神经元形态重建工具的研究进展

近年来,分子标记和显微光学成像技术的系列突破,使得单细胞分辨的全脑尺度神经群落成像成为现实.然而,现有神经元形态重建工具的发展速度远远滞后于海量数据的产生速度,难以满足现阶段成像数据的分析需求.在此背景下,我们首先分析了神经元形态重建工具发展滞后的原因,简述现有半自动和全自动神经元形态重建工具的特点和最新发展,并结合现有工具的特点分析其向高通量、高准确度重建工具发展时面临的挑战.最后,我们对未来形态重建工具的发展趋势及应用前景做出展望.     

Feasibility Study of the Elaboration of a Biodegradable and Bioactive Ligament Made of Poly(ε-caprolactone)-pNaSS Grafted Fibers for the Reconstruction of Anterior Cruciate Ligament: In Vivo Experiment

Background

The anterior cruciate ligament rupture is a common injury which mainly affects young and active population. Faced to this problem, the development of synthetic structures for ligament reconstruction is increasing. The most recent researches focused on the development of biodegradable structures that could be functionalized to enhance host integration. This work describes the elaboration of different poly(ε-caprolactone) prototypes for the rat anterior cruciate ligament replacement in order to found the best design for further in vivo assays.

Automated system for gene annotation and metabolic pathway reconstruction using general sequence databases

Despite the growing number of genomes published or currently being sequenced, there is a relative paucity of software for functional classification of newly discovered genes and their assignment to metabolic pathways. Available software for such analyses has a very steep learning curve and requires the installation, configuration, and maintenance of large amounts of complex infrastructure, including complementary software and databases. Many such tools are restricted to one or a few data sources and classification schemes. In this work, we report an automated system for gene annotation and metabolic pathway reconstruction (ASGARD), which was designed to be powerful and generalizable, yet simple for the biologist to install and run on centralized, commonly available computers. It avoids the requirement for complex resources such as relational databases and web servers, as well as the need for administrator access to the operating system. Our methodology contributes to a more rapid investigation of the potential biochemical capabilities of genes and genomes by the biological researcher, and is useful in biochemical as well as comparative and evolutionary studies of pathways and networks.     

Organelle association visualized by three-dimensional ultrastructural imaging of the yeast cell

This study was aimed at a better understanding of organelle organization in the yeast Saccharomyces cerevisiae with special emphasis on the interaction and physical association of organelles. For this purpose, a computer aided method was employed to generate three-dimensional ultrastructural reconstructions of chemically and cryofixed yeast cells. This approach showed at a high level of resolution that yeast cells were densely packed with organelles that had a strong tendency to associate at a distance of <30 nm. The methods employed here also allowed us to measure the total surface area and volume of organelles, the number of associations between organelles, and the ratio of associations between organelles per surface area. In general, the degree of organelle associations was found to be much higher in chemically fixed cells than in cryofixed cells, with endoplasmic reticulum/plasma membrane, endoplasmic reticulum/mitochondria and lipid particles/nuclei being the most prominent pairs of associated fractions. In cryofixed cells, similar preferences for organelle association were seen, although at lower frequency. The occurrence of specific organelle associations is believed to be important for intracellular translocation and communication. Membrane contact as a possible means of interorganelle transport of cellular components, especially of lipids, is discussed.     

Land use intensification increasingly drives the spatiotemporal patterns of the global human appropriation of net primary production in the last century

Land use has greatly transformed Earth's surface. While spatial reconstructions of how the extent of land cover and land-use types have changed during the last century are available, much less information exists about changes in land-use intensity. In particular, global reconstructions that consistently cover land-use intensity across land-use types and ecosystems are missing. We, therefore, lack understanding of how changes in land-use intensity interfere with the natural processes in land systems. To address this research gap, we map land-cover and land-use intensity changes between 1910 and 2010 for 9 points in time. We rely on the indicator framework of human appropriation of net primary production (HANPP) to quantify and map land-use-induced alterations of the carbon flows in ecosystems. We find that, while at the global aggregate level HANPP growth slowed down during the century, the spatial dynamics of changes in HANPP were increasing, with the highest change rates observed in the most recent past. Across all biomes, the importance of changes in land-use areas has declined, with the exception of the tropical biomes. In contrast, increases in land-use intensity became the most important driver of HANPP across all biomes and settings. We conducted uncertainty analyses by modulating input data and assumptions, which indicate that the spatial patterns of land use and potential net primary production are the most critical factors, while spatial allocation rules and uncertainties in overall harvest values play a smaller role. Highlighting the increasing role of land-use intensity compared to changes in the areal extent of land uses, our study supports calls for better integration of the intensity dimension into global analyses and models. On top of that, we provide important empirical input for further analyses of the sustainability of the global land system.     

Probing intracellular vesicle trafficking and membrane remodelling by cryo-EM

Protein transport between the membranous compartments of the eukaryotic cells is mediated by the constant fission and fusion of the membrane-bounded vesicles from a donor to an acceptor membrane. While there are many membrane remodelling complexes in eukaryotes, COPII, COPI, and clathrin-coated vesicles are the three principal classes of coat protein complexes that participate in vesicle trafficking in the endocytic and secretory pathways. These vesicle-coat proteins perform two key functions: deforming lipid bilayers into vesicles and encasing selective cargoes. The three trafficking complexes share some commonalities in their structural features but differ in their coat structures, mechanisms of cargo sorting, vesicle formation, and scission. While the structures of many of the proteins involved in vesicle formation have been determined in isolation by X-ray crystallography, elucidating the proteins' structures together with the membrane is better suited for cryogenic electron microscopy (cryo-EM). In recent years, advances in cryo-EM have led to solving the structures and mechanisms of several vesicle trafficking complexes and associated proteins.     

Effect of stochastic resonance on proprioception and kinesthesia in anterior cruciate ligament reconstructed patients

Low amplitude mechanical noise vibration has been shown to improve somatosensory acuity in various clinical groups with comparable deficiencies through a phenomenon known as Stochastic Resonance (SR). This technology showed promising outcomes in improving somatosensory acuity in other clinical patients (e.g., Parkinson’s disease and osteoarthritis). Some degree of chronic somatosensory deficiency in the knee has been reported following anterior cruciate ligament (ACL) reconstruction surgery. In this study, the effect of the SR phenomenon on improving knee somatosensory acuity (proprioception and kinesthesia) in female ACL reconstructed (ACLR) participants (n = 19) was tested at three months post-surgery, and the results were compared to healthy controls (n = 28). Proprioception was quantified by the measure of joint position sense (JPS) and kinesthesia with the threshold to detection of passive movement (TDPM).The results based on the statistical analysis demonstrated an overall difference between the somatosensory acuity in the ACLR limb compared to healthy controls (p = 0.007). A larger TDPM was observed in the ACLR limb compared to the healthy controls (p = 0.002). However, the JPS between the ACLR and healthy limbs were not statistically significantly different (p = 0.365). SR significantly improved JPS (p = 0.006) while the effect was more pronounced in the ACLR cohort. The effect on the TDPM did not reach statistical significance (p = 0.681) in either group.In conclusion, deficient kinesthesia in the ACLR limb was observed at three months post-surgery. Also, the positive effects of SR on somatosensory acuity in the ACL reconstructed group warrant further investigation into the use of this phenomenon to improve proprioception in ACLR and healthy groups.     

Reconstruction of tricarboxylic acid cycle in Corynebacterium glutamicum with a genome-scale metabolic network model for trans-4-hydroxyproline production

trans-4-Hydroxy- l -proline (Hyp) is an abundant component of mammalian collagen and functions as a chiral synthon for the syntheses of anti-inflammatory drugs in the pharmaceutical industry. Proline 4-hydroxylase (P4H) can catalyze the conversion of l -proline to Hyp; however, it is still challenging for the fermentative production of Hyp from glucose using P4H due to the low yield and productivity. Here, we report the metabolic engineering of Corynebacterium glutamicum for the fermentative production of Hyp by reconstructing tricarboxylic acid (TCA) cycle together with heterologously expressing the p4h gene from Dactylosporangium sp. strain RH1. In silico model-based simulation showed that α-ketoglutarate was redirected from the TCA cycle toward Hyp synthetic pathway driven by P4H when the carbon flux from succinyl-CoA to succinate descended to zero. The interruption of the TCA cycle by the deletion of sucCD-encoding the succinyl-CoA synthetase (SUCOAS) led to a 60% increase in Hyp production and had no obvious impact on the growth rate. Fine-tuning of plasmid-borne ProB* and P4H abundances led to a significant increase in the yield of Hyp on glucose. The final engineered Hyp-7 strain produced up to 21.72 g/L Hyp with a yield of 0.27 mol/mol (Hyp/glucose) and a volumetric productivity of 0.36 g·L ⁻¹·hr ⁻¹ in the shake flask fermentation. To our knowledge, this is the highest yield and productivity achieved by microbial fermentation in a glucose-minimal medium for Hyp production. This strategy provides new insights into engineering C. glutamicum by flux coupling for the fermentative production of Hyp and related products.     

Three-dimensional ultrastructure and quantitative analysis of the human Sertoli cell nucleolus

The nucleolus of the human Sertoli cell displays a spontaneous segregation of its components and has only one or 2 large fibrillar centers. The 3-dimensional reconstruction and quantitative analysis of its components was undertaken using a Quantimet 900 image analysis system in order to define the spatial relationships between the dense fibrillar component and the fibrillar center and especially to investigate whether threads of dense fibrillar component exist independently, without being linked to a fibrillar center. Our 3D reconstructions demonstrated that the dense fibrillar threads or sheets were never independent of fibrillar centers. These structures belonged to a continuous network that joined the layer of dense fibrils surrounding the fibrillar center. When the nucleolus contained 2 different-sized fibrillar centers, quantitative analysis showed that there was a proportional relationship between the volume of the dense fibrillar component and the volume of the fibrillar center. These data, compared with those previously obtained by means of autoradiographic techniques, suggest that the rDNA-containing chromatin passes through the fibrillar center and unwinds from there into the dense fibrillar component.