C-ME: a 3D community-based, real-time collaboration tool for scientific research and training

The need for effective collaboration tools is growing as multidisciplinary proteome-wide projects and distributed research teams become more common. The resulting data is often quite disparate, stored in separate locations, and not contextually related. Collaborative Molecular Modeling Environment (C-ME) is an interactive community-based collaboration system that allows researchers to organize information, visualize data on a two-dimensional (2-D) or three-dimensional (3-D) basis, and share and manage that information with collaborators in real time. C-ME stores the information in industry-standard databases that are immediately accessible by appropriate permission within the computer network directory service or anonymously across the internet through the C-ME application or through a web browser. The system addresses two important aspects of collaboration: context and information management. C-ME allows a researcher to use a 3-D atomic structure model or a 2-D image as a contextual basis on which to attach and share annotations to specific atoms or molecules or to specific regions of a 2-D image. These annotations provide additional information about the atomic structure or image data that can then be evaluated, amended or added to by other project members.     

Determination of molecular conformation and permeation in skin via IR spectroscopy, microscopy, and imaging

Skin tissue, in addition to its specific use in dermal research, provides an excellent model for developing the techniques of vibrational microscopy and imaging for biomedical applications. In addition to permitting characterization of various regions of skin, the relative paucity of major biological constituents in the stratum corneum (the outermost layer of skin), permits us to image, with microscopic resolution, conformational alterations and concentration variations in both the lipid and protein components. Thus we are able to monitor the effects of exogenous materials such as models for drug delivery agents (liposomes) and permeation enhancers (DMSO) on stratum corneum lipid organization and protein structure. In addition, we are able to monitor protein conformational changes in single corneocytes. The current article demonstrates these procedures, ranging from direct univariate measures of lipid chain conformational disorder, to factor analysis which permits us to image conformational differences between liposomes that have permeated through the stratum corneum from those which have remained on the surface in a reservoir outside the skin.     

SwarmPS: rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that approximately 10(4)-10(5) particle projections are required to attain a 3A resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present Swarm(PS), a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (approximately 10(2)), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. Swarm(PS) is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.     

Programmable illumination and high-speed, multi-wavelength, confocal microscopy using a digital micromirror

Confocal microscopy is routinely used for high-resolution fluorescence imaging of biological specimens. Most standard confocal systems scan a laser across a specimen and collect emitted light passing through a single pinhole to produce an optical section of the sample. Sequential scanning on a point-by-point basis limits the speed of image acquisition and even the fastest commercial instruments struggle to resolve the temporal dynamics of rapid cellular events such as calcium signals. Various approaches have been introduced that increase the speed of confocal imaging. Nipkov disk microscopes, for example, use arrays of pinholes or slits on a spinning disk to achieve parallel scanning which significantly increases the speed of acquisition. Here we report the development of a microscope module that utilises a digital micromirror device as a spatial light modulator to provide programmable confocal optical sectioning with a single camera, at high spatial and axial resolution at speeds limited by the frame rate of the camera. The digital micromirror acts as a solid state Nipkov disk but with the added ability to change the pinholes size and separation and to control the light intensity on a mirror-by-mirror basis. The use of an arrangement of concave and convex mirrors in the emission pathway instead of lenses overcomes the astigmatism inherent with DMD devices, increases light collection efficiency and ensures image collection is achromatic so that images are perfectly aligned at different wavelengths. Combined with non-laser light sources, this allows low cost, high-speed, multi-wavelength image acquisition without the need for complex wavelength-dependent image alignment. The micromirror can also be used for programmable illumination allowing spatially defined photoactivation of fluorescent proteins. We demonstrate the use of this system for high-speed calcium imaging using both a single wavelength calcium indicator and a genetically encoded, ratiometric, calcium sensor.     

Differential expression of acetylcholinesterase in the brainstem, ventrobasal thalamus and primary somatosensory cortex of perinatal rats, mice, and hamsters

Acetylcholinesterase (AChE) is transiently expressed by thalamocortical axons in the rat, and staining for this enzyme has been used extensively to study the development of thalamocortical projections. In the present study, patterns of AChE staining were compared in the trigeminal brainstem, thalami and primary somatosensory cortices of perinatal rats, mice, and hamsters. As previously reported, the ventral posteromedial nucleus (VPM) of rats showed dense AChE staining from P-0 at least through P-8. The ventral posterolateral nucleus (VPL) contained heavy AChE staining at least through P-60. In the cortex, there was also dense AChE staining which was organized somatotopically in patches similar to those observed with other methods such as cytochrome oxidase (CO) staining. However, by adulthood, AChE staining revealed a negative image of the CO staining pattern in lamina IV. In the mouse and hamster, there was dense AChE staining inVPL from P-0 through adulthood, but VPM was much less heavily stained for this enzyme. Moreover, the staining in VPL of mice was markedly reduced after transection of axons that travel to the thalamus in the medial lemniscus, suggesting that much of it was contained in these afferent fibers. In the cortices of both perinatal and adult mice and hamsters, AChE staining yielded a negative image of the somatotopically organized patches demonstrable with CO staining. This negative image was apparent by P-2 in the mouse and P-4 in the hamster. These results document a dramatic species difference with respect to the expression of AChE in the thalami and cortices of developing rodents. The differences between the patterns observed in rats vs mice and hamsters probably reflect the fact that cortical AChE in the latter species is not contained in thalamocortical afferents arising from either VPM or VPL.     

Cryo-EM density maps adjustment for subtraction,consensus and sharpening

Electron cryomicroscopy (cryo-EM) has emerged as a powerful structural biology instrument to solve near-atomic three-dimensional structures. Despite the fast growth in the number of density maps generated from cryo-EM data, comparison tools among these reconstructions are still lacking. Current proposals to compare cryo-EM data derived volumes perform map subtraction based on adjustment of each volume grey level to the same scale. We present here a more sophisticated way of adjusting the volumes before comparing, which implies adjustment of grey level scale and spectrum energy, but keeping phases intact inside a mask and imposing the results to be strictly positive. The adjustment that we propose leaves the volumes in the same numeric frame, allowing to perform operations among the adjusted volumes in a more reliable way. This adjustment can be a preliminary step for several applications such as comparison through subtraction, map sharpening, or combination of volumes through a consensus that selects the best resolved parts of each input map. Our development might also be used as a sharpening method using an atomic model as a reference. We illustrate the applicability of this algorithm with the reconstructions derived of several experimental examples. This algorithm is implemented in Xmipp software package and its applications are user-friendly accessible through the cryo-EM image processing framework Scipion.     

Auto-align - multi-modality fluorescence microscopy image co-registration

Multi-modality microscopes incorporate multiple microscopy techniques into one module, imaging through a common objective lens. Simultaneous or consecutive image acquisition of a single specimen, using multiple techniques, increases the amount of measurable information available. In order to benefit from each modality, it is necessary to accurately co-register data sets. Intrinsic differences in the image formation process employed by each modality result in images which possess different characteristics. In addition, as a result of using different measurement devices, images often differ in size and can suffer relative geometrical deformations including rotation, scale and translation, making registration a complex problem. Current methods generally rely on manual input and are therefore subject to human error. Here, we present an automated image registration tool for fluorescence microscopy. We show that it successfully registers images obtained via total internal reflection fluorescence (TIRF), or epi-fluorescence, and confocal microscopy. Furthermore, we provide several other applications including channel merging following image acquisition through an emission beam splitter, and lateral stage drift correction. We also discuss areas of membrane trafficking which could benefit from application of Auto-Align. Auto-Align is an essential item in the advanced microscopist's toolbox which can create a synergy of single or multi-modality image data.     

A neural mechanism for adjustment to optimal conditions,with possible reference to visual accommodation

A general mechanism is studied which adapts the value of some biological parameter so as to maximize or to minimize the value of another parameter. In the process of visual accommodation, the thickness of the lens is determined by the maximum sharpness of the image on the retina. A neural mechanism which provides for such an optimum adjustment is described. A similar mechanism may play a role in such phenomena as hedonistic behavior where activity is adjusted to a maximum of satisfaction. The mechanism discussed here does not provide for an absolutely sharp retinal image, but leads to a conclusion that the sharpness of that image fluctuates within narrow limits which are determined by the parameters of the systems.     

Small-angle X-ray scattering reveals structural dynamics of the botulinum neurotoxin associating protein, nontoxic nonhemagglutinin

In cell culture supernatants, the botulinum neurotoxin (BoNT) exists as part of a toxin complex (TC) in which nontoxic nonhemagglutinin (NTNHA) and/or hemagglutinins (HAs) are assembled onto the BoNT. A series of investigations indicated that formation of the TC is vital for delivery of the toxin to nerve cells through the digestive tract. In the assembly process, BoNT binds to NTNHA yielding M-TC, and it then matures into L-TC by further association with the HAs via NTNHA in the M-TC. Here, we report a crystal structure of the NTNHA from Clostridium botulinum serotype D strain 4947. Additionally, we performed small-angle X-ray scattering (SAXS) analysis of the NTNHA and the M-TC to elucidate the solution structure. The crystal structure of D-4947 NTNHA revealed that BoNT and NTNHA share a closely related structure consisting of three domains. The SAXS image indicated that, even though the N-terminal two-thirds of the NTNHA molecule had an apparently similar conformation in both the crystal and solution structures, the C-terminal third of the molecule showed a more extended structure in the SAXS image than that seen in the crystallographic image. The discrepancy between the crystal and solution structures implies a high flexibility of the C-terminal third domain of NTNHA, which is involved in binding to BoNT. Structural dynamics of the NTNHA molecule revealed by SAXS may explain its binding to BoNT to form the BoNT/NTNHA complex.     

The functional coupling of the mechanisms for the selection of significant signals and the motor reactions they induce]

The data are described in favour of forming the integrative image of the significant signals in the mammalian brain. This image is created as a summary of the significant at this moment information, selected in the specialized areas of the cortex. The hypothesis is founded on the investigations of the cortico-striatal interrelations. They suggest that the results of the cortical analysis, which are dispersed through the specialized cortical fields, enter the striatum via the corticofugal pathways and transform into an integrative form in its neuronal network. The experimental data show that the striatal activity recorded during instrumental behaviour does not contain motor programs or commands, but reflects the peculiarity of the sensory environment, in which the movements are realized.     

The emerging role of miR-200 family in metastasis: focus on EMT,CSCs, angiogenesis,and anoikis

Introduction

Cancer is the second major threat to human society and one of the main challenges facing healthcare systems. One of the main problems of cancer care is the metastases of cancer cells that cause 90% of deaths due to cancer. Multiple molecular mechanisms are involved in cancer cell metastasis. Therefore, a better understanding of these molecular mechanisms is necessary for designing restrictive strategies against cancer cell metastasis. Accumulating data suggests that MicroRNAs (miRNAs) are involved in metastasis and invasion of human tumors through regulating multiple genes expression levels that are involved in molecular mechanisms of metastasis. The goal of this review is to present the molecular pathways by which the miR 200 family manifests its effects on EMT, cancer stem cells, angiogenesis, anoikis, and the effects of tumor cell metastases.

Methods

A detailed literature search was conducted to find information about the role of the miR-200 family in the processes involved in metastasis in various databases.

Results

Numerous lines of evidence revealed an association between the mir-200 family and metastasis of human tumors by impressing processes such as cancer stem cells, EMT, angiogenesis, and anoikis.

Conclusions

Understanding the molecular mechanisms associated with metastasis in which the miR-200 family is involved can be effective in treating metastatic cancers.

Graphic abstract

     

利用原子力显微镜对A型流感病毒的形态学研究

利用透射电子显微镜(TEM)和原子力显微镜(AFM)观察流感病毒(H1N1),探讨AFM在病毒形态研究中的应用,为病毒形态学研究提供一种新型、简便、快捷的工具.TEM采用磷钨酸负染方法,AFM采用轻敲模式在大气常温下扫描成像,并对主要指标长度(直径)、Ra、Rq等进行测量.两种方法最终得到相似的形态学结果,流感病毒呈球状、丝状,并有一些形状介于两者之间.TEM提供了流感病毒二维图像,可见钉状突起,AFM则呈现了流感病毒三维图像,且可见病毒表面有凹凸不平的特征和边缘有齿轮状的突起,同时获得表面粗糙度等可以量化指标.与TEM观察相比,原子力显微镜是一种制样简单、观察直观的新型病毒形态学研究工具,其表征参数可以作为病毒形态学研究的量化指标.     

Molecular Reproduction & Development Volume 79, Issue 6, June 2012 cover image

Maturation in bovine oocytes is triggered by a single surge of gonadotropins, i.e., luteinizing hormone (LH) and follicle‐stimulating hormone (FSH), which cause changes in the intraooplasmic concentrations of second messengers such as cyclic adenosine 3′,5′‐ monophosphate and Ca²+ through their activity on cumulus cells (see Silvestre et al., this issue). This time‐sequence shows a representative fluorescent intensity profile of the Ca²+ wave triggered in cumulus cells by the addition of FSH in an immature bovine cumulusoocyte complex loaded with the fluorescent Ca²+ indicator Fluo‐4 FF/AM. The top image shows the cumulus‐oocyte complex at the time of FSH addition, and the bottom image shows the same cumulus‐oocyte complex 162 sec after exposure; intermediate images were taken at 48, 66, 84, 108, 132 sec from the addition of FSH, respectively.     

Oufti: an integrated software package for high‐accuracy,high‐throughput quantitative microscopy analysis

With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re‐emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today's single‐cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand‐alone, open‐source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non‐diffraction‐limited fluorescence signals and is scalable for high‐throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis and post‐processing analysis, makes the software broadly accessible to users irrespective of their computational skills.     

A new concept for medical imaging centered on cellular phone technology

According to World Health Organization reports, some three quarters of the world population does not have access to medical imaging. In addition, in developing countries over 50% of medical equipment that is available is not being used because it is too sophisticated or in disrepair or because the health personnel are not trained to use it. The goal of this study is to introduce and demonstrate the feasibility of a new concept in medical imaging that is centered on cellular phone technology and which may provide a solution to medical imaging in underserved areas. The new system replaces the conventional stand-alone medical imaging device with a new medical imaging system made of two independent components connected through cellular phone technology. The independent units are: a) a data acquisition device (DAD) at a remote patient site that is simple, with limited controls and no image display capability and b) an advanced image reconstruction and hardware control multiserver unit at a central site. The cellular phone technology transmits unprocessed raw data from the patient site DAD and receives and displays the processed image from the central site. (This is different from conventional telemedicine where the image reconstruction and control is at the patient site and telecommunication is used to transmit processed images from the patient site). The primary goal of this study is to demonstrate that the cellular phone technology can function in the proposed mode. The feasibility of the concept is demonstrated using a new frequency division multiplexing electrical impedance tomography system, which we have developed for dynamic medical imaging, as the medical imaging modality. The system is used to image through a cellular phone a simulation of breast cancer tumors in a medical imaging diagnostic mode and to image minimally invasive tissue ablation with irreversible electroporation in a medical imaging interventional mode.     

Partner Choice Drives the Evolution of Cooperation via Indirect Reciprocity

Indirect reciprocity potentially provides an important means for generating cooperation based on helping those who help others. However, the use of ‘image scores’ to summarize individuals’ past behaviour presents a dilemma: individuals withholding help from those of low image score harm their own reputation, yet giving to defectors erodes cooperation. Explaining how indirect reciprocity could evolve has therefore remained problematic. In all previous treatments of indirect reciprocity, individuals are assigned potential recipients and decide whether to cooperate or defect based on their reputation. A second way of achieving discrimination is through partner choice, which should enable individuals to avoid defectors. Here, I develop a model in which individuals choose to donate to anyone within their group, or to none. Whereas image scoring with random pairing produces cycles of cooperation and defection, with partner choice there is almost maximal cooperation. In contrast to image scoring with random pairing, partner choice results in almost perfect contingency, producing the correlation between giving and receiving required for cooperation. In this way, partner choice facilitates much higher and more stable levels of cooperation through image scoring than previously reported and provides a simple mechanism through which systems of helping those who help others can work.     

Observation of objects under intense plasma background illumination

Experiments on the observation of a brightness-amplified image of an object through a masking arc discharge are presented. The copper-vapor laser active medium was used as an image brightness amplifier. It is shown that the image quality does not worsen under plasma background illumination.     

Multispectral/hyperspectral image enhancement for biological cell analysis.

BACKGROUND: Microscopes form projected images from illuminated objects, such as cellular tissue, which are recorded at a distance through the optical system's field of view. A telescope on a satellite or airplane also forms images with a similar optical projection of objects on the ground. Typical visible illuminations form a displayed set of three-color channels (Red Green Blue [RGB]) that are combined from three image sensor arrays (e.g., focal plane arrays) into a single pixel coding for each color present in the image. Analysis of these RGB color images develops a qualitative image representation of the objects. METHODS: Independent component analysis (ICA) is used for analysis and enhancement of multispectral images, and compared with the similar and widely used principal component analysis. RESULTS: The data examples indicate that the ICA enhancement, and the resulting RGB image combination display, can be useful in processing datacubes of cellular data where isolation of unknown subtle image elements representing objects is desired. CONCLUSIONS: ICA image enhancement can aid processing of datacubes of cellular data by clarifying subtle image elements. These parallelizable algorithms can be implemented for real-time, online analysis.     

Determination of molecular conformation and permeation in skin via IR spectroscopy, microscopy, and imaging

Skin tissue, in addition to its specific use in dermal research, provides an excellent model for developing the techniques of vibrational microscopy and imaging for biomedical applications. In addition to permitting characterization of various regions of skin, the relative paucity of major biological constituents in the stratum corneum (the outermost layer of skin), permits us to image, with microscopic resolution, conformational alterations and concentration variations in both the lipid and protein components. Thus we are able to monitor the effects of exogenous materials such as models for drug delivery agents (liposomes) and permeation enhancers (DMSO) on stratum corneum lipid organization and protein structure. In addition, we are able to monitor protein conformational changes in single corneocytes. The current article demonstrates these procedures, ranging from direct univariate measures of lipid chain conformational disorder, to factor analysis which permits us to image conformational differences between liposomes that have permeated through the stratum corneum from those which have remained on the surface in a reservoir outside the skin.