Flow patterns and endothelial cell morphology in a simplified model of an artificial ventricle

The aim of this study was to delineate the flow patterns in a non-unidirectional flow field inside a ventricle-shaped cell culture chamber, and examine the resulting morphology and integrity of the endothelium in select regions of the monolayer. The chamber was perfused by pulsatile flow, and the coherent motion of the fluid was studied using flow visualization aided by image analysis. Four distinct flow patterns were discerned and examined: central jet, flow impingement, flow separation, and recirculating eddies. The influence of these patterns on endothelial cell morphology was assessed after 20 h of exposure to flow. There were no signs of damage to the endothelium in the jet region nor was there evidence of cell alignment with the flow. Yet, there were changes in cell morphology and cytoskeletal architecture as compared to control. By contrast, within the eddies where the flow was highly disturbed, there was apparent damage to the endothelium. Thus, exposure of cells to random velocity fluctuations in regions of quasi-static flow compromises the integrity of the monolayer. Identification of such sites and acquisition of the knowledge necessary to protect the cells from denudation will be valuable for the endothelialization efforts of cardiac prostheses.     

Visualization of thrombin receptors on mouse embryo fibroblasts using fluorescein-amine conjugated human α-thrombin

The localization of thrombin receptors on mouse embryo (ME) cells has been examined by direct fluorescence microscopy using a fluorescein aminelabeled thrombin. Two fluorescein amines, 4-(N-6-aminoethyl thioureal)-fluorescein and 4-(N-6-aminohexyl thioureal)-fluorescein, were synthesized and attached to the carbohydrate moiety of highly purified human α-thrombin by periodate oxidation of the carbohydrate and selective reduction of the Schiff's base using sodium cyanoborohydride. Preparations of fluorescent thrombin with from 1 to 4 fluoresceins per molecule of thrombin retained their ability to proteolytically cleave fibrinogin to form fibrin clots, to bind to thrombin receptors on ME cells, and to initiate cell division. After incubating mitogenic concentrations of the fluorescein amine labeled thrombin with ME cells at 4°C, a diffuse fluorescent pattern was observed over the surface of the ME cells. This diffuse pattern was specific: it was not observed on cells from parallel cultures incubated with fluorescent thrombin plus a 20-fold excess of unlabeled thrombin. Thus, thrombin receptors appear to be distributed randomly over the surface of ME cells prior to interaction with thrombin. Increasing the temperature to 37°C following binding at 4° C resulted in a rapid dissociation of the fluorescent pattern from the cells leaving only the autofluorescent vesicles. This result may reflect the unique ability of thrombin to proteolytically cleave its own receptor.     

StructureSelector: A web‐based software to select and visualize the optimal number of clusters using multiple methods

Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program structure has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (medmedk , medmeak , maxmedk and maxmeak ) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data. However, the lack of easy‐to‐use software limits the use of these appealing new estimators. Here, we developed a web‐based user‐friendly software structureselector to calculate the four appealing alternative statistics together with the commonly used Ln Pr(X|K) and ΔK statistics. structureselector accepts the result files of structure , admixture or faststructure as input files. It reports the “best” K for each estimator, and the results are available as HTML or tab separated tables. The program can also generate graphical representations for specific K, which can be easily downloaded from the server. The software is freely available at http://lmme.qdio.ac.cn/StructureSelector/ .     

神经递质的可视化荧光检测技术研究进展

神经递质是神经系统中至关重要的组成部分,神经递质释放的时间和空间变化是神经网络中信息处理的核心,可视化监测神经递质的生物传感器是探究各类生理和病理活动的重要工具。文中综述了近年来具有较高时间和空间分辨率的监测神经递质时空分布变化技术的研究进展,介绍了对谷氨酸、多巴胺、γ-氨基丁酸和乙酰胆碱这4类重要的神经递质的检测方法,并归纳总结了各类检测方法的基本原理和优缺点,为设计具有高时空分辨率的神经递质传感器提供一个较为系统的参考。     

Integrative visualization of the molecular structure of a cellular microdomain

An integrative approach to visualization is used to create a visual snapshot of the structural biology of the polar microdomain of Caulobacter crescentus. The visualization is based on the current state of molecular and cellular knowledge of the microdomain and its cellular context. The collaborative process of researching and executing the visualization has identified aspects that are well determined and areas that require further study. The visualization is useful for dissemination, education, and outreach, and the study lays the groundwork for future 3D modeling and simulation of this well‐studied example of a cellular condensate.     

Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson‐Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two‐dimensional external molecular visualization software. This process has inherent limitations: visualization of three‐dimensional objects using a two‐dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol‐APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.     

A practical guide to amplicon and metagenomic analysis of microbiome data

Advances in high-throughput sequencing(HTS)have fostered rapid developments in the field of microbiome research,and massive microbiome datasets are now being generated.However,the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field.Here,we systematically summarize the advantages and limitations of micro-biome methods.Then,we recommend specific pipelines for amplicon and metagenomic analyses,and describe commonly-used software and databases,to help researchers select the appropriate tools.Furthermore,we introduce statistical and visualization methods suit-able for microbiome analysis,including alpha-and beta-diversity,taxonomic composition,difference compar-isons,correlation,networks,machine learning,evolu-tion,source tracing,and common visualization styles to help researchers make informed choices.Finally,a step-by-step reproducible analysis guide is introduced.We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the bio-logical significance behind the data.     

DAPI: a DNA-Specific Fluorescent Probe

DAPI (4′,6-diamidino-2-phenylin-dole) is a DNA-specific probe which forms a fluorescent complex by attaching in the minor grove of A-T rich sequences of DNA. It also forms nonfluorescent intercalative complexes with double-stranded nucleic acids. The physicochemical properties of the dye and its complexes with nucleic acids and history of the development of this dye as a biological stain are described. The application of DAPI as a DNA-specific probe for flow cytometry, chromosome staining, DNA visualization and quantitation in histochemistry and biochemistry is reviewed. The mechanisms of DAPI-nucleic acid complex formation including minor groove binding, intercalation and condensation are discussed.     

Visualizing RNA base-pairing probabilities with RNAbow diagrams

There are many effective ways to represent a minimum free energy RNA secondary structure that make it easy to locate its helices and loops. It is a greater challenge to visualize the thermal average probabilities of all folds in a partition function sum; dot plot representations are often puzzling. Therefore, we introduce the RNAbows visualization tool for RNA base pair probabilities. RNAbows represent base pair probabilities with line thickness and shading, yielding intuitive diagrams. RNAbows aid in disentangling incompatible structures, allow comparisons between clusters of folds, highlight differences between wild-type and mutant folds, and are also rather beautiful.     

Subtype Identification in Acutely Dissociated Rat Nodose Ganglion Neurons Based on Morphologic Parameters

Nodose ganglia are composed of A-, Ah- and C-type neurons. Despite their important roles in regulating visceral afferent function, including cardiovascular, pulmonary, and gastrointestinal homeostasis, information about subtype-specific expression, molecular identity, and function of individual ion transporting proteins is scarce. Although experiments utilizing the sliced ganglion preparation have provided valuable insights into the electrophysiological properties of nodose ganglion neuron subtypes, detailed characterization of their electrical phenotypes will require measurements in isolated cells. One major unresolved problem, however, is the difficulty to unambiguously identify the subtype of isolated nodose ganglion neurons without current-clamp recording, because the magnitude of conduction velocity in the corresponding afferent fiber, a reliable marker to discriminate subtypes in situ, can no longer be determined. Here, we present data supporting the notion that application of an algorithm regarding to microscopic structural characteristics, such as neuron shape evaluated by the ratio between shortest and longest axis, neuron surface characteristics, like membrane roughness, and axon attachment, enables specific and sensitive subtype identification of acutely dissociated rat nodose ganglion neurons, by which the accuracy of identification is further validated by electrophysiological markers and overall positive predictive rates is 89.26% (90.04%, 76.47%, and 98.21% for A-, Ah, and C-type, respectively). This approach should aid in gaining insight into the molecular correlates underlying phenotypic heterogeneity of nodose ganglia. Additionally, several critical points that help for neuron identification and afferent conduction calibration are also discussed.