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Cattle

Cattle are large, domesticated, hoofed mammals that belong to the Bovidae family.
They are raised for their meat, milk, and other agricultural products.
Cattle are known for their four-chambered stomachs, which allow them to efficiently digest grass and other vegetation.
They typically have a distinctive hump on their shoulders and long, curved horns.
Cattle play an important role in many cultures and economies around the world, providing a valuable source of food and income for farmers and ranchers.
Resaerch into cattle health, breeding, and production can lead to important advancements in the cattle industry and improved outcomes for consumers.

Most cited protocols related to «Cattle»

We simulated data with varying number of sequences and sites (table 1) to assess the performance of UFBoot. For each setting, we used IQ-TREE (Nguyen L-T, Minh BQ, Schmidt HA, von Haeseler A, in preparation) to generate 200 random trees (true trees) under the Yule–Harding model (Harding 1971 ) where the branch lengths follow an exponential distribution with the mean of 0.1. Seq-Gen (Rambaut and Grassly 1997 (link)) was used to evolve the DNA or protein sequences along the tree under the GTR + (Lanave et al. 1984 (link); Yang 1994 (link)) and WAG + (Yang 1994 (link); Whelan and Goldman 2001 (link)) model, respectively. The GTR model parameters are:

. The distribution parameter is . In total, we simulated 600 DNA alignments and 400 amino acid alignments for five settings (table 1).
For each simulated alignment, we then performed UFBoot with , , and . To compare the UFBoot results, we conducted SBS as implemented in RAxML-SSE3 7.3.0 with 100 replicates (Stamatakis 2006 (link)), RBS with 1,000 replicates (Stamatakis et al. 2008 (link)), and PhyML SH-aLRT (Guindon et al. 2010 (link)). For each bootstrap method, the inferred split support values were mapped onto the ML tree reconstructed by IQ-TREE.
Finally, we collected the set of unique splits occurring in the 1,000 ML trees reconstructed from the 1,000 alignments generated and classified them as true or false splits (i.e., splits that occur in the corresponding true tree or not). Each split was associated with four support values: , , , and rounded as integers between and . Then, we computed the fraction, , of true splits with support value against all splits with the same support value , thus we computed:

Similarly, we computed , , and . This ratio is coined “accuracy” (Hillis and Bull 1993 ) and was used recently by Anisimova et al. (2011) (link).
Publication 2013
Amino Acids Amino Acid Sequence Cattle Trees
The QTLdb accepts either curated public data from journal papers or private laboratory reports subject to publication. More than 50 parameters/data types are subject to collection to describe a QTL, as reported earlier (3 ). We have recently added a number of new data types to enhance our ability to be more inclusive in QTL/association data collection. These new types include ‘association’ data for candidate gene or single marker associations; ‘eQTL’ from microarray-based QTL scan analysis; ‘test scale’ to differentiate genome-wise, chromosome-wise, comparison-wise and experiment-wise QTL/association reports; ‘test model’ to indicate epistatic or maternally or paternally imprinted QTL; new test statistics such as Bayes value and likelihood ratio, etc. We have also added animal breed information for future breed-associated QTL analysis. The backbone maps to record QTL are from USDA-Meat Animal Research Center (MARC; for pigs and cattle), Wageningen University (for chicken), University of Melbourne (for sheep) and the National Center for Cool and Cold Water Aquaculture (NCCCWA; for rainbow trout). Reported QTL genome locations were obtained by interpolating their linkage map positions via anchor markers.
QTL are mapping features recorded as linkage distances. In order for GBrowse to display QTL and for users to easily port QTL data for customized analysis, we established a process to convert the QTL linkage map locations (centimorgan, cM) to the corresponding physical locations (megabase pair, Mbp). The data conversion is a mathematical process built in a Perl script, whereby interpolation or extrapolation is performed with reference to the nearest common anchoring marker locations on both maps.
The QTLdb has a three-tiered data curation structure so that curators, editors and database administrators can work together and share responsibilities in a workflow to ensure data quality and smooth process control. In the past few years, a set of new data debugging tools, process control mechanisms and functions for the ease of use of the tools have been developed in response to lessons learned during data curation and debugging.
Publication 2012
Administrators Animals Cattle CCL7 protein, human Chickens Chromosome Mapping Chromosomes Common Cold Domestic Sheep Genes Genome Inclusion Bodies Meat Microarray Analysis Microtubule-Associated Proteins Oncorhynchus mykiss Physical Examination Pigs Radionuclide Imaging Vertebral Column
We tested SNeP with two published datasets that had been previously used to describe trends in Ne over time using LD, Bos indicus [54,436 SNPs of 423 East African Shorthorn Zebu (SHZ)–Mbole-Kariuki et al., 2014 (link), data available at Dryad Digital Repository: doi:10.5061/dryad.bc598.] and Ovis aries [49,034 SNPs genotyped in 24 Swiss White Alpine (SWA), 24 Swiss Black-Brown Mountain sheep (SBS), 24 Valais Blacknose sheep (VBS), 23 Valais Red sheep (VRS), 24 Swiss Mirror sheep (SMS) and 24 Bundner Oberländer sheep (BOS)–Burren et al., 2014 (link)]. The r2 estimates for the cattle datasets were obtained by the authors using GenABLE (Aulchenko et al., 2007 (link)) using a minimum allele frequency (MAF) < 0.01 and adjusting the recombination rate using Haldane's mapping function (Haldane, 1919 ). The r2 estimates of the sheep data were calculated by the authors using PLINK-1.07 (Purcell et al., 2007 (link)), with a MAF < 0.05 and no further corrections. For both autosomal datasets r2 estimates where corrected for sample size using equation (4) with β = 2. For these comparative analyses the SNeP command line included the same parameters used for the published data apart from the r2 estimates, calculated through genotype count and the use of SNeP's novel binning strategy.
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Publication 2015
Bos indicus Cattle Domestic Sheep East African People Fingers Genotype Recombination, Genetic Single Nucleotide Polymorphism
The Iso-Seq method for sequencing full-length transcripts was developed by PacBio during the same time period as the genome assembly. We therefore used this technique to improve characterization of transcript isoforms expressed in cattle tissues using a diverse set of tissues collected from L1 Dominette 0 1449 upon euthanasia. The data were collected using an early version of the Iso-Seq library protocol [26 ] as suggested by PacBio. Briefly, RNA was extracted from each tissue using Trizol reagent as directed (Thermo Fisher). Then 2 μg of RNA were selected for PolyA tails and converted into complementary DNA (cDNA) using the SMARTer PCR cDNA Synthesis Kit (Clontech). The cDNA was amplified in bulk with 12–14 rounds of PCR in 8 separate reactions, then pooled and size-selected into 1–2, 2–3, and 3–6 kb fractions using the BluePippin instrument (Sage Science). Each size fraction was separately re-amplified in 8 additional reactions of 11 PCR cycles. The products for each size fraction amplification were pooled and purified using AMPure PB beads (Pacific Biosciences) as directed, and converted to SMRTbell libraries using the Template Prep Kit v1.0 (PacBio) as directed. Iso-Seq was conducted for 22 tissues including abomasum, aorta, atrium, cerebral cortex, duodenum, hypothalamus, jejunum, liver, longissimus dorsi muscle, lung, lymph node, mammary gland, medulla oblongata, omasum, reticulum, rumen, subcutaneous fat, temporal cortex, thalamus, uterine myometrium, and ventricle from the reference cow, as well as the testis of her sire. The size fractions were sequenced in either 4 (for the smaller 2 fractions) or 5 (for the largest fraction) SMRTcells on the RS II instrument. Isoforms were identified using the Cupcake ToFU pipeline [27 ] without using a reference genome.
Short-read–based RNA-seq data derived from tissues of Dominette were available in the GenBank database because her tissues have been a freely distributed resource for the research community. To complement and extend these data and to ensure that the tissues used for Iso-Seq were also represented by RNA-seq data for quantitative analysis and confirmation of isoforms observed in Iso-Seq, we generated additional data, avoiding overlap with existing public data. Specifically, the TruSeq stranded mRNA LT kit (Illumina, Inc.) was used as directed to create RNA-seq libraries, which were sequenced to ≥30 million reads for each tissue sample. The Dominette tissues that were sequenced in this study include abomasum, anterior pituitary, aorta, atrium, bone marrow, cerebellum, duodenum, frontal cortex, hypothalamus, KPH fat (internal organ fat taken from the covering on the kidney capsule), lung, lymph node, mammary gland (lactating), medulla oblongata, nasal mucosa, omasum, reticulum, rumen, subcutaneous fat, temporal cortex, thalamus, uterine myometrium, and ventricle. RNA-seq libraries were also sequenced from the testis of her sire. All public datasets, and the newly sequenced RNA-seq and Iso-Seq datasets, were used to annotate the assembly, to improve the representation of low-abundance and tissue-specific transcripts, and to properly annotate potential tissue-specific isoforms of each gene.
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Publication 2020
Abomasum Anabolism Aorta Bone Marrow Capsule Cattle cDNA Library Cerebellum Cerebral Ventricles Cortex, Cerebral Dietary Fiber DNA, Complementary Duodenum Euthanasia Genes Genome Heart Atrium Hypothalamus Jejunum Kidney Liver Lobe, Frontal Lung Mammary Gland Medulla Oblongata Muscle Tissue Myometrium Nasal Mucosa Nodes, Lymph Omasum Pituitary Hormones, Anterior Poly(A) Tail Protein Isoforms Reticulum RNA, Messenger RNA-Seq Rumen Subcutaneous Fat Temporal Lobe Testis Thalamus Tissues Tissue Specificity Tofu trizol Uterus
The genomes of strains DSM 27638, DSM 27639 and DSM 27640 were compared with finished closed references genomes selected as members of the corresponding RTs, Comparative genomics included three strains belonging to the most virulent RT 027 (non-epidemic strain CD196, the epidemic and highly virulent strain R20291 [14 (link)], and the bovine isolate 2,007,855), three other strains belong to recently emerging RTs 017 (CF5 and M68) and RT 078 (M120). The RT 012 is represented by strain 630 [23 , 27 (link)]. All analyzed strains are listed in Table 2. Orthologous proteins were determined with ProteinOrtho [28 (link)] applying default parameters. Circular visualizations and comparisons of shared nucleotide regions of the genomes have been produced with BRIG [29 (link)] and linear visualizations with MAUVE [30 (link)]. Identification of genomic islands has been done with Island viewer 3 [31 (link)]. All identified regions have been manually curated using UniProtKB/Swiss-Prot and TrEMBL database (www.uniprot.org). In detail, comparison of related genome regions have been done with ACT and Artemis [32 (link)]. Phylogenomics based on whole genome alignments has been performed by using Phylomark [33 (link)]. Synteny analysis and SNP prediction have been performed with nucmer from the mummer program suite [34 (link)].

Genome sequences used in this study

StrainRibotypeToxino-typeGenome sizeIsolation (year/country)Accession numberReference
DSM 27638a027III4,229,6982015/GermanyCP011846.1This study
DSM 27639a01204,263,9972015/GermanyCP011847.1This study
DSM 27640a027III4,229,6292015/GermanyCP011848.1This study
630a01204,274,7821982/SwitzerlandCP010905.2[27 (link)]
CF5b017VIII4,159,5171995/BelgiumFN665652.1[14 (link)]
M68b017VIII4,308,3252006/IrelandNC_017175.1[14 (link)]
CD196c027III4,110,5541985/FranceNC_013315.1[49 (link)]
R20291d027III4,191,3392006/UKFN545816.1[14 (link)]
2007855d027III4,179,8672007/USFN665654.1[14 (link)]
M120b078V4,047,7292007/UKNC_017174.1[51 (link)]

aPacBio/Illumina hybrid assembly

b454/Illumina hybrid assembly

c454/Sanger sequencing

d454 sequencing

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Publication 2018
Cattle Epidemics Genome Genomic Islands Hybrids Nucleotides Proteins Strains Synteny

Most recents protocols related to «Cattle»

Not available on PMC !

Example 8

The SFME sample processing can be done in fused silica tubing of smaller diameter which are commonly used as liquid line in liquid chromatography system (e.g., tubing having an inner diameter of 500 μm or less). The extraction can be induced by applying a push and pull force on one side of the tubing. The extract can be either directly analyzed by nanoESI or stored for further operations.

FIG. 10 show analysis of 50 ng/mL amitriptyline in bovine whole blood. MS/MS spectrum of the molecular ion was collected. The blood sample was first 10× diluted using H2O as a reduction of viscosity. For extraction, 5 μL of the diluted sample was processed in a fused silica tubing (i.d. 500 μm) using methods of the invention. The extract was then infused into a nanoESI emitter and analyzed by nanoESI.

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Patent 2024
Amitriptyline BLOOD Cattle Liquid Chromatography Silicon Dioxide Tandem Mass Spectrometry Viscosity

Example 3

In this example, non-mouse TdT variants were constructed from publicly available genes and were tested to determine their ability to incorporate 3′-O-amino-dNTPs into a test polynucleotide (p877) in hairpin completion assays as described above. The TdT variants are identified in Table 9 along with their incorporation capacity as compared to mouse TdT variant, M27.

TABLE 9
Characteristics of Non-Mouse TdT Variants
Percent
PercentActivity
Accession NumberIdentityRelativeSEQ
SpeciesOf sources speciesto M27to M27*ID NO
BovineNP_803461.18248427
Related toXP_005999893.1803128
Latmeria
PumaXP_026918530.1815429
N139 reptilianXP_016851390.16813130
ShrewXP_006880141.1825731
Mouse M2710032
*Hairpin completion assay

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Patent 2024
Biological Assay Cattle Genes Mice, House NP-27 Polynucleotides Puma Shrews
Not available on PMC !

Example 6

Oil content in the dicotyledonous plant species Trifolium repens (clover), a legume commonly used as a pasture species, was increased by expressing the combination of WRI1, DGAT and Oleosin genes in vegetative parts. The construct pJP3502 was used to transform T. repens by Agrobacterium-mediated transformation (Larkin et al., 1996). Briefly, the genetic construct pJP3502 was introduced into A. tumefaciens via a standard electroporation procedure. The binary vector also contained a 35S:NptII selectable marker gene within the T-DNA. The transformed Agrobacterium cells were grown on solid LB media supplemented with kanamycin (50 mg/L) and rifampicin (25 mg/L) and incubated at 28° C. for two days. A single colony was used to initiate a fresh culture. Following 48 hours vigorous culture, the Agrobacterium cells was used to treat T. repens (cv. Haifa) cotyledons that had been dissected from imbibed seed as described by Larkin et al. (1996). Following co-cultivation for three days the explants were exposed to 25 mg/L kanamycin to select transformed shoots and then transferred to rooting medium to form roots, before transfer to soil.

Six transformed plants containing the T-DNA from pJP3502 were obtained and transferred to soil in the glasshouse. Increased oil content was observed in the non-seed tissue of some of the plants, with one plant showing greater than 4-fold increase in TAG levels in the leaves. Such plants are useful as animal feed, for example by growing the plants in pastures, providing feed with an increased energy content per unit weight (energy density) and resulting in increased growth rates in the animals.

The construct pJP3502 is also used to transform other leguminous plants such as alfalfa (Medicago sativa) and barrel medic (Medicago truncatula) by the method of Wright et al. (2006) to obtain transgenic plants which have increased TAG content in vegetative parts. The transgenic plants are useful as pasture species or as hay or silage as a source of feed for animals such as, for example, cattle, sheep and horses, providing an increased energy density in the feed.

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Patent 2024
Agrobacterium Alfalfa Animals Cattle Cells Cloning Vectors Cotyledon Domestic Sheep Electroporation Equus caballus Fabaceae Genes Kanamycin Magnoliopsida Markers, DNA Medicago truncatula Plant Embryos Plant Oils Plant Roots Plants Plants, Transgenic Reproduction Rifampin Silage Tissues Trifolium Trifolium repens

Example 4

For viscous biofluid samples, dilution of the sample was applied to allow the operation with systems and methods of the invention. As an example, blood samples containing drugs were diluted 10 times before analysis by SFME nanoESI. The data in FIG. 4 panels A-B show that methods of the invention were able to analyze analytes from a blood sample. FIG. 4 panels A-B show MS/MS spectra obtained using slug flow microextraction nanoESI. Bovine blood samples, each containing 40 ng/mL nicotine (FIG. 4 panel A) and 40 ng/mL methamphetamine (FIG. 4 panel B) were diluted 10 times with water and then analyzed using SFME nanoESI. 10 μL of diluted sample, 5 μL ethyl acetate used.

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Patent 2024
BLOOD Cattle ethyl acetate Methamphetamine Nicotine Pharmaceutical Preparations Slugs Tandem Mass Spectrometry Technique, Dilution Viscosity
The contents of DM, fat, protein, and lactose in milk were measured using a MilkoScan FT2 instrument (Foss, Hillerød, Denmark), which was calibrated using bovine milk.
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Publication 2023
Cattle FOS protein, human Lactose Milk, Cow's Proteins

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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
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The BovineHD BeadChip is a high-density genotyping array designed for genetic analysis in cattle. It provides comprehensive genome-wide coverage with over 777,000 genetic markers. The BovineHD BeadChip is a tool for researchers to study the bovine genome and investigate genetic variations.
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The BovineSNP50 BeadChip is a lab equipment product designed for genetic analysis of bovine samples. It provides a comprehensive set of single nucleotide polymorphisms (SNPs) for bovine genome-wide association studies and other genetic research applications.
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The RNeasy Mini Kit is a laboratory equipment designed for the purification of total RNA from a variety of sample types, including animal cells, tissues, and other biological materials. The kit utilizes a silica-based membrane technology to selectively bind and isolate RNA molecules, allowing for efficient extraction and recovery of high-quality RNA.
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The HiSeq 2000 is a high-throughput DNA sequencing system designed by Illumina. It utilizes sequencing-by-synthesis technology to generate large volumes of sequence data. The HiSeq 2000 is capable of producing up to 600 gigabases of sequence data per run.

More about "Cattle"

Bovine, ruminants, dairy cows, beef cattle, livestock, Bovidae, FBS (Fetal Bovine Serum), TRIzol reagent, BovineHD BeadChip, BovineSNP50 BeadChip, RNeasy Mini Kit, TRIzol, SAS 9.4, BD Vacutainer, Agilent 2100 Bioanalyzer, HiSeq 2000.
Cattle are large, domesticated, hoofed mammals that belong to the Bovidae family.
They are raised for their meat, milk, and other agricultural products.
Cattle are known for their four-chambered stomachs, which allow them to efficiently digest grass and other vegetation.
They typically have a distinctive hump on their shoulders and long, curved horns.
Cattle play an important role in many cultures and economies around the world, providing a valuable source of food and income for farmers and ranchers.
Researchers in the cattle industry utilize various tools and techniques to study cattle health, breeding, and production.
FBS (Fetal Bovine Serum) is a commonly used supplement in cell culture media, providing essential nutrients for cell growth and proliferation.
The TRIzol reagent is a popular method for extracting high-quality RNA from cattle samples, enabling gene expression analysis.
Genetic studies in cattle often employ microarray platforms like the BovineHD BeadChip and the BovineSNP50 BeadChip to identify genetic markers and variants associated with important traits.
To ensure high-quality RNA extraction and analysis, researchers may use the RNeasy Mini Kit and the Agilent 2100 Bioanalyzer.
Statistical software like SAS 9.4 is commonly used for data analysis, while sample collection devices like the BD Vacutainer help ensure proper sample handling and preservation.
Advanced sequencing technologies, such as the HiSeq 2000, enable in-depth genomic and transcriptomic studies in cattle, leading to important advancements in the industry.
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