Quantitative and analytical tools to analyze the spatiotemporal population dynamics of microbial consortia

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Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories

The Unit-vector RMS (URMS) is a new technique to compare protein chains and to detect similarities of chain segments. It is limited to comparison of C(alpha) chains. However, it has a number of unique features that include exceptionally weak dependence on the length of the chain and efficient detection of substructure similarities. Two molecular dynamics simulations of proteins in the neighborhood of their native states are used to test the performance of the URMS. The first simulation is of a solvated myoglobin and the second is of the protein MHC. In accord with previous studies the secondary structure elements (helices or sheets) are found to be moving relatively rigidly among flexible loops. In addition to these tests, folding trajectories of C peptides are analyzed, revealing a folding nucleus of seven amino acids.     

The transitional junction: a new functional subcellular domain at the intercalated disc

We define here a previously unrecognized structural element close to the heart muscle plasma membrane at the intercalated disc where the myofibrils lead into the adherens junction. At this location, the plasma membrane is extensively folded. Immunofluorescence and immunogold electron microscopy reveal a spectrin-rich domain at the apex of the folds. These domains occur at the axial level of what would be the final Z-disc of the terminal sarcomere in the myofibril, although there is no Z-disc-like structure there. However, a sharp transitional boundary lies between the myofibrillar I-band and intercalated disc thin filaments, identifiable by the presence of Z-disc proteins, alpha-actinin, and N-terminal titin. This allows for the usual elastic positioning of the A-band in the final sarcomere, whereas the transduction of the contractile force normally associated with the Z-disc is transferred to the adherens junctions at the plasma membrane. The axial conjunction of the transitional junction with the spectrin-rich domains suggests a mechanism for direct communication between intercalated disc and contractile apparatus. In particular, it provides a means for sarcomeres to be added to the ends of the cells during growth. This is of particular relevance to understanding myocyte elongation in dilated cardiomyopathy.     

Use of TSAR as a new tool to analyze the molecular dynamics trajectories of proteins

There is a lack of tools to analyze simulations of protein molecular dynamics quantitatively. Our aim is to use calmodulin, a prototypical calcium-binding protein, to describe a strategy and some tools for extracting relevant information from dynamics calculations. Our main conclusions are as follows:

• •• Autocorrelation vectors may be used to represent a 3D conformation in an n-dimensional space, where n is variable (n ⩽ 20–30).
• •• On such a transformation, classic statistical tools (PCA, clustering, etc.) may be used to differentiate or characterize dynamics trajectories quantitatively.
• •• TSAR, an integrated package used for quantitative structure-activity relationships, is well suited (after minor modifications) for such a purpose.

Finally, this type of strategy is able to point out the effects of the solvent screening parameters of the Amber software on the dynamics trajectories of calmodulin.     

GFP as a tool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassa

We report the construction of a versatile GFP expression plasmid and demonstrate its utility in Neurospora crassa. To visualize nuclei and microtubules, we generated carboxy-terminal fusions of sgfp to Neurospora histone H1 (hH1) and beta-tubulin (Bml). Strong expression of GFP fusion proteins was achieved with the inducible Neurospora ccg-1 promoter. Nuclear and microtubule organization and dynamics were observed in live vegetative hyphae, developing asci, and ascospores by conventional and confocal laser scanning fluorescence microscopy. Observations of GFP fusion proteins in live cells largely confirmed previous results obtained by examination of fixed cells with various microscopic techniques. H1-GFP revealed dynamic nuclear shapes. Microtubules were mostly aligned parallel to the growth axis in apical compartments but more randomly arranged in sub-apical compartments. Time-lapse imaging of beta-tubulin-GFP in germinating macroconidia revealed polymerization and depolymerization of microtubules. In heterozygous crosses, H1-GFP and beta-tubulin-GFP expression was silenced, presumably by meiotic silencing. H1-GFP was translated in the vicinity of hH1+-sgfp+ nuclei in the common cytoplasm of giant Banana ascospores, but it diffused into all nuclei, another illustration of the utility of GFP fusion proteins.     

Monitoring the dynamics of Src activity in response to anti-invasive dasatinib treatment at a subcellular level using dual intravital imaging

Optimising response to tyrosine kinase inhibitors in cancer remains an extensive field of research. Intravital imaging is an emerging tool, which can be used in drug discovery to facilitate and fine-tune maximum drug response in live tumors. A greater understanding of intratumoural delivery and pharmacodynamics of a drug can be obtained by imaging drug target-specific fluorescence resonance energy transfer (FRET) biosensors in real time. Here, we outline our recent work using a Src-FRET biosensor as a readout of Src activity to gauge optimal tyrosine kinase inhibition in response to dasatinib treatment regimens in vivo. By simultaneously monitoring both the inhibition of Src using FRET imaging, and the modulation of the surrounding extracellular matrix using second harmonic generation (SHG) imaging, we were able to show enhanced drug penetrance and delivery to live pancreatic tumors. We discuss the implications of this dual intravital imaging approach in the context of altered tumor-stromal interactions, while summarising how this approach could be applied to assess other combination strategies or tyrosine kinase inhibitors in a preclinical setting.     

BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes

Microarray technology has become employed widely for biological researchers to identify genes associated with conditions such as diseases and drugs. To date, many methods have been developed to analyze data covering a large number of genes, but they focus only on statistical significance and cannot decipher the data with biological concepts. Gene Ontology (GO) is utilized to understand the data with biological interpretation; however, it is restricted to specific ontology such as biological process, molecular function, and cellular component. Here, we attempted to apply MeSH (Medical Subject Headings) to interpret groups of genes from biological viewpoint. To assign MeSH terms to genes, in this study, contexts associated with genes are retrieved from full set of MEDLINE data using machine learning, and then extracted MeSH terms from retrieved articles. Utilizing the developed method, we implemented a software called BioCompass. It generates high-scoring lists and hierarchical lists for diseases MeSH terms associated with groups of genes to utilize MeSH and GO tree, and illustrated a wiring diagram by linking genes with extracted association from articles. Researchers can easily retrieve genes and keywords of interest, such as diseases and drugs, associated with groups of genes. Using retrieved MeSH terms and OMIM in conjunction with, we could obtain more disease information associated with target gene. BioCompass helps researchers to interpret groups of genes such as microarray data from a biological viewpoint.     

Extinction antagonizes olfactory memory at the subcellular level

Memory loss occurs by diverse mechanisms, as different time constants of performance decrement and sensitivities to experimental manipulations suggest. While the phenomena of memory decay, interference, and extinction are well established behaviorally, little is known about them at the circuit or molecular level. In Drosophila, odorant memories lasting up to 3 hr can be localized to mushroom body Kenyon cells, a single neuronal level in the olfactory pathway. The plasticity underlying this memory trace can be induced without Kenyon cell synaptic output. Experimental extinction, i.e., presentation of the conditioned stimulus without the reinforcer, reduces memory performance and does so at the same circuit level as memory formation. Thus, unreinforced presentation of learned odorants antagonizes intracellularly the signaling cascade underlying memory formation.     

Probing the spatiotemporal patterns of HBV multiplication reveals novel features of its subcellular processes

Through evolution, Hepatitis B Virus (HBV) developed highly intricate mechanisms exploiting host resources for its multiplication within a constrained genetic coding capacity. Yet a clear picture of viral hitchhiking of cellular processes with spatial resolution is still largely unsolved. Here, by leveraging bDNA-based fluorescence in situ hybridization (FISH) combined with immunofluorescence, we developed a microscopic approach for multiplex detection of viral nucleic acids and proteins, which enabled us to probe some of the key aspects of HBV life cycle. We confirmed the slow kinetics and revealed the high variability of viral replication at single-cell level. We directly visualized HBV minichromosome in contact with acetylated histone 3 and RNA polymerase II and observed HBV-induced degradation of Smc5/6 complex only in primary hepatocytes. We quantified the frequency of HBV pregenomic RNAs occupied by translating ribosome or capsids. Statistics at molecular level suggested a rapid translation phase followed by a slow encapsidation and maturation phase. Finally, the roles of microtubules (MTs) on nucleocapsid assembly and virion morphogenesis were analyzed. Disruption of MTs resulted in the perinuclear retention of nucleocapsid. Meanwhile, large multivesicular body (MVB) formation was significantly disturbed as evidenced by the increase in number and decrease in volume of CD63⁺ vesicles, thus inhibiting mature virion secretion. In conclusion, these data provided spatially resolved molecular snapshots in the context of specific subcellular activities. The heterogeneity observed at single-cell level afforded valuable molecular insights which are otherwise unavailable from bulk measurements.     

RECA immunological assay as a tool to analyze the SOS response

The content of RECA protein, one of the SOS genes product, was determined in a bacterial extract by a two site-radioimmunometric assay. The variation of the RECA concentration after induction by physical or chemical treatments was used as a probe to analyze the SOS response. Relationships between either the number or the nature of DNA lesions and the level of the relative amplification of RECA have been established. The modulation of the recA gene expression is discussed.     

Proteome analysis at the level of subcellular structures.

The targeting of proteins to particular subcellular sites is an important principle of the functional organization of cells at the molecular level. In turn, knowledge about the subcellular localization of a protein is a characteristic that may provide a hint as to the function of the protein. The combination of classic biochemical fractionation techniques for the enrichment of particular subcellular structures with the large-scale identification of proteins by mass spectrometry and bioinformatics provides a powerful strategy that interfaces cell biology and proteomics, and thus is termed 'subcellular proteomics'. In addition to its exceptional power for the identification of previously unknown gene products, the analysis of proteins at the subcellular level is the basis for monitoring important aspects of dynamic changes in the proteome such as protein transloction. This review summarizes data from recent subcellular proteomics studies with an emphasis on the type of data that can retrieved from such studies depending on the design of the analytical strategy.     

Proteomic profiles of induced hepatotoxicity at the subcellular level

In the present study proteomes of liver samples were analyzed after administration of phenobarbital (PB) or 3-methylcholantrene (3-MC) to mice. Liver cell homogenates were subfractionated by differential ultracentrifugation into cytosol and microsomes, which were subjected to 2-DE to generate the proteomic maps of these fractions. 2-DE yielded 1100 and 800 protein spots for microsomes and cytosol, respectively. General trends of the fraction-specific alterations after 3-MC or PB treatment were evaluated using the Student's t-test and the principal component analysis (PCA). According to the PCA-derived data, the microsomal changes after 3-MC and PB treatment were quite similar. However, in the case of the cytosol data, the specificities of 3-MC- and PB-induced responses could be clearly distinguished from each other. Protein spots, whose expression levels differed from control, were identified by MALDI-TOF PMF. Proteomic studies such as those reported herein can be useful in identifying the molecular-based toxicity of lead drug candidates.     

The dynamics of recycled acetylcholine receptors at the neuromuscular junction in vivo

At the peripheral neuromuscular junction (NMJ), a significant number of nicotinic acetylcholine receptors (AChRs) recycle back into the postsynaptic membrane after internalization to intermingle with not-yet-internalized ;pre-existing' AChRs. However, the way in which these receptor pools are maintained and regulated at the NMJ in living animals remains unknown. Here, we demonstrate that recycled receptors in functional synapses are removed approximately four times faster than pre-existing receptors, and that most removed recycled receptors are replaced by new recycled ones. In denervated NMJs, the recycling of AChRs is significantly depressed and their removal rate increased, whereas direct muscle stimulation prevents their loss. Furthermore, we show that protein tyrosine phosphatase inhibitors cause the selective accumulation of recycled AChRs in the peri-synaptic membrane without affecting the pre-existing AChR pool. The inhibition of serine/threonine phosphatases, however, has no effect on AChR recycling. These data show that recycled receptors are remarkably dynamic, and suggest a potential role for tyrosine dephosphorylation in the insertion and maintenance of recycled AChRs at the postsynaptic membrane. These findings may provide insights into long-term recycling processes at less accessible synapses in the central nervous system in vivo.     

Vivipary as a tool to analyze late embryogenic events in maize

In maize vivipary, the precocious germination of the seed while still attached to the ear, is the diagnostic phenotype of mutants, which are impaired in the biosynthesis or response to abscisic acid (ABA). Of the 15 genes so far described, 12 control specific steps in ABA biosynthesis, two mediate hormone response and one still has an undefined role. We have analyzed a collection of 25 independent vp isolates with the aim of determining the degree of mutational saturation that has so far been reached. Of the 25 viviparous mutants complementation tested, 22 correspond to known loci: six are allelic to vp1, another six to vp5, one to vp7, two to vp9, six to vp10 and one to w3. The remaining three represent genes not previously identified. All mutants so far tested except rea show a decrease in ABA content. As to the only two mutants (vp1 and rea) whose endogenous ABA content is not impaired, the reduction in sensitivity of the double mutant compared to the single ones suggests that the two genes control separate pathways in the ABA signal transduction. Some of the mutants in this collection have a characteristic incomplete germination that allows the embryo of the mature dry seed to resume germination. By exploiting this feature it is possible to infer, through a germination test, whether the mutant has been impaired in the acquisition of desiccation tolerance. This information provides the starting point for the dissection of the genetic basis of desiccation tolerance.     

Acetylcholinesterase dynamics at the neuromuscular junction of live animals

At cholinergic synapses, acetylcholinesterase (AChE) is critical for ensuring normal synaptic transmission. However, little is known about how this enzyme is maintained and regulated in vivo. In this work, we demonstrate that the dissociation of fluorescently-tagged fasciculin 2 (a specific and selective peptide inhibitor of AChE) from AChE is extremely slow. This fluorescent probe was used to study the removal and insertion of AChE at individual synapses of living adult mice. After a one-time blockade of AChEs with fluorescent fasciculin 2, AChEs are removed from synapses initially at a faster rate (t(1/2) of approximately 3 days) and later at a slower rate (t(1/2) of approximately 12 days). Most of the removed AChEs are replaced by newly inserted AChEs over time. However, when AChEs are continuously blocked with fasciculin 2, the removal rate increases substantially (t(1/2) of approximately 12 h), and most of the lost AChEs are not replaced by newly inserted AChE. Furthermore, complete one-time inactivation of AChE activity significantly increases the removal of postsynaptic nicotinic acetylcholine receptors (AChRs). Finally, time lapse imaging reveals that synaptic AChEs and AChRs that are removed from synapses are co-localized in the same pool after being internalized. These results demonstrate a remarkable AChE dynamism and argue for a potential link between AChE function and postsynaptic receptor lifetime.     

The spatiotemporal dynamics of microglia across the human lifespan

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Measuring endothelial glycocalyx dimensions in humans: a potential novel tool to monitor vascular vulnerability.

The endothelial glycocalyx is increasingly considered as an intravascular compartment that protects the vessel wall against pathogenic insults. The purpose of this study was to translate an established experimental method of estimating capillary glycocalyx dimension into a clinically useful tool and to assess its reproducibility in humans. We first evaluated by intravital microscopy the relation between the distance between the endothelium and erythrocytes, as a measure of glycocalyx thickness, and the transient widening of the erythrocyte column on glycocalyx compression by passing leukocytes in hamster cremaster muscle capillaries. We subsequently assessed sublingual microvascular glycocalyx thickness in 24 healthy men using orthogonal polarization spectral imaging. In parallel, systemic glycocalyx volume (using a previously published tracer dilution technique) as well as cardiovascular risk profiles were assessed. Estimates of microvascular glycocalyx dimension from the transient erythrocyte widening correlated well with the size of the erythrocyte-endothelium gap (r = 0.63). Measurements in humans were reproducible (0.58 +/- 0.16 and 0.53 +/- 0.15 microm, coefficient of variance 15 +/- 5%). In univariate analysis, microvascular glycocalyx thickness significantly correlated with systemic glycocalyx volume (r = 0.45), fasting plasma glucose (r = 0.43), and high-density lipoprotein-cholesterol (r = 0.40) and correlated negatively with low-density lipoprotein-cholesterol (r = -0.41) as well as body mass index (r = -0.45) (all P < 0.05). In conclusion, the dimension of the endothelial glycocalyx can be measured reproducibly in humans and is related to cardiovascular risk factors. It remains to be tested whether glycocalyx dimension can be used as an early marker of vascular damage and whether therapies aimed at glycocalyx repair can protect the vasculature against pathogenic challenges.     

Atomic force microscopy: a tool to analyze the structural organization of pathogenic protozoa

The fine structure of parasitic protozoa has been the subject of intense investigation with the use of electron microscopy. The recent development of atomic force microscopy (AFM) and all of the techniques associated with AFM has created new ways to further analyze the structure of cells. In this review, the various, presently-available modalities of AFM are discussed, as well as the results obtained in analysis of: (i) the structure of intact and detergent-extracted protozoa; (ii) the surface of infected cells; (iii) the structure of parasite macromolecules; (iv) the measurement of surface potential; and (v) force spectroscopy, the measurement of elasticity and ligand-receptor interactions.