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Rodent

Rodents are a diverse group of small to medium-sized mammals characterized by their continuously growing incisors and efficient digestive systems.
They include mice, rats, hamsters, gerbils, guinea pigs, and many others.
Rodents are widely used in biomedical research due to their genetic and physiological similarities to humans, as well as their rapid reproduction and ease of handling.
Researchers utilize rodent models to study a variety of topics, such as disease pathogenesis, drug development, and behavioral neuroscience.
Proper experimental design and the selection of appropriate rodent strains are crucial for ensuring the reliability and reproducibility of research findings.
PubCompare.ai can help optimize rodent research by identifying the best protocols from literature, preprints, and patents, enhanceing the accuracy and reproducibility of your studies.

Most cited protocols related to «Rodent»

1
BUSCO v3: Comprehensive Genome Assessment
Details of the new and updated lineage data sets as well as the new software developments that make up BUSCO v3 are presented in the Supplementary Material online and in the user guide online at http://busco.ezlab.org. BUSCO has been developed and tested on Linux, the codebase is written for Python and runs with the standard Python packages. BUSCO is licensed and freely distributed under the MIT Licence. The BUSCO v3 source code is available through the GitLab project, https://gitlab.com/ezlab/busco, and built as a virtual machine with dependencies preinstalled.
Versions and accessions of all the genome assemblies, annotated gene sets, or transcriptomes assessed by BUSCO as part of this study are detailed in the Supplementary Material online, along with the settings used for each analysis. The Augustus ab initio gene prediction analyses are described in detail in the Supplementary Material online, to compute the coverage scores the predicted protein sequences were aligned against their respective reference annotations using BLASTp (e.g., a coverage score of 100% means that every amino acid of a reference protein is found in the predicted protein with no insertions, deletions, or substitutions). Details of the preprocessing, BUSCO completeness analyses, and postprocessing of the rodent data sets for the phylogenomics study are all presented in the Supplementary Material online, proteins selected for the superalignment were aligned using MAFFT (Katoh and Standley 2013 (link)) and filtered with trimAl (Capella-Gutiérrez et al. 2009 (link)), and the maximum likelihood tree was built using RAxML (Stamatakis 2014 (link)).
Waterhouse R.M., Seppey M., Simão F.A., Manni M., Ioannidis P., Klioutchnikov G., Kriventseva E.V, & Zdobnov E.M. (2017). BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics. Molecular Biology and Evolution, 35(3), 543-548.
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Publication 2017
Amino Acids Amino Acid Sequence Gene Deletion Genes Genome Insertion Mutation Proteins Python Rodent Staphylococcal Protein A Strains Transcriptome Trees
2
Differentiation and Characterization of Midbrain Dopaminergic Neurons
Human ESC (H9, H1) and iPSC lines (2C6 and SeV6) were subjected to a modified dual SMAD-inhibition13 (link) based FP induction12 (link) protocol. Exposure to SHH C25II, Purmorphamine, FGF8 and CHIR99021 were optimized for midbrain FP and DA neuron yield (see Figure 1d). Following FP induction, further maturation was carried out in Neurobasal/B27 medium supplemented with AA, BDNF, GDNF, TGFβ3 and dbcAMP (see full methods for details). The resulting DA neurons were subjected to extensive phenotypic characterization via immunocytochemistry, qRT-PCR, gene expression profiling, HPLC analysis for DA and in vitro electrophysiological recordings. In vivo studies were performed in 6-hydroxydopamine lesioned, hemiparkinsonian rodents (adult NOD-SCID IL2Rgc mice and Sprague Dawley rats) as well as in two adult rhesus monkeys treated with carotid injections of MPTP. DA neurons were injected stereotactically in the striata of the animals (150 × 103 cells in mice, 250 × 103 cells in rats) and a total of 7.5 × 106 cells (distributed in 6 tracts; 3 on each side of brain) in monkeys. Behavioral assays were performed at monthly intervals post grafting, including amphetamine mediated rotational analysis as well as a test for focal akinesia (“stepping test”) and forelimb use (cylinder test). Rats and mice were sacrificed at 18–20 weeks and the primates at 1 month post grafting. Characterization of the grafts was performed via stereological analyses of cell numbers and graft volumes and comprehensive immunohistochemistry.
Kriks S., Shim J.W., Piao J., Ganat Y.M., Wakeman D.R., Xie Z., Carrillo-Reid L., Auyeung G., Antonacci C., Buch A., Yang L., Beal M.F., Surmeier D.J., Kordower J.H., Tabar V, & Studer L. (2011). Floor plate-derived dopamine neurons from hESCs efficiently engraft in animal models of PD. Nature, 480(7378), 547-551.
Publication 2011
1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine Adult Amphetamine Animals Biological Assay Brain Bucladesine Carotid Arteries Cells Chir 99021 FGF8 protein, human Forelimb Glial Cell Line-Derived Neurotrophic Factor Grafts High-Performance Liquid Chromatographies Homo sapiens Hydroxydopamine Immunocytochemistry Immunohistochemistry Induced Pluripotent Stem Cells Macaca mulatta Mesencephalon Mice, Inbred NOD Monkeys Mus Neurons Phenotype Primates purmorphamine Rats, Sprague-Dawley Rattus Rodent SCID Mice Step Test Striatum, Corpus
3
Improved Protein Family Clustering in PANTHER
PANTHER version 3.0 (1 (link),2 (link)) used seed-based clustering to define protein families. The advantage of this approach was its modularity: new families could be easily added in areas that were inadequately covered in previous versions. However, the seed-based clustering resulted in significant redundancy for a number of large protein families, such as protein kinases and G-protein-coupled receptors, which were covered by a number of families that overlapped to varying degrees.
The current version, PANTHER version 5.0, addresses this issue by implementing a global clustering of proteins. Proteins from PANTHER version 4.0 were clustered using a similarity metric derived from the pairwise BLASTP scores:
where S(a, b) is the BLASTP raw score for the alignment of sequences a and b using the BLOSUM62 matrix and masked for low-complexity segments. The denominator is the largest self-alignment score, and therefore, the similarity is the fraction of the maximum score possible for an alignment of sequences a and b. In cases where there were multiple high-scoring pairs (HSPs; i.e. partial alignments), S(a, b) was set equal to the sum of the scores for the maximal set of non-overlapping HSPs.
This pairwise similarity was used to define single-linkage clusters (maximal clusters in which each protein is connected to at least one other protein in the cluster by a non-zero similarity score). A dendrogram was built for each single-linkage cluster using the UPGMA algorithm (17 ). The family labels from the PANTHER version 4.0 library were then used to define the optimal cut of each UPGMA dendrogram into family clusters, to maximize the correspondence to previous versions of PANTHER. In the great majority of cases, the PANTHER version 5.0 family was almost identical to the corresponding family in the previous version of the library. Only about 40 subtrees in the UPGMA dendrograms, primarily those that were represented by overlapping clusters in the previous version, had to be broken further into functionally homogeneous clusters using manual curation. Overall, the family clusters identified from the UPGMA dendrograms covered over 96% of the version 4.0 training sequences. The rest of the sequences were either singletons according to Equation 1 (often due to low-complexity masking), or lay outside the family boundaries defined by PANTHER version 4.0 family labels on the UPGMA dendrograms. Each of these ‘leftover’ sequences (unmasked) was scored against SAM HMMs built for the family clusters, and was brought into the family of the best scoring HMM if the NLL-NULL score was less than −50. Those leftovers not meeting this criterion were added as singleton families if they were from a primate or rodent species; otherwise they were removed from the library.
Mi H., Lazareva-Ulitsky B., Loo R., Kejariwal A., Vandergriff J., Rabkin S., Guo N., Muruganujan A., Doremieux O., Campbell M.J., Kitano H, & Thomas P.D. (2004). The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Research, 33(Database Issue), D284-D288.
Publication 2004
cDNA Library G-Protein-Coupled Receptors Hypertelorism, Severe, With Midface Prominence, Myopia, Mental Retardation, And Bone Fragility Primates Protein Kinases Proteins Rodent Staphylococcal Protein A
4
Standardized Rodent NASH Histological Scoring
Briefly, the two key features of NASH, steatosis and inflammation, were categorized as follows: steatosis was determined by analyzing hepatocellular vesicular steatosis, i.e. macrovesicular steatosis and microvesicular steatosis separately, and by hepatocellular hypertrophy as defined below (Fig. 2). Inflammation was scored by analyzing the amount of inflammatory cell aggregates (Fig. 2). The proposed rodent scoring system is shown in Table 4 and options for its use in diagnosis are shown in S1 Fig. The purpose of this scoring system is however not to derive a single score, but to score the individual features.
Macrovesicular steatosis and microvesicular steatosis were both separately scored and the severity was graded, based on the percentage of the total area affected, into the following categories: 0 (<5%), 1 (5–33%), 2 (34–66%) and 3 (>66%). The difference between macrovesicular and microvesicular steatosis was defined by whether the vacuoles displaced the nucleus to the side (macrovesicular) or not (microvesicular). Similarly, the level of hepatocellular hypertrophy, defined as cellular enlargement more than 1.5 times the normal hepatocyte diameter, was scored, based on the percentage of the total area affected, into the following categories: 0 (<5%), 1 (5–33%), 2 (34–66%) and 3 (>66%). For hepatocellular hypertrophy the evaluation was merely based on abnormal enlargement of the cells, irrespective of rounding of the cells and/or changes in cytoplasm or the number of vacuoles, and is therefore not a substitute of ballooning. The unweight sum of the scores for steatosis (macrovesicular steatosis, microvesicular steatosis and hypertrophy) thus ranged from 0–9. Both steatosis and hypertrophy were evaluated at a 40 to 100× magnification and only the sheets of hepatocytes were taken into account (terminal hepatic venules and portal tracts etc were excluded).
Inflammation was evaluated by counting the number of inflammatory foci per field using a 100 x magnification (view size of 3.1 mm2). A focus was defined a cluster, not a row, of ≥5 inflammatory cells. Five different fields were counted and the average was subsequently scored into the following categories: normal (<0.5 foci), slight (0.5–1.0 foci), moderate (1.0–2.0 foci), severe (>2.0 foci).
Hepatic fibrosis was identified using Sirius Red stained slides at 40 x magnification and evaluated by scoring whether pathologic collagen staining was absent (only in vessels) or collagen staining observed within the liver slide, the latter further defined as mild, moderate or massive. In addition, the percentage of the total area affected was evaluated using using image analysis of surface area on Sirius red stained slides.
Liang W., Menke A.L., Driessen A., Koek G.H., Lindeman J.H., Stoop R., Havekes L.M., Kleemann R, & van den Hoek A.M. (2014). Establishment of a General NAFLD Scoring System for Rodent Models and Comparison to Human Liver Pathology. PLoS ONE, 9(12), e115922.
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Publication 2014
Blood Vessel Cell-Derived Microparticles Cell Enlargement Cell Nucleus Cells Collagen Cytoplasm Diagnosis Fibrosis, Liver Hepatocyte Hypertrophy Inflammation Liver Nonalcoholic Steatohepatitis Portal System Rodent Steatohepatitis Vacuole Venules
5
Computational Toxicity Prediction Protocol
To predict the toxicity of the input compound, a 2D similarity search is performed on an updated version of the in-house toxicity database SuperToxic (17 (link)) and the most similar compounds to the input molecule are considered. The set used for prediction consists of approximately 38 000 unique compounds with known oral LD50 values measured in rodents. The data was gathered from public sources and literature and prepared using Instant JChem 6.2.0 (January 2014), ChemAxon (http://www.chemaxon.com), for standardization purposes.
From the standardized molecule structures, InChI keys were calculated and used to remove duplicates in the dataset. In the case of multiple LD50 values measured for one compound, the lowest dose value was kept to represent the worst-case toxicity of a compound. Six toxicity classes were defined based on the GHS classification scheme using the LD50 thresholds of 5, 50, 300, 2000 and 5000 mg/kg body weight. Each compound of the dataset was represented using a concatenated fingerprint consisting of the ‘FP2’ and ‘FP4’ fingerprints of Mychem (http://mychem.sourceforge.net/) as well as the ECFP4 fingerprint (18 (link)). The fingerprints were calculated using Open Babel (19 (link)) and JChem 6.1.3 (November 2013), ChemAxon (http://www.chemaxon.com), respectively. The similarity between two compounds was calculated using the Tanimoto Index.
In addition to the similarity search, the prediction method takes into account the presence of toxic fragments. All compounds in the database were fragmented using RECAP (20 (link)) as well as the in-house method ROTBONDS (21 (link)). The occurrence of each distinct fragment in molecules of the prediction dataset was tested using its SMILES string, computed with JChem 6.1.3 (November 2013) in a substructure search which was implemented using Open Babel's (19 (link)) fast search. To determine fragments over-represented in the most toxic classes, a propensity analysis (22 (link)) was performed. Propensity scores (PS) were calculated for every fragment and toxicity class. Toxic fragments were defined as those showing a PS above a threshold of 3 in classes I, II or III, and a PS below 1 in classes IV–VI. Based on these conditions, a total number of 1591 and 1580 fragments specific to toxicity classes I–III, generated with the ROTBONDS and RECAP fragmentation method, respectively, were contemplated for prediction.
Drwal M.N., Banerjee P., Dunkel M., Wettig M.R, & Preissner R. (2014). ProTox: a web server for the in silico prediction of rodent oral toxicity. Nucleic Acids Research, 42(Web Server issue), W53-W58.
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Publication 2014
Body Weight Molecular Structure Rodent

Most recents protocols related to «Rodent»

1
Evaluating mRNA Vaccines Against Lethal hMPV Challenge in Cotton Rats
Not available on PMC !

Example 16

The instant study was designed to test the efficacy in cotton rats of hMPV vaccines against a lethal challenge. mRNA vaccines encoding hMPV fusion protein were used. The mRNA polynucleotide encodes a full-length fusion protein and comprises the wild-type nucleotide sequence obtained from the hMPV A2a strain.

Cotton rats were immunized intramuscularly (IM) at week 0 and week 3 with the mRNA vaccines encoding hMPV fusion protein with either 2 μg or 10 μg doses for each immunization. The animals were then challenged with a lethal dose of hMPV in week 7 post initial immunization via IV, IM or ID. The endpoint was day 13 post infection, death or euthanasia. Viral titers in the noses and lungs of the cotton rats were measured. The results (FIGS. 9A and 9B) show that a 10 μg dose of mRNA vaccine protected the cotton mice 100% in the lung and drastically reduced the viral titer in the nose after challenge (˜2 log reduction). Moreover, a 2 μg dose of mRNA vaccine showed a 1 log reduction in lung viral titer in the cotton mice challenged.

Further, the histopathology of the lungs of the cotton mice immunized and challenged showed no pathology associated with vaccine-enhanced disease (FIG. 10).

US11872278B2. Combination HMPV/RSV RNA vaccines (2024-01-16). ModernaTX, Inc. [US]. Inventors: Giuseppe Ciaramella [US], Sunny Himansu [US].
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Patent 2024
Animals Base Sequence Euthanasia Gossypium Human Metapneumovirus Immunization Infection Lung mRNA Vaccine mRNA Vaccines Mus Nose Pneumonia, Viral Polynucleotides Proteins Rats, Cotton RNA, Messenger Rodent Strains vaccin Vaccines
2
Evaluation of mRNA-based hMPV Vaccines
Not available on PMC !

Example 13

The instant study is designed to test the efficacy in cotton rats of candidate hMPV vaccines against a lethal challenge using an hMPV vaccine comprising mRNA encoding Fusion (F) glycoprotein, major surface glycoprotein G, or a combination of both antigens obtained from hMPV. Cotton rats are challenged with a lethal dose of the hMPV.

Animals are immunized intravenously (IV), intramuscularly (IM), or intradermally (ID) at week 0 and week 3 with candidate hMPV vaccines with and without adjuvant. Candidate vaccines are chemically modified or unmodified. The animals are then challenged with a lethal dose of hMPV on week 7 via IV, IM or ID. Endpoint is day 13 post infection, death or euthanasia. Animals displaying severe illness as determined by >30% weight loss, extreme lethargy or paralysis are euthanized. Body temperature and weight are assessed and recorded daily.

In experiments where a lipid nanoparticle (LNP) formulation is used, the formulation may include a cationic lipid, non-cationic lipid, PEG lipid and structural lipid in the ratios 50:10:1.5:38.5. The cationic lipid is DLin-KC2-DMA (50 mol %) or DLin-MC3-DMA (50 mol %), the non-cationic lipid is DSPC (10 mol %), the PEG lipid is PEG-DOMG (1.5 mol %) and the structural lipid is cholesterol (38.5 mol %), for example.

US11872278B2. Combination HMPV/RSV RNA vaccines (2024-01-16). ModernaTX, Inc. [US]. Inventors: Giuseppe Ciaramella [US], Sunny Himansu [US].
Full text: Click here
Patent 2024
Animals Antigens Body Temperature Cations Cholesterol Euthanasia Glycoproteins Human Metapneumovirus Infection Lethargy Lipid Nanoparticles Lipids Membrane Glycoproteins Pharmaceutical Adjuvants Rats, Cotton RNA, Messenger Rodent Vaccines
3
Acclimation and Housing of Female ICR Mice
Not available on PMC !

Example 6

SPF female ICR mice were obtained at 3 weeks of age from Taconic Farms (Hudson, NY), and used for the experiments after one-week acclimation. Mice were housed at the Isolation Unit of the Central Animal Facility (University of Guelph) in a temperature controlled environment with a 12 h light/dark cycle. Animal care was provided in accordance with the animal utilization protocol no. 04R030 (University of Guelph) and the Guide to the Care and Use of Experimental Animals (1). Mice were fed sterilized solid rodent chow and water. When needed, water was supplemented with Amp and Km at a concentration of 400 mg L−1 and 200 mg L−1, respectively. Each mouse was assessed daily for weight, body temperature, signs of dehydration, posture and alertness.

US11857581B2. Antiviral methods and compositions comprising probiotic bacterial molecules (2024-01-02). MicroSintesis Inc. [CA]. Inventors: Mansel Griffiths [CA].
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Patent 2024
Acclimatization Animals Body Temperature Dehydration Females isolation Mice, House Mice, Inbred ICR Rodent
4
Yeast-based Galactose Degradation in Foods
Not available on PMC !

Example 4

As part of evaluating the feasibility of a yeast-based approach as a treatment to mitigate the effects of elevated concentrations of galactose in foods and beverages, several evolved clones were tested for their capability of degrading galactose when present in food. Milk was tested because it represents the most challenging food for galactosemia patients considering its high level of galactose (2-4 g per 100 mL of milk). Food spiked with galactose was tested in parallel.

For this study, three evolved yeast strains obtained by adaptive evolution followed by UV treatment, Clone Y-C201-1, Clone Y-C202-1, and Clone Y-C202-2, one evolved yeast strain obtained by adaptive evolution, Clone Y-C202, as well as the initial parent strain Yi were compared for their galactose consumption activity. Cultures were initiated from a single colony on agar plates and grown in 15 mL of liquid YP medium (1% yeast extract, 2% peptone; Teknova, Hollister, CA) in a 50-mL mini-bioreactor by incubation at 30° C. with an agitation of 225 rpm supplemented with 2% galactose (Teknova). Strain Saccharomyces boulardii (SB) was prepared similarly to the evolved clones except that it was grown in YP medium supplemented with 2% glucose.

The testing of galactose consumption was started with yeast cells obtained from a culture volume containing 1.0×109 Colony Forming Units (CFU) pelleted by centrifugation at 1000 rpm (Sorval, RT7) for 10 min at room temperature. Cell pellets were resuspended either in 1.0 mL of milk already pre-treated with lactase (LACTAID milk where lactose is transformed into galactose and glucose) or in 1 mL rodent diet (Teklad, Envigo) spiked with a solution of 5% galactose or a solution of 5% galactose+1% glucose. All the reactions were incubated at 37° C. Aliquots of the reactions were taken at multiple time points and stored at −20° C. until galactose concentration determination.

[Figure (not displayed)]

US11865151B2. Live biotherapeutics for the treatment of carbohydrate disorders (2024-01-09). GUTSYBIO INC. [US]. Inventors: Genevieve Hansen [US].
Full text: Click here
Patent 2024
Acclimatization Agar Beverages Biological Evolution Bioreactors Cells Centrifugation Clone Cells Diet Food Galactose Galactosemias Glucose Lactaid Lactase Lactose Milk, Cow's Parent Patients Pellets, Drug Peptones Rodent Saccharomyces boulardii Strains Yeast, Dried
5
Yeast-Based Fructose Degradation Potential
Not available on PMC !

Example 10

As part of evaluating the feasibility of a yeast-based approach as a treatment to mitigate the effects of elevated concentrations of fructose in foods and beverages, several evolved clones obtained by adaptive evolution were tested for their ability of degrading fructose when present in food.

For this study, two evolved yeast strains obtained by adaptive evolution, G1_1A and G2_1A were tested for their ability to degrade dietary fructose. The testing of fructose consumption was started with yeast cells obtained from a culture initiated from a single colony on agar plates and grown in 15 mL of liquid YP medium in a 50-mL mini-bioreactor by incubation at 30° C. with an agitation of 225 rpm supplemented with 4% fructose. Cells were pelleted by centrifugation at 1000 rpm (Sorval, RT7) for 10 min at room temperature. Cell pellets were resuspended in 5 mL rodent diet (Teklad, Envigo) spiked with a solution of 10% fructose (=555 mM). Reactions were incubated at 37° C. to mimic human gastrointestinal temperature conditions. Aliquots of the reactions were taken at multiple time points and stored at −20° C. until fructose concentration determination using the colorimetric Fructose Assay Kit (Cat. No. EFRU-100; BioAssay Systems, Hayward, CA).

As shown in Table 12, the evolved clones were able to rapidly decrease fructose concentration when present in diet.

TABLE 12
Remaining Fructose (%) after Exposure for 0.5 to 3 Hours to a Solution
of 10% Fructose with Evolved Clones G1_1A and G2_1A
CloneG1_1AG1_1AG1_1AG2_1AG2_1AG2_1A
CFU/mL3.10E+096.21E+092.17E+103.39E+096.78E+092.37E+10
Time point: 0.5 hr111.1%88.2%45.9%91.3%76.8%37.8%
Time point: 2.0 hr78.0%53.2%6.3%77.2%53.3%5.6%
Time point: 3.0 hr60.8%35.2%−1.5%59.7%34.7%−0.5%

US11865151B2. Live biotherapeutics for the treatment of carbohydrate disorders (2024-01-09). GUTSYBIO INC. [US]. Inventors: Genevieve Hansen [US].
Full text: Click here
Patent 2024
Acclimatization Agar Beverages Biological Assay Biological Evolution Bioreactors Cells Centrifugation Clone Cells Colorimetry Diet Food Fructose Gastrointestinal Diseases Homo sapiens Pellets, Drug Rodent Strains Yeast, Dried

Top products related to «Rodent»

1
C57bl 6j mice by Jackson ImmunoResearch
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C57BL/6J mice are a widely used inbred mouse strain. They are a commonly used model organism in biomedical research.
2
C57bl 6j by Jackson ImmunoResearch
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C57BL/6J is a mouse strain commonly used in biomedical research. It is a common inbred mouse strain that has been extensively characterized.
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Sprague dawley rat by Charles River Laboratories
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The Total OXPHOS Rodent WB Antibody Cocktail is a combination of antibodies designed for the detection of oxidative phosphorylation (OXPHOS) proteins in rodent samples through Western blotting. The cocktail includes antibodies that target different subunits of the five OXPHOS complexes, allowing for the simultaneous detection of these key mitochondrial proteins.

More about "Rodent"

Rodents are a diverse group of small to medium-sized mammals characterized by their continuously growing incisors and efficient digestive systems.
This includes a wide variety of species such as mice, rats, hamsters, gerbils, guinea pigs, and many others.
Rodents are widely utilized in biomedical research due to their genetic and physiological similarities to humans, as well as their rapid reproduction and ease of handling.
Researchers often utilize rodent models, such as C57BL/6J mice, C57BL/6, C57BL/6J male mice, and Sprague-Dawley rats, to study a variety of topics, including disease pathogenesis, drug development, and behavioral neuroscience.
The Total OXPHOS Rodent WB Antibody Cocktail is a useful tool for researchers working with rodent samples.
Proper experimental design and the selection of appropriate rodent strains are crucial for ensuring the reliablity and reproducibility of research findings.
PubCompare.ai can help optimize rodent research by identifying the best protocols from literature, preprints, and patents, enhanceing the accuracy and reproducibility of your studies.
This can lead to more reliable and accurate research outcomes, streamlining the research process.