggested cellular adaptations to the space environment persisting months post-flight.Conclusion Our findings provide valuable insights into the physiological consequences of short-duration spaceflight,with telomere dynamics and immune cell gene expression adapting to spaceflight and persisting after return to Earth.CHIP sequencing data will serve as a reference point for studying the early development of CHIP in astronauts,an understudied phenomenon as previous studies have focused on career astronauts.This study will serve as a reference point for future commercial and non-commercial spaceflight,low Earth orbit(LEO)missions,and deep-space exploration.
基金Chongqing Science Fund for Distinguished Young Scholars(No.CSTB2022NSCQJQX0032)Chongqing University Innovation Research Group Project(No.CXQT21011)+2 种基金Chongqing Medical University Youth Innovation in Future Medicine(No.W0156)the National Natural Science Foundation of China(No.82200123)Natural Science Foundation of Chongqing,China,(No.CSTB2023NSCQ-MSX0280).
文摘Hematopoiesis represents a meticulously regulated and dynamic biological process.Genetic aberrations affecting blood cells,induced by various factors,frequently give rise to hematological tumors.These instances are often accompanied by a multitude of abnormal post-transcriptional regulatory events,including RNA alternative splicing,RNA localization,RNA degradation,and storage.Notably,post-transcriptional regulation plays a pivotal role in preserving hematopoietic homeostasis.The DEAD-Box RNA helicase genes emerge as crucial post-transcriptional regulatory factors,intricately involved in sustaining normal hematopoiesis through diverse mechanisms such as RNA alternative splicing,RNA modification,and ribosome assembly.This review consolidates the existing knowledge on the role of DEAD-box RNA helicases in regulating normal hematopoiesis and underscores the pathogenicity of mutant DEADBox RNA helicases in malignant hematopoiesis.Emphasis is placed on elucidating both the positive and negative contributions of DEAD-box RNA helicases within the hematopoietic system.
文摘In the present experiments the changes in levels of ribosome,polysome and 3H-leucine incorporation rate in liver post-mitochondrial supernatant (PM-supernatant) were investigated in Sedericient and Se-supplented rats.The results demonstrated that the amounts of ribosome and polysome as well as the ratio of polysome to ribosome in liver PM-supernatant from the Se-deficient rats were all remarkahly decreased.In the meantime,the rate of protein synthesis expressed as radioactivity or 3H-leucine incorporated into protein in the PM-supernatant system also decreased significantly.The results suggest that the decreases of ribosomes and proportion of ribosomal aggregates in PM-supernatant may be responsible for the decrease of the protein synthesis activity in liver of the Se-deficient animals.
基金supported by research grants R01GM12367 and R35GM140819 from the National Institutes of General Medical Sciences,NIH.
文摘Conformational dynamics contribute importantly to enzyme catalysis,such that targeted conformational constraint may affect catalysis.Firefly luciferases undergo extensive structural change during catalysis;key residues form a hydrophobic pocket,excluding water and enabling maximally energetic light production.Point mutants almost always luminesce at longer wavelengths(lower energy)than the wild type.Conformational constraint,using dipeptide analogue 3 at a position critical for optimized excited state structure,produced luciferase emission at a shorter wavelength by∼10 nm.Incomparison,introduction of conformationally constrained analogues 4,5,or 7 afforded luciferases emitting at longer wavelengths,while a related unconstrained luciferase(analogue 6)exhibited wild-type emission.The constrained luciferases tested were more stable than the wild type.Protein modeling demonstrated that the“inside”or“outside”orientation of the conformationally constrained dipeptide led to the shorter or longer emission wavelength,respectively.More broadly,these results suggest that local conformational constraint can control specific elements of enzyme behavior,both in vitro and in vivo.This represents the first example of studying enzyme function by introducing conformationally constrained dipeptides at a specific protein position.The principles discovered here in luciferase modification will enable studies to control the wavelength emission and photophysical properties of modified luciferases.
文摘目的构建库容量大、多样性好的核糖体展示单链抗体库,为进一步筛选单链抗体奠定基础。方法对2006年10月1日至11月31日收集于中山大学附属第二医院的人外周血(健康成人2名,胃癌3例,肠癌3例,胰腺癌1例,每例各5mL,新生儿2名各2mL)分离淋巴细胞,提取RNA;利用RT-PCR克隆出全套重链可变区基因(variable region of heavy chain,VH)、轻链可变区基因(variable region of light chain,VL);然后利用重叠延伸PCR技术连接构建VH-VL单链抗体库。并通过连接T-Vector转化E.coli JM109大肠埃希菌,经蓝白筛选,挑取阳性克隆测序以鉴定单链抗体组装。结果试验成功构建了单链抗体核糖体展示模板,其库容达1.1×1013。结论大容量核糖体展示单链抗体库的构建为筛选多种人源性单链抗体奠定了基础。
文摘The structure and function of BNS(bionanosystems)such as macromolecules,viruses and ribosomes are strongly affected by electrostatic interactions.Yet their supra-million atom size makes them difficult to simulate via a straightforward PoissonBoltzmann(PB)approach.Here we explore a multiscale approach that results in a coarse-grained PB equation that follows rigorously from the all-atom PB equation.The derivation of the coarse-grained equation follows from an ansatz on the dependence of the electrical potential in two distinct ways,i.e.one reflecting atomic-scale variations and the other capturing nanometer-scale features.With this ansatz and a series expansion of the potential in a length-scale ratio,the coarse-grained PB equation is obtained.This multiscale methodology and an efficient computational methodology provide a way to efficiently simulate BNS electrostatics with atomic-scale resolution for the first time,avoiding the need for excessive supercomputer resources.The coarse-grained PB equation contains a tensorial dielectric constant that mediates the channeling of the electric field along macromolecules in an aqueous medium.The multiscale approach and novel salinity connections to the PB equation presented here should enhance the accuracy and wider applicability of PB modeling。
基金the Tender Subject of Key Research Areas of Xinxiang Medical Uuniversity in 2011,No.ZD2011-16Key Projects in Scientific Research of Henan Provincial Education Department,No.13A180850~~
