Dissecting tumor maintenance requirements using bioluminescence imaging of cell proliferation in a mouse glioma model

Bioluminescence imaging has previously been used to monitor the formation of grafted tumors in vivo and measure cell number during tumor progression and response to therapy. The development and optimization of successful cancer therapy strategies may well require detailed and specific assessment of biological processes in response to mechanistic intervention. Here, we use bioluminescence imaging to monitor the cell cycle in a genetically engineered, histologically accurate model of glioma in vivo. In these platelet-derived growth factor (PDGF)-driven oligodendrogliomas, G1 cell-cycle arrest is generated by blockade of either the PDGF receptor or mTOR using small-molecule inhibitors.     

Dissecting spindle architecture with a laser

Microtubules in spindles are too dense to resolve by light microscopy, even with super-resolution methods. Using a new method based on laser-ablation techniques, Brugués et?al. present the first quantitative characterization of the vertebrate meiotic spindle and propose an assembly mechanism for building this architecture.     

Microscope-based techniques to study cell adhesion and migration

Modern light microscopy has evolved to provide a variety of quantitative imaging techniques and also the capability to perturb structure-function relationships in living cells. The advances have been especially useful in the study of cell adhesion and migration. This review will focus on how such microscopy-based techniques can be useful in situ to study the molecular interactions and dynamics, to locally perturb actin-based structures and to measure the traction forces exerted by motile cells.     

Higher-order architecture of cell adhesion mediated by polymorphic synaptic adhesion molecules neurexin and neuroligin

Polymorphic adhesion molecules neurexin and neuroligin (NL) mediate asymmetric trans-synaptic adhesion, which is crucial for synapse development and function. It is not known whether or how individual synapse function is controlled by the interactions between variants and isoforms of these molecules with differing ectodomain regions. At a physiological concentration of Ca(2+), the ectodomain complex of neurexin-1 β isoform (Nrx1β) and NL1 spontaneously assembled into crystals of a lateral sheet-like superstructure topologically compatible with transcellular adhesion. Correlative light-electron microscopy confirmed extracellular sheet formation at the junctions between Nrx1β- and NL1-expressing non-neuronal cells, mimicking the close, parallel synaptic membrane apposition. The same NL1-expressing cells, however, did not form this higher-order architecture with cells expressing the much longer neurexin-1 α isoform, suggesting a functional discrimination mechanism between synaptic contacts made by different isoforms of neurexin variants.     

Dissecting the cosegregation probability from genome architecture mapping

Genome architecture mapping (GAM) is a recently developed methodology that offers the cosegregation probability of two genomic segments from an ensemble of thinly sliced nuclear profiles, enabling us to probe and decipher three-dimensional chromatin organization. The cosegregation probability from GAM binned at 1 Mb, which thus probes the length scale associated with the genomic separation greater than 1 Mb, is, however, not identical to the contact probability obtained from Hi-C, and its correlation with interlocus distance measured with fluorescence in situ hybridization is not so good as the contact probability. In this study, by using a polymer-based model of chromatins, we derive a theoretical expression of the cosegregation probability as well as that of the contact probability and carry out quantitative analyses of how they differ from each other. The results from our study, validated with in silico GAM analysis on three-dimensional genome structures from fluorescence in situ hybridization, suggest that to attain strong correlation with the interlocus distance, a properly normalized version of cosegregation probability needs to be calculated based on a large number of nuclear slices ($n>{10}^3$).     

Dissecting the genetic architecture of a stepwise infection process

How a host fights infection depends on an ordered sequence of steps, beginning with attempts to prevent a pathogen from establishing an infection, through to steps that mitigate a pathogen's control of host resources or minimize the damage caused during infection. Yet empirically characterizing the genetic basis of these steps remains challenging. Although each step is likely to have a unique genetic and environmental signature, and may therefore respond to selection in different ways, events that occur earlier in the infection process can mask or overwhelm the contributions of subsequent steps. In this study, we dissect the genetic architecture of a stepwise infection process using a quantitative trait locus (QTL) mapping approach. We control for variation at the first line of defence against a bacterial pathogen and expose downstream genetic variability related to the host's ability to mitigate the damage pathogens cause. In our model, the water‐flea Daphnia magna, we found a single major effect QTL, explaining 64% of the variance, that is linked to the host's ability to completely block pathogen entry by preventing their attachment to the host oesophagus; this is consistent with the detection of this locus in previous studies. In susceptible hosts allowing attachment, however, a further 23 QTLs, explaining between 5% and 16% of the variance, were mapped to traits related to the expression of disease. The general lack of pleiotropy and epistasis for traits related to the different stages of the infection process, together with the wide distribution of QTLs across the genome, highlights the modular nature of a host's defence portfolio, and the potential for each different step to evolve independently. We discuss how isolating the genetic basis of individual steps can help to resolve discussion over the genetic architecture of host resistance.     

Relating connectional architecture to grey matter function using diffusion imaging

Understanding brain function in terms of connectional architecture is a major goal of neuroimaging. However, direct investigation of the influence of brain circuitry on function has been hindered by the lack of a technique for exploring anatomical connectivity in the in vivo brain. Recent advances in magnetic resonance diffusion imaging have given scientists access to data relating to local white matter architecture and, for the first time, have raised the possibility of in vivo investigations into brain circuitry. This review investigates whether diffusion imaging may be used to identify regions of grey matter that are distinct in their connectional architecture, and whether these connectional differences are reflected either in local cytoarchitecture or in local grey matter function.Establishing a direct relationship between regional boundaries based on diffusion imaging and borders between regions that perform different functions would not only be of great significance when interpreting functional results, but would also provide a first step towards the validation of diffusion-based anatomical connectivity studies.     

Dissecting membrane protein architecture: An annotation of structural complexity

α‐Helical membrane proteins exist in an anisotropic environment which strongly influences their folding, stability, and architecture, which is far more complex than a simple bundle of transmembrane helices, notably due to helix deformations, prosthetic groups and extramembrane structures. However, the role and the distribution of such heterogeneity in the supra molecular organization of membrane proteins remains poorly investigated. Using a nonredundant subset of α‐helical membrane proteins, we have annotated and analyze the statistics of several types of new elements such as incomplete helices, intramembrane loops, helical extensions of helical transmembrane domains, extracellular loops, and helices lying parallel to the membrane surface. The relevance of the annotation scheme was studied using residue composition, statistics, physical chemistry, and symmetry of their distribution in relation to the immediate membrane environment. Calculation of hydrophobicity using different scales show that different structural elements appear to have affinities coherent with their position in the membrane. Examination of the annotation scheme suggests that there is considerable information content in the amino acid compositions of the different elements suggesting that it might be useful for structural prediction. More importantly, the proposed annotation will help to decipher the complex hierarchy of interactions involved in membrane protein architecture. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 815–829, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Water quality assessment using diatom assemblages and advanced modelling techniques

1. Two types of artificial neural networks procedures were used to define and predict diatom assemblage structures in Luxembourg streams using environmental data. 2. Self‐organising maps (SOM) were used to classify samples according to their diatom composition, and multilayer perceptron with a backpropagation learning algorithm (BPN) was used to predict these assemblages using environmental characteristics of each sample as input and spatial coordinates (X and Y) of the cell centres of the SOM map identified as diatom assemblages as output. Classical methods (correspondence analysis and clustering analysis) were then used to identify the relations between diatom assemblages and the SOM cell number. A canonical correspondence analysis was also used to define the relationship between these assemblages and the environmental conditions. 3. The diatom‐SOM training set resulted in 12 representative assemblages (12 clusters) having different species compositions. Comparison of observed and estimated sample positions on the SOM map were used to evaluate the performance of the BPN (correlation coefficients were 0.93 for X and 0.94 for Y). Mean square errors of 12 cells varied from 0.47 to 1.77 and the proportion of well predicted samples ranged from 37.5 to 92.9%. This study showed the high predictability of diatom assemblages using physical and chemical parameters for a small number of river types within a restricted geographical area.     

Dissecting in vitro host cell infection by Plasmodium sporozoites using flow cytometry

The study of the liver stage of malaria has been hampered by limitations in the experimental approaches required to effectively dissect and quantify hepatocyte infection by Plasmodium . Here, we report on the use of flow cytometry, in conjunction with GFP-expressing Plasmodium sporozoites, to assess the various steps that constitute a successful malaria liver infection: cell traversal, hepatocyte invasion and intrahepatocyte parasite development. We show that this rapid, efficient and inexpensive method can be used to overcome current limitations in the independent quantification of those steps, facilitating routine or large-scale studies of host–pathogen molecular interactions.     

Dissecting tumor cell invasion: epithelial cells acquire invasive properties after the loss of uvomorulin-mediated cell-cell adhesion

The generation of invasiveness in transformed cells represents an essential step of tumor progression. We show here, first, that nontransformed Madin-Darby canine kidney (MDCK) epithelial cells acquire invasive properties when intercellular adhesion is specifically inhibited by the addition of antibodies against the cell adhesion molecule uvomorulin; the separated cells then invade collagen gels and embryonal heart tissue. Second, MDCK cells transformed with Harvey and Moloney sarcoma viruses are constitutively invasive, and they were found not to express uvomorulin at their cell surface. These data suggest that the loss of adhesive function of uvomorulin (which is identical to E-cadherin and homologous to L-CAM) is a critical step in the promotion of epithelial cells to a more malignant, i.e., invasive, phenotype. Similar modulation of intercellular adhesion might also occur during invasion of carcinoma cells in vivo.     

Three-dimensional imaging of plant cuticle architecture using confocal scanning laser microscopy

Full appreciation of the roles of the plant cuticle in numerous aspects of physiology and development requires a comprehensive understanding of its biosynthesis and deposition; however, much is still not known about cuticle structure, trafficking and assembly. To date, assessment of cuticle organization has been dominated by 2D imaging, using histochemical stains in conjunction with light and fluorescence microscopy. This strategy, while providing valuable information, has limitations because it attempts to describe a complex 3D structure in 2D. An imaging technique that could accurately resolve 3D architecture would provide valuable additions to the growing body of information on cuticle molecular biology and biochemistry. We present a novel application of 3D confocal scanning laser microscopy for visualizing the architecture, deposition patterns and micro-structure of plant cuticles, using the fluorescent stain auramine O. We demonstrate the utility of this technique by contrasting the fruit cuticle of wild-type tomato ( Solanum lycopersicum cv. M82) with those of cutin-deficient mutants. We also introduce 3D cuticle modeling based on reconstruction of serial optical sections, and describe its use in identification of several previously unreported features of the tomato fruit cuticle.     

Study of cell-matrix adhesion dynamics using surface plasmon resonance imaging ellipsometry

The interaction of cells with extracellular matrix, termed cell-matrix adhesions, importantly governs multiple cellular phenomena. Knowledge of the functional dynamics of cell-matrix adhesion could provide critical clues for understanding biological phenomena. We developed surface plasmon resonance imaging ellipsometry (SPRIE) to provide high contrast images of the cell-matrix interface in unlabeled living cells. To improve the contrast and sensitivity, the null-type imaging ellipsometry technique was integrated with an attenuated total reflection coupler. We verified that the imaged area of SPRIE was indeed a cell-matrix adhesion area by confocal microscopy imaging. Using SPRIE, we demonstrated that three different cell types exhibit distinct features of adhesion. SPRIE was applied to diverse biological systems, including during cell division, cell migration, and cell-cell communication. We imaged the cell-matrix anchorage of mitotic cells, providing the first label-free imaging of this interaction to our knowledge. We found that cell-cell communication can alter cell-matrix adhesion, possibly providing direct experimental evidence for cell-cell communication-mediated changes in cell adhesion. We also investigated shear-stress-induced adhesion dynamics in real time. Based on these data, we expect that SPRIE will be a useful methodology for studying the role of cell-matrix adhesion in important biological phenomena.     

Dissecting cell biology with chemical scalpels

Understanding complex cellular processes requires methods for specifically perturbing protein function in a temporally defined fashion. In recent years a variety of chemical tools have been used to study the cytoskeleton and cell division, protein trafficking, and the destruction of proteins by the ubiquitin-proteasome system. The ability to use combinations of reversible inhibitors is proving to be especially helpful in dissecting complex cellular events. Furthermore, the identification of novel inhibitors through unbiased screening approaches is revealing novel drugable steps in important cellular pathways.     

Regulation of cell adhesion using a signal-responsive membrane substrate

We have developed a novel cell culture material that regulates cell adhesion by changes in potassium ion concentration. The material is a polyethylene substrate grafted to a copolymer of the thermoresponsive polymer N-isopropylacrylamide (NIPAM) and benzo-18-crown- 6-acrylamide (BCAm), with a pendant crown ether as sensor. The crown ether recognizes potassium ion concentrations and NIPAM conformational changes lead to changes in the hydrophobicity/hydrophilicity balance of the entire polymer at constant cell culture temperatures. Although cells were successfully cultured on the ion recognition material in normal culture medium at 37 degrees C, the cells could be detached from the material surface by adding potassium ions alone, without proteolytic enzymes, because the surface to which the cells were attached altered its surface characteristics to a more hydrophilic state. Therefore, cell layers with intact cell-to-cell junctions and high activities were successfully recovered. Furthermore, by changing the target sensors, this material will be able to control cell adhesion through various cellular signals.     

Dissecting cell death with proteomic scalpels

Programmed cell deaths (PCD), including apoptosis, autophagy and programmed necrosis, are genetically determined, complex processes in multi-cellular organisms. Problems with the regulation of PCD have been implicated in a number of diseases including myocardial infarction, cancer and autoimmune disease. As a result, the investigation on PCD regulation has stirred considerable interest. In the past decades, many PCD-involved proteins had been identified as being modulated by post-translational mechanisms, including post-translational modification, protein-protein interactions and protein cleavage, which fall precisely within the range of proteomic analysis. Contemporary quantitative proteomics, interactomics, PTMomics, degradomics, chemical proteomics and pharmacoproteomics have been quickly applied in the field of PCD research, and possess the potential to be the driving forces of the field. This review attempts to highlight some of the major achievements in the application of proteomics in PCD research to trigger further thinking and application.