Mice were sacrificed by CO2 suffocation within 24 h after the endoscopic procedure. The large intestine was removed and its length measured when it was in a relaxed position without stretching; it was weighed after removal of the feces. The colon density [mg/cm] was calculated by dividing the weight by the length of the large intestine. The intestine was opened longitudinally and washed thoroughly with phosphate-buffered saline [PBS] then processed as a ‘Swiss roll’ in paraffin. Five-micrometer slides were cut and stained with hematoxylin and eosin [H&E] using a standard protocol. Slides were scored for tissue quality [‘poor’ or ‘moderate to perfect’]. Based on the existing literature, eight histological components were assessed: ‘inflammatory infiltrate’, ‘goblet cell loss’, ‘hyperplasia’, ‘crypt density’, ‘muscle thickness’, ‘submucosal infiltration’, ‘ulcerations’ and ‘crypt abscesses’ [all categorized from 0–3, Table 1 /Figure 1 ]. A total histological severity score, ranging from 0 to 24, was obtained by summing the eight item scores.
Large Intestine
The large intestine, also known as the colon, is the final segment of the digestive tract.
It plays a crucial role in the absorption of water and electrolytes, as well as the storage and elimination of waste products.
Spanning approximately 5 feet in length, the large intestine consists of the cecum, colon, rectum, and anal canal.
It is responsible for the formation and expulsion of feces, making it an essential component of the body's waste management system.
Researchers studying the large intestine can leverage PubCompare.ai's AI-driven platform to optimize their research protocols, explore the latest literature, preprints, and patents, and identify the best approaches for their large intestine studies.
Unlock new insights and revolutionize your understanding of this vital organ today!
It plays a crucial role in the absorption of water and electrolytes, as well as the storage and elimination of waste products.
Spanning approximately 5 feet in length, the large intestine consists of the cecum, colon, rectum, and anal canal.
It is responsible for the formation and expulsion of feces, making it an essential component of the body's waste management system.
Researchers studying the large intestine can leverage PubCompare.ai's AI-driven platform to optimize their research protocols, explore the latest literature, preprints, and patents, and identify the best approaches for their large intestine studies.
Unlock new insights and revolutionize your understanding of this vital organ today!
Most cited protocols related to «Large Intestine»
Abscess
Asphyxia
CFC1 protein, human
Colon
Eosin
Feces
Goblet Cells
Hyperplasia
Inflammation
Intestines
Large Intestine
Mus
Muscle Tissue
Paraffin
Phosphates
Saline Solution
Surgical Endoscopy
Tissues
Ulcer
Strictly, the tissue-specific gene is defined as gene whose function and expression is restricted to a particular tissue or cell type. However, in many cases, the specificity concept is broadened to tissue selectivity that gene expression is enriched in one or several tissues/cell types (Shuang et al., 2006 (link)). In TiSGeD, we presented genes of both strictly specific and highly selective in tissues.
Briefly, the tissue-specific gene is detected by solving a linear algebra problem of scalar projection in this study. First, transform each expression profile of gene x into a vector Xp:
where n is the number of tissues in the profile and xi is the gene expression level in tissue i. For each element in the profile Xp, the expression xi can also be represented by a vector Xi in high-dimension tissue spaces:
Then, the tissue specificity of gene x in tissue i is determined by calculating the ratio of vector Xi's scalar projection in the direction of vector Xp (i.e. ‖X‖) against the length of Xp (i.e. ‖Xp‖):
Theoretically, the SPM ranges from 0 to 1.0. A value close to 1.0 indicates that element xi is the major contributor to the length of profile Xp in high-dimension tissue spaces; in biological term, high tissue specificity.
In practice, user can rely on the SPM value to quantitatively estimate the tissue specificity of a gene in a profile regardless of its absolute expression level. The larger the SPM value, the higher the tissue specificity is. However, in the cases of profiles with ‘spiked’ expression patterns (which gene expressions are highly selective in several similar tissues), a large SPM value may not be achieved. As a feasible solution, the original gene expression profiles are reformatted by merging several similar subtissues into an ‘integrative’ tissue (individual expressions are summed up as the expression of the representative) according to the organ hierarchy tree adopted in this study. For example, intestine represents for small intestine, large intestine, etc. As a result, the ‘spiked’ expression pattern can then be detected by SPM analysis as an enriched expression.
Briefly, the tissue-specific gene is detected by solving a linear algebra problem of scalar projection in this study. First, transform each expression profile of gene x into a vector Xp:
where n is the number of tissues in the profile and xi is the gene expression level in tissue i. For each element in the profile Xp, the expression xi can also be represented by a vector Xi in high-dimension tissue spaces:
Then, the tissue specificity of gene x in tissue i is determined by calculating the ratio of vector Xi's scalar projection in the direction of vector Xp (i.e. ‖X‖) against the length of Xp (i.e. ‖Xp‖):
Theoretically, the SPM ranges from 0 to 1.0. A value close to 1.0 indicates that element xi is the major contributor to the length of profile Xp in high-dimension tissue spaces; in biological term, high tissue specificity.
In practice, user can rely on the SPM value to quantitatively estimate the tissue specificity of a gene in a profile regardless of its absolute expression level. The larger the SPM value, the higher the tissue specificity is. However, in the cases of profiles with ‘spiked’ expression patterns (which gene expressions are highly selective in several similar tissues), a large SPM value may not be achieved. As a feasible solution, the original gene expression profiles are reformatted by merging several similar subtissues into an ‘integrative’ tissue (individual expressions are summed up as the expression of the representative) according to the organ hierarchy tree adopted in this study. For example, intestine represents for small intestine, large intestine, etc. As a result, the ‘spiked’ expression pattern can then be detected by SPM analysis as an enriched expression.
Biopharmaceuticals
Cells
Cloning Vectors
Gene Expression
Genes
Histocompatibility Testing
Intestines
Intestines, Small
Large Intestine
Tissues
Tissue Specificity
Trees
alpha HML-1
Antibodies
Bicarbonates
BLOOD
Buffers
CD44 protein, human
Cells
Cervix Uteri
Collagenase, Clostridium histolyticum
Dithioerythritol
Enzymes
Female Reproductive System
Flow Cytometry
Hemoglobin, Sickle
HEPES
Hyperostosis, Diffuse Idiopathic Skeletal
Intestines
Intestines, Small
isolation
Kidney
Lamina Propria
Large Intestine
Liver
Lung
Lymphocyte
Matrix Metalloproteinase 2
Mucus
Mus
Needles
Nodes, Lymph
Nylons
Pancreas
Passive Immunization
Percoll
Polystyrenes
Salivary Glands
Spleen
Stomach
Streptavidin
Syringes
Thymus Plant
Tissues
Uterine Cornua
Vagina
K18 hACE2 transgenic and WT C57BL/6 mice were either mock (PBS)-infected (controls) or infected intranasally (i.n.) with 1 × 105 PFU of SARS-CoV-2 in a final volume of 50 µl following isoflurane sedation. Limited numbers of available K18 hACE2 transgenic mice reduced the study to a single exposure dose of SARS-CoV-2. After viral infection, mice were monitored daily for morbidity (body weight) and mortality (survival). Mice showing >25% loss of their initial body weight were defined as reaching experimental end-point and humanely killed.
In parallel, K18 hACE2 transgenic or WT C57BL/6 mice were infected and euthanized at 2, 4, or 6 DPI. For viral titers, chemokine/cytokine, histopathology and IHC analyses, seven female and seven male for 2 and 4 DPI, and three female and three male for 6 DPI SARS-CoV-2-infected; and one female and one male mock-infected K18 hACE2 mice were used. As controls for these analyses, four female and four male SARS-CoV-2-infected for 2 and for 4 DPI, and one male and one female for mock WT C57BL/6 mice were used. Ten tissues (nasal turbinate, trachea, lung, heart, kidney, liver, spleen, small intestine, large intestine, and brain) were harvested from each mouse. Half organ was fixed in 10% neutral buffered formalin solution for molecular pathology analyses and the other half was homogenized in 1 mL of PBS using a Precellys tissue homogenizer (Bertin Instruments) for viral titration. Tissue homogenates were centrifuged at 21,500 × g for 5 min and supernatants were collected for measurement of viral load and chemokine/cytokine analyses.
In parallel, K18 hACE2 transgenic or WT C57BL/6 mice were infected and euthanized at 2, 4, or 6 DPI. For viral titers, chemokine/cytokine, histopathology and IHC analyses, seven female and seven male for 2 and 4 DPI, and three female and three male for 6 DPI SARS-CoV-2-infected; and one female and one male mock-infected K18 hACE2 mice were used. As controls for these analyses, four female and four male SARS-CoV-2-infected for 2 and for 4 DPI, and one male and one female for mock WT C57BL/6 mice were used. Ten tissues (nasal turbinate, trachea, lung, heart, kidney, liver, spleen, small intestine, large intestine, and brain) were harvested from each mouse. Half organ was fixed in 10% neutral buffered formalin solution for molecular pathology analyses and the other half was homogenized in 1 mL of PBS using a Precellys tissue homogenizer (Bertin Instruments) for viral titration. Tissue homogenates were centrifuged at 21,500 × g for 5 min and supernatants were collected for measurement of viral load and chemokine/cytokine analyses.
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Animals, Transgenic
Body Weight
Brain
Chemokine
Cytokine
Females
Formalin
Heart
Human Body
Intestines, Small
Isoflurane
Kidney
Large Intestine
Liver
Lung
Males
Mice, Inbred C57BL
Mice, Laboratory
Mice, Transgenic
SARS-CoV-2
Sedatives
Spleen
Tissues
Titrimetry
Trachea
Turbinates
Virus Diseases
As a safety precaution against infection, our institute developed a COVID‐19‐optimised autopsy protocol in line with recently published recommendations.22 Two hours prior to autopsy, 4% phosphate‐buffered formalin was instilled into the mouth, nose, and pharynx. Autopsies were performed in a room with adequate airflow (more than six air changes per hour of total room volume) under conditions similar to those recommended for autopsies of those who have died from suspected Creutzfeld–Jakob disease (i.e. hazmat suits, boots, goggles, and FFP2/3 masks) with an in‐corpore technique analogous to that used in forensic institutions. Thoracic organs were eviscerated (see below), and the heart was separately dissected in the direction of blood flow. Parenchymal organs (liver, spleen, kidney, and pancreas) were dissected within the body. After mobilisation of the small and large intestines, their exterior surfaces were inspected; if there were any outstanding findings, tissue was excised for further macroscopic and histological examination. In all cases, tissue samples from the liver, heart and kidney were histologically examined. Other organs, as well as bone marrow and the brain, were analysed upon specific clinical indication (younger age; neurological symptoms). To avoid aerosolisation, the brain was removed by opening the skull with a handsaw; bone marrow from the iliac crest was also procured with a handsaw. A detailed description of this in‐corpore protocol is provided in Doc. S1 .
The lungs, trachea and larynx were exenterated intact and perfused via the trachea with 4% refrigerated (4°C) phosphate‐buffered formalin. The trachea was then closed with a clamp, and the specimens immersed in formalin at room temperature for 72 h before dissection. The lungs were subsequently cut into 5–10‐mm parasagittal slices and examined macroscopically. Two sections of each lobe, as well as the trachea, were submitted for histological examination.
The lungs, trachea and larynx were exenterated intact and perfused via the trachea with 4% refrigerated (4°C) phosphate‐buffered formalin. The trachea was then closed with a clamp, and the specimens immersed in formalin at room temperature for 72 h before dissection. The lungs were subsequently cut into 5–10‐mm parasagittal slices and examined macroscopically. Two sections of each lobe, as well as the trachea, were submitted for histological examination.
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Autopsy
Blood Circulation
Bone Marrow
Brain
COVID 19
Cranium
Dissection
Formalin
Heart
Human Body
Iliac Crest
Infection
Kidney
Large Intestine
Larynx
Liver
Lung
Marrow
Neurologic Symptoms
Nose
Oral Cavity
Pancreas
Pharynx
Phosphates
Safety
Spleen
Tissues
Trachea
Youth
Most recents protocols related to «Large Intestine»
Example 2
Next, the expression of Chl1 was confirmed using various tissues or cells.
(B) The intestinal epithelium (EpCAM-positive CD45-negative), fibroblasts (COL1a2-GFP-positive CD45-negative podoplanin-positive), macrophages (F480-positive CD11b-positive), CD4-positive T cells, B cells (CD19-positive B220-positive), and lamina propria cells of the large intestine (whole colon cells) were isolated in the same way as above. RNA was purified from each cell using TRIZOL (Thermo Fisher Scientific Inc./Invitrogen: 15596018) and subsequently reverse-transcribed using VILO (Thermo Fisher Scientific Inc./Invitrogen: 11755500). The expression analysis of Chl1 was conducted using Universal Probe Library (Roche Life Science) and LightCycler™ 480 system (Roche Life Science). Comparison with the expression of Gapdh is shown (n=3). The results were as shown in
As shown in
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B-Lymphocytes
CD4 Positive T Lymphocytes
cDNA Library
Cells
COL1A2 protein, human
Colon
Fibroblasts
GAPDH protein, human
Inflammation
Intestinal Epithelium
ITGAM protein, human
Lamina Propria
Large Intestine
Macrophage
TACSTD1 protein, human
Tissues
trizol
Peyer’s patches were first removed from the small intestine (duodenum, jejunum and ileum) and large intestine (cecum and colon). The intestinal sections were flushed with 1xPBS, opened longitudinally, then cut into 1cm sections, washed in PBS, followed by incubation in RPMI-1640 +1mM Dithiotriol (DTT) for 10mins (both Sigma-Aldrich (St Louis, MI, USA)). Cells were pelleted and suspended in HBSS (Calcium- and Magnesium-free) containing 25mM HEPES, 1mM DTT and 1mM EDTA (all Sigma-Aldrich), followed by incubation for 30 minutes at 37°C on a shaker at 140 rpm. Post-incubation, cells were vortexed vigorously for 10 seconds and filtered through a 100μm nylon membrane, to obtain the intestinal epithelial lymphocytes (IELs). Remaining tissues were further digested for 1hr at 37°C, with shaking at 250 rpm, in RPMI-1640 containing 1mg/ml Collagenase from Clostridium Histolyticum (Sigma-Aldrich). Post-incubation, cells were vortexed vigorously for 10 seconds and nylon membrane-filtered, to obtain the lamina propria lymphocytes (LPs). IELs and LPs were washed twice and resuspended in 30% Ficoll (GE HealthCare, Chicago, IL, USA), then layered on a 70% Ficoll solution prior to density centrifugation (469 xg, 20 mins, room temperature). Isolated IELs were washed and resuspended in RPMI complete media (RPMI-1640 + L-glutamine containing 5% FBS, 1mM HEPES, 1x MEM NEAA, 1mM Sodium pyruvate, 50μM 2-mercaptoethanol and 25μg Gentamycin sulfate (all Sigma-Aldrich)).
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2-Mercaptoethanol
Calcium
Cecum
Cells
Centrifugation
Collagenase, Clostridium histolyticum
Colon
Duodenum
Edetic Acid
Ficoll
Glutamine
Hemoglobin, Sickle
HEPES
Ileum
Intestines
Intestines, Small
Jejunum
Lamina Propria
Large Intestine
Lymphocyte
Magnesium
Neoplasm Metastasis
Nylons
Peyer Patches
Pyruvate
Sodium
Sulfate, Gentamicin
Tissue, Membrane
Tissues
A total of 99 faecal or intestinal samples from deer mice (Peromyscus maniculatus) were collected between 2018 and 2021 for this and other research projects. Adult deer mice were sampled in six locations spanning four environment types, two each for free-living and captive conditions (table 1 ; electronic supplementary material, figure S1). These samples were donated by collaborators, causing slight variations in collection procedure between populations. Some samples were collected as fresh faecal samples and others were dissected from the large intestine postmortem. However, the effect of sample type on microbial composition was minimal compared to our main variables of interest (i.e. environment type and condition; table 2 ), so this discrepancy is not expected to confound our main findings. Greater detail regarding collection procedures for each population can be found in the electronic supplemental material.
Sample information.
| environment type | location ID | condition | number of samples | sample type | collection site | collection year and season | sex | subspecies | diet |
|---|---|---|---|---|---|---|---|---|---|
| undeveloped | UN1 | free-living | 11 | intestinal | Wallace Woods, PA | summer 2018 | 4F, 2 M, 5 unknown | unknown | wild (omnivorous, likely insects, seeds, grains, etc.) |
| UN2 | free-living | 7 | faecal | Yancey County, NC | spring-summer 2021 | unknown | unknown | wild (omnivorous, likely insects, seeds, grains, etc.) | |
| urban | FU | free-living | 10 | intestinal | Bronx, NY | summer 2020 | 2F, 1 M, 7 unknown | unknown | unknown, likely found materials in and around zoo |
| zoo | CZ | captive | 29 | faecal | Bronx, NY | summer 2020 | unknown | unknown | mixture of rodent chow and fresh vegetables |
| laboratory | CL1 | captive | 22 | faecal | Cambridge, MA | winter 2020 | 11F, 11M | 11 bairdii, 11 gambelii | irradiated Prolab Isopro RMH 3000 + sunflower seeds |
| CL2 | captive | 20 | faecal | Columbia, SC | winter 2021 | unknown | bairdii | irradiated Harlan 8904 Teklad Rodent Diet |
PERMANOVA statistical results for Bray–Curtis, unweighted UniFrac and weighted UniFrac distances analysed by environment type, condition (captive or free-living) and sample type (intestinal or faecal). All p-values are Holm corrected.
| variable | Bray–Curtis | unweighted UniFrac | weighted UniFrac | ||||||
|---|---|---|---|---|---|---|---|---|---|
| p-value | F | R2 | p-value | F | R2 | p-value | F | R2 | |
| environment | 0.012 | 12.87 | 0.29 | 0.012 | 12.39 | 0.28 | 0.012 | 10.77 | 0.25 |
| condition | 0.012 | 19.55 | 0.17 | 0.012 | 18.73 | 0.16 | 0.012 | 14.06 | 0.13 |
| sample type | 0.012 | 13.39 | 0.12 | 0.012 | 11.67 | 0.11 | 0.012 | 7.81 | 0.07 |
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Adult
Autopsy
Cereals
Feces
Helianthus annuus
Insecta
Intestines
Large Intestine
Mice, Deer
Plant Embryos
Rodent
Computed tomography planning was done at 2.0-mm intervals for PBT planning. When contouring of the recurrent tumor was unclear on CT, pelvic magnetic resonance imaging (MRI) was performed. The PBT machine used was the Hitachi proton‐type particle therapy system (Hitachi, Kashiwa, Japan). The PBT planning system used was the XiO‐M (Hitachi). Gross tumor volume (GTV) was defined as a recurrent tumor. The median clinical target volume (CTV) margin was 5 mm (range, 2-7 mm) around the GTV. The median planning target volume (PTV) margin was 5 mm (range, 3-10 mm) around the CTV. The supine position is the standard treatment position because of the high morbidity rate of the postoperative colonic stoma. Irradiation was performed 5 days a week and at least 4 days a week, even on holidays. PBT was administered using the passive scattering method. The basic policy of dose and fractionation at our institution was as follows: if possible, the dose per fraction was >2.2 Gy and the total dose was >70 Gy. The maximum doses for the small and large bowels were 50 and 60 Gy, respectively. Moreover, the dose for the bladder, urethra, pelvic bone, and skin was not over the 100% isodose line. However, the radiation oncologist in charge decided the radiation dose and fractionation based on tumor location, the distance between tumors and organs at risk, and the patient's condition. The relative biological effectiveness (RBE) value of 1.1 was used in this study. Replanning, including a boost plan to reduce dose to organs at risk, was adopted for most patients during PBT.
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Colon
Hip Bone
Large Intestine
Neoplasms
Neoplasms by Site
Patients
Pelvis
Proton Therapy
Radiation Oncologists
Radiotherapy
Radiotherapy Dose Fractionations
Skin
Surgical Stoma
Urethra
Urinary Bladder
X-Ray Computed Tomography
The effect of intestinal preparation was regarded as the main outcome indicator and was scored using the Boston Bowel Preparation Scale (BBPS). As a commonly used clinical bowel preparation assessment scale, the BBPS score divides the large intestine into 3 segments (rectum and sigmoid colon, transverse colon and descending colon, ascending colon and cecum) and scores after adequate bowel preparation. Each intestinal segment was scored from 0 to 3 points, and the total score ranges from 0 to 9 points. The indications of scorings were as follows: 0 points, the entire intestinal mucosa cannot be observed due to irremovable solid or liquid feces; 1 point, parts of the intestinal mucosa cannot be observed due to the presence of stains, turbid liquid, and residual feces; 2 points, the intestinal mucosa is well observed, but a small amount of stains, cloudy liquid, and feces remain; and 3 points, the intestinal mucosa is well observed, and there are no residual stains, cloudy liquids, and stools [39 (link)]. In this study, the total score of BBPS score is > 5, and any intestinal segment ≥ 2 points can be considered satisfactory intestinal preparation.
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Cecum
Colon, Ascending
Colon, Descending
Feces
Intestinal Mucosa
Intestines
Large Intestine
Rectum
Sigmoid Colon
Staining
Transverse Colon
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Collagenase VIII is a laboratory enzyme used for the digestion and dissociation of collagen-rich tissues. It is effective in breaking down the extracellular matrix, facilitating the isolation and extraction of cells from various sources.
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