bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving Spatial Conformations of Immuno-Proteins with Cryo-Atomic Force Microscopy (Cryo-Afm)
Authors: Shaon Zhifeng , Sheng Sitong 
Published: July 2020

Abstract
A major advantage of atomic force microscopy (AFM) is its intrinsic high contrast, owing to its extremely high sensitivity to height variations. For clean, flat specimens, high-resolution images of a variety of bio-molecules have been obtained, demonstrating the usefulness of AFM in structural biology. However, for large molecular complexes, the effectiveness of AFM is seriously limited, partly owing to the excessive deformation induced by the probe force exerted on the specimen. To overcome this difficulty, we have developed a cryo-AFM, operated under liquid nitrogen vapor at a temperature only a few degrees above 77K. In this system, specimen or tip contamination is significantly reduced, and the resolution achieved with isolated macromolecules is generally higher than that obtainable at room temperature with AFM. Therefore, cryo-AFM has been proven to be a worthy alternative for conventional electron microscopy (EM) with the potential of higher resolution without image averaging.
A particularly fruitful application of cryo-AFM is the study of the spatial structure of several immuno-proteins, where the 3D surface topology of the molecule has been obtained.
Micro & Nano-Scale Structure of Enamel and Dentin-Enamel Junction of Human Teeth
Authors: Fong Hanson , Sarikaya Mehmet , White Shane , Snead Malcolm 
Published: July 2020

Abstract
Enamel, which covers the anatomical crown of the tooth, is the hardest tissue in human body. Supported by a soft but tough dentin structure, the tooth is an advanced nanocomposite that can endure mastication stresses throughout a lifetime. A detail understanding the structure of the tooth, and sepecifically detin-enamel junction (DEJ), not only provides a sound basis for a model for synthetic dental restoration, but also provides lessons from nature on biomimetic regeneration with mechanical integrity. Enamel is a non-growing mineralized tissue and is subjected to most mechanical abuse. Dentin-enamel junction plays a critical role of distributing load between two very dissimilar materials - enamel and dentin. Bulk scale mechanical tests have shown that induced cracks on enamel tend to be arrested DEJ. Furthermore, nanoindentation measurements have also shown that there is a gradual decrease in hardness from enamel to dentin in the DEJ zone suggests a strong mechanical coupling in both deciduous and adult incisors. The objective of this investigation, through microscopical study, is to understand how these two dental hard tissues structurally couple through their junction zone.
Localization Of Camkiiα mrnas to Dendritic Spines Visualized By High Resolution In Situ Hybridization
Authors: Byrd AL , Shenoy SM , Martinez M , Plociniak M , Zhang H L , Singer RH , Bassell G J 
Published: July 2020

Abstract
Observations that polyribosomes are localized near dendritic spines and beneath synapses has led to a hypothesis of synapse-specific gene expression in which local synthesis would provide a mechanism to influence synaptic structure and strength (l).The active transport of specific mRNAs into dendrites and spines may be a regulated mechanism to target synaptic and regulatory proteins to postsynaptic locations and influence synaptic activity. RNA granules labeled with the vital dye, SYT014, were observed to localize into developing neurites in response to the neurotrophin, NT-3 (2). Neurotrophins have been shown to enhance synaptic activity by a process which requires new protein synthesis (3). The identity and source of newly synthesized proteins which are required to enhance synaptic strength in response to NT-3 are unknown. CaMKIIαRNA localization into dendrites has been shown to occur during long term potentiation (4).
Imaging Protein Interactions and Gene Expression in Individual Cells by Fluorescence Resonance Energy Transfer
Authors: Tsien RY , Miyawaki A , Kerr R , Baird G , Griffin BA , Adams SR , Zlokarnik G , Whitney M , Negulescu PA , Li W-H 
Published: July 2020

Abstract
Interactions between proteins or protein domains can be imaged by fusing them to cyan (CFP) and yellow (YFP) mutants of Green Fluorescent Protein and observing fluorescence resonance energy transfer (FRET). For example, fusions of CFP, calmodulin, a calmodulin-binding peptide, and YFP are transfectable emission-ratioing Ca2+ indicators with many uses. They are highly suitable for twophoton excitation at 770-810 nm, even at video rates. Applications not possible with previous indicators include detection of submicroscopic domains of Ca2+ by fusion of the indicators to key proteins, and dynamic imaging of Ca2+ in transgenic animals. YFPs have been improved as FRET acceptors by reducing their sensitivity to pH changes. Many other applications of GFP mutants to detect fluctuating protein-protein interactions are underway.
A synthetic alternative to GFPs for protein tagging arises from the ability of membrane-permeant biarsenical dyes to seek out and light up alpha-helical Cys-Cys-X-X-Cys-Cys motifs placed in recombinant proteins in live cells. The new system is much smaller than GFP (6 residues vs. 238), can label internal domains not just N- and C-terminii, and offers novel readouts (e.g. red emission peaking &gt; 600 nm) and better temporal control of the labeling.
Protein Dynamics During Apoptosis
Authors: Herman Brian 
Published: July 2020

Abstract
Apoptosis is an actively regulated process of cell death necessary for proper control of tissue growth. The phenomenon is characterized by plasma membrane blebbing, cell shrinkage, chromatin condensation, and degradation of DNA. Apoptosis is distinctly different from necrosis. Unlike necrosis, which is a passive form of cell death, apoptosis appears to be an active physiological process using a controlled genetic “program” of gene expression. Furthermore, apoptosis does not involve severe tissue damage or inflammation. Membrane integrity is preserved, and there is no loss of cellular contents before phagocytosis. Apoptosis is also distinct from necrosis in that it can be triggered or suppressed by tissue-specific hormones and growth factors.
Apoptosis plays a critical role in tissue homeostasis by counterbalancing mitosis. It is an essential component of many physiological processes, including embryonic development, clonal selection in thymocytes, and in protection against disease.
Elastic Properties of Erythrocyte's Membrane Measured by Atomic Force Stretching Method
Authors: Rafi Korenstein , Arkady Bitler , Luana Scheffer , Eshel Ben-Jacob 
Published: July 2020

Abstract
We employed force-distance measurements, carried out by Atomic Force Microscopy (AFM), to explore the local elastic properties of the membrane-skeleton of human erythrocytes. To calculate the elastic constant of the membrane-skeleton we chose that part of the withdraw region in the force-distance curve which corresponds to the stretching of the membrane-skeleton complex. In order to achieve efficient stretching of the membrane we increased the adhesion of the tip to the membrane by polysine coating of the tip.
Fig. 1 is presents the method of stretching AFM on which our measurements are based, and in Fig.2 one can see the theoretical model of the deformation of a circular plate with fixed boundaries by an external force (AFM probe ) used for recalculating the membrane's bending modulus from the experimental data.
Since we obtained different detachment patterns of tip from the membrane, we set selection criteria for the choice of appropriate curves corresponding to membrane stretching.
Imaging the Lateral Distribution of Fluorescently Labeled Membrane Components of Human Erythrocytes Under Deformation
Authors: Knowles DW , Mohandas N , Ortiz de Solorzano C , Lockett SJ 
Published: July 2020

Abstract
The human erythrocyte membrane comprises many different biological macromolecules arranged into a cohesive two dimensional structure. It has long been a model system for studying cell membrane component interactions and their related underlying cell biology. Erythrocyte membrane rigidity emanates from its hexagonal semi-solid cytoskeletal network of spectrin polymers joined at junctional complexes by globular proteins. The network supports a 2D fluid double layer of lipid in which is dissolved a large array of receptor proteins some of which completely span the lipid bilayer and link to the underlying cytoskeletal network.
To study membrane component - component interactions, we have used the technique of fluorescence imaged microdeformation (1). This technique combines fluorescence labeling of specific membrane components, single cell microdeformation and state-of-the-art image collection and analysis to map the distribution of labeled components on the surface of the cell.
Quantitative Phase Contrast Microscopy of Living Astrocytes By Numerical Reconstruction of Digital Holograms
Authors: Marquet P , Cuche E , Chatton J-Y , Depeursinge Ch , Magistretti PJ 
Published: July 2020

Abstract
We have developed a method of numerical holography which allows simultaneous intensity and quantitative phase contrast imaging. Measurement of optical path length provides precise information about the cell morphology. As presented in Fig. 1, the experimental set-up for the recording of digital holograms is basically a Mach-Zender interferometer. At the exit of the interferometer, a CCD camera records a hologram which is made by the interference between a reference wave R and the object wave O that is transmitted by the biological sample. In order to obtain a plane wave as reference, a beam expander (B.E.) including a pinhole is introduced in the reference arm and enlarges the beam diameter to about 2cm. A similar system which produces a smaller beam diameter (≈5mm) is inserted in the objet arm. To perform holography in the off-axis geometry, the mirror in the reference arm is oriented in such a way that the reference wave reaches the CCD camera with a small incidence angle.
All-Solid-State Diode-Pumped Fluorescence Lifetime Imaging System for Biomedicaine and Microscopy
Authors: Cole M J , Dowling K , French P M W , Jones R , Parsons-Karavassilis D , Lever M J , Dymoke-Bradshaw A K L , Hares J D , Neil M A A , Ju_kaitis R , Wilson T 
Published: July 2020

Abstract
The determination of fluorescence lifetime requires only relative measurements of intensity and so is especially useful for biomedical samples in which the heterogeneous nature of tissue and autofluorescence cause significant problems. Since fluorescence lifetime is dependent upon both radiative and non-radiative decay rates, it may be used to distinguish between different fluorophore molecules (with different radiative decay rates) and to monitor local environmental perturbations that affect the non-radiative decay rate. Fluorescence lifetime probes have been demonstrated for many biologically significant analytes including [O2], [Ca2+] and pH. Fluorescence lifetime imaging (FLIM) can be applied to almost any optical imaging modality, including microscopy and potentially to non-invasive optical biopsy. Fluorescence lifetime data may be acquired in the frequency or time domain. The recent development of user-friendly and relatively portable ultrafast laser technology and the availability of ultrafast gated optical image intensifiers (GOI’s) enable the development of potentially inexpensive time domain FLIM instruments that may be deployed outside specialist laser laboratories.
The Effects of Spaceflight Conditions on Calcium-Dependent Secretion and Cytoskeletal Organization During Fertilization and Cell Divisions In the Sea Urchin Lytechinus Pictus
Authors: Schatten Heide , Chakrabarti Amitabha , Levine Howard , Runco Mario , Anderson Ken , Taylor Meghan 
Published: July 2020

Abstract
Calcium loss and muscle atrophy are two of the main metabolic changes experienced by astronauts and crew members during exposure to microgravity in space. To investigate the effects of spaceflight on calcium-dependent secretion and cytoskeletal formation in a less complex system we utilized sea urchin eggs and embryos which were fertilized and cultured under spaceflight conditions during the STS-77 shuttle mission. Sea urchin eggs were fertilized and cultured in the newly developed aquatic research facility (ARF) which allowed culture of eggs and embryos in microgravity and in a 1g centrifuge in space. This allowed analysis of the comparison of microgravity and 1g spaceflight treatments with samples cultured on ground. Eggs and embryos were maintained in Standard Container Assemblies (SCAs) with identical sets prepared for culture in microgravity, and at 1g in the middeck compartment of the shuttle Endeavor, as well as for ground observations at the Kennedy Space Center.
Soma/Germline Interactions In Caenorhabditis Elegans Gonad
Authors: Hall David H , Winfrey Virginia P , Blaeuer Gareth , Hoffman Loren H , Furuta Tokiko , Rose Kimberly L , Hobert Oliver , Greenstein David 
Published: July 2020

Abstract
A combination of microscopical methods (TEM, SEM, freeze fracture, confocal, immunoEM) are utilized to demonstrate functional interactions between somatic cells and the germline in the model organism, C. elegans.A variety of signaling mechanisms are required to coordinate activity of maturing oocytes and the somatic sheath of the gonad. Communication via gap junctions allows direct coordination of sheath cell motility and oocyte development. Gap junctions link adjoining sheath cells, and link the sheath to the most mature oocyte. Yolk protein produced in the intestine passes from the pseudocoelom through the basal lamina of the proximal gonad and then through fenestrations (sheath pores) in the gonad sheath before being endocytosed into the most mature oocytes. Myoepithelial specializations anchored by hemi-adherens junctions in the proximal sheath act to squeeze the primary oocyte out of the gonad to the spermatheca for fertilization.
Applications of Confocal Microscopy to Study the Roles of the Cytoskeleton During Early Embryogenesis In Amphibians
Authors: Danilchik M V , Brown E E , Larkin K , Ray K 
Published: July 2020

Abstract
Because of their great size, availability, and capacity to develop autonomously in culture, amphibian eggs have become a productive system for a wide variety of experimental studies of animal cells. Their use has advanced our understanding of fundamental molecular and cellular processes such as transcription and translation, regulation of the cell cycle, and the function of the cytoskeleton. The amphibian egg, particularly that of the frog Xenopus laevis,has further served as an excellent system for studying complex developmental phenomena, including the roles of growth factors, signal transduction, and transcription regulation in cell determination, morphogenesis, and tissue differentiation.
Despite these advantages, the frog egg's great size and opacity have made it a challenging subject for microscopy. Thus, many problems in early development, such as how maternal cytoplasmic determinants become localized during cell division, have resisted traditional optical approaches.
Ultrastructural Pathology of Aids: an Overview
Authors: Orenstein Jan M 
Published: July 2020

Abstract
The ultrastructural pathology of HIV infection is a broad subject, owing to the fact that the transmission electron microscope has played an integral part in our understanding of HIV disease. The subject can be divided into three basic areas: HIV pathogenesis, opportunistic infections (OI), and neoplastic disease. Once HIV was determined to be a retrovirus, TEM confirmed its membership in the Lentivirus family and showed that it has a conical nucleoid. TEM has played a key role in our understanding of: 1) the CNS as a target of HIV, 2) the macrophage as a “trojan horse” for HIV, 3) how lymphocytes and macrophages differ in their HIV expression, 4) attachment of virions to the processes of follicular dendritic cells via complement and Fc receptors, and 5) the formation of multinucleated giant cells.
Microsporidia Infection Results In Redistribution of Host Cell Mitochondria
Authors: Shaw Andrew P , Scanlon Mary , Leitch Gordon J 
Published: July 2020

Abstract
Microsporidia are obligate intracellular parasites that lack mitochondria. Until recently, their importance was primarily limited to fish and insects; but with the onset of the AIDS epidemic, understanding their role as human pathogens has become increasingly important. Encephalitozoon microsporidia develop and mature within a membrane bound parasitophorous vacuole (pv). Following initial infection of the host cell, the developing stages (meronts) of the parasite proliferate in close proximity to the pv membrane. Later, they differentiate through a sporogonial stage and finally into environmentally resistant mature spores located more centrally in the vacuole.
Previous work done in our laboratory has shown that the pv membrane does not act as a significant diffusion barrier to the movement of ions between the host cell cytoplasm and the parasite, permitting the free-acid form of calcein, a fluorescent dye, loaded into the host cell to enter the pv.
The Efects of Spaceflight on Mitochondria in Human Lymphocytes (Jurkat).
Authors: Schatten Heide , Lewis Marian 
Published: July 2020

Abstract
Spaceflight induced mitochondrial alterations have been reported for muscle and may be associated with altered physiological functions in space. Mitochondrial alterations are also indicative of preapoptotic events which are seen in greater amounts in cells exposed to spaceflight when compared with cells cultured at 1 g. Preapoptotic mitochondrial changes include alterations of processes at the inner mitochondrial membrane and can result in changes in mitochondrial volume. Higher amounts of oxidative stress during space flight may be one of the causes for changes which lead to apoptosis. Jurkat cells flown on the STS-76 space shuttle mission showed an increase in the number of cells with apoptotic bodies early in the mission and a time-dependent, microgravity-related increase in the Fas/APO-1 cell death factor. Here we investigated the morphology of mitochondria in Jurkat cells exposed to spaceflight during the STS-76 mission.
Localization of Tissue Factor Pathway Inhibitor In Endothelial Cells: Pitfalls and Challenges
Authors: Olsen R , Hansen J-B , Webster P 
Published: July 2020

Abstract
Tissue Factor Pathway Inhibitor (TFPI) is a potent inhibitor of the extrinsic coagulation system, synthesized in endothelial cells. Membrane bound TFPI has recently been shown to play an important role in the degradation of activated coagulation factors in the endothelium. Comparison of subcellular TFPI localization patterns and TFPI production between Human Umbilical Vein Endothelial Cells (HUVEC) and an immortalized cell line (ECV 304) are presented here, as are the essential protocol modifications that we used to obtain labeling results by both light- and electron microscopy. We show that ECV 304 cells are similar to HUVEC in that TFPI is present in the Golgi complex (fig. 1) as well as in the endocytic pathway of ECV cells. Additionally, they secrete higher levels of TFPI into the culture medium than HUVEC. A colocalization of anti-TFPI with endocytosed BSA-gold, as well as with accumulated DAMP, demonstrated the presence of TFPI in the endocytic pathway.
CIV, An Iridovirus With a Pseudo T=147 Capsid Structure
Authors: Yan X , Olson N H , Bergoin M , Rossmann M G , Baker T S 
Published: July 2020

Abstract
Chilo iridescent virus (CIV), the type species of the genus Iridovirusin the family Iridoviridae,was first isolated from the rice stem borer, Chilo suppressalis,a member of Lepidoptera insect order. ‘2 CIV is being considered as a potential pest control agent because of its wide host range which includes leafhoppers and some arthropods. The virion (∼lxl09 daltons) encapsidates a 209 kbp, dsDNA genome within its fiber-covered, icosahedral shell. The virion is composed of about 26 structural proteins, two (P50 and P'50, 50kDa each) of which are the major capsid proteins. P50 migrates as a monomer in either a reducing or non-reducing SDS-PAGE gel and is exposed to the surface, whereas P'50 exists as a disulfide-bond, stabilized trimer in a non-reducing gel and is only partially exposed. Virions contain 9% lipid present as a lipid bilayer within the protein capsid.
Infection of Tick Cells By Two Nonpathogenic Strains of Rickettsia
Authors: Palmer Ann T , Munderloh Ulrike G , Kurtti Timothy J 
Published: July 2020

Abstract
Ticks harbor several different genera of endosymbiotic bacteria. These obligate intracellular bacteria, most of which appear to be nonpathogenic for the tick, persist in nature by being transmitted transovarially from generation to generation. Those in the genus Rickettsiabelong to the spotted fever group (SFG) of rickettsia which includes both mammalian pathogenic and nonpathogenic species. The species that cause spotted fevers in humans, e.g. Rickettsia rickettsii, are well characterized but those not known to cause disease remain poorly understood. Transmission electron microscopy on SFG rickettsia cultured in tick cell cultures offers a powerful way to examine dynamic host parasite interactions in these apparently nonpathogenic SFG species.
We have successfully isolated two unknown, nonpathogenic rickettsia strains in tick cell lines. T2 was isolated from an Ixodes ricinus tick collected in the English Garden in Munich, Germany and is propagated in an Ixodes scapularis cell line, ISE6.
First Report of a Putative Cyanophage, Mc-1, of Microcoleus Sp.
Authors: Rosowski J R , Shaffer J J , Martin E L , Kokjohn T A , Lee K W 
Published: July 2020

Abstract
A current review (1) lists 21 cyanophages of coccoid and filamentous heterocystic and non-heterocystic blue-green algae (BGA). The capsid diameters of these viruses range from 50-90 nm, and none have been previously reported for Microcoleus,a sheath-producing, filamentous, surface colonizing BGA (Fig. 1), of the order Oscillatoriales, and class Cyanophyceae (= Cyanobacteria). From a freshwater culture of Microcoleussp. we report here a putative cyanophage with a side-to-side hexagonal capsid diameter of 140 nm, based on measurements from thin sections of algal filaments prepared for transmission electron microscopy (TEM).
An earlier report (2) documented the ultrastructure of mucilage secretion, and its role in sheath, trichome and filament formation in an isolate of the BGA Microcoleus sp. grown in soil-water medium. Now we report large cyanophage-like particles in a majority of cells making up the trichomes. These putative hexagonal viral capsids (Figs. 2-5) are mainly clustered in the center or to one side of the nucleoplasm.
Infrared Spectroscopic Micro-Imaging of Macromolecular Leakage In Acute Lung Injury Tissue
Authors: Wang J , Fata P , Yip B , Oppenheimer L , O’Connor R , Stimpson R , Mantsch H H 
Published: July 2020

Abstract
Acute lung injury is defined as a syndrome of inflammation resulting in increased capillary-alveolar permeability that is associated with a constellation of clinical, radiological and physiological abnormalities. Adult respiratory distress syndrome (ARDS), relatively common in the intensive care, is a more specific, severe form of ALI, with diverse causes. Diffuse alveolar damage is the pathognomonic feature of the syndrome. Under the pathophysiologic conditions of increasing capillary membrane permeability, large macromolecules can gain access to the interstitium, resulting in pulmonary interstitial edema, and from there enter the alveolar space in severe cases. Detecting the distribution of macromolecules in lung tissue, therefore, constitutes evidence of the injury. Traditional pathologic examination of biopsy/autopsy materials is the only route to provide pathologic evidence of the capillary-alveolar membrane damage induced lung injury. Although morphometric analyses are more laborious, they provide qualitative assessment of morphological changes that is an important aspect of acute lung injury, see Fig.l.