Clean localization super-resolution microscopy for 3D biological imaging

We propose clean localization microscopy (a variant of fPALM) using a molecule filtering technique. Localization imaging involves acquiring a large number of images containing single molecule signatures followed by one-to-one mapping to render a super-resolution image. In principle, this process can be repeated for other z-planes to construct a 3D image. But, single molecules observed from off-focal planes result in false representation of their presence in the focal plane, resulting in incorrect quantification and analysis. We overcome this with a single molecule filtering technique that imposes constraints on the diffraction limited spot size of single molecules in the image plane. Calibration with sub-diffraction size beads puts a natural cutoff on the actual diffraction-limited size of single molecules in the focal plane. This helps in distinguishing beads present in the focal plane from those in the off-focal planes thereby providing an estimate of the single molecules in the focal plane. We study the distribution of actin (labeled with a photoactivatable CAGE 552 dye) in NIH 3T3 mouse fibroblast cells. (C) 2016 Author(s).

Stimuli-responsive protamine-based biodegradable nanocapsules for enhanced bioavailability and intracellular delivery of anticancer agents

Enzyme-and pH-responsive polyelectrolyte nanocapsules having diameters in the range of 200 +/- 20 nm were fabricated by means of Layer-by-Layer assembly of biopolymers, protamine, and heparin, and then loaded with anticancer drug doxorubicin. The incorporation of the FDA-approved peptide drug protamine as a wall component rendered the capsules responsive to enzyme stimuli. The stimuli-responsive drug release from these nanocapsules was evaluated, and further modulation of capsule permeability to avoid premature release was demonstrated by crosslinking the wall components. The interaction of the nanocapsules with cancer cells was studied using MCF-7 breast cancer cells. These capsules were readily internalized and disintegrated inside the cells, culminating in the release of the loaded doxorubicin and subsequent cell death as observed by confocal microscopy and MTT Assay. The bioavailability studies performed using BALB/c mice revealed that the encapsulated doxorubicin exhibited enhanced bioavailability compared to free doxorubicin. Our results indicate that this stimuli-responsive system fabricated from clinically used FDA-approved molecules and exhibiting minimal premature release has great potential for drug-delivery applications.

Stimuli-responsive protamine-based biodegradable nanocapsules for enhanced bioavailability and intracellular delivery of anticancer agents

Enzyme-and pH-responsive polyelectrolyte nanocapsules having diameters in the range of 200 +/- 20 nm were fabricated by means of Layer-by-Layer assembly of biopolymers, protamine, and heparin, and then loaded with anticancer drug doxorubicin. The incorporation of the FDA-approved peptide drug protamine as a wall component rendered the capsules responsive to enzyme stimuli. The stimuli-responsive drug release from these nanocapsules was evaluated, and further modulation of capsule permeability to avoid premature release was demonstrated by crosslinking the wall components. The interaction of the nanocapsules with cancer cells was studied using MCF-7 breast cancer cells. These capsules were readily internalized and disintegrated inside the cells, culminating in the release of the loaded doxorubicin and subsequent cell death as observed by confocal microscopy and MTT Assay. The bioavailability studies performed using BALB/c mice revealed that the encapsulated doxorubicin exhibited enhanced bioavailability compared to free doxorubicin. Our results indicate that this stimuli-responsive system fabricated from clinically used FDA-approved molecules and exhibiting minimal premature release has great potential for drug-delivery applications.

Intracellular delivery of antibodies by chimeric Sesbania mosaic virus (SeMV) virus like particles

The therapeutic potential of antibodies has not been fully exploited as they fail to cross cell membrane. In this article, we have tested the possibility of using plant virus based nanoparticles for intracellular delivery of antibodies. For this purpose, Sesbania mosaic virus coat protein (CP) was genetically engineered with the B domain of Staphylococcus aureus protein A (SpA) at the beta H-beta I loop, to generate SeMV loop B (SLB), which self-assembled to virus like particles (VLPs) with 43 times higher affinity towards antibodies. CP and SLB could internalize into various types of mammalian cells and SLB could efficiently deliver three different monoclonal antibodies-D6F10 (targeting abrin), anti-a-tubulin (targeting intracellular tubulin) and Herclon (against HER2 receptor) inside the cells. Such a mode of delivery was much more effective than antibodies alone treatment. These results highlight the potential of SLB as a universal nanocarrier for intracellular delivery of antibodies.

Damage evolution, localization and failure of solids subjected to impact loading

In order to reveal the underlying mesoscopic mechanism governing the experimentally observed failure in solids subjected to impact loading, this paper presents a model of statistical microdamage evolution to macroscopic failure, in particular to spallation. Based on statistical microdamage mechanics and experimental measurement of nucleation and growth of microcracks in an Al alloy subjected to plate impact loading, the evolution law of damage and the dynamical function of damage are obtained. Then, a lower bound to damage localization can be derived. It is found that the damage evolution beyond the threshold of damage localization is extremely fast. So, damage localization can serve as a precursor to failure. This is supported by experimental observations. On the other hand, the prediction of failure becomes more accurate, when the dynamic function of damage is fitted with longer experimental observations. We also looked at the failure in creep with the same idea. Still, damage localization is a nice precursor to failure in creep rupture.

Intracellular demography and the dynamics of Salmonella enterica infections.

An understanding of within-host dynamics of pathogen interactions with eukaryotic cells can shape the development of effective preventive measures and drug regimes. Such investigations have been hampered by the difficulty of identifying and observing directly, within live tissues, the multiple key variables that underlay infection processes. Fluorescence microscopy data on intracellular distributions of Salmonella enterica serovar Typhimurium (S. Typhimurium) show that, while the number of infected cells increases with time, the distribution of bacteria between cells is stationary (though highly skewed). Here, we report a simple model framework for the intensity of intracellular infection that links the quasi-stationary distribution of bacteria to bacterial and cellular demography. This enables us to reject the hypothesis that the skewed distribution is generated by intrinsic cellular heterogeneities, and to derive specific predictions on the within-cell dynamics of Salmonella division and host-cell lysis. For within-cell pathogens in general, we show that within-cell dynamics have implications across pathogen dynamics, evolution, and control, and we develop novel generic guidelines for the design of antibacterial combination therapies and the management of antibiotic resistance.

A dynamic view of the spread and intracellular distribution of Salmonella enterica.

The events that determine the dynamics of proliferation, spread and distribution of microbial pathogens within their hosts are surprisingly heterogeneous and poorly understood. We contend that understanding these phenomena at a sophisticated level with the help of mathematical models is a prerequisite for the development of truly novel, targeted preventative measures and drug regimes. We describe here recent studies of Salmonella enterica infections in mice which suggest that bacteria resist the antimicrobial environment inside host cells and spread to new sites, where infection foci develop, and thus avoid local escalation of the adaptive immune response. We further describe implications for our understanding of the pathogenic mechanism inside the host.

Bacterial growth rate and host factors as determinants of intracellular bacterial distributions in systemic Salmonella enterica infections.

Bacteria of the species Salmonella enterica cause a range of life-threatening diseases in humans and animals worldwide. The within-host quantitative, spatial, and temporal dynamics of S. enterica interactions are key to understanding how immunity acts on these infections and how bacteria evade immune surveillance. In this study, we test hypotheses generated from mathematical models of in vivo dynamics of Salmonella infections with experimental observation of bacteria at the single-cell level in infected mouse organs to improve our understanding of the dynamic interactions between host and bacterial mechanisms that determine net growth rates of S. enterica within the host. We show that both bacterial and host factors determine the numerical distributions of bacteria within host cells and thus the level of dispersiveness of the infection.

Nature of disorder and localization in amorphous carbon

The electronic structure of amorphous diamond-like carbon is studied. Analysis of the participation ratio shows that π states within the σ-σ* gap are localized. The localization arises from dihedral angle disorder. The localization of π states causes the mobility gap to exceed the optical gap, which accounts for the low carrier mobility and the flat photoluminesence excitation spectrum. © 1998 Elsevier Science B.V. All rights reserved.

Shear localization and recrystallization in dynamic deformation of 8090 Al-Li alloy

The microstructural evolution in localized shear deformation was investigated in an 8090 Al-Li alloy by split Hopkinson pressure bar (strain rate of approximately 10(3) s(-1)) at ambient temperature and 77 K. The alloy was tested in the peak-, over-, under-, and natural-aged conditions, that provide a wide range of microstructural parameters and mechanical properties. Two types of localized shear bands were distinguished by optical microscopy: the deformed shear band and the white-etching shear band. They form at different stages of deformation during localization. There are critical strains for the occurrence of deformed and white-etching localized shear deformation, at the imposed strain rate. Observations by transmission electron microscopy reveal that the white-etching bands contain fine equiaxed grains; it is proposed that they are the result of recrystallization occurring during localization. The deformed-type bands are observed after testing at 77 K in all heat treatment conditions, but they are not as well defined as those developed at ambient temperature. Cracking often occurs along the localized shear at ambient temperature. The decrement in temperature is favorable for the nucleation, growth and coalescence of the microcracks along the shear bands, inducing fracture.

Enhanced virulence of Salmonella enterica serovar typhimurium after passage through mice.

The interaction between Salmonella enterica and the host immune system is complex. The outcome of an infection is the result of a balance between the in vivo environment where the bacteria survive and grow and the regulation of fitness genes at a level sufficient for the bacteria to retain their characteristic rate of growth in a given host. Using bacteriological counts from tissue homogenates and fluorescence microscopy to determine the spread, localization, and distribution of S. enterica in the tissues, we show that, during a systemic infection, S. enterica adapts to the in vivo environment. The adaptation becomes a measurable phenotype when bacteria that have resided in a donor animal are introduced into a recipient naïve animal. This adaptation does not confer increased resistance to early host killing mechanisms but can be detected as an enhancement in the bacterial net growth rate later in the infection. The enhanced growth rate is lost upon a single passage in vitro, and it is therefore transient and not due to selection of mutants. The adapted bacteria on average reach higher intracellular numbers in individual infected cells and therefore have patterns of organ spread different from those of nonadapted bacteria. These experiments help in developing an understanding of the influence of passage in a host on the fitness and virulence of S. enterica.

Intracellular demography and the dynamics of Salmonella enterica infections.

An understanding of within-host dynamics of pathogen interactions with eukaryotic cells can shape the development of effective preventive measures and drug regimes. Such investigations have been hampered by the difficulty of identifying and observing directly, within live tissues, the multiple key variables that underlay infection processes. Fluorescence microscopy data on intracellular distributions of Salmonella enterica serovar Typhimurium (S. Typhimurium) show that, while the number of infected cells increases with time, the distribution of bacteria between cells is stationary (though highly skewed). Here, we report a simple model framework for the intensity of intracellular infection that links the quasi-stationary distribution of bacteria to bacterial and cellular demography. This enables us to reject the hypothesis that the skewed distribution is generated by intrinsic cellular heterogeneities, and to derive specific predictions on the within-cell dynamics of Salmonella division and host-cell lysis. For within-cell pathogens in general, we show that within-cell dynamics have implications across pathogen dynamics, evolution, and control, and we develop novel generic guidelines for the design of antibacterial combination therapies and the management of antibiotic resistance.

Efficient topological localization using orientation adjacency coherence histograms

This paper describes an efficient vision-based global topological localization approach that uses a coarse-to-fine strategy. Orientation Adjacency Coherence Histogram (OACH), a novel image feature, is proposed to improve the coarse localization. The coarse localization results are taken as inputs for the fine localization which is carried out by matching Harris-Laplace interest points characterized by the SIFT descriptor. Computation of OACHs and interest points is efficient due to the fact that these features are computed in an integrated process. We have implemented and tested the localization system in real environments. The experimental results demonstrate that our approach is efficient and reliable in both indoor and outdoor environments. © 2006 IEEE.

Coarse-to-fine vision-based localization by indexing scale-invariant features

This paper presents a novel coarse-to-fine global localization approach inspired by object recognition and text retrieval techniques. Harris-Laplace interest points characterized by scale-invariant transformation feature descriptors are used as natural landmarks. They are indexed into two databases: a location vector space model (LVSM) and a location database. The localization process consists of two stages: coarse localization and fine localization. Coarse localization from the LVSM is fast, but not accurate enough, whereas localization from the location database using a voting algorithm is relatively slow, but more accurate. The integration of coarse and fine stages makes fast and reliable localization possible. If necessary, the localization result can be verified by epipolar geometry between the representative view in the database and the view to be localized. In addition, the localization system recovers the position of the camera by essential matrix decomposition. The localization system has been tested in indoor and outdoor environments. The results show that our approach is efficient and reliable. © 2006 IEEE.

Vision-based global localization using a visual vocabular

This paper presents a novel coarse-to-fine global localization approach that is inspired by object recognition and text retrieval techniques. Harris-Laplace interest points characterized by SIFT descriptors are used as natural land-marks. These descriptors are indexed into two databases: an inverted index and a location database. The inverted index is built based on a visual vocabulary learned from the feature descriptors. In the location database, each location is directly represented by a set of scale invariant descriptors. The localization process consists of two stages: coarse localization and fine localization. Coarse localization from the inverted index is fast but not accurate enough; whereas localization from the location database using voting algorithm is relatively slow but more accurate. The combination of coarse and fine stages makes fast and reliable localization possible. In addition, if necessary, the localization result can be verified by epipolar geometry between the representative view in database and the view to be localized. Experimental results show that our approach is efficient and reliable. ©2005 IEEE.