Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm

The starchy endosperm of cereals is a priori taken as a metabolically uniform tissue. By applying a noninvasive assay based on (13)C/(1)H-magnetic resonance imaging (MRI) to barley (Hordeum vulgare) grains, we uncovered metabolic compartmentation in the endosperm. (13)C-Suc feeding during grain filling showed that the primary site of Ala synthesis was the central region of the endosperm, the part of the caryopsis experiencing the highest level of hypoxia. Region-specific metabolism in the endosperm was characterized by flux balance analysis (FBA) and metabolite profiling. FBA predicts that in the central region of the endosperm, the tricarboxylic acid cycle shifts to a noncyclic mode, accompanied by elevated glycolytic flux and the accumulation of Ala. The metabolic compartmentation within the endosperm is advantageous for the grain's carbon and energy economy, with a prominent role being played by Ala aminotransferase. An investigation of caryopses with a genetically perturbed tissue pattern demonstrated that Ala accumulation is a consequence of oxygen status, rather than being either tissue specific or dependent on the supply of Suc. Hence the (13)C-Ala gradient can be used as an in vivo marker for hypoxia. The combination of MRI and metabolic modeling offers opportunities for the noninvasive analysis of metabolic compartmentation in plants.     

组学技术在核盘菌研究中的应用

核盘菌Sclerotinia sclerotiorum是一种典型的死体营养型植物病原真菌,全球分布且寄主范围广泛,严重危害多种植物,对农业生产造成严重损失。核盘菌研究主要集中在真菌生物学及病理学等方面。近年来,随着高通量分析技术的不断改进,多种组学技术为系统生物学研究提供了平台。文中主要综述利用多种组学研究方法在植物病原真菌核盘菌研究中的应用及研究进展,探讨开展植物病原物及病害发展的系统性研究思路,以期为核盘菌的分子生物学及致病机理等研究提供参考,同时也为其他植物病原物及病害系统研究提供理论依据。     

In vivo biofluid dynamic imaging in the developing zebrafish

Flow-structure interactions are ubiquitous in nature, and are important factors in the proper development of form and function in living organisms. In order to uncover the mechanisms by which flow-structure interactions affect vertebrate development, we first need to establish the techniques necessary to quantitatively describe the fluid flow environment within the embryo. To do this, we must bring dynamic, in vivo imaging methods to bear on living systems. Traditional avian and mammalian model systems can be problematic in this regard. The zebrafish (Danio rerio) is widely accepted as an excellent model organism for the study of vertebrate biology, as it shows substantial anatomical and genetic conservation with higher vertebrates, including humans. Their small size, optical transparency, and external development make zebrafish the ideal model system for dynamic imaging. This article reviews the current state of research in imaging biofluid flow within and around developing zebrafish embryos, with an emphasis on dynamic imaging modalities.     

In vivo imaging of embryonic vascular development using transgenic zebrafish

In this study we describe a model system that allows continuous in vivo observation of the vertebrate embryonic vasculature. We find that the zebrafish fli1 promoter is able to drive expression of enhanced green fluorescent protein (EGFP) in all blood vessels throughout embryogenesis. We demonstrate the utility of vascular-specific transgenic zebrafish in conjunction with time-lapse multiphoton laser scanning microscopy by directly observing angiogenesis within the brain of developing embryos. Our images reveal that blood vessels undergoing active angiogenic growth display extensive filopodial activity and pathfinding behavior similar to that of neuronal growth cones. We further show, using the zebrafish mindbomb mutant as an example, that the expression of EGFP within developing blood vessels permits detailed analysis of vascular defects associated with genetic mutations. Thus, these transgenic lines allow detailed analysis of both wild type and mutant embryonic vasculature and, together with the ability to perform large scale forward-genetic screens in zebrafish, will facilitate identification of new mutants affecting vascular development.     

Combined approaches to reveal genes associated with litter size in Yunshang black goats

Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two subpopulations (polytocous group, PG, and monotocous group, MG) with evident differences of litter size. Following the mapping to reference genome, and SNP calling and pruning, three approaches – GWAS, ROH analysis and detection of signatures of selection – were employed to unveil candidate genes responsible for litter size. Consequently, 12 candidate genes containing OSBPL8 with the minimum P-value were uncovered by GWAS. Differences were observed in the pattern of ROH between two subpopulations that shared similar low inbreeding coefficients. Two ROH hotspots and 12 corresponding genes emerged from ROH pool association analysis. Based on the nS_L statistic, 15 and 61 promising genes were disclosed under selection for MG and PG respectively. Of them, some promising genes participate in ovarian function (PPP2R5C, CDC25A, ESR1, RPS26 and SERPINBs), seasonal reproduction (DIO3, BTG1 and CRYM) and metabolism (OSBPL8, SLC39A5 and SERPINBs). Our study pinpointed some novel promising genes influencing litter size, provided a comprehensive insight into genetic makeup of litter size and might facilitate selective breeding in goats.     

Using imaging and genetics in zebrafish to study developing spinal circuits in vivo

Imaging and molecular approaches are perfectly suited to young, transparent zebrafish (Danio rerio), where they have allowed novel functional studies of neural circuits and their links to behavior. Here, we review cutting-edge optical and genetic techniques used to dissect neural circuits in vivo and discuss their application to future studies of developing spinal circuits using living zebrafish. We anticipate that these experiments will reveal general principles governing the assembly of neural circuits that control movements.     

Confocal imaging of metabolism in vivo: pitfalls and possibilities

Confocal laser scanning microscopy (CLSM) has had wide application in morphological studies and ion imaging in plants, but little impact so far on biochemical investigations. This position is likely to change as the range of fluorescent probes increases. To illustrate the type of kinetic information that can be obtained using CLSM in an intact, living system, an analysis has been made of the two-step detoxification of monochlorobimane (MCB) following conjugation to glutathione (GSH) by a glutathione S-transferase in the cytoplasm and vacuolar sequestration of the fluorescent glutathione S-bimane (GSB) by a glutathione S-conjugate (GSX) pump. Fluorescence from the cytoplasm and vacuole of individual trichoblasts and atrichoblasts was measured from time-series of (x, y) optical sections in the elongation zone of Arabidopsis root tips. Intensity changes were calibrated and converted to amounts using compartment volumes, measured by stereological techniques. The data were well described using pseudo-first-order kinetics for the conjugation reaction and either Michaelis-Menten kinetics (Model I), or, as the GSX-pump was operating close to V(max), a pseudo-zero-order reaction (Model II), for the GSX-pump. Analysis of 15 individual cells from two roots gave [GSH](cyt) in the range 1.8-4 mM. GST activity was relatively constant on a cell basis in one root, but increased markedly in the other, giving a net increase in conjugation activity as cells progressed through the elongation zone. In contrast, GSX-pump activity increased in parallel with the increase in cell size in both roots, effectively maintaining a constant transport activity per unit root length or estimated vacuole surface area.     

Combined proteome and metabolite-profiling analyses reveal surprising insights into yeast sulfur metabolism

Metabolomics is considered as an emerging new tool for functional proteomics in the identification of new protein function or in projects aiming at modeling whole cell metabolism. When combined with proteome studies, metabolite-profiling analyses revealed unanticipated insights into the yeast sulfur pathway. In response to cadmium, the observed overproduction of glutathione, essential for the detoxification of the metal, can be entirely accounted for by a marked drop in sulfur-containing protein synthesis and a redirection of sulfur metabolite fluxes to the glutathione pathway. A kinetic analysis showed sequential and dramatic changes in intermediate sulfur metabolite pools within the first hours of the treatment. Strikingly, whereas proteome and metabolic data were positively correlated under cadmium conditions, proteome and metabolic data were negatively correlated during other growth conditions, i.e. methionine supplementation or sulfate starvation. These differences can be explained by alternative mechanisms in the regulation of Met4, the activator of the sulfur pathway. Whereas Met4 activity is controlled by the cellular cysteine content in response to sulfur source and availability, the present study suggests that Met4 activation under cadmium conditions is cysteine-independent. The results clearly indicate that the metabolic state of a cell cannot be safely predicted based solely on proteomic and/or gene expression data. Combined metabolome and proteome studies are necessary to draw a comprehensive and integrated view of cell metabolism.     

Surface functionalization of barium titanate SHG nanoprobes for in vivo imaging in zebrafish

To address the need for a bright, photostable labeling tool that allows long-term in vivo imaging in whole organisms, we recently introduced second harmonic generating (SHG) nanoprobes. Here we present a protocol for the preparation and use of a particular SHG nanoprobe label, barium titanate (BT), for in vivo imaging in living zebrafish embryos. Chemical treatment of the BT nanoparticles results in surface coating with amine-terminal groups, which act as a platform for a variety of chemical modifications for biological applications. Here we describe cross-linking of BT to a biotin-linked moiety using click chemistry methods and coating of BT with nonreactive poly(ethylene glycol) (PEG). We also provide details for injecting PEG-coated SHG nanoprobes into zygote-stage zebrafish embryos, and in vivo imaging of SHG nanoprobes during gastrulation and segmentation. Implementing the PROCEDURE requires a basic understanding of laser-scanning microscopy, experience with handling zebrafish embryos and chemistry laboratory experience. Functionalization of the SHG nanoprobes takes ～3 d, whereas zebrafish preparation, injection and imaging setup should take approximately 2-4 h.     

In vivo time-lapse imaging and serial section electron microscopy reveal developmental synaptic rearrangements

Dendrites, axons, and synapses are dynamic during circuit development; however, changes in microcircuit connections as branches stabilize have not been directly demonstrated. By combining in?vivo time-lapse imaging of Xenopus tectal neurons with electron microscope reconstructions of imaged neurons, we report the distribution and ultrastructure of synapses on individual vertebrate neurons and relate these synaptic properties to dynamics in dendritic and axonal arbor structure over hours or?days of imaging. Dynamic dendrites have a high density of immature synapses, whereas stable dendrites have sparser, mature synapses. Axons initiate contacts from multisynapse boutons on stable branches. Connections are refined by decreasing convergence from multiple inputs to postsynaptic dendrites and by decreasing divergence from multisynapse boutons to postsynaptic sites. Visual deprivation or NMDAR antagonists decreased synapse maturation and elimination, suggesting that coactive input activity promotes microcircuit development by concurrently regulating synapse elimination and maturation of remaining contacts.     

Skeletal muscle regeneration in Xenopus tadpoles and zebrafish larvae

Background

Mammals are not able to restore lost appendages, while many amphibians are. One important question about epimorphic regeneration is related to the origin of the new tissues and whether they come from mature cells via dedifferentiation and/or from stem cells. Several studies in urodele amphibians (salamanders) indicate that, after limb or tail amputation, the multinucleated muscle fibres do dedifferentiate by fragmentation and proliferation, thereby contributing to the regenerate. In Xenopus laevis tadpoles, however, it was shown that muscle fibres do not contribute directly to the tail regenerate. We set out to study whether dedifferentiation was present during muscle regeneration of the tadpole limb and zebrafish larval tail, mainly by cell tracing and histological observations.

Results

Cell tracing and histological observations indicate that zebrafish tail muscle do not dedifferentiate during regeneration. Technical limitations did not allow us to trace tadpole limb cells, nevertheless we observed no signs of dedifferentiation histologically. However, ultrastructural and gene expression analysis of regenerating muscle in tadpole tail revealed an unexpected dedifferentiation phenotype. Further histological studies showed that dedifferentiating tail fibres did not enter the cell cycle and in vivo cell tracing revealed no evidences of muscle fibre fragmentation. In addition, our results indicate that this incomplete dedifferentiation was initiated by the retraction of muscle fibres.

Conclusions

Our results show that complete skeletal muscle dedifferentiation is less common than expected in lower vertebrates. In addition, the discovery of incomplete dedifferentiation in muscle fibres of the tadpole tail stresses the importance of coupling histological studies with in vivo cell tracing experiments to better understand the regenerative mechanisms.     

In vivo time-lapse imaging of cell divisions during neurogenesis in the developing zebrafish retina

Two-photon excitation microscopy was used to reconstruct cell divisions in living zebrafish embryonic retinas. Contrary to proposed models for vertebrate asymmetric divisions, no apico-basal cell divisions take place in the zebrafish retina during the generation of postmitotic neurons. However, a surprising shift in the orientation of cell division from central-peripheral to circumferential occurs within the plane of the ventricular surface. In the sonic you (syu) and lakritz (lak) mutants, the shift from central-peripheral to circumferential divisions is absent or delayed, correlating with the delay in neuronal differentiation and neurogenesis in these mutants. The reconstructions here show that mitotic cells always remain in contact with the opposite basal surface by means of a thin basal process that can be inherited asymmetrically.     

Structure and function of skeletal muscle in zebrafish early larvae

Zebrafish muscles were examined at an early developmental stage (larvae 5-7 d). Using aluminum clips, preparations (approximately 1.5 mm length, 150 microm diameter) were mounted for force registration and small angle x-ray diffraction. Sarcomeres were oriented mainly in parallel with the preparation long axis. Electrical stimulation elicited fast and reproducible single twitch contractions. Length-force relations showed an optimal sarcomere length of 2.15 microm. X-ray diffraction revealed clear equatorial 1.1/1.0 reflections, showing that myofilaments are predominantly arranged along the preparation long axis. In contrast, reflections from older (2 mo) zebrafish showed two main filament orientations each at an approximately 25 degrees angle relative to the preparation long axis. Electrical stimulation of larvae muscles increased the 1.1/1.0 intensity ratio, reflecting mass transfer to thin filaments during contraction. The apparent lattice volume was 3.42 x 10(-3) microm(3), which is smaller than that of mammalian striated muscle and more similar to that of frog muscles. The relation between force and stimulation frequency showed fusion of responses at a comparatively high frequency (approximately 186 Hz), reflecting a fast muscle phenotype. Inhibition of fast myosin with N-benzyl-p-toluene sulphonamide (BTS) showed that the later phase of the tetanus was less affected than the initial peak. This suggests that, although the main contractile phenotype is fast, slow twitch fibers can contribute to sustained contraction. A fatigue stimulation protocol with repeated 220 ms/186 Hz tetani showed that tetanic force decreased to 50% at a train rate of 0.1 s(-1). In conclusion, zebrafish larvae muscles can be examined in vitro using mechanical and x-ray methods. The muscles and myofilaments are mainly orientated in parallel with the larvae long axis and exhibit a significant fast contractile component. Sustained contractions can also involve a small contribution from slower muscle types.     

Combined 1H and 31P NMR studies of cerebral metabolism in vivo

NMR spectroscopic methods have recently been developed for measurement of several concentrated cerebral metabolites in vivo. At present, 31P spectra from the brain permit detection of ATP, PCr, Pi, and certain sugar and lipid phosphates. The resonant frequency of Pi also provides a measure of cerebral pHi, and under some conditions ADP concentration can be calculated from information available in the 31P spectrum. The 1H spectrum of brain provides measurements of lactate, creatine, and several amino acids and choline-containing compounds. Both kinds of spectra can be obtained from the same subject. Our group at Yale used combined 31P and 1H methods to demonstrate that loss and recovery of phosphate energy stores and concomitant changes in cerebral amino acids during hypoglycemic coma in rodents could be observed in vivo. We then used the same methods to show that cerebral pHi can be normal while lactate is elevated in status epilepticus. NMR spectroscopy performed in vivo provides an array of chemically specific measurements unavailable by any other non-invasive method. It is thought to be entirely free of deleterious biological effects; hence, its potential for use in humans is considerable.     

The enantioselective enrichment,metabolism, and toxicity of fenoxaprop-ethyl and its metabolites in zebrafish

To investigate the impacts of the widely used chiral herbicide fenoxaprop-ethyl (FE) on aquatic organisms, the enrichment, metabolism, acute toxicity, and oxidative stress of fenoxaprop-ethyl and its main metabolites fenoxaprop (FA), ethyl-2-(4-hydroxyphenoxy)propanoate (EHPP), 2-(4-hydroxyphenoxy)propanoic acid (HPPA), and 6-chloro-2,3-dihydrobenzoxazol-2-one (CDHB) in zebrafish were studied. The enantioselectivity of fenoxaprop-ethyl and its chiral metabolites was also determined. Fenoxaprop-ethyl quickly degraded in zebrafish by aquatic exposure. FA, HPPA, and CDHB were the main metabolites that were enriched in the zebrafish. In the metabolism experiment, the half-lives of the metabolites were 0.92–1.72 days in zebrafish. The R-enantiomers of FA and HPPA were preferentially enriched and metabolized with enantiomeric fractions (EFs) of 0.65–0.85. According to the 96-h acute toxicity, FA, HPPA, EHPP, and CDHB were less toxic to zebrafish than FE, following the order of FE > CDHB > EHPP > FA > HPPA. The S-enantiomers of FE, FA, CDHB, and EHPP were more toxic than the R-enantiomers. FE and its metabolites could significantly increase catalase (CAT) and superoxide dismutase (SOD) activity and the malondialdehyde (MDA) content in gill and liver tissues, indicating their oxidative stress, and these effects were also enantioselective. This work could supply more information for evaluating the risks of fenoxaprop-ethyl on aquatic organisms concerning their metabolites and enantiomers.