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181 results for “formalin”
Deconvolved STED nanoscopy images of the nuclear phosphatidylinositol 4,5-bisphosphate and nuclear speckle marker SON together with deconvolved confocal images of DAPI stained nuclei in human formalin-fixed paraffin-embedded skin warts sections
<p>The collection and analysis of formalin-fixed paraffin-embedded (FFPE) human skin sections was approved by the local ethics-committee at the Department of Pathology, University of Cologne, Germany. Written informed consentwas obtained from all patients in accordance with the Declaration of Helsinki. For biopsy materials from archival paraffin blocks of human skin, an informed consent was obtained from all the subjects and ethical approval obtained from the Ethics Committee at the University of Cologne. Surgically removed human FFPE skin biopsies were sectioned into 4 µm sections. Sections were dewaxed, and indirectly immunofluorescently labeled against nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) using 5 µg/mL rabbit primary polyclonal antibody (Echelon Biosciences Inc. Z-A045, clone 2C11). The primary antibody against nPI(4,5)P2 was recognized by the goat secondary antibody conjugated with Abberrior Star 635P (Abberior 2-0002-007-5). Sections were indirectly immunofluorescently labeled against nuclear speckle marker SON using 1 µg/mL rabbit primary polyclonal antibody (Abcam ab121759). The primary antibody against SON was recognized by the goat secondary antibody conjugated with Abberrior Star 580 (Abberrior ST580-1002). Sections were co-stained by DAPI 1:1000 in PBS for 5 min.</p> <p>Imaging of nPI(4,5)P2-635P channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 7% 633 nm laser; 775 Notch filter; 50% 775 nm STED laser; 30% 3D STED; HyD 639-698 nm, photon-counting mode, gain 100, gating 0.3-10 ns. Imaging of SON-580 channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 10% 585 nm laser; 775 Notch filter; 80% 775 nm STED laser, 30% 3D STED; Hybrid detector (HyD) 589-616 nm, photon-counting mode, gain 100, gating 0.4-10 ns.</p> <p>Z-stacks of STED images were deconvolved using Huygens Professional 22.10 software (Scientific Imaging B.V.). Data sets were processed using Workflow Processor. The workflow consisted of selecting images, setting up the microscopy and deconvolution parameters and saving deconvolved images as 8-bit TIFF single files for individual channels (which were later used for the quantitative analyses; see below). Microscopy parameters were optimized and set as follows. Sampling intervals were ≤20 nm in X and Y and ≤20 nm in Z. Numerical aperture was 1.4; refractive indexes of the lens immersion oil was 1.518 and of the embedding media 1.458; objective quality was good, coverslip position was 0 µm and imaging direction was downward. For nPI(4,5)P2-635P STED channel the backprojected pinhole was 216 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 633 and 651 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 25, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 5.1. For SON-580 STED channel the backprojected pinhole was 195 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 585 and 602 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 20, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 4.</p>
Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference
<p>The known biodiversity of Asia and Australasia is continuously expanding with more focused studies on systematics of various groups and the respective biogeography. Historically, fluctuating sea-levels and cyclic connection and separation of now-disjunct landmasses have been invoked to explain the accumulation of biodiversity via species pump mechanisms. However, recent research has shown that geological shifts of the mainland and dispersal events may be better explanations of the biodiversity in these regions. We investigate these processes using the poorly-studied and geographically widespread Mud Snakes (Serpentes: Homalopsidae) using a target capture approach of ~4,800 nuclear loci from fresh tissues and supplemental mitochondrial data from formalin tissues from museum specimens. We use these datasets to reconstruct the first resolved phylogeny of the group, identify their biogeographic origins, and test hypotheses regarding the roles of sea-level change and habitat selection on their diversification. Divergence dating and ancestral range estimation yielded support for an Oligocene origin and diversification from mainland Southeast Asia and Sundaland in the rear-fanged group ~20 million years ago, followed by eastward and westward dispersal. GeoHiSSE models indicate that niche expansion of ancestral rear-fanged lineages into aquatic environments did not impact their diversification rates. Our results highlight that Pleistocene sea-level changes and habitat specificity did not primarily lead to the extant species richness of Homalopsidae, and that, alternatively, geological shifts in mainland Southeast Asia may be a major driver of diversity in this group. We also emphasize the importance of using fresh and degraded tissues, and both nuclear and mitochondrial DNA, for filling in knowledge gaps in poorly known, but highly diverse and conceptually important groups, constituting a non-traditional model study system for understanding transitions between terrestrial, marine, and freshwater environments.</p>
Fig. 1 in Effect of 80% ethanol or 10% formalin fixation, freezing at - 20 C and staining on Myxobolus (Myxosporea) spores to be deposited in parasitological collections
Fig. 1. Myxospores of Myxobolus bramae treated in different ways. (a) Fresh spore, (b) Spore fixed in 80% ethanol, (c) Spore fixed in 10% formalin solution, (d) Spore freezing at – 20 ◦C for 3 months, (e) Spore stained with Giemsa stain, (f) Spore stained with Ziehl–Neelsen stain.
Fig. 3 in Effect of 80% ethanol or 10% formalin fixation, freezing at - 20 C and staining on Myxobolus (Myxosporea) spores to be deposited in parasitological collections
Fig. 3. Myxospores of Myxobolus bliccae treated in different ways. (a) Fresh spore, (b) Spore fixed in 80% ethanol, (c) Spore fixed in 10% formalin solution, (d) Spore freezing at – 20 ◦C for 3 months, (e) Spore stained with Giemsa stain, (f) Spore stained with Ziehl–Neelsen stain.
Fig. 4 in Effect of 80% ethanol or 10% formalin fixation, freezing at - 20 C and staining on Myxobolus (Myxosporea) spores to be deposited in parasitological collections
Fig. 4. Length and width (n = 795 and 729, respectively) of differently treated spores of Myxobolus bramae. Medians and interquartile ranges are indicated by thick middle lines and boxes, respectively, whereas the whiskers represent maximum and minimum values, and the open circles refer to outliers.
Fig. 2 in Effect of 80% ethanol or 10% formalin fixation, freezing at - 20 C and staining on Myxobolus (Myxosporea) spores to be deposited in parasitological collections
Fig. 2. (a) Myxospore of M. bramae treated with Lugol's solution. (b) Myxospore of M. bliccae treated with Lugol's solution.
Fig. 1 in Length correction for early-juvenile Brazilian herring Sardinella janeiro (Eigenmann, 1894) after preservation in formalin, ethanol and freezing
Fig. 1. Mean percentage shrinkage of total length for earlyjuvenile of Sardinella janeiro during storage in freezing (open triangle), 2.5% formalin (full circle), 5% formalin (open circle), 70% ethanol (full square) and 95% ethanol (open square).
Fig. 3 in Length correction for early-juvenile Brazilian herring Sardinella janeiro (Eigenmann, 1894) after preservation in formalin, ethanol and freezing
Fig. 3. The relationship between fresh total length and relative (%) shrinkage in total length after 60 days of preservation for early-juvenile of Sardinella janeiro. (a) Freezing (open triangle), (b) 2.5% formalin (full circle), 5% formalin (open circle), (c) 70% ethanol (full square) and 95% ethanol (open square).
Fig. 2 in Length correction for early-juvenile Brazilian herring Sardinella janeiro (Eigenmann, 1894) after preservation in formalin, ethanol and freezing
Fig. 2. Mean percentage shrinkage of body mass for earlyjuvenile of Sardinella janeiro during storage in freezing (open triangle), 2.5% formalin (full circle), 5% formalin (open circle), 70% ethanol (full square) and 95% ethanol (open square).
Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference
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Data for: Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain
<p>Tissue clearing and labeling techniques have revolutionized brain-wide imaging and analysis, yet their application to clinical formalin-fixed paraffin-embedded (FFPE) blocks remains challenging. We introduce HIF-Clear, a novel method for efficiently clearing and labeling centimeter-thick FFPE specimens using elevated temperature and concentrated detergents. HIF-Clear with multi-round immunolabeling reveals neuron circuitry regulating multiple neurotransmitter systems in a whole FFPE mouse brain, and is able to be used as the evaluation of disease treatment efficiency. HIF-Clear also supports expansion microscopy and can be performed on a non-sectioned 15-year-old FFPE specimen, as well as a 3-month formalin-fixed mouse brain. Thus, HIF-Clear represents a feasible approach for researching archived FFPE specimens for future neuroscientific and 3D neuropathological analyses.</p>
Data from: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens
Open the record for dataset details and reuse information.
Data for: Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain
Open the record for dataset details and reuse information.
Delta Smelt Formalin Fixation and Preservation Effects on Fish Weight and Length
Natural history museum specimen are invaluable for a variety of conservation and ecological applications. Fishes are commonly preserved in formalin; however, formalin preservation is associated with reduced fish length and increased weight, but the magnitude and timing of these changes may vary among species. Unaccounted for preservation-driven shifts in fish length and weight may have drastic effects on any conservation or ecological conclusions drawn from specimen preserved for various durations as well as when compared to fresh, unpreserved specimen. The purpose of this study was to test whether formalin fixation and preservation affects endangered Delta Smelt, Hypomesus transpacificus, lengths and weights with implications for the use of data collected on preserved and fresh specimen. Fresh Delta Smelt were lengthed and weighted, then fixed and preserved in 10% buffered formalin. Repeated measures of specimen length and weight were recorded weekly for 4 weeks, fortnightly from preservation week 4 through preservation week 24, and then approximately annually through 6 total years of preservation.
Transverse section of a whale earplug showing the alternating light and dark laminae. Stephen Trumble, left, and Sascha Usenko, right, with a jar containing whale earplugs in 10 percent formalin at the Natural History Museum in London. Photographs: Sascha Usenko. in The Evolution of Natural History Collections
Transverse section of a whale earplug showing the alternating light and dark laminae. Stephen Trumble, left, and Sascha Usenko, right, with a jar containing whale earplugs in 10 percent formalin at the Natural History Museum in London. Photographs: Sascha Usenko.
Deconvolved STED nanoscopy images of the nuclear phosphatidylinositol 4,5-bisphosphate and nuclear speckle marker SON together with deconvolved confocal images of DAPI stained nuclei in human formalin-fixed paraffin-embedded skin sections
<p>The collection and analysis of formalin-fixed paraffin-embedded (FFPE) human skin sections was approved by the local ethics-committee at the Department of Pathology, University of Cologne, Germany. Written informed consentwas obtained from all patients in accordance with the Declaration of Helsinki. For biopsy materials from archival paraffin blocks of human skin, an informed consent was obtained from all the subjects and ethical approval obtained from the Ethics Committee at the University of Cologne. Surgically removed human FFPE skin biopsies were sectioned into 4 µm sections. Sections were dewaxed, and indirectly immunofluorescently labeled against nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) using 5 µg/mL rabbit primary polyclonal antibody (Echelon Biosciences Inc. Z-A045, clone 2C11). The primary antibody against nPI(4,5)P2 was recognized by the goat secondary antibody conjugated with Abberrior Star 635P (Abberior 2-0002-007-5). Sections were indirectly immunofluorescently labeled against nuclear speckle marker SON using 1 µg/mL rabbit primary polyclonal antibody (Abcam ab121759). The primary antibody against SON was recognized by the goat secondary antibody conjugated with Abberrior Star 580 (Abberrior ST580-1002). Sections were co-stained by DAPI 1:1000 in PBS for 5 min.</p> <p>Imaging of nPI(4,5)P2-635P channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 7% 633 nm laser; 775 Notch filter; 50% 775 nm STED laser; 30% 3D STED; HyD 639-698 nm, photon-counting mode, gain 100, gating 0.3-10 ns. Imaging of SON-580 channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 10% 585 nm laser; 775 Notch filter; 80% 775 nm STED laser, 30% 3D STED; Hybrid detector (HyD) 589-616 nm, photon-counting mode, gain 100, gating 0.4-10 ns.</p> <p>Z-stacks of STED images were deconvolved using Huygens Professional 22.10 software (Scientific Imaging B.V.). Data sets were processed using Workflow Processor. The workflow consisted of selecting images, setting up the microscopy and deconvolution parameters and saving deconvolved images as 8-bit TIFF single files for individual channels (which were later used for the quantitative analyses; see below). Microscopy parameters were optimized and set as follows. Sampling intervals were ≤20 nm in X and Y and ≤20 nm in Z. Numerical aperture was 1.4; refractive indexes of the lens immersion oil was 1.518 and of the embedding media 1.458; objective quality was good, coverslip position was 0 µm and imaging direction was downward. For nPI(4,5)P2-635P STED channel the backprojected pinhole was 216 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 633 and 651 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 25, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 5.1. For SON-580 STED channel the backprojected pinhole was 195 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 585 and 602 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 20, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 4.</p>
Unlocking the genomes of formalin-fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality
<p>DNA quality and quantity metrics (Microsoft Excel worksheet with 3 sheets, one per species).</p> <p>We compared two protocols developed to extract DNA from formalin-fixed tissues using specimens of three freshwater fishes: Southern Brook Lamprey <em>Ichthyomyzon gagei</em>, Slimy Sculpin <em>Cottus cognatus</em>, and Brown Trout <em>Salmo trutta</em>. Extractions were attempted using hot alkali digestion with and without buffer wash pretreatments to compare the DNA concentration, purity, and fragment length of DNA recovered between extraction protocols, tissue types (muscle and caudal fin tissue for Brown Trout and Slimy Sculpin), and preservation periods (5 or 7 years for Southern Brook Lamprey).</p> <p>Four metrics were collected: DNA quantity (measured using Qubit 3.0 instrument with dsDNA high sensitivity kit); DNA purity measured by A260/A280 ratio (measured using NanoDrop 2000 spectrophotometer); DNA purity measured by A260/A230 ratio (measured using NanoDrop 2000 spectrophotometer); and percent fragments >= 300 base pairs (measured using ImageJ). For spectrophotometric absorbance ratios, an A260/A280 ratio of 1.8 and an A260/ A230 ratio of 2.0 were considered to represent “pure” DNA (i.e., free of contaminants). For analyses of DNA purity, deviations from 1.8 for the A260/A280 ratio and from 2.0 for the A260/A230 ratio were used as the response variables, such that larger deviation values corresponded to less-pure DNA.</p> <p>Please see attached README.md file for additional information.</p>
Infectious Outcomes of Povidone-iodine Rectal Cleansing Plus Formalin Disinfection of Needle During Prostate Biopsy
ClinicalTrials.gov study NCT03879486. IPD Sharing: Not stated. Countries: 1. Publications: 24.
Data from: DNA extraction method affects the detection of a fungal pathogen in formalin-fixed specimens using qPCR
Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80–90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.
Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression
The identification of gene fusions promises to play an important role in personalized cancer treatment decisions. Many rare gene fusion events have been identified in fresh frozen solid tumors from common cancers employing next-generation sequencing technology. However the ability to detect transcripts from gene fusions in RNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissues, which exist in very large sample repositories for which disease outcome is known, is still limited due to the low complexity of FFPE libraries and the lack of appropriate bioinformatics methods. We sought to develop a bioinformatics method, named gFuse, to detect fusion transcripts in FFPE tumor tissues. An integrated, cohort based strategy has been used in gFuse to examine single-end 50 base pair (bp) reads generated from FFPE RNA-Sequencing (RNA-Seq) datasets employing two breast cancer cohorts of 136 and 76 patients. In total, 118 fusion events were detected transcriptome-wide at base-pair resolution across the 212 samples. We selected 77 candidate fusions based on their biological relevance to cancer and supported 61% of these using TaqMan assays. Direct sequencing of 19 of the fusion sequences identified by TaqMan confirmed them. Three unique fused gene pairs were recurrent across the 212 patients with 6, 3, 2 individuals harboring these fusions respectively. We show here that a high frequency of fusion transcripts detected at the whole transcriptome level correlates with poor outcome (P<0.0005) in human breast cancer patients. This study demonstrates the ability to detect fusion transcripts as biomarkers from archival FFPE tissues, and the potential prognostic value of the fusion transcripts detected.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.