Full-color imaging is essential in digital pathology for accurate tissue analysis.Utilizing advanced optical modulation and phase retrieval algorithms,Fourier ptychographic microscopy(FPM)offers a powerful solution fo...Full-color imaging is essential in digital pathology for accurate tissue analysis.Utilizing advanced optical modulation and phase retrieval algorithms,Fourier ptychographic microscopy(FPM)offers a powerful solution for high-throughput digital pathology,combining high resolution,large field of view,and extended depth of field(DOF).However,the full-color capabilities of FPM are hindered by coherent color artifacts and reduced computational efficiency,which significantly limits its practical applications.Color-transferbased FPM(CFPM)has emerged as a potential solution,theoretically reducing both acquisition and reconstruction threefold time.Yet,existing methods fall short of achieving the desired reconstruction speed and colorization quality.In this study,we report a generalized dual-color-space constrained model for FPM colorization.This model provides a mathematical framework for model-based FPM colorization,enabling a closed-form solution without the need for redundant iterative calculations.Our approach,termed generalized CFPM(gCFPM),achieves colorization within seconds for megapixel-scale images,delivering superior colorization quality in terms of both colorfulness and sharpness,along with an extended DOF.Both simulations and experiments demonstrate that gCFPM surpasses state-of-the-art methods across all evaluated criteria.Our work offers a robust and comprehensive workflow for high-throughput full-color pathological imaging using FPM platforms,laying a solid foundation for future advancements in methodology and engineering.展开更多
The spider monkey, a fruit specialist and important seed dispersal agent in the Neotropics, is an endangered primate due to habitat loss, hunting and the pet trade. Spider monkeys have been the subject of a few studie...The spider monkey, a fruit specialist and important seed dispersal agent in the Neotropics, is an endangered primate due to habitat loss, hunting and the pet trade. Spider monkeys have been the subject of a few studies in Central and South Ame- rica, but little is known about the diet and ranging for this primate in southern Mexico. Here we report the results of a six-month long study （October 2010 to March 2011） of the feeding preferences and ranging patterns of the Yucatan spider monkey Ateles geoffroyi yucatanensis living in the ＂Ya＇ax＇che＂ reserve by the Caribbean coast in northeast Yucatan peninsula. Focal animal and scan sampling as well as GPS tracking were used to document spider monkey feeding behavior, location of food trees and ranging in the reserve. The spider monkeys used 36 species of plants （94% trees; n = 432） and six non tree morphospecies as a source of food. Six tree species accounted for 〉~80% of total feeding time and for 74% of all trees used. Fruits accounted for 59% of total feeding time, followed by leaves （35%）, palm piths （5%） and other plant parts （1%）. Total range used by the monkeys was esti- mated at 43% of semievergreen rainforest habitat available （ca 40ha）. Range use was not random with segments showing light, moderate and heavy use; the use of different areas of their range varied monthly and was closely linked to the spatial dispersion of the trees used for food [Current Zoology 59 （1）： 125-134, 2013].展开更多
A consensus sequence, encoding a putative DNA polymerase type B derived from a Polinton transposon, was assembled from the sex determination region of Xiphophorus maculatus. This predicted protein, which is 1,158 aa i...A consensus sequence, encoding a putative DNA polymerase type B derived from a Polinton transposon, was assembled from the sex determination region of Xiphophorus maculatus. This predicted protein, which is 1,158 aa in length, contains a DNAA_pol_B_2 domain and a DTDS motif. The DNA polymerase type B gene has about 10 copies in the haploid X. maculatus genome with one Y-specific copy. Interestingly, it has specific copies on the W chromosome in the X. maculatus Usumacinta strain （sex determination with female het- erogamety）, which represent new markers for this type of sex chromosome in platyfish. This marker with W- and Y-specific copies suggests relationship between different types of gonosomes and allows comparing male and female heterogameties in the platyfish. Further molecular analysis of the DNA polymerase type B gene in X. maculatus will shed new light on the evolution of sex chromosomes in platyfish.展开更多
Ataxia telangiectasia(AT)is an autosomal recessive multisystem disorder with increased radiosensitivity and cancer susceptibility.The responsible gene(ATM)consists of 66 exons and a coding region of 9171 bp which prec...Ataxia telangiectasia(AT)is an autosomal recessive multisystem disorder with increased radiosensitivity and cancer susceptibility.The responsible gene(ATM)consists of 66 exons and a coding region of 9171 bp which precludes direct seq uencing as a screening assay for confirmation or exclusion of the clinical suspi cion of AT.Peripheral blood mononuclear cells of 330 patients referred for the exclusion of AT were exposed to ionizing radiation(IR)and incubated for 72 h i n the presence of phytohemagglutinin.Using bivariate BrdUHoechst/ethidium brom ide flowcytometry,the following cell cycle parameters were ascertained:(1)pro portion of non-proliferating(G0,G1)cells as a measure of mitogen response,(2)proportion of first-cycle G2-phase cells relative to the growth fraction(G2 /GF)as a measure of radiosensitivity.Of the cases tested,94.2%could be unequ ivocally assigned either to the AT-negative or the AT-positive group of patien ts.Of the AT-positive cases,11 were confirmed by ATM mutation analysis.Ninet een cases presented with non-conclusive results,mostly due to poor mitogen res ponse;however,a combination of cellcycle data with serum AFP concentrations le d to the exclusion of AT in all but two of the uncertain cases.Substitution of ionizing radiation by the radiomimetic bleomycin was additionally tested in a sm all series of patients.We conclude that cell-cycle testing complemented by ser um AFP measurements fulfills the criteria as a rapid and economical screening pr ocedure for the differential diagnosis of juvenile ataxias.展开更多
The molecular mechanisms underlying gonadal differentiation in vertebrates have long intrigued researchers.However,studies in this field have predominantly focused on mammals,with limited attention given to non-mammal...The molecular mechanisms underlying gonadal differentiation in vertebrates have long intrigued researchers.However,studies in this field have predominantly focused on mammals,with limited attention given to non-mammalian vertebrates,particularly at the cellular level.To address this knowledge gap,we selected the Chinese tongue sole as our research model.We collected samples from six developmental stages of ovaries and testes and performed in-depth transcriptomic analyses of 123,344 single-cell nuclei.This study identified 34 major cell types,including five gonadal cell types,enabling us to outline the early sex differentiation roadmap in a non-model teleost species.Both somatic and germ cells in the gonads were systematically studied using bioinformatics methods.Numerous sex-biased genes and markers were identified and experimentally validated,contributing to our understanding of the dynamic development and differentiation processes of gonadal supporting cells and germ cells in teleosts.Weighted Gene Co-expression Network Analysis(WGCNA)networks emphasized the critical roles of foxl2a and dmrt1 in sex differentiation.Pseudotime analysis revealed the early differentiation processes between male and female germ cells.We discovered a new germ cell marker gene,gpat2,and elucidated the differentiation pathway of gonadal stem cells in teleost fish.Our results highlight the significance of pathways such as oocyte meiosis,Target of Rapamycin(TOR)complex,oxytocin signaling,cGMP-PKG signaling,and arginine signaling in the differentiation of oocytes and spermatogonial stem cells.Cell-cell communication analyses further revealed interactions among different gonadal cell types,identifying the WNT and Notch pathways as crucial for the development of female and male gonads.Furthermore,we verified a feedback loop between dmrt1 and zfpm2 for the first time in teleosts,suggesting potential roles for zfpm2 in the formation and development of the teleost testis.Our findings provide a comprehensive transcriptomic resource for investigating the early sex differentiation processes of teleosts at the single-cell level and bridge the knowledge gap in research on non-mammalian vertebrates.展开更多
Biogenesis of photosynthetic pigment/protein complexes is a highly regulated process that requires various assisting factors. Here, we report on the molecular analysis of the Pitt gene （sir1644） from the cyanobacter...Biogenesis of photosynthetic pigment/protein complexes is a highly regulated process that requires various assisting factors. Here, we report on the molecular analysis of the Pitt gene （sir1644） from the cyanobacterium Synechocystis sp. PCC 6803 （Synechocystis 6803） that encodes a membrane-bound tetratricopeptide repeat （TPR） protein of formerly unknown function. Targeted inactivation of Pitt affected photosynthetic performance and light-dependent chlorophyll synthesis. Yeast two-hybrid analyses and native PAGE strongly suggest a complex formation between Pitt and the light-dependent protochlorophyllide oxidoreductase （POR）. Consistently, POR levels are approximately threefold reduced in the pitt insertion mutant. The membrane sublocalization of Pitt was found to be dependent on the presence of the periplasmic photosystem Ⅱ （PSⅡ） biogenesis factor PratA, supporting the idea that Pitt is involved in the early steps of photosynthetic pigment/protein complex formation.展开更多
All members of the YidC/Oxal/Alb3 protein family are evolutionarily conserved and appear to function in membrane protein integration and protein complex stabilization. Here, we report on a second thylakoidal isoform o...All members of the YidC/Oxal/Alb3 protein family are evolutionarily conserved and appear to function in membrane protein integration and protein complex stabilization. Here, we report on a second thylakoidal isoform of Alb3, named Alb4. Analysis of Arabidopsis knockout mutant lines shows that AIb4 is required in assembly and/or stability of the CF1CF0-ATP synthase （ATPase）. alb4 mutant lines not only have reduced steady-state levels of ATPase subunits, but also their assembly into high-molecular-mass complexes is altered, leading to a reduction of ATP synthesis in the mutants. Moreover, we show that Alb4 but not AIb3 physically interacts with the subunits CF1β and CF0ll. Summarizing, the data indicate that AIb4 functions to stabilize or promote assembly of CF1 during its attachment to the membrane-embedded CF0 part.展开更多
Chloroplast-located proteins which are encoded by the nuclear genome have to be imported from the cytosol into the organelle in a posttranslational manner. Among these nuclear-encoded chloroplast proteins are the ligh...Chloroplast-located proteins which are encoded by the nuclear genome have to be imported from the cytosol into the organelle in a posttranslational manner. Among these nuclear-encoded chloroplast proteins are the light- harvesting chlorophyll a/b-binding proteins （LHCPs）. After translation in the cytosol, precursor proteins of LHCPs are imported via the TOC/TIC translocase, processed to their mature size to insert into thylakoid membranes where they recruit chlorophylls a and b to form pigment-protein complexes. The translocation of proteins is a highly regulated process which employs several regulators. To analyze whether CAO （chlorophyll a oxigenase） which converts chlorophyll a to chlorophyll b at the inner chloroplast membrane, is one of these regulators, we performed import reactions utilizing a homozygous loss-of-function mutant （cao-1）. We imported in vitro translated and 35S-labeled precursor proteins of light- harvesting proteins of photosystem II LHCB1, LHCB4, and LHCB5 into chloroplasts isolated from cao-1 and show that import of precursor proteins and their processing to mature forms are not impaired in the mutant. Therefore, regulation of the import machinery cannot be responsible for the decreased steady-state levels of light-harvesting complex （LHC） proteins. Regulation does not take place at the transcriptional level either, because Lhcb mRNAs are not down-regulated. Additionally, reduced steady-state levels of LHCPs also do not occur due to posttranslational turnover of non-functional LHCPs in chloroplasts. Taken together, our data show that plants in the absence of CAO and therefore devoid of chlorophyll b are not influenced in their import behavior of LHC proteins.展开更多
The chemokine receptor CCR7 and its ligands CCL19 and CCL21 guide the homing and positioning of dendritic and T cells in lymphoid organs,thereby contributing to several aspects of adaptive immunity and immune toleranc...The chemokine receptor CCR7 and its ligands CCL19 and CCL21 guide the homing and positioning of dendritic and T cells in lymphoid organs,thereby contributing to several aspects of adaptive immunity and immune tolerance.In the present study,we investigated the role of CCR7 in the pathogenesis of collagen-induced arthritis(CIA).By using a novel anti-human CCR7 antibody and humanized CCR7 mice,we evaluated CCR7 as a target in this autoimmune model of rheumatoid arthritis(RA).Ccr7-deficient mice were completely resistant to CIA and presented severely impaired antibody responses to collagen II(CII).Selective CCR7 expression on dendritic cells restored arthritis severity and anti-CII antibody titers.Prophylactic and therapeutic treatment of humanized CCR7 mice with anti-human CCR7 mAb 8H3-16A12 led to complete resistance to CIA and halted CIA progression,respectively.Our data demonstrate that CCR7 signaling is essential for the induction of CIA and identify CCR7 as a potential therapeutic target in RA.展开更多
P-glycoprotein(ABCB1)is the first discovered mammalian member of the large family of ATP binding cassette(ABC)transporters.It facilitates the movement of compounds(called allocrites)across membranes,using the energy o...P-glycoprotein(ABCB1)is the first discovered mammalian member of the large family of ATP binding cassette(ABC)transporters.It facilitates the movement of compounds(called allocrites)across membranes,using the energy of ATP binding and hydrolysis.Here,we review the thermodynamics of allocrite binding and the kinetics of ATP hydrolysis by ABCB1.In combination with our previous molecular dynamics simulations,these data lead to a new model for allocrite transport by ABCB1.In contrast to previous models,we take into account that the transporter was evolutionarily optimized to operate within a membrane,which dictates the nature of interactions.Hydrophobic interactions drive lipid-water partitioning of allocrites,the transport process’s first step.Weak dipolar interactions(including hydrogen bonding,π-π stacking,and π-cation interactions)drive allocrite recognition,binding,and transport by ABCB1 within the membrane.Increasing the lateral membrane packing density reduces allocrite partitioning but enhances dipolar interactions between allocrites and ABCB1.Allocrite flopping(or reorientation of the polar part towards the extracellular aqueous phase)occurs after hydrolysis of one ATP molecule and opening of ABCB1 at the extracellular side.Rebinding of ATP re-closes the transporter at the extracellular side and expels the potentially remaining allocrite into the membrane.The high sensitivity of the steady-state ATP hydrolysis rate to the nature and number of dipolar interactions,as well as to the dielectric constant of the membrane,points to a flopping process,which occurs to a large extent at the membrane-transporter interface.The proposed unidirectional ABCB1 transport cycle,driven by weak dipolar interactions,is consistent with membrane biophysics.展开更多
Background:Blood-based biomarkers have proven to be a reliable measure of the severity and outcome of traumatic brain injury(TBI)in both murine models and patients.In particular,neuronspecific enolase(NSE),neurofilame...Background:Blood-based biomarkers have proven to be a reliable measure of the severity and outcome of traumatic brain injury(TBI)in both murine models and patients.In particular,neuronspecific enolase(NSE),neurofilament light(NFL)and S100 beta(S100B)have been investigated in the clinical setting post-injury.Ethanol intoxication(EI)remains a significant comorbidity in TBI,with 30–40%of patients having a positive blood alcohol concentration post-TBI.The effect of ethanol on blood-based biomarkers for the prognosis and diagnosis of TBI remains unclear.In this study,we investigated the effect of EI on NSE,NFL and S100B and their correlation with blood–brain barrier integrity in a murine model of TBI.Methods:We used ultra-sensitive single-molecule array technology and enzyme-linked immunosorbent assay methods to measure NFL,NSE,S100B and claudin-5 concentrations in plasma 3 hours post-TBI.Results:We showed that NFL,NSE and S100B were increased at 3 hours post-TBI.Interestingly,ethanol blood concentrations showed an inverse correlation with NSE but not with NFL or S100B.Claudin-5 levels were increased post-injury but no difference was detected compared to ethanol pretreatment.The increase in claudin-5 post-TBI was correlated with NFL but not with NSE or S100B.Conclusions:Ethanol induces an effect on biomarker release in the bloodstream that is different from TBI not influenced by alcohol.This could be the basis of investigations into humans.展开更多
Cells encountering hypoxic stress conserve resources and energy by downregulating the protein synthesis. Here we demonstrate that one mechanism in this response is the translational repression of TOP mRNAs that encode...Cells encountering hypoxic stress conserve resources and energy by downregulating the protein synthesis. Here we demonstrate that one mechanism in this response is the translational repression of TOP mRNAs that encode components of the translational apparatus. This mode of regulation involves TSC and Rheb, as knockout of TSC1 or TSC2 or overexpression of Rheb rescued TOP mRNA translation in oxygen-deprived celts. Stress-induced translational repression of these mRNAs closely correlates with the hypophosphorylated state of 4E-BP, a translational repressor. However, a series of 4E-BP loss- and gain-of-function experiments disprove a cause-and- effect relationship between the phosphorylation status of 4E-BP and the translational repression of TOP mRNAs under oxygen or growth factor deprivation. Furthermore, the repressive effect of anoxia is similar to that attained by the very efficient inhibition of mTOR activity by Torin 1, but much more pronounced than roptor or rictor knockouL Likewise, deficiency of raptor or rictor, even though it mildly downregulated basal translation efficiency of TOP mRNAs, failed to suppress the oxygen-mediated translational activation of TOP mRNAs. Finally, co-knockdown of TIA-1 and TIAR, two RNA-binding proteins previously implicated in translational repression of TOP mRNAs in amino acid-starved cells, failed to relieve TOP mRNA translation under other stress conditions. Thus, the nature of the proximal translational regulator of TOP m RNAs remains elusive.展开更多
E-selectin is a cell-adhesion molecule of the vascular endothelium that promotes essential leukocyte rolling in the early inflammatory response by binding to glycoproteins containing the tetrasaccharide sialyl Lewisx(...E-selectin is a cell-adhesion molecule of the vascular endothelium that promotes essential leukocyte rolling in the early inflammatory response by binding to glycoproteins containing the tetrasaccharide sialyl Lewisx(sLex).Efficient leukocyte recruitment under vascular flow conditions depends on an increased lifetime of E-selectin/ligand complexes under tensile force in a so-called catch-bond binding mode.Co-crystal structures of a representative fragment of the extracellular E-selectin region with sLex and a glycomimetic antagonist thereof reveal an extended E-selectin conformation,which is identified as a high-affinity binding state of E-selectin by molecular dynamics simulations.Small-angle X-ray scattering experiments demonstrate a direct link between ligand binding and E-selectin conformational transition under static conditions in solution.This permits tracing a series of concerted structural changes connecting ligand binding to conformational stretching as the structural basis of E-selectin catch-bond-mediated leukocyte recruitment.The detailed molecular view of the binding site paves the way for the design of a new generation of selectin antagonists.This is of special interest,since their therapeutic potentialwas recently demonstrated with the pan-selectin antagonists GMI-1070(Rivipansel).展开更多
Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling pa...Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling path- ways have been described that are thought to be triggered by reactive oxygen species, photosynthesis redox imbalance, tetrapyrrole intermediates, and other metabolic traits. Here we report a meta-analysis based on transcriptome and pro- tein interaction data. Comparing the output of these pathways reveals the commonalities and peculiarities stimulated by six different sources impinging on operational retrograde signaling. Our study provides novel insights into the interplay of these pathways, supporting the existence of an as-yet unknown core response module of genes being regulated under all conditions tested. Our analysis further highlights affiliated regulatory cis-elements and classifies abscisic acid and auxin-based signaling as secondary components involved in the response cascades following a plastidial signal. Our study provides a global analysis of structure and interfaces of different pathways involved in plastid-to-nucleus signaling and a new view on this complex cellular communication network.展开更多
Background:Dispersal is an important event for most organisms at least once in their life cycle.The evolution of dispersal can be infuenced by local adaptation,landscape structure,and perceived temporal and spatial va...Background:Dispersal is an important event for most organisms at least once in their life cycle.The evolution of dispersal can be infuenced by local adaptation,landscape structure,and perceived temporal and spatial variation.The interaction between local adaptation,landscape heterogeneity,temporal variability and rules of dispersal may be more complex than previously assumed.Therefore,we sought to understand the infuence of emigration rules and landscape structure on emerging dispersal rates and traits.Here,we implemented an individual-based model(IBM)of trait evolution in scenarios characterized by diferent landscape structures and diferent degrees of spatial heterogeneity and global temporal variation.Individuals could evolve two traits coding for their environmental niche(position of niche optimum and niche width),and two traits determining nearest-neighbor dispersal:an individual emigrates with a probability defned by the frst trait(random emigration),but emigrates with certainty if the fertility expected in the patch of residence falls below a threshold specifed by the second trait(habitat-dependent emigration).Results:We note an interaction efect between dispersal strategy and spatial variance—lower emigration under habitat-dependent than under random emigration if spatial heterogeneity is low,but eventually a reversal of this ranking if heterogeneity becomes large.Landscapes with sharp transition of habitat attributes result in a high degree of spatial sorting,while fractal landscapes do not.Emigration rates are overall lowest,when spatial variation is highest.Conclusions:We conclude that emergent emigration rates are infuenced more by landscape structure and spatiotemporal heterogeneity than by the emigration strategy.With the ongoing land use change more research into this topic could help highlight the difculties species might face under the change from landscapes characterized by gradual transition zones to landscapes dominated by abrupt ecotones,the latter typical for agricultural and urban settings.展开更多
Memory is a term used in two important systems:the nervous system and the immune system.Both systems need to recognize alterations and threats in an ever-changing environment.As a consequence,both systems during their...Memory is a term used in two important systems:the nervous system and the immune system.Both systems need to recognize alterations and threats in an ever-changing environment.As a consequence,both systems during their evolution perfected their abilities to recall earlier challenges in mounting protective responses.This ability gives both systems the power to facilitate these protective responses if confronted with the same or similar challenges again.展开更多
Human action famously transforms the Earth and its biosphere and geosphere.1 While most literature consider plowing,burning,debris,and other products and by-products of our activities,direct effects of changing human ...Human action famously transforms the Earth and its biosphere and geosphere.1 While most literature consider plowing,burning,debris,and other products and by-products of our activities,direct effects of changing human biomass might merit further study.Humans are now the dominant terrestrial vertebrate,composing about 1/3 of land vertebrate biomass,which translates to 1/10 of total vertebrate biomass.2 The other terrestrial 2/3 consists nearly entirely of livestock kept by humans for food.Non-domesticated land vertebrates,from shrews to elephants to swallows,form a mere 3%.Human and domestic animal sequences,commonly detected in environmental DNA(eDNA)metabarcoding studies,are routinely excluded from analysis.Here,we hypothesize that extending eDNA analysis to include human and domesticated animal eDNA(hdaDNA)will provide insight into present-day and potentially historical human impacts on the biosphere(Figure 1).We think the distribution and abundance of hdaDNA are features of the Anthropocene worthy of study.展开更多
Single-molecule localization microscopy(SMLM)aims for maximized precision and a high signal-to-noise ratio1.Both features can be provided by placing the emitter in front of a metal-dielectric nanocoating that acts as ...Single-molecule localization microscopy(SMLM)aims for maximized precision and a high signal-to-noise ratio1.Both features can be provided by placing the emitter in front of a metal-dielectric nanocoating that acts as a tuned mirror2–4.Here,we demonstrate that a higher photon yield at a lower background on biocompatible metal-dielectric nanocoatings substantially improves SMLM performance and increases the localization precision by up to a factor of two.The resolution improvement relies solely on easy-to-fabricate nanocoatings on standard glass coverslips and is spectrally and spatially tunable by the layer design and wavelength,as experimentally demonstrated for dual-color SMLM in cells.展开更多
Our work focuses on the development of simpler and effective production of nanofluidic devices for high-throughput charged single nanoparticle trapping in an aqueous environment.Single nanoparticle confinement using e...Our work focuses on the development of simpler and effective production of nanofluidic devices for high-throughput charged single nanoparticle trapping in an aqueous environment.Single nanoparticle confinement using electrostatic trapping has been an effective approach to study the fundamental properties of charged molecules under a controlled aqueous environment.Conventionally,geometry-induced electrostatic trapping devices are fabricated using SiOx-based substrates and comprise nanochannels imbedded with nanoindentations such as nanopockets,nanoslits and nanogrids.These geometry-induced electrostatic trapping devices can only trap negatively charged particles,and therefore,to trap positively charged particles,modification of the device surface is required.However,the surface modification process of a nanofluidic device is cumbersome and time consuming.Therefore,here,we present a novel approach for the development of surface-modified geometry-induced electrostatic trapping devices that reduces the surface modification time from nearly 5 days to just a few hours.We utilized polydimethylsiloxane for the development of a surface-modified geometry-induced electrostatic trapping device.To demonstrate the device efficiency and success of the surface modification procedure,a comparison study between a PDMS-based geometry-induced electrostatic trapping device and the surface-modified polydimethylsiloxane-based device was performed.The device surface was modified with two layers of polyelectrolytes(1:poly(ethyleneimine)and 2:poly(styrenesulfonate)),which led to an overall negatively charged surface.Our experiments revealed the presence of a homogeneous surface charge density inside the fluidic devices and equivalent trapping strengths for the surface-modified and native polydimethylsiloxane-based geometry-induced electrostatic trapping devices.This work paves the way towards broader use of geometry-induced electrostatic trapping devices in the fields of biosensing,disease diagnosis,molecular analysis,fluid quality control and pathogen detection.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.12104500 and 82430062)the Key Research and Development Projects of Shaanxi Province(Grant No.2023-YBSF-263),the Shenzhen Engineering Research Centre(Grant No.XMHT20230115004)the Shenzhen Science and Technology Innovation Commission(Grant No.KCXFZ20201221173207022).
文摘Full-color imaging is essential in digital pathology for accurate tissue analysis.Utilizing advanced optical modulation and phase retrieval algorithms,Fourier ptychographic microscopy(FPM)offers a powerful solution for high-throughput digital pathology,combining high resolution,large field of view,and extended depth of field(DOF).However,the full-color capabilities of FPM are hindered by coherent color artifacts and reduced computational efficiency,which significantly limits its practical applications.Color-transferbased FPM(CFPM)has emerged as a potential solution,theoretically reducing both acquisition and reconstruction threefold time.Yet,existing methods fall short of achieving the desired reconstruction speed and colorization quality.In this study,we report a generalized dual-color-space constrained model for FPM colorization.This model provides a mathematical framework for model-based FPM colorization,enabling a closed-form solution without the need for redundant iterative calculations.Our approach,termed generalized CFPM(gCFPM),achieves colorization within seconds for megapixel-scale images,delivering superior colorization quality in terms of both colorfulness and sharpness,along with an extended DOF.Both simulations and experiments demonstrate that gCFPM surpasses state-of-the-art methods across all evaluated criteria.Our work offers a robust and comprehensive workflow for high-throughput full-color pathological imaging using FPM platforms,laying a solid foundation for future advancements in methodology and engineering.
文摘The spider monkey, a fruit specialist and important seed dispersal agent in the Neotropics, is an endangered primate due to habitat loss, hunting and the pet trade. Spider monkeys have been the subject of a few studies in Central and South Ame- rica, but little is known about the diet and ranging for this primate in southern Mexico. Here we report the results of a six-month long study （October 2010 to March 2011） of the feeding preferences and ranging patterns of the Yucatan spider monkey Ateles geoffroyi yucatanensis living in the ＂Ya＇ax＇che＂ reserve by the Caribbean coast in northeast Yucatan peninsula. Focal animal and scan sampling as well as GPS tracking were used to document spider monkey feeding behavior, location of food trees and ranging in the reserve. The spider monkeys used 36 species of plants （94% trees; n = 432） and six non tree morphospecies as a source of food. Six tree species accounted for 〉~80% of total feeding time and for 74% of all trees used. Fruits accounted for 59% of total feeding time, followed by leaves （35%）, palm piths （5%） and other plant parts （1%）. Total range used by the monkeys was esti- mated at 43% of semievergreen rainforest habitat available （ca 40ha）. Range use was not random with segments showing light, moderate and heavy use; the use of different areas of their range varied monthly and was closely linked to the spatial dispersion of the trees used for food [Current Zoology 59 （1）： 125-134, 2013].
基金supported by the grants from the Biofuture Programme of the German Federal Ministry for Education and Research (BMBF,to JNV),the French Research Agency (ANR to JNV)the Scientific Research Foundation for the Returned Overseas Chinese Scholars,the Ministry of Education of China (to QZ)
文摘A consensus sequence, encoding a putative DNA polymerase type B derived from a Polinton transposon, was assembled from the sex determination region of Xiphophorus maculatus. This predicted protein, which is 1,158 aa in length, contains a DNAA_pol_B_2 domain and a DTDS motif. The DNA polymerase type B gene has about 10 copies in the haploid X. maculatus genome with one Y-specific copy. Interestingly, it has specific copies on the W chromosome in the X. maculatus Usumacinta strain （sex determination with female het- erogamety）, which represent new markers for this type of sex chromosome in platyfish. This marker with W- and Y-specific copies suggests relationship between different types of gonosomes and allows comparing male and female heterogameties in the platyfish. Further molecular analysis of the DNA polymerase type B gene in X. maculatus will shed new light on the evolution of sex chromosomes in platyfish.
文摘Ataxia telangiectasia(AT)is an autosomal recessive multisystem disorder with increased radiosensitivity and cancer susceptibility.The responsible gene(ATM)consists of 66 exons and a coding region of 9171 bp which precludes direct seq uencing as a screening assay for confirmation or exclusion of the clinical suspi cion of AT.Peripheral blood mononuclear cells of 330 patients referred for the exclusion of AT were exposed to ionizing radiation(IR)and incubated for 72 h i n the presence of phytohemagglutinin.Using bivariate BrdUHoechst/ethidium brom ide flowcytometry,the following cell cycle parameters were ascertained:(1)pro portion of non-proliferating(G0,G1)cells as a measure of mitogen response,(2)proportion of first-cycle G2-phase cells relative to the growth fraction(G2 /GF)as a measure of radiosensitivity.Of the cases tested,94.2%could be unequ ivocally assigned either to the AT-negative or the AT-positive group of patien ts.Of the AT-positive cases,11 were confirmed by ATM mutation analysis.Ninet een cases presented with non-conclusive results,mostly due to poor mitogen res ponse;however,a combination of cellcycle data with serum AFP concentrations le d to the exclusion of AT in all but two of the uncertain cases.Substitution of ionizing radiation by the radiomimetic bleomycin was additionally tested in a sm all series of patients.We conclude that cell-cycle testing complemented by ser um AFP measurements fulfills the criteria as a rapid and economical screening pr ocedure for the differential diagnosis of juvenile ataxias.
基金supported by the National Natural Science Foundation of China(32230107)Key Research and Development Project of Shandong Province(2021LZGC028,2023ZLYS02)+2 种基金Central Public-interest Scientific Institution Basal Research Fund,CAFS(2020TD20,2022CG01)Shandong Taishan Scholar Climbing Projectthe Key Research and Development Project of Shandong Province(2022ZLGX01)。
文摘The molecular mechanisms underlying gonadal differentiation in vertebrates have long intrigued researchers.However,studies in this field have predominantly focused on mammals,with limited attention given to non-mammalian vertebrates,particularly at the cellular level.To address this knowledge gap,we selected the Chinese tongue sole as our research model.We collected samples from six developmental stages of ovaries and testes and performed in-depth transcriptomic analyses of 123,344 single-cell nuclei.This study identified 34 major cell types,including five gonadal cell types,enabling us to outline the early sex differentiation roadmap in a non-model teleost species.Both somatic and germ cells in the gonads were systematically studied using bioinformatics methods.Numerous sex-biased genes and markers were identified and experimentally validated,contributing to our understanding of the dynamic development and differentiation processes of gonadal supporting cells and germ cells in teleosts.Weighted Gene Co-expression Network Analysis(WGCNA)networks emphasized the critical roles of foxl2a and dmrt1 in sex differentiation.Pseudotime analysis revealed the early differentiation processes between male and female germ cells.We discovered a new germ cell marker gene,gpat2,and elucidated the differentiation pathway of gonadal stem cells in teleost fish.Our results highlight the significance of pathways such as oocyte meiosis,Target of Rapamycin(TOR)complex,oxytocin signaling,cGMP-PKG signaling,and arginine signaling in the differentiation of oocytes and spermatogonial stem cells.Cell-cell communication analyses further revealed interactions among different gonadal cell types,identifying the WNT and Notch pathways as crucial for the development of female and male gonads.Furthermore,we verified a feedback loop between dmrt1 and zfpm2 for the first time in teleosts,suggesting potential roles for zfpm2 in the formation and development of the teleost testis.Our findings provide a comprehensive transcriptomic resource for investigating the early sex differentiation processes of teleosts at the single-cell level and bridge the knowledge gap in research on non-mammalian vertebrates.
文摘Biogenesis of photosynthetic pigment/protein complexes is a highly regulated process that requires various assisting factors. Here, we report on the molecular analysis of the Pitt gene （sir1644） from the cyanobacterium Synechocystis sp. PCC 6803 （Synechocystis 6803） that encodes a membrane-bound tetratricopeptide repeat （TPR） protein of formerly unknown function. Targeted inactivation of Pitt affected photosynthetic performance and light-dependent chlorophyll synthesis. Yeast two-hybrid analyses and native PAGE strongly suggest a complex formation between Pitt and the light-dependent protochlorophyllide oxidoreductase （POR）. Consistently, POR levels are approximately threefold reduced in the pitt insertion mutant. The membrane sublocalization of Pitt was found to be dependent on the presence of the periplasmic photosystem Ⅱ （PSⅡ） biogenesis factor PratA, supporting the idea that Pitt is involved in the early steps of photosynthetic pigment/protein complex formation.
文摘All members of the YidC/Oxal/Alb3 protein family are evolutionarily conserved and appear to function in membrane protein integration and protein complex stabilization. Here, we report on a second thylakoidal isoform of Alb3, named Alb4. Analysis of Arabidopsis knockout mutant lines shows that AIb4 is required in assembly and/or stability of the CF1CF0-ATP synthase （ATPase）. alb4 mutant lines not only have reduced steady-state levels of ATPase subunits, but also their assembly into high-molecular-mass complexes is altered, leading to a reduction of ATP synthesis in the mutants. Moreover, we show that Alb4 but not AIb3 physically interacts with the subunits CF1β and CF0ll. Summarizing, the data indicate that AIb4 functions to stabilize or promote assembly of CF1 during its attachment to the membrane-embedded CF0 part.
文摘Chloroplast-located proteins which are encoded by the nuclear genome have to be imported from the cytosol into the organelle in a posttranslational manner. Among these nuclear-encoded chloroplast proteins are the light- harvesting chlorophyll a/b-binding proteins （LHCPs）. After translation in the cytosol, precursor proteins of LHCPs are imported via the TOC/TIC translocase, processed to their mature size to insert into thylakoid membranes where they recruit chlorophylls a and b to form pigment-protein complexes. The translocation of proteins is a highly regulated process which employs several regulators. To analyze whether CAO （chlorophyll a oxigenase） which converts chlorophyll a to chlorophyll b at the inner chloroplast membrane, is one of these regulators, we performed import reactions utilizing a homozygous loss-of-function mutant （cao-1）. We imported in vitro translated and 35S-labeled precursor proteins of light- harvesting proteins of photosystem II LHCB1, LHCB4, and LHCB5 into chloroplasts isolated from cao-1 and show that import of precursor proteins and their processing to mature forms are not impaired in the mutant. Therefore, regulation of the import machinery cannot be responsible for the decreased steady-state levels of light-harvesting complex （LHC） proteins. Regulation does not take place at the transcriptional level either, because Lhcb mRNAs are not down-regulated. Additionally, reduced steady-state levels of LHCPs also do not occur due to posttranslational turnover of non-functional LHCPs in chloroplasts. Taken together, our data show that plants in the absence of CAO and therefore devoid of chlorophyll b are not influenced in their import behavior of LHC proteins.
基金supported by Deutsche Forschungsgemeinschaft(DFG)grant KFO 250-FO 334/2-1 to R.Forster.
文摘The chemokine receptor CCR7 and its ligands CCL19 and CCL21 guide the homing and positioning of dendritic and T cells in lymphoid organs,thereby contributing to several aspects of adaptive immunity and immune tolerance.In the present study,we investigated the role of CCR7 in the pathogenesis of collagen-induced arthritis(CIA).By using a novel anti-human CCR7 antibody and humanized CCR7 mice,we evaluated CCR7 as a target in this autoimmune model of rheumatoid arthritis(RA).Ccr7-deficient mice were completely resistant to CIA and presented severely impaired antibody responses to collagen II(CII).Selective CCR7 expression on dendritic cells restored arthritis severity and anti-CII antibody titers.Prophylactic and therapeutic treatment of humanized CCR7 mice with anti-human CCR7 mAb 8H3-16A12 led to complete resistance to CIA and halted CIA progression,respectively.Our data demonstrate that CCR7 signaling is essential for the induction of CIA and identify CCR7 as a potential therapeutic target in RA.
基金Stiftung zur Forderung der biologischen Forschung,Basel,Switzerland.
文摘P-glycoprotein(ABCB1)is the first discovered mammalian member of the large family of ATP binding cassette(ABC)transporters.It facilitates the movement of compounds(called allocrites)across membranes,using the energy of ATP binding and hydrolysis.Here,we review the thermodynamics of allocrite binding and the kinetics of ATP hydrolysis by ABCB1.In combination with our previous molecular dynamics simulations,these data lead to a new model for allocrite transport by ABCB1.In contrast to previous models,we take into account that the transporter was evolutionarily optimized to operate within a membrane,which dictates the nature of interactions.Hydrophobic interactions drive lipid-water partitioning of allocrites,the transport process’s first step.Weak dipolar interactions(including hydrogen bonding,π-π stacking,and π-cation interactions)drive allocrite recognition,binding,and transport by ABCB1 within the membrane.Increasing the lateral membrane packing density reduces allocrite partitioning but enhances dipolar interactions between allocrites and ABCB1.Allocrite flopping(or reorientation of the polar part towards the extracellular aqueous phase)occurs after hydrolysis of one ATP molecule and opening of ABCB1 at the extracellular side.Rebinding of ATP re-closes the transporter at the extracellular side and expels the potentially remaining allocrite into the membrane.The high sensitivity of the steady-state ATP hydrolysis rate to the nature and number of dipolar interactions,as well as to the dielectric constant of the membrane,points to a flopping process,which occurs to a large extent at the membrane-transporter interface.The proposed unidirectional ABCB1 transport cycle,driven by weak dipolar interactions,is consistent with membrane biophysics.
文摘Background:Blood-based biomarkers have proven to be a reliable measure of the severity and outcome of traumatic brain injury(TBI)in both murine models and patients.In particular,neuronspecific enolase(NSE),neurofilament light(NFL)and S100 beta(S100B)have been investigated in the clinical setting post-injury.Ethanol intoxication(EI)remains a significant comorbidity in TBI,with 30–40%of patients having a positive blood alcohol concentration post-TBI.The effect of ethanol on blood-based biomarkers for the prognosis and diagnosis of TBI remains unclear.In this study,we investigated the effect of EI on NSE,NFL and S100B and their correlation with blood–brain barrier integrity in a murine model of TBI.Methods:We used ultra-sensitive single-molecule array technology and enzyme-linked immunosorbent assay methods to measure NFL,NSE,S100B and claudin-5 concentrations in plasma 3 hours post-TBI.Results:We showed that NFL,NSE and S100B were increased at 3 hours post-TBI.Interestingly,ethanol blood concentrations showed an inverse correlation with NSE but not with NFL or S100B.Claudin-5 levels were increased post-injury but no difference was detected compared to ethanol pretreatment.The increase in claudin-5 post-TBI was correlated with NFL but not with NSE or S100B.Conclusions:Ethanol induces an effect on biomarker release in the bloodstream that is different from TBI not influenced by alcohol.This could be the basis of investigations into humans.
文摘Cells encountering hypoxic stress conserve resources and energy by downregulating the protein synthesis. Here we demonstrate that one mechanism in this response is the translational repression of TOP mRNAs that encode components of the translational apparatus. This mode of regulation involves TSC and Rheb, as knockout of TSC1 or TSC2 or overexpression of Rheb rescued TOP mRNA translation in oxygen-deprived celts. Stress-induced translational repression of these mRNAs closely correlates with the hypophosphorylated state of 4E-BP, a translational repressor. However, a series of 4E-BP loss- and gain-of-function experiments disprove a cause-and- effect relationship between the phosphorylation status of 4E-BP and the translational repression of TOP mRNAs under oxygen or growth factor deprivation. Furthermore, the repressive effect of anoxia is similar to that attained by the very efficient inhibition of mTOR activity by Torin 1, but much more pronounced than roptor or rictor knockouL Likewise, deficiency of raptor or rictor, even though it mildly downregulated basal translation efficiency of TOP mRNAs, failed to suppress the oxygen-mediated translational activation of TOP mRNAs. Finally, co-knockdown of TIA-1 and TIAR, two RNA-binding proteins previously implicated in translational repression of TOP mRNAs in amino acid-starved cells, failed to relieve TOP mRNA translation under other stress conditions. Thus, the nature of the proximal translational regulator of TOP m RNAs remains elusive.
基金supported by the Swiss National Science Foundation(grant number 200020_129935 and R’EQUIP 145023).
文摘E-selectin is a cell-adhesion molecule of the vascular endothelium that promotes essential leukocyte rolling in the early inflammatory response by binding to glycoproteins containing the tetrasaccharide sialyl Lewisx(sLex).Efficient leukocyte recruitment under vascular flow conditions depends on an increased lifetime of E-selectin/ligand complexes under tensile force in a so-called catch-bond binding mode.Co-crystal structures of a representative fragment of the extracellular E-selectin region with sLex and a glycomimetic antagonist thereof reveal an extended E-selectin conformation,which is identified as a high-affinity binding state of E-selectin by molecular dynamics simulations.Small-angle X-ray scattering experiments demonstrate a direct link between ligand binding and E-selectin conformational transition under static conditions in solution.This permits tracing a series of concerted structural changes connecting ligand binding to conformational stretching as the structural basis of E-selectin catch-bond-mediated leukocyte recruitment.The detailed molecular view of the binding site paves the way for the design of a new generation of selectin antagonists.This is of special interest,since their therapeutic potentialwas recently demonstrated with the pan-selectin antagonists GMI-1070(Rivipansel).
文摘Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling path- ways have been described that are thought to be triggered by reactive oxygen species, photosynthesis redox imbalance, tetrapyrrole intermediates, and other metabolic traits. Here we report a meta-analysis based on transcriptome and pro- tein interaction data. Comparing the output of these pathways reveals the commonalities and peculiarities stimulated by six different sources impinging on operational retrograde signaling. Our study provides novel insights into the interplay of these pathways, supporting the existence of an as-yet unknown core response module of genes being regulated under all conditions tested. Our analysis further highlights affiliated regulatory cis-elements and classifies abscisic acid and auxin-based signaling as secondary components involved in the response cascades following a plastidial signal. Our study provides a global analysis of structure and interfaces of different pathways involved in plastid-to-nucleus signaling and a new view on this complex cellular communication network.
基金funded by the German Research Foundation DFG,KU 3384-1/1.
文摘Background:Dispersal is an important event for most organisms at least once in their life cycle.The evolution of dispersal can be infuenced by local adaptation,landscape structure,and perceived temporal and spatial variation.The interaction between local adaptation,landscape heterogeneity,temporal variability and rules of dispersal may be more complex than previously assumed.Therefore,we sought to understand the infuence of emigration rules and landscape structure on emerging dispersal rates and traits.Here,we implemented an individual-based model(IBM)of trait evolution in scenarios characterized by diferent landscape structures and diferent degrees of spatial heterogeneity and global temporal variation.Individuals could evolve two traits coding for their environmental niche(position of niche optimum and niche width),and two traits determining nearest-neighbor dispersal:an individual emigrates with a probability defned by the frst trait(random emigration),but emigrates with certainty if the fertility expected in the patch of residence falls below a threshold specifed by the second trait(habitat-dependent emigration).Results:We note an interaction efect between dispersal strategy and spatial variance—lower emigration under habitat-dependent than under random emigration if spatial heterogeneity is low,but eventually a reversal of this ranking if heterogeneity becomes large.Landscapes with sharp transition of habitat attributes result in a high degree of spatial sorting,while fractal landscapes do not.Emigration rates are overall lowest,when spatial variation is highest.Conclusions:We conclude that emergent emigration rates are infuenced more by landscape structure and spatiotemporal heterogeneity than by the emigration strategy.With the ongoing land use change more research into this topic could help highlight the difculties species might face under the change from landscapes characterized by gradual transition zones to landscapes dominated by abrupt ecotones,the latter typical for agricultural and urban settings.
文摘Memory is a term used in two important systems:the nervous system and the immune system.Both systems need to recognize alterations and threats in an ever-changing environment.As a consequence,both systems during their evolution perfected their abilities to recall earlier challenges in mounting protective responses.This ability gives both systems the power to facilitate these protective responses if confronted with the same or similar challenges again.
文摘Human action famously transforms the Earth and its biosphere and geosphere.1 While most literature consider plowing,burning,debris,and other products and by-products of our activities,direct effects of changing human biomass might merit further study.Humans are now the dominant terrestrial vertebrate,composing about 1/3 of land vertebrate biomass,which translates to 1/10 of total vertebrate biomass.2 The other terrestrial 2/3 consists nearly entirely of livestock kept by humans for food.Non-domesticated land vertebrates,from shrews to elephants to swallows,form a mere 3%.Human and domestic animal sequences,commonly detected in environmental DNA(eDNA)metabarcoding studies,are routinely excluded from analysis.Here,we hypothesize that extending eDNA analysis to include human and domesticated animal eDNA(hdaDNA)will provide insight into present-day and potentially historical human impacts on the biosphere(Figure 1).We think the distribution and abundance of hdaDNA are features of the Anthropocene worthy of study.
基金supported by the Deutsche Forschungsgemeinschaft(DFG,German Research Foundation)TRR 166 projects A04(to M.S.)and C06(to K.G.H.)the Rudolf Virchow Center of the University of Würzburg(H.S.H.)+2 种基金the Elite Network of Bavaria(ENB)with project K-BM-2013-247(to B.S.)the University of Würzburg(M.E.,M.K.,S.H.,and R.G.)the State of Bavaria(clean room facilities).
文摘Single-molecule localization microscopy(SMLM)aims for maximized precision and a high signal-to-noise ratio1.Both features can be provided by placing the emitter in front of a metal-dielectric nanocoating that acts as a tuned mirror2–4.Here,we demonstrate that a higher photon yield at a lower background on biocompatible metal-dielectric nanocoatings substantially improves SMLM performance and increases the localization precision by up to a factor of two.The resolution improvement relies solely on easy-to-fabricate nanocoatings on standard glass coverslips and is spectrally and spatially tunable by the layer design and wavelength,as experimentally demonstrated for dual-color SMLM in cells.
基金The work was funded by the Swiss Nanoscience Institute,Basel,Switzerland(SNI PhD Graduate School)under project P1310.
文摘Our work focuses on the development of simpler and effective production of nanofluidic devices for high-throughput charged single nanoparticle trapping in an aqueous environment.Single nanoparticle confinement using electrostatic trapping has been an effective approach to study the fundamental properties of charged molecules under a controlled aqueous environment.Conventionally,geometry-induced electrostatic trapping devices are fabricated using SiOx-based substrates and comprise nanochannels imbedded with nanoindentations such as nanopockets,nanoslits and nanogrids.These geometry-induced electrostatic trapping devices can only trap negatively charged particles,and therefore,to trap positively charged particles,modification of the device surface is required.However,the surface modification process of a nanofluidic device is cumbersome and time consuming.Therefore,here,we present a novel approach for the development of surface-modified geometry-induced electrostatic trapping devices that reduces the surface modification time from nearly 5 days to just a few hours.We utilized polydimethylsiloxane for the development of a surface-modified geometry-induced electrostatic trapping device.To demonstrate the device efficiency and success of the surface modification procedure,a comparison study between a PDMS-based geometry-induced electrostatic trapping device and the surface-modified polydimethylsiloxane-based device was performed.The device surface was modified with two layers of polyelectrolytes(1:poly(ethyleneimine)and 2:poly(styrenesulfonate)),which led to an overall negatively charged surface.Our experiments revealed the presence of a homogeneous surface charge density inside the fluidic devices and equivalent trapping strengths for the surface-modified and native polydimethylsiloxane-based geometry-induced electrostatic trapping devices.This work paves the way towards broader use of geometry-induced electrostatic trapping devices in the fields of biosensing,disease diagnosis,molecular analysis,fluid quality control and pathogen detection.
