Erratum: Author Correction: Skull optical clearing window for in vivo imaging of the mouse cortex at synaptic resolution.

[This corrects the article DOI: 10.1038/lsa.2017.153.].

Skull optical clearing window for in vivo imaging of the mouse cortex at synaptic resolution.

Imaging cells and microvasculature in the living brain is crucial to understanding an array of neurobiological phenomena. Here, we introduce a skull optical clearing window for imaging cortical structures at synaptic resolution. Combined with two-photon microscopy, this technique allowed us to repeatedly image neurons, microglia and microvasculature of mice. We applied it to study the plasticity of dendritic spines in critical periods and to visualize dendrites and microglia after laser ablation. Given its easy handling and safety, this method holds great promise for application in neuroscience research.

[Effect of wound to growth of larva of host to Ophiocordyceps sinensis during artificial breeding].

To clear the effect of the wound to the growth of the larva of the host to the Ophiocordyceps sinensis, the wounds of same severity at the same position were made artificially to the larva and which were artificial fed at the same environment and condition. The results indicated that, over the winter, the survival rate of the wounded of the infection larva was lower than that of the healthy larva, but the weight had no significant difference between the wounded and the healthy larva. The survival rate of the wounded of the no infection larva was lower than that of the healthy larva, but except with black skin, the wounded larva with offwhite and dusty red had no influence on the variety of the weight. In summery, wound had no advantage to the survival rate, but had no influence to the weight. The result had provided theoretical basis to the reforming of the system of the artificial culture O. sinensis.

Microglial migration mediated by ATP-induced ATP release from lysosomes.

Microglia are highly motile cells that act as the main form of active immune defense in the central nervous system. Attracted by factors released from damaged cells, microglia are recruited towards the damaged or infected site, where they are involved in degenerative and regenerative responses and phagocytotic clearance of cell debris. ATP release from damaged neural tissues has been suggested to mediate the rapid extension of microglial process towards the site of injury. However, the mechanisms of the long-range migration of microglia remain to be clarified. Here, we found that lysosomes in microglia contain abundant ATP and exhibit Ca(2+)-dependent exocytosis in response to various stimuli. By establishing an efficient in vitro chemotaxis assay, we demonstrated that endogenously-released ATP from microglia triggered by local microinjection of ATPγS is critical for the long-range chemotaxis of microglia, a response that was significantly inhibited in microglia treated with an agent inducing lysosome osmodialysis or in cells derived from mice deficient in Rab 27a (ashen mice), a small GTPase required for the trafficking and exocytosis of secretory lysosomes. These results suggest that microglia respond to extracellular ATP by releasing ATP themselves through lysosomal exocytosis, thereby providing a positive feedback mechanism to generate a long-range extracellular signal for attracting distant microglia to migrate towards and accumulate at the site of injury.

Special method to prepare quantum dot probes with reduced cytotoxicity and increased optical property.

Quantum dots (QDs) are widely used in the life sciences because of their novel physicochemical properties. However, the cytotoxity of these nonoparticles have attracted great attention recently because this has not been well resolved. Four probes were synthesized by chemical coupling and protein denaturation with CdSeZnS, CdTe QDs, and transferrin. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and capillary electrophoresis were used to verify the conjugation of these luminescent probes. The cytotoxicity of these four luminescent probes and the original QDs were evaluated in HeLa cells. The results showed that over 92% of HeLa cells were still alive after being exposed to 3.2-microM CdSeZnS QDs capped with denatured transferrin for 72 h. Furthermore, while the probe preparation was very simple, the photoluminescence quantum yield of this probe was 7% higher than the original CdSeZnS QDs. This provides a new way for exploiting QD probes with low cytotoxicity, which will expand applications of nanocomposite assembly in biolabeling and imaging.

High-sensitivity quantum dot-based fluorescence resonance energy transfer bioanalysis by capillary electrophoresis.

Here a new method for high-sensitivity quantum dot (QD)-based fluorescence resonance energy transfer (FRET) bioanalysis was developed. In this method, capillary electrophoresis (CE) with fluorescence detection was applied. The FRET system consisted of water-soluble 532-nm emitting CdTe QDs donor and 632-nm emitting CdSe/ZnS QDs acceptor which were covalently conjugated with mouse IgG and goat anti-mouse IgG, respectively. The bio-affinity between antigen and antibody brought two kinds of QDs close enough to make the FRET happen between them. In the CE experiments, highly efficient separation of donor-acceptor immunocomplexes was obtained, and the process of FRET was monitored. Results showed that FRET efficiency obtained by CE (38.56-69.58%) improved substantially in comparison with that obtained by ensemble measurement (12.77-52.37%). The high efficient separation of donor-acceptor immunocomplexes and the possible conformation change of antigen and antibody, contributes to the lower analysis uncertainty (variance) and higher FRET efficiency obtained in CE and consequentially, this makes the analysis of FRET more sensitive. This novel CE-based technique can be easily extended to other FRET system based on QDs and may have potential application in the study of biomolecule conformation change.

[Micro-CT system based on the flat panel detector for small animal imaging].

A high resolution Micro-CT system for small animal imaging is introduced in this paper. Micro-focus X-ray tube with focal diameter of 100 microm and flat panel detector with imaging area of 13cm x 13cm are adopted in this system. The data acquired in rotation scanning is reconstructed with cone beam algorithm. The resolving power of the detector is measured to be 31 lp/cm at 10% of the MTF. The resolution of the Micro-CT system could achieve 185 m when the magnification factor is 1.94. Thighbone of a rabbit is used as sample imaging with the system. The trabecular bone could be imaged clearly. And the ability of small animal imaging of the system has been demonstrated.

Study on molecular interactions between proteins on live cell membranes using quantum dot-based fluorescence resonance energy transfer.

Mouse anti-human CD71 monoclonal antibody (anti-CD71) was conjugated with red quantum dots (QDs; 5.3 nm, emission wavelength lambda(em) = 614 nm) and used to label HeLa cells successfully. Then green QD-labeled goat anti-mouse immunoglobulin G (IgG; the size of the green QDs was 2.2 nm; lambda(em) = 544 nm) was added to bind the red-QD-conjugated anti-CD71 on the cell surface by immunoreactions. Such interaction between anti-CD71 and IgG lasted 4 min and was observed from the fluorescence spectra: the fluorescence intensity of the "red" peak at 614 nm increased by 32%; meanwhile that of the "green" one at 544 nm decreased by 55%. The ratio of the fluorescence intensities (I(544 nm)/I(614 nm)) decreased from 0.5 to 0.2. The fluorescence spectra as well as cell imaging showed that fluorescence resonance energy transfer took place between these two kinds of QDs on the HeLa cells through interactions between the primary antibody and the secondary antibody.

Bioconjugate recognition molecules to quantum dots as tumor probes.

Transferrin and mouse anti-human CD71 monoclonal antibody were respectively conjugated covalently to the core/shell CdSe/ZnS quantum dots with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride and N-hydrocylsulfo-succinimide (Sulfo-NHS). The conjugation worked well and the bioactivities of these macromolecules still remained, which was verified by column filtration, sodium dodecyl sulfate polyacrylamide gel electrophoresis, absorption spectra, fluorescence spectra, and circular dichroism spectrometry. Thus, these two kinds of quantum dot conjugates were used to recognize the tumor cells involved. In case of pseudo positivity, FITC-labeling secondary antibody IgG was used, and the results showed that as-prepared fluorescent quantum dot bioprobes were highly specific to tumor cells.

Acetylene-substituted two-photon absorbing molecules with rigid elongated pi-conjugation: synthesis, spectroscopic properties and two-photon fluorescence cell imaging applications.

Two asymmetrical molecules with substituted acetylene as central rigid elongated conjugation are reported as potential chromophores for two-photon microscopic imaging. These molecules consist of a typical D-pi-A structure, have different donors (D), the same pi-conjugated center (pi) and the same acceptor (A). Structural characterization and spectroscopic properties, including single-photon (linear) absorption, quantum yields, single-photon fluorescence, and two-photon absorption spectra, were studied in solvents with different polarity. These acetylene-substituted molecules were found to have high two-photon absorption cross-sections (for example, 690 GM for molecule 1 in toluene), which were determined by a two-photon induced fluorescence method using a femtosecond Ti: sapphire laser as excitation source. Single- and two-photon cellular imaging experiments demonstrate that the substituted acetylene derivatives could be one kind of promising two-photon fluorescence probes for cellular imaging.

Optimization of the methods for introduction of amine groups onto the silica nanoparticle surface.

The luminescent silica nanoparticle has attracted the researchers' concentration in bioanalysis recently. Its extensive application is based on the immobilization of various biomolecules such as deoxyribonucleic acid, antibody, and so forth onto the surface. By comparing different introduction methods of amine groups, it was confirmed that the "two-step" route is more preferable by adding tetraethyl orthosilicate and 3-aminopropyl-(triethoxyl)silane in sequence, to attain ideal amine-modified silica nanoparticles. On this basis, carboxyl groups were derived from amine groups on the nanoparticle surface and then were activated by 1-ethyl-3-3-(3-dimethylaminopropyl) carbodiimide hydrochloride and N-hydroxy-succinimide. Finally, mouse monoclonal antihuman CD71 antibody (McAb CD71) and transferrin were effectively linked with the carboxyl groups and successfully labeled the receptors in the membrane of fibroblast cells, respectively.

Quantum dot optical encoded polystyrene beads for DNA detection.

A novel multiplex analysis technology based on quantum dot (QD) optical encoded beads was studied. Carboxyl functionalized polystyrene beads, about 100 microm in size, were precisely encoded by the various ratios of two types of QDs whose emission wavelengths are 576 and 628 nm, respectively. Then the different encoded beads were covalently immobilized with different probes in the existing of sulfo-NHS and 1-[3-(Dimethylamino) propyl]-3-ethylcarbodiimide methiodide, and the probe density could reach to 3.1 mmol/g. These probe-linked encoded beads were used to detect the target DNA sequences in complex DNA solution by hybridization. Hybridization was visualized using fluorescein isothiocynate-labeled DNA sequences. The results show that the QDs and target signals can be obviously identified from a single-bead-level spectrum. This technology can detect DNA targets effectively with a detection limit of 0.2 microg/mL in complex solution.

[Progress in tissue optical imaging].

In this review, we introduce the basic principle and technology progress of tissue optical imaging from both diffuse optical imaging and coherence domain imaging, which include the continuous-wave imaging, time-resolved optical tomography, diffuse photon density waves tomography, ultrasound-modulated optical tomography, optical coherence tomography and laser speckle imaging. Applications of optical imaging in brain activity and tissue function are also discussed.

Comparisons of graph-structure clustering methods for gene expression data.

Although many numerical clustering algorithms have been applied to gene expression data analysis, the essential step is still biological interpretation by manual inspection. The correlation between genetic co-regulation and affiliation to a common biological process is what biologists expect. Here, we introduce some clustering algorithms that are based on graph structure constituted by biological knowledge. After applying a widely used dataset, we compared the result clusters of two of these algorithms in terms of the homogeneity of clusters and coherence of annotation and matching ratio. The results show that the clusters of knowledge-guided analysis are the kernel parts of the clusters of Gene Ontology (GO)-Cluster software, which contains the genes that are most expression correlative and most consistent with biological functions. Moreover, knowledge-guided analysis seems much more applicable than GO-Cluster in a larger dataset.

Operon prediction based on SVM.

The operon is a specific functional organization of genes found in bacterial genomes. Most genes within operons share common features. The support vector machine (SVM) approach is here used to predict operons at the genomic level. Four features were chosen as SVM input vectors: the intergenic distances, the number of common pathways, the number of conserved gene pairs and the mutual information of phylogenetic profiles. The analysis reveals that these common properties are indeed characteristic of the genes within operons and are different from that of non-operonic genes. Jackknife testing indicates that these input feature vectors, employed with RBF kernel SVM, achieve high accuracy. To validate the method, Escherichia coli K12 and Bacillus subtilis were taken as benchmark genomes of known operon structure, and the prediction results in both show that the SVM can detect operon genes in target genomes efficiently and offers a satisfactory balance between sensitivity and specificity.

Preparation of silica encapsulated quantum dot encoded beads for multiplex assay and its properties.

Novel -COOH modified polystyrene beads were prepared by sulfonation grafting, and the surface area and pore volume are greatly improved in comparison with the swelling-treated beads. The optimization coating time is 4 h, and the corresponding -COOH content is approximately 2.1 mmol/g. The scanning electron microscope results show that the silica particles deposited on the beads and formed a silica shell that decreases the leakage of quantum dots (QDs) preferably and improves the bar code stability greatly. The anti-photobleaching of silica-coated beads was studied systemically, and the results show that the half-decay time (t1/2) of the coated beads increases to 537 s--seven times longer than that of the uncoated ones. Further DNA probe hybridization experiments indicated that the coding signal and target signal can be detected simultaneously and that the assays based on these probe-conjugated silica/QD/polystyrene beads have good specificity and sensitivity that can detect a concentration as low as 0.01 microg/ml target DNA in denatured calf thymus DNA solution, indicating that it is feasible to use this kind of bead for multiplex analysis.

KDE Bioscience: platform for bioinformatics analysis workflows.

Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.

[Relationship between respiration exchange ratio and muscle oxygen content measured by near-infrared spectroscopy].

OBJECTIVE: To study the relationship between respiration exchange ratio (RER) and tissue oxygen content in human skeletal muscle. METHOD: Using a portable tissue oximeter based on near-infrared spectroscopy (NIRS), the relative changes of skeletal muscle oxygen content were measured non-invasively and in vivo when healthy volunteers were performing an incremental intensity running protocol. The results were compared with heart rate (HR), VO2, VCO2, and RER. RESULT: In the experiment, the change in skeletal muscle oxygenation content of the volunteers was regular and has a significant close relationship to HR, VO2 and RER (P=0.01). CONCLUSION: It shows that NIRS is a new photonic technology which provides a measurable biomedical parameter for the evaluation of athlete's physique and training effect. It offers reference for monitoring and assessing training effect in vivo, real-time and non-invasively.

The interface behavior of hemoglobin at carbon nanotube and the detection for H(2)O(2).

Direct electrochemistry of hemoglobin (Hb) is observed at carbon nanotube (CNT) interface. The adsorbing Hb can transfer electron directly at CNT interface compared with common carbon material. The heterogeneous electron transfer rate constant k of Hb can be calculated as 0.062s(-1), the transfer coefficient alpha is 0.21 and the average surface coverage of Hb on CNT surface is 3.58 x 10(-9) +/- 2.7 x 10(-10)mol/cm(2). It is found that the adsorbing Hb still keeps its catalytic activity to H(2)O(2). This sensor was used to detect H(2)O(2). The apparent Michaelis-Menten constant is calculated as 6.75 x 10(-4)molL(-1).

[Blood oxygen and lactate concentrations in skeletal muscles during exercise].

OBJECTIVE: To study the relationship between blood lactate and blood oxygenation in human skeletal muscle. METHOD: Using a portable tissue oximeter based on Near-Infrared Spectroscopy (NIRS), concentration of HbO2, blood lactate and blood volume were measured non-invasively and continuously when the subjects were doing incremental exercise on a bicycle ergometer. RESULT: As the intensity of exercise was increased, blood lactate concentration, blood volume in tissue increased, while concentration of HbO2 decreased. CONCLUSION: It is possible to assess the fatigue state with tissue oximeter by monitoring intensity of exercise non-invasively and dynamically. By studying their correlations, a novel approach for measuring blood lactate non-invasively and assessing sports ability could be provided.