Focus: A Multifaceted Battle Against Cancer: Extracting Knowledge from Chemical Imaging Data Using Computational Algorithms for Digital Cancer Diagnosis

Fourier transform infrared (FTIR) spectroscopic imaging is an emerging microscopy modality for clinical histopathologic diagnoses as well as for biomedical research. Spectral data recorded in this modality are indicative of the underlying, spatially resolved biochemical composition but need computerized algorithms to digitally recognize and transform this information to a diagnostic tool to identify cancer or other physiologic conditions. Statistical pattern recognition forms the backbone of these recognition protocols and can be used for highly accurate results. Aided by biochemical correlations with normal and diseased states and the power of modern computer-aided pattern recognition, this approach is capable of combating many standing questions of traditional histology-based diagnosis models. For example, a simple diagnostic test can be developed to determine cell types in tissue. As a more advanced application, IR spectral data can be integrated with patient information to predict risk of cancer, providing a potential road to precision medicine and personalized care in cancer treatment. The IR imaging approach can be implemented to complement conventional diagnoses, as the samples remain unperturbed and are not destroyed. Despite high potential and utility of this approach, clinical implementation has not yet been achieved due to practical hurdles like speed of data acquisition and lack of optimized computational procedures for extracting clinically actionable information rapidly. The latter problem has been addressed by developing highly efficient ways to process IR imaging data but remains one that has considerable scope for progress. Here, we summarize the major issues and provide practical considerations in implementing a modified Bayesian classification protocol for digital molecular pathology. We hope to familiarize readers with analysis methods in IR imaging data and enable researchers to develop methods that can lead to the use of this promising technique for digital diagnosis of cancer.     

Oviduct histochemistry and site of synthesis of a 29.7 kDa jelly coat glycoprotein in the anuran Lepidobatrachus laevis

The oviduct of the anuran Lepidobatrachus laevis contains three morphological regions, each of which contains a histochemically distinct luminal mucosa. In the pars recta, the most anterior portion of the oviduct, there are periodic acid-Schiff base (PAS)-positive simple glands and epithelia. In the pars convoluta, there are alcian blue-positive, combined alcian blue- and PAS-positive and PAS-positive gland types. The most posterior region, the pars uterina, contains alcian blue-positive and alcian blue-negative epithelial cells. Previous work has shown that solubilized egg jelly contains a major 29.7 kDa glycoprotein subunit that was detected in oviduct tissue extracts from the pars convoluta in the present study. Rabbit antisera to the 29.7 kDa egg jelly glycoprotein of L. laevis reacted with the major pars convoluta glycoprotein and there were no immunoreactive components in the pars uterina. The slight immunoreactivity detected at 29.0–37.0 kDa in pars recta extracts is not believed to be the jelly molecule, based on low immunoreactivity and subunit molecular weight measurements. We conclude that the synthesis of the 29.7 kDa egg jelly glycoprotein is restricted to the pars convoluta region of the oviduct.     

Single-file diffusion through K+ channels in frog skin epithelium

Summary The ratio between the unidirectional fluxes of K⁺ across the frog skin with K-permeable outer membranes was determined in the absence of Na⁺ in the apical solutions. The experiments were performed under presteady-state conditions to be able to separate the flux ratio for K⁺ through the cells from contributions to the fluxes through extracellular leaks. The cellular flux ratio deviated strongly from the value calculated from the flux ratio for electrodiffusion. The experiments can be explained if the passive K transport through the epithelial cells proceeds through specific channels by single-file diffusion with a flux ratio exponent of about 2.5.     

A click chemistry approach for the synthesis of cyclic ureido tethered coumarinyl and 1-aza coumarinyl 1,2,3-triazoles as inhibitors of Mycobacterium tuberculosis H37Rv and their in silico studies

Nucleoside bases like uracil, pharmacophoric triazoles and benzimidazolones have been used during the present study to design molecular matrices for antitubercular activity, employing Click Chemistry. Click triazoles 4/7/10 have been obtained by the reaction of 4-(Azidomethyl)-2H-chromen-2-ones/quinolin-2(1H)-ones 3 and propargyl ethers 2/6/9 derived from theophylline/6-methyl uracil/2-benzimidazolone respectively. In addition to spectral data structures have been confirmed by single crystal X-ray diffraction studies in case of uracil bis alkyne (6) and theophylline mono triazole (4c). Theophylline linked mono triazoles, 4(a-d) and 6-methyl uracil linked bis triazoles, 7(a-e) have been found to inhibit Mycobacterium tuberculosis H37Rv with MIC values in the range 55.62–115.62 μM. Benzimidazolone bis triazoles, 10(a-n) showed better activity with MIC in the range 2.33–18.34 μM. Molecular modeling studies using Surflex-Dock algorithm supported our results.     

De novo inference of protein function from coarse‐grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high‐throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse‐grained (CG) molecular dynamics trajectories were used to compute normalized root‐mean‐square‐fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three‐dimensional autocorrelation vectors. Our in‐house custom‐built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics‐signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof‐of‐principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom‐made CG FF, useful to all. Proteins 2014; 82:2443–2454. © 2014 Wiley Periodicals, Inc.     

Elektronenmikroskopische Untersuchungen an der Froschlunge

Zusammenfassung Das Alveolarepithel der Froschlunge weist nur einen einzigen Zelltyp auf. Die Zellkörper sitzen in den Nischen zwischen den Kapillaren, die sie mit Zytoplasmaausläufern überdecken. Die Epithelzellen enthalten große Zytosomen mit osmiophilen Lamellen mit einer Periode von 40–42 Å. Sie sind den Typ II-Pneumozyten der Säugerlunge vergleichbar.Das Alveolarepithel der Froschlunge ist mit einer Grenzschicht bedeckt, die in Abhängigkeit von der Fixierung eine 40–42 Å-Periode aufweist oder aus einer oder mehreren Doppelmembranen zusammengesetzt ist. Gittermuster und Myelinfiguren sind vorhanden. Das bedeutet, daß Surfactant in der Froschlunge in gleicher Weise wie in der Säugerlunge dargestellt werden kann.

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Electron microscopic studies on the lung of the frogI. Demonstration of the alveolar lining layer (surfactant)

Summary The alveolar epithelium of the frog exhibits only one type of cells. The cell-bodies are situated in the spaces among the capillaries, which they cover with cytoplasmic extensions. The epithelial cells contain large bodies (cytosomes) with osmiophilic lamellae having a period of 40–42 Å. The alveolar cells are considered to be similar to the type II-pneumocytes of mammalian lungs.The alveolar epithelium of the lung of the frog is covered with a lining layer, which depending on the method of fixation consists of periods of 40–42 Å or of one or more double membranes. Lattice formations and myelin figures are seen. This means that the surfactant in the lung of the frog can be demonstrated in the same way as in mammalian lungs.

     

An electron microscopic study of stellate cells and cavities in the pars distalis of frog pituitary

Stellate cells in the pars distalis of adult Rana ridibunda were observed electron microscopically under normal and experimental conditions (TRH injection). The stellate cells have lengthy processes extending into the intercellular spaces between the secretory cells and scanty cytoplasm surrounding the nucleus. Occasional desmosomes link stellate cells to adjacent secretory cells. In the pars distalis of animals injected with thyrotropic-releasing hormone (TRH), the stellate cells form large cavities (2-6 mum) filled with heterogeneous material. Their cytoplasm contains well-developed Golgi complexes and some lysosomes; these are the principal morphological alterations as compared to those observed in control animals. It is suggested that stellate cells could play an active role in addition to providing a structural framework for the pars distalis.