bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blind Deconvolution of Low and High Signal-to-noise 3-D Images of Fluorescent Subcellular Structures
Authors: Rajwa B , Czyz J , Dobrucki J 
Published: July 2020

Abstract
This report summarizes our experiences gained with deconvolving 3-d images of various types of biological samples - animal and plant cells; live and fixed. We compared raw, unmodified images with images processed with standard filtering methods and images improved by using deconvolution. The blind decovolution software package from AutoQuant, Inc. was used. All images were acquired using a BioRad MRC 1024 confocal microscope (attached to a Nikon Diaphot microscope), using fluorescence or reflected light. For thin (up to 25 μm) flat specimens a 60x PlanApo NA1.4 lens was used while for thick (25-200 μm) water containing samples a 40x Fluor NA1.15 water immersion lens was used.
In an attempt to test the usefulness and validity of deconvolution for various types of biological samples we adopted the following approaches:
1. collect images of structures that are known to be both fluorescent and reflective - compare the results of deconvolution of fluorescence images with reflected light images that are not deconvolved.
Patterning of Surface Chemistry and Topography for Biological Applications
Authors: Craighead H G , Davis R C , Foquet M , Isaacson M , James C , Turner S , Kam L , Turner J N , Shain W , Banker G 
Published: July 2020

Abstract
The technologies of nanofabrication as applied to inorganic materials and substrates are advanced and continue to develop. These sophisticated processes enable the formation of complex electronic, optical and mechanical devices with feature sizes down to tens of nanometers. Adaptation of these types of processes to surface chemical patterning and topographical patterning provides a new set of experimental tools for investigating biological systems and realizing sensors and devices that require the interaction of biological systems and fluids with inorganic materials and surfaces.
In this talk we discuss methods of pattering self assembled monolayers, proteins and antibodies on silicon and glass surfaces by lithography and microcontact printing. This is of utility in a variety of experiments in cell-surface interactions and in sensor devices. In certain types of devices the manipulation of fluids and sieving of molecules is a critical function such as in DNA sequencing6 by electrophoretic separation.
The Confocal Microscope: How to Choose it and Use it
Authors: Drazba JA 
Published: July 2020

Abstract
The decision to buy a confocal microscope presents the huge task of wading through designs and options from a number of excellent companies. While the principle of confocal imaging - rejection of out-of-focus light - is consistently achieved, each manufacturer does so with a unique design. There is strong competition among manufacturers to have the microscope with the best possible resolution and light transfer efficiency so that maximum specimen detail is detected with the least light damage. There are a number of excellent instruments currently available. In deciding among them consideration should be given to the following: type and number of users, types of imaging required, and your budget. If the microscope is going to be used by a single lab for a single purpose i.e. gfp expression in embryos, you should consider one of the less elaborate “personal confocals” with one laser, one or two detectors and a price tag under $150,000.
The Importance of Optimizing Operational Procedures and Calibrations in Materials Characterization Using an Analytical Electron Microscope
Authors: Echer CJ 
Published: July 2020

Abstract
When managing multi-disciplinary materials characterization facilities to help solve scientific materials problems, one needs to confidently operate the instrumentation knowing that the calibrations and operational procedures are as accurate as possible and optimized by periodic evaluation. An overview of the calibrations and some operational pitfalls will be reviewed for the Analytical Electron Microscope. I intend to show examples of various results produced over the years characterizing materials, including some recent data. A short chronological history of my career pertaining to image documentation will show examples from the old days to the present. I pride myself on having a top-notch laboratory so when scientists need relatively fast answers, one knows which direction to proceed and the equipment is capable of achieving the results. When scientific users come to an AEM laboratory, each individual brings a potpourri of materials problems to try and solve.
Corrosion Casting in the Reproduction of the Micro-Surface Topography of Fibrillar Collagen
Authors: Sims PA , Albrecht RM 
Published: July 2020

Abstract
The interaction of cells with biomaterials is influenced by a number of factors including the chemical composition, surface charge, hydrophobicity, porosity and texture of the biomaterial. Changes in texture alone have been shown to result in reduced platelet adhesion on ventricular assist devices, reduced scar tissue formation around implanted prostheses, and enhanced biocompatability of vascular stents. In vitro growth of certain cells requires extracellular matrix components to provide the right physical and chemical stimuli for adherence, growth and differentiation. What role the texture of these materials plays, and the mechanisms responsible for the effects of substrate texture on the behavior of cells are not well understood. Previously we have used microcorrosion casting technology to replicate lymph node and other vasculature. More recently, we have used corrosion casting to replicate of the subendothelial matrix exposed when cells are damaged due to the passage of air emboli through a vessel.
Microvascularization of the uterine tube in the rabbit (Oryctolagus cuniculus)
Authors: R. P. Chopard , I. Watanabe , C. I. Conegero 
Published: July 2020

Abstract
Several authors have been studying the microvascularization pattern of the ovary in different animals. To determine the microvascularization pattern using the corrosive-resin casting method, casts of the vascular network were prepared and examined by scanning electron microscopy. However, the same procedure has rarely been used to study the microvascularization pattern of the uterine tube itself. The microvascularization of the uterine tube has always been associated microvascularization studies of the ovary. This study analyses the microvascularization of the uterine tube, pointing out differences between the region of the tube itself and it's infundibulum. In this study we used uterine tubes from adult female rabbits. Anesthesia was carried out with Ketalar (5mg/kg body weight); after that saline solution and 2,5% glutaraldehyde were injected through the left ventricle. This procedure was followed by mercox 2B injection. After polymerization the samples were collected and immersed in warm water (60°C). Then samples underwent tissue digestion.
Formation of Proteasome-PA700 Complexes Directly Correlates with Activation of Peptidase Activity
Authors: Adams G , Crotchett B , Slaughter C , DeMartino G , Gogol E 
Published: July 2020

Abstract
The eukaryotic 20S proteasome (700 kDa) serves as the core complex for the breakdown of most cytosolic proteins by the ubiquitin-dependent pathway. This cylinder-shaped proteolytic assembly (17 nm long, 11 nm diameter) consists of four stacked heptameric rings that help to form a central cavity where degradation occurs. The catalytic sites are located on the cavity surface of the two middle β rings while the outer α rings serve as docking sites for various regulatory complexes.
PA700 (700 kDa, 20 protein subunits) is the major regulatory complex of the proteasome, forming a “cap” that attaches to either or both proteasome ends. The resulting superassembly structurally resembles the larger, more active 26S proteasome and exhibits both a higher intrinsic peptidase activity as well as a wider range of substrate specificity, including ubiquitin-tagged proteins. A second regulatory complex, the modulator (300 kDa), further stimulates the effects of PA700 at subsaturating concentrations of the activator with no detectable effect on the proteasome in the absence of PA700.
Green Fluorescent Protein as a Non-Invasive Probe of Viscosity and pH in Cell Cytoplasm and Organelles
Authors: Verkman AS 
Published: July 2020

Abstract
Green fluorescent protein (GFP) was evaluated as a non-invasive probe to quantify the rheological properties and pH of intracellular aqueous compartments. Spectroscopic studies were done on several bacterially-expressed and purified GFP mutants. GFP-S65T was brightly fluorescent in solution (ƛex 492 nm, ƛem 509 nm) with lifetime 2.9 ns and rotational correlation time ( tc ) ∼20 ns. Recovery of GFP fluorescence after photobleaching was complete with a half-time (t1/2) in aqueous saline of 30 ± 2 ms (5 μm diameter spot) giving a diffusion coefficient of 8.7 x 10-7 cm2/s. The t1/2 was proportional to solution viscosity and was dependent on spot diameter. In contrast to fluorescein, GFP photobleaching efficiency was not affected by solution O2 content, triplet state quenchers, singlet oxygen scavengers, and general radical quenchers. In solutions of higher viscosity, an additional, rapid GFP recovery process was detected and ascribed to reversible photobleaching. The t1/2 for reversible photobleaching was 1.5-5.5 ms (relative viscosity 5-250), independent of spot diameter, and not affected by O2 or quenchers.
Efficient, Retro Viral-Mediated Expression Of GFP Fusion Proteins as Inhibitors of Intracellular Signal Transduction Pathways: A Case Study
Authors: Murphy TJ , Wang Xiaofei 
Published: July 2020

Abstract
A variety of extracellular signals, including hormones, neurotransmitters, growth factors and cytokines, are capable of activating vascular smooth muscle cells (VSMC). These can modulate the VSMC phenotype, which underlies the progression of vascular diseases. We study gene expression control responses in VSMC that are regulated by different classes of cell surface receptors. Taken as simpler model systems for the pleiotropic sensitivity of VSMC to extracellular stimuli, we focus on understanding the elements of intracellular signal transduction pathways involved in controlling gene expression. In particular, we are interested in identifying signaling elements that can be activated by multiple classes of cell surface receptors.
Previous studies had supported both a role of protein kinase A (PKA) activity and transcriptional induction of an unknown factor in control of ATI angiotensin receptor gene expression in VSMC (1). The mRNA from this gene is down-regulated by a variety of extracellular stimuli, and we hypothesized that stimulation of PKA by several classes of receptors might explain the apparently pleiotropic nature of ATI-receptor down regulation.
Optical Mesurements of Presynaptic Function: What Keeps Vesicle Traffic Going
Authors: Ryan Timothy A 
Published: July 2020

Abstract
The nervous system has evolved to make use of a variety of mechanisms that allow information to flow and be processed among a large collection of individual cells. The communication between individual brain cells occurs largely at chemical synapses. In these compartments, chemical messengers are packaged into small vesicles that fuse with the cell membrane upon stimulation, releasing neurotransmitter.. The average total number of synaptic vesicles in a typical central nervous system synapse is only a few hundred and as a result an efficient local recycling mechanism operates in order to replenish this pool during periods of even modest neuronal activity. Without this membrane recycling, synapses quickly become depleted of vesicles, and soon fail to communicate information between cells.
We make use of optical techniques to follow the trafficking of synaptic vesicles at synapses formed between hippocampal neurons grown in culture. Recycling synaptic vesicles can be readily labeled using the fluorescent amphipathic membrane dye FM 1-43.
Characterization of Endocytic Pathways by Quantitative Fluorescence Microscopy
Authors: Maxfield Frederick R , Ghosh Richik N , Mallet William G , Thwe Soe Thwe , Leopold Philip L , Cohen-Gould Leona , Mayor Satyajit , Mukherjee Sushmita , Zha Xiaohui , McGraw Timothy E 
Published: July 2020

Abstract
We have used light and electron microscopy to analyze endocytic trafficking pathways. In one set of studies, we have used fluorescently labeled antibodies to trace an endocytic pathway from the cell surface to the trans- Golgi network (TGN). Cells were transfected with a construct consisting of the transmembrane and cytoplasmic domains of TGN38 and the extracellular domain of Tac. TGN38 is predominantly in the TGN, but a small fraction is found on the cell surface. We used FITC-labeled anti-Tac monoclonal IgG to analyze the pathway from the surface to the TGN. We compared the distribution of internalized Tac-TGN38 to internalized transferrin. We found that most Tac-TGN38 enters the same early endosomes as transferrin. Furthermore, most Tac-TGN38 returns to the cell surface from the endocytic recycling compartment (ERC) at the same rate as transferrin. However, on each pass through the cell approximately 18% of Tac-TGN is retained, and this Tac-TGN38 is delivered to the TGN.
Fluorescent and Electron Microscopic Studies Suggest That Confronting Cisternae Arise from Nuclear Envelope in Mitotic Cells
Authors: Palisano J R , Thacker J L , Piromalli C S , Morrison A M , Tate J E 
Published: July 2020

Abstract
The origin and role of confronting cisternae (CC) have been clouded in mystery since their discovery in 1955. Early investigations suggested that CC arose from either nuclear envelope (NE) or by stacking of endoplasmic reticulum (ER) cisternae. Electron microscopic studies of mitotic HeLa cells suggest that CC are fragments of NE (Fig. 1) that arise as portions of the NE fold back on one another. Because lamin B is a NE specific protein, a monoclonal antibody to lamin B was used to probe the origin of CC. The monoclonal antibody to lamin B was then detected by utilizing a secondary antibody conjugated to the fluorochrome rhodamine which fluoresces red when exposed to UV light. Fluorescent microscopy of interphase HeLa cells demonstrates that only the NE fluoresces red when the cells are probed with a monoclonal antibody to lamin B (Fig. 2). There is no label localized in the cytoplasm which supports the evidence that lamin B is only localized to the NE in interphase cells.
Electron Microscopy of Bound Polysomes on in Vitro Rough Endoplasmic Reticulum Prepared by Cryohomogenization
Authors: Kent Christensen A 
Published: July 2020

Abstract
We have previously described a cryohomogenization method for making in vitropreparations of rough endoplasmic reticulum (RER) and other organelles. The goal of that approach was to minimize the extensive vesicular fragmentation of the endoplasmic reticulum that occurs during homogenization for conventional cell fractionation. The microsome fraction of cell fractionation consists primarily of small vesicles derived from rough and smooth endoplasmic reticulum, and has been of great value in biochemical studies of protein synthesis and secretion. However, the small size of the microsome vesicles has made them less useful for in vitro studies of bound polysomes by electron microscopy. As a further development of our cryohomogenization approach, we here describe a method for removing larger particles and debris from the cryohomogenate by filtration, and the application of in vitro RER and other organelles to EM grid membranes for negative staining and viewing by electron microscopy.
Nature of ADH-Induced Endosomes In Toad Urinary Bladder Granular Epithelial Cells
Authors: Mia AJ , Oakford LX , Dibas A , Yorio T 
Published: July 2020

Abstract
Serosal ADH stimulation enhances water flow under an imposed osmotic gradient through insertion of water channels (aggrephores) into the mucosal plasma membrane of toad urinary bladder sacs. Following cessation of ADH actions, water channels are retrieved as endosomes that can be visualized by mucosal inclusion of horseradish peroxidase (HRP) into round vesicles, long tubules and multivesicular bodies within the cytosol (1,2,3). Endosomes also occur adjacent to golgi bodies or lysosomes (1,2,3). However, true nature of endosomes including their formation at the mucosal surface and their shuttling in granular cells is still unclear (4,5). Current studies were undertaken to understand the role of endosomes in water channel cycling in this renal membrane model.
Urinary bladder sacs removed surgically from doubly-pithed toads, were suspended at ends of glass tubes. Control (no hormone) and experimental bladder sacs were exposed to ADH for 10 min in the absence of osmotic gradient.
Ultrastructural Changes in Hepatocellular Rough Endoplasmic Reticulum in Rats Given a Pyrimidine Derivative
Authors: Maleeff Beverly E , Newsholme Stephen J , Hart Timothy K 
Published: July 2020

Abstract
Hepatomegaly, characterized by increased liver weight due to hyperplasia or hypertrophy, can be induced in many species by various drugs or environmental toxins. In rats, hepatomegaly is more usually associated with increases of smooth endoplasmic reticulum in hepatocytes and the associated induction of cytochrome P450 enzymes or with hepatocellular peroxisomal proliferation. In this study, a substituted pyrimidine derivative given to rats resulted in hepatomegaly with an unusual selective increase in hepatocellular rough endoplasmic reticulum (RER).
Female Sprague-Dawley rats were given repeated oral doses of a substituted pyrimidine derivative for 28 consecutive days. Livers were collected at necropsy, weighed, fixed in 10% neutral buffered formalin and processed to paraffin sections stained with hematoxylin and eosin (H&E) for light microscopic evaluation. Portions of formalin-fixed liver were transferred to buffered 2.5% glutaraldehyde for ultrastructural evaluation. Specimens were processed into epoxy resin and thin sections were examined with a JEOL 1200EX transmission electron microscope.
Morphometry of Liver Lesions in an Ultrastructural Pathology Study
Authors: Singh A , Ireland WP , Chu I 
Published: July 2020

Abstract
Some pathologic alterations in animal tissue sections, because of low resolution, are not identified using light microscopy. Availability of higher resolution in electron microscopy (EM) confers a decisive role on EM for diagnostic pathology that is well accepted. Much has already been contributed by EM in understanding of liver diseases. However, EM has been further refined by adding a quantitative facet to the results. Morphometric technique allows transfer of facts acquired from 2-dimensional samples, e.g., electron micrographs, to a 3-dimensional perspective. In addition, the technique is valuable in determining the significance of the alterations especially in instances where the changes numerically are either scanty or indistinguishable from a normal appearance of the cells or tissues (Fig. 1).
In our work on the effects of several different PCB congeners, one of the compounds, namely, congener number 153 was studied to obtain morphometric data on the lesions in the liver of rats given the congener in the diets for 13 weeks.
Muscle Biopsy: Use of Cryosections, Histochemistry, and Electron Microscopy for Diagnosis
Authors: Hastings Cindy L , Jones Yvonne M , Mrak Robert E 
Published: July 2020

Abstract
Modern diagnosis of biopsied muscle requires a multidisciplinary approach, including routine histology and immunohistochemistry, cryosectioning for histochemistry, and (in selected cases) electron microscopy or biochemical evaluation. Routine paraffin embedding offers excellent histological detail. Cryosections provide fresh tissue for histochemical reactions that delineate fiber types and reveal special architectural alterations. Electron microscopy is applied in selected instances to provide diagnostic detail not otherwise apparent. Biochemical analysis of frozen tissue is used to define certain inborn errors of metabolism. This integrated approach allows diagnostic precision far beyond the limited information available from routine paraffin sections. We present examples of diagnoses made possible using these special techniques.
Chronic, slowly progressive neuropathies show grouping of fiber types and target fiber formation, apparent in special histochemical preparations. Routine histological preparations may be normal or show only nonspecific changes. Central core disease shows areas of pallor evident in the central areas of many myofibers in histochemical preparations.
Macrophage Targeted Photodynamic Regulation of Wound Healing
Authors: Coleno Mariah , Wallace Vincent P , Tromberg Bruce J , Hasan Tayyaba 
Published: July 2020

Abstract
Wound healing is coordinated by the diverse activities of cells of the monocyte/macrophage lineage.1 Macrophage depletion impairs wound healing, while overexpression of macrophage products is associated with chronic inflammatory states. If light-activatable pharmacologic agents could be selectively targeted to macrophages, clinical conditions resulting from overexpression such as postsurgical adhesions, hypertrophic scarring, and the formation of intimal hyperplasia could be suppressed. Similarly, adjusting light dose parameters to provide a stimulatory effect could selectively enhance wound repair processes.
To test these hypothesis, photoactivatable cytotoxins (photosensitizers, PS) coupled to specific receptor ligands have been evaluated for localization in cells found in cutaneous tissue using a non-invasive imaging method, two-photon microscopy.
The two-photon microscope (TPM) has been found to be a useful tool for imaging cells with submicron resolution thus allowing for the determination of photosensitizer localization within cells. Additional uses of the TPM will include imaging into epithelial tissue grown in culture and tracking cells in wounds.
Subcellular Localization of an Oncoprotein using Immunofluorescence, Confocal Imaging and Immuno Electron Microscopy
Authors: Murti K , Caslini C , Domer PH , Korsmeyer S J , Boer J , Grosveld G , Look AT 
Published: July 2020

Abstract
The mixed-lineage leukemia (MLL) gene is associated with more than 25 translocations of chromosome band 1 lq23 in the human leukemias. In certain unusually aggressive leukemias, the N-terminal portion of MLL fuses in frame to a portion of the transcription factor AF4. As a part of our investigation of the role of the MLL-AF4 fusion oncoprotein in Leukemogenesis, we studied the cellular sites of distribution of MLL-AF4 in the Hela carcinoma cells and U937 myeloid cells by immunofluorscene, confocal imaging and immuno-electron microscopy. Hela and U937 cells were stably transfected with a FLAG epitope-tagged MLL-AF4 (F-MLL-AF4) under the control of a tetracycline-responsive promoter and the expression of F-MLL-AF4 detected by indirect immunofluorescence (IF) with an anti-FLAG monoclonal antibody. These studies revealed that in both cell types the antibodies labeled two nuclear components, the nucleoli in an intense manner and the nucleoplasm in a punctate (100 to 200 dots) pattern. No antibody staining was observed in control (in the presence of tetracycline) cells.