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https://www.readbyqxmd.com/read/29347011/luminescence-from-cavitation-bubbles-deformed-in-uniform-pressure-gradients
#1
Outi Supponen, Danail Obreschkow, Philippe Kobel, Mohamed Farhat
Presented here are observations that demonstrate how the deformation of millimetric cavitation bubbles by a uniform pressure gradient quenches single-collapse luminescence. Our innovative measurement system captures a broad luminescence spectrum (wavelength range, 300-900 nm) from the individual collapses of laser-induced bubbles in water. By varying the bubble size, driving pressure, and perceived gravity level aboard parabolic flights, we probed the limit from aspherical to highly spherical bubble collapses...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346801/early-gene-expression-profile-in-retinal-ganglion-cell-layer-after-optic-nerve-crush-in-mice
#2
Satoru Ueno, Azusa Yoneshige, Yoshiki Koriyama, Man Hagiyama, Yoshikazu Shimomura, Akihiko Ito
Purpose: Optic nerve crush (ONC) induces retinal ganglion cell (RGC) death, which causes vision loss in glaucoma. To investigate early events leading to apoptosis of RGCs, we performed gene expression analysis of injured retinas in the period before RGC loss. Methods: The temporal changes of gene profiles at 0, 1, and 4 days after ONC were determined by DNA microarray. To verify the gene expression changes in RGCs, we enriched RGCs by laser-captured microdissection and performed real-time RT-PCR of 14 selected genes...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29344874/laser-capture-microdissection-based-rna-seq-of-barley-grain-tissues
#3
Ronny Brandt, Martin Mascher, Johannes Thiel
Spatiotemporal patterning throughout the plant body depends to a large degree on cell- and tissue-specific expression of genes. Subsequently, for a better understanding of cell and tissue differentiation processes during plant development it is important to conduct transcript analyses in individual cells or tissue types rather than in bulk tissues. Laser capture microdissection (LCM) provides a useful method for isolating specific cell types from complex tissue structures for downstream applications. Contrasting to mammalian cells, the texture of plant cells is more critical due to hard, cellulose-rich cell walls, large vacuoles, and air spaces which complicates tissue preparation and extraction of macromolecules, like DNA and RNA...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344873/laser-capture-microdissection-and-rna-extraction-from-perfusion-fixed-cartilage-and-bone-tissue-from-mice-implanted-with-human-ipsc-derived-mscs-in-a-calvarial-defect-model
#4
Xiaonan Xin, Xi Jiang, Alexander Lichtler, Mark Kronenberg, David Rowe, Joel S Pachter
Laser-capture microdissection (LCM) coupled to downstream RNA analysis poses unique difficulties for the evaluation of mineralized tissues. A rapid protocol was thus developed to enable sufficient integrity of bone and cartilage tissue for reliable sectioning, while minimizing RNA loss associated with prolonged decalcification and purification steps. Specifically, the protocol involves pump-assisted, cardiac perfusion-fixation with paraformaldehyde, and moderate digestion of LCM-acquired tissue with proteinase K followed by DNase treatment and separation of RNA using magnetic beads...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344871/laser-capture-microdissection-for-layer-specific-analysis-of-enteric-ganglia
#5
Corinna Rosenbaum, Martina Böttner, Thilo Wedel, Marco Metzger
The enteric nervous system (ENS) is the division of the autonomic nervous system that innervates the gastrointestinal (GI) tract and controls central intestinal functions such as peristalsis and fluid movement. Enteric nerve cell bodies (neurons and glia) are predominantly organized in ganglionated networks that are present along the entire length of the GI tract in multiple tissue layers. Most cell bodies are organized in the myenteric plexus allocated between the longitudinal and the circular muscle layers or in the submucosal plexus between muscle tissue and mucosa...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344869/isolation-of-amyloid-plaques-and-neurofibrillary-tangles-from-archived-alzheimer-s-disease-tissue-using-laser-capture-microdissection-for-downstream-proteomics
#6
Eleanor Drummond, Shruti Nayak, Geoffrey Pires, Beatrix Ueberheide, Thomas Wisniewski
Here, we describe a new method that allows localized proteomics of amyloid plaques and neurofibrillary tangles (NFTs), which are the two pathological hallmarks of Alzheimer's disease (AD). Amyloid plaques and NFTs are visualized using immunohistochemistry and microdissected from archived, formalin-fixed paraffin-embedded (FFPE) human tissue samples using laser-capture microdissection. The majority of human tissue specimens are FFPE; hence the use of this type of tissue is a particular advantage of this technique...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344868/laser-capture-microdissection-for-the-analysis-of-rat-and-human-spinal-cord-ependyma-by-qpcr
#7
Daniel Garcia-Ovejero, Beatriz Paniagua-Torija, Angel Arevalo-Martin, Beatriz Navarro-Galve, Eduardo Molina-Holgado
In the last few decades many efforts have been dedicated to decipher the nature and regenerative potential of neurogenic niches and endogenous stem cells after damage of the central nervous system. In the spinal cord, it has been largely focused on the ependymal region, which hosts neural precursors/stem cells (NSC) in rodents but differs between species and ages. In the current chapter, we detail our protocol to study the gene expression profile of this region using fresh frozen blocks of rat and human post-mortem spinal cords...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344867/immuno-laser-capture-microdissection-for-the-isolation-of-enriched-glial-populations-from-frozen-post-mortem-human-brain
#8
Julie E Simpson, Stephen B Wharton, Paul R Heath
Laser-capture microdissection (LCM) has revolutionized the isolation of defined regions and specific cell populations from human tissue. This approach used in combination with immunohistochemistry (immuno-LCM) has become a valuable method for isolating individual cell-types from a complex heterogeneous population. Here, we describe the detailed methodology required for the isolation of enriched populations of GFAP+ astrocytes, OSP+ oligodendrocytes, and CD68+ microglia from frozen post-mortem human central nervous system tissue using immuno-LCM...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344866/immuno-guided-laser-capture-microdissection-of-glial-cells-for-mrna-analysis
#9
Arnaud B Nicot, Justine Rambeau, Flora Guillot, Alexandra Garcia, David A Laplaud
Laser-capture microdissection (LCM) allows for retrieval of specific cell populations in situ. By combining immunofluorescent labeling with LCM, mRNAs can be probed by qRT-PCR for determining in situ gene expression during health and disease. This approach permits obtaining and analyzing histologically enriched cell populations in a tissue that can be hardly obtained from other methods such as white matter astrocytes from rodents or any individual cell population from archival human or rodent brain tissues...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344864/laser-capture-microdissection-in-traumatic-brain-injury-research-obtaining-hippocampal-subregions-and-pools-of-injured-neurons-for-genomic-analyses
#10
Deborah R Boone, Harris A Weisz, Stacy L Sell, Helen L Hellmich
The methods presented here are based on our laboratory's 15 years of experience using laser capture microdissection to obtain samples for the study of gene expression after traumatic brain injury (TBI) using a well-established rat model of experimental TBI. Here, we describe how to use the ArcturusXT laser capture microdissection system to capture swaths of specific regions of the rat hippocampus as well as specific neuronal populations defined by Fluoro-Jade C staining. Staining with Fluoro-Jade C identifies a neuron that is in the process of degeneration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344863/the-isolation-of-pure-populations-of-neurons-by-laser-capture-microdissection-methods-and-application-in-neuroscience
#11
Renée Morris, Prachi Mehta
In mammals, the central nervous system (CNS) is constituted of various cellular elements, posing a challenge to isolating specific cell types to investigate their expression profile. As a result, tissue homogenization is not amenable to analyses of motor neurons profiling as these represent less than 10% of the total spinal cord cell population. One way to tackle the problem of tissue heterogeneity and obtain meaningful genomic, proteomic, and transcriptomic profiling is to use laser capture microdissection technology (LCM)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344862/cell-type-specific-laser-capture-microdissection-for-gene-expression-profiling-in-the-human-brain
#12
Sarah A Mauney, Tsung-Ung W Woo, Kai C Sonntag
Cell type-specific laser microdissection technologies in combination with molecular techniques to determine gene expression profiles have become powerful tools to gain insight into the neurobiological basis of neural circuit disturbances in various neurologic or psychiatric diseases. To identify specific cell populations in human postmortem brain tissue, one can use the inherent properties of the cells, such as pigmentation and morphology or their structural composition through immunohistochemistry (IHC). Here, we describe the isolation of homogeneous neurons and oligodendrocytes and the extraction of high-quality RNA from these cells in human postmortem brain using a combination of rapid IHC, Nissl staining, or simple morphology with Laser Capture Microdissection (LCM), or Laser Microdissection (LMD)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344861/laser-capture-microdissection-and-transcriptional-analysis-of-sub-populations-of-the-osteoblast-lineage-from-undecalcified-bone
#13
Efrain Pacheco, Rong Hu, Scott Taylor
Transcriptional analysis of tissue samples is a useful and widely applied approach to provide insight into the molecular mechanisms engaged in response to phenotypic changes or external stimuli. We describe a method that overcomes the technical challenges associated with the application of Laser Capture Microdissection to undecalcified bone enabling us to collect high-quality bone tissue with maintained cellular morphology that is suitable for cryosectioning, fixation, and cutting. Using this method, we obtain samples enriched for specific cell types from the mature osteoblast lineage (osteoblasts, lining cells, i...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344860/laser-microdissection-for-human-papillomavirus-hpv-genotyping-attribution-and-methylation-pattern-analyses-of-squamous-intraepithelial-lesions
#14
Monica Molano, Suzanne M Garland, Alyssa M Cornall
Human papillomavirus (HPV) is a nearly ubiquitous infectious organism. It is estimated that 80% of sexually active adults will be exposed to anogenital HPVs in their lifetime, and detection of multiple genotypes in an anogenital sample is common. Detection and genotyping of HPV is usually performed by DNA testing, and less frequently by mRNA testing. HPV genotype testing and characterization of DNA methylation patterns of HPV-related lesions can provide important biological, epidemiological, and potentially relevant clinical information in individuals and populations...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344859/laser-capture-microdissection-and-isolation-of-high-quality-rna-from-frozen-endometrial-tissue
#15
Michele Cummings, Georgia Mappa, Nicolas M Orsi
Laser capture microdissection (LCM) allows expression profiling of specific cell populations within tissues. However, isolation of high-quality RNA from laser capture microdissected frozen tissue is beset by problems arising from intrinsic tissue RNase activity. Herein, we describe an optimized staining/LCM/RNA extraction protocol developed for the isolation of epithelial RNA from frozen tissue sections using human endometrial cancer as a model tissue. This method combines excellent, reproducible visualization of tissue morphology with the isolation of high-integrity RNA suitable for downstream applications such as expression microarray analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344858/laser-capture-microdissection-as-a-tool-to-study-the-mucosal-immune-response-in-celiac-disease
#16
Giuseppe Iacomino, Vera Rotondi Aufiero, Pasquale Marena, Antonella Venezia, Riccardo Troncone, Salvatore Auricchio, Giuseppe Mazzarella
Laser capture microdissection (LCM) is a powerful tool for selection and isolation of single cells or compartments from complex primary tissues to perform molecular analyses. Celiac disease is a genetic autoimmune disorder where the ingestion of gluten leads to damage in the small intestine. Increased intraepithelial lymphocytes and the presence of the lamina propria inflammatory infiltrate of the duodenal mucosa is a common part of the disease. These cells promote inflammatory processes through the release of cytokines...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344857/adaptation-of-laser-microdissection-technique-to-nanostring-rna-analysis-in-the-study-of-a-spontaneous-metastatic-mammary-carcinoma-mouse-model
#17
Nadia P Castro, Yelena G Golubeva
The mouse model characterized by spontaneous lung metastasis from JygMC (A) cells closely resembles the human triple negative breast cancer (TNBC) subtype. The primary tumors morphologically present both epithelial and spindle-like cells, but metastases in lung parenchyma display only adenocarcinoma properties. In the study of molecular signatures, laser capture microdissection (LCM) on frozen tissue sections was used to separate the following regions of interest: the epithelial-mesenchymal transition (EMT), mesenchymal-epithelial transition (MET), carcinoma, lung metastases, normal mammary gland and normal lung parenchyma...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344855/protocol-for-the-analysis-of-laser-capture-microdissected-fresh-frozen-tissue-homogenates-by-silver-stained-1d-sds-page
#18
DaRue A Prieto, Gordon Whitely, Donald J Johann, Josip Blonder
The heterogeneity present in solid tumors adds significant difficulty to scientific analysis and improved understanding. Fundamentally, solid tumor formation consists of cancer cells proper along with stromal elements. The burgeoning malignant process is dependent upon modified stromal elements. Collectively, the stroma forms an essential microenvironment, which is indispensable for the survival and growth of the malignant neoplasm. This cellular heterogeneity makes molecular profiling of solid tumors via mass spectrometry (MS)-based proteomics a daunting task...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344854/laser-microdissection-workflow-for-isolating-nucleic-acids-from-fixed-and-frozen-tissue-samples
#19
Yelena G Golubeva, Andrew C Warner
Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344852/laser-capture-microdissection-insights-into-methods-and-applications
#20
Meera Mahalingam
Laser capture microdissection is a non-molecular, minimally disruptive method to obtain cytologically and/or phenotypically defined cells or groups of cells from heterogeneous tissues. Its advantages include efficient rapid and precise procurement of cells. The potential disadvantages include time consuming, expensive, and limited by the need for a pathologist for recognition of distinct subpopulations within a specified sample. Overall it is versatile allowing the preparation of homogenous isolates of specific subpopulations of cells from which DNA/RNA or protein can be extracted for RT-PCR, quantitative PCR, next-generation sequencing, immunoblot blot analyses, and mass spectrometry...
2018: Methods in Molecular Biology
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