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Brassica napus

Brassica napus, also known as rapeseed or canola, is a widely cultivated plant species belonging to the Brassicaceae family.
It is an important oilseed crop grown for its edible oil and high-protein meal.
Brassica napus is characterized by its lobed leaves, yellow flowers, and distinctive seed pods.
The plant is native to Europe and is now grown extensively around the world, including in North America, Europe, and Asia.
Reseach on Brassica napus focuses on improving yield, oil quality, and disease resistance to enhance its agricultural and commercial value.
With PubCompare.ai, researchers can easily locate the most accurate and reproducible protocols from literature, pre-prints, and patents to optimize their Brassica napus studies and enhnace the reliability of their findings.

Most cited protocols related to «Brassica napus»

To validate amplification specificity and to check for the presence of non-specific amplicons, qPCR assays were performed using 66 randomly selected genes from thale cress, oilseed rape, rice (Oryza sativa), sweet orange (Citrus sinensis), silkworm (Bombyx mori) and zebrafish (Danio rerio). In these qPCR experiments, only the best primer pair for each gene from qPrimerDB was selected, as summarized in Supplementary Table S2. To ensure the reliability of experimental results, the setup and validation of qPCR were performed, as prescribed in the MIQE guidelines (26 (link)). Based on the results of melting curve analysis and gel electrophoresis, all selected primer pairs were demonstrated to be of high specificity and amplification efficiency (Supplementary Figure S1).
In addition, to test the specificity and accuracy of the primer design workflow used in qPrimerDB, we collected 454 and 137 qPCR primer pairs for A. thaliana and B. mori, respectively, from 55 previously published studies (Supplementary Table S3). Using the validation and classification steps in the qPrimerDB workflow, the specificity and classification of all collected primers were determined. The results showed that the ratios of gene-specific primers were 75.87% for A. thaliana and 98.23% for B. mori in qPrimerDB, whereas values collected from the published studies were only 71.09 and 79.65%, respectively (Supplementary Table S4). These assays established that the automatic primer design workflow developed in qPrimerDB generated high quality gene-specific qPCR primers, whose specificity and consistency were superior to those of manually designed primers.
We also compared the qPCR primers for H. sapiens generated with MRPrimer and qPrimerDB workflows. For both two methods, only the best pre-commutated primers were retained and used for specificity and classification comparison. The results showed that a total of 14 500 MRPrimer and 17 632 qPrimerDB qPCR primers were gene-specific, and the ratio of level 1 primer in qPrimerDB was 50.36%, much higher than that in MRPrimer (13.14%) (Supplementary Table S5), indicating that the qPrimerDB workflow might well be one of the most effective gene-specific qPCR primer design tools, suitable for automatic primer design for newly sequenced genomes.
Publication 2017
Arabidopsis thalianas Biological Assay Bombyx Bombyx mori Brassica napus Citrus sinensis Electrophoresis Genes Genome Oligonucleotide Primers Oryza sativa Rice Zebrafish
All solvents used for sample preparation and analyses were of LC/MS-grade quality (CHROMASOLV, Fluka). A list of standard compounds used for the recovery experiment including sum formulas, molar masses, PubChem IDs and suppliers can be found in the Supplemental Information S3. L-Tryptophan-2′,4′,5′,6′,7′-D5 (98%) was purchased from Cambridge Isotope Laboratories. Arabidopsis thaliana (ecotype Col-0) was grown for six weeks on a soil/vermiculite mixture (3/2) in a growth cabinet with 8 h light ( 150 μE m−2s−1) at 22°C and 16 h dark at 20°C. Seeds of Brassica napus, Brassica oleracera and Brassica rapa were kindly provided by D. Strack, Department of Secondary Metabolism, Leibniz Institute of Plant Biochemistry, Halle. All other seeds were obtained from local distributors. Procedures for extraction of leaf and seed material are provided in Supplemental Information S4.
Publication 2011
11-dehydrocorticosterone Arabidopsis thalianas Brassica Brassica napus Brassica rapa Diet, Formula Ecotype Isotopes Light Molar Plant Leaves Plants Secondary Metabolism Solvents Tryptophan vermiculite
Several sequence resources were combined, forming a custom, redundant protein database. Expressed Sequence Tags (EST) databases from A. thaliana (release 12.1), Brassica napus (release 1), C. reinhardtii (release 5), G. max (release 10), Lotus japonicus (release 3), Lycopersicum esculentum (release 10.1), M. truncatula (release 8), Nicotiana tabacum (release 2), O. sativa (release 16), Solanum tuberosum (release 10), and Z. mays (release 16) were downloaded from the TIGR Gene Indices (now available at the Dana-Farber Cancer Institute gene index project) [49 (link)]. TIGR Transcript Assemblies (TA) from A. thaliana, Brassica napus, C. reinhardtii, P. patens, G. max, Glycine soja, Lotus corniculatus, Lupinus albus, Lycopersicum esculentum, M. sativa, M. truncatula, Nicotiana tabacum, O. sativa, Phaseolus coccineus, Phaseolus vulgaris, Pisum sativum, Solanum tuberosum, and Z. mays were added to this set (all release 1, 15 August 2005) [50 (link)]. The proteins predicted from the plant genomes of A. thaliana (NCBI Genbank release 5, 03 May 2006) [57 (link)], C. reinhardtii (JGI, release 3) [58 (link)], M. truncatula (Genome Sequencing Project release 17 July 2006) [59 (link)], O. sativa (release 4, 30 December 2005) [60 (link)], and P. trichocarpa (JGI, release 1) [61 (link)] were also included.
Sequence names were truncated to a unique identifier. Information about the database origin of each sequence was added to the unique identifier (i.e. OS-TA, OSEST, OSGEN for O. sativa TA, EST or genomic sequences respectively). Nucleotide sequences were translated into protein sequences in all six reading frames (universal code), and frame information was appended to the sequence identifier (e.g. "_+2"). The translated nucleotide sequences and modified protein sequences derived from genomic data were combined into a single file and formatted using Formatdb (options: -p T and -o T) [43 (link)]. The resulting database contained 3,631,558 sequences. To determine whether CLE sequences were specific to plants, a separate search was based on the non-redundant protein database (NCBI nr, version 15 June 2006.).
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Publication 2008
Amino Acid Sequence Base Sequence Brassica napus Expressed Sequence Tags Gene, Cancer Genes Genome Genome, Plant Glycine Lotus japonicus Lupinus Nicotiana tabacum Phaseolus Phaseolus vulgaris Pisum sativum Plants Proteins Reading Frames Solanum tuberosum Soybeans
There were 98 foods and non-alcoholic beverages listed on the FFQ. These were combined into 48 food groups on the basis of similarity of nutrient composition and comparable usage. For example, carrots, parsnips, swedes and turnips were combined in the ‘root vegetables’ group; bacon, ham, corned beef, meat pies and sausages were combined in the ‘processed meats’ group.
Principal component analysis is a statistical technique that produces new variables that are uncorrelated linear combinations of the dietary variables with maximum variance (20 (link)). PCA was performed on the reported frequencies of consumption of the 48 foods and food groups at the before, early and late pregnancy time points. The principal component analyses were based on the correlation matrix in order to adjust for unequal variances of the original variables. Natural dietary pattern scores were calculated by multiplying the coefficients for the 48 food groups at one time point by each individual’s standardized reported frequencies of consumption at the same time point. In order to calculate applied dietary pattern scores, frequencies of consumption in early and late pregnancy were standardized to the mean and standard deviation (SD) observed before pregnancy (since standardizing to the frequencies at the early or late pregnancy time point would remove information about increases or decreases in consumption between time points). Applied dietary pattern scores were then calculated by multiplying the coefficients from the PCA at the before-pregnancy time point by each individual’s standardized reported frequencies of consumption at the early and late pregnancy time points.
Natural PCA dietary scores are generated by definition with a mean of zero. The natural scores were divided by their standard deviation in order that the units of the scores were meaningful (standard deviation units). The applied scores were divided by the standard deviation of the before-pregnancy score, so that comparisons could be made in terms of change in standard deviation units.
Publication 2009
Alcoholic Beverages Bacon Beef Brassica napus Daucus carota Diet Food Meat Nutrients Parsnips Plant Roots Pregnancy Vegetables
The NCS-A interviews and parent SAQs assessed twelve CAs. These included three types of interpersonal loss (parental death, parental divorce, and other loss of contact with parents or caregivers), four types of parental maladjustment (mental illness, substance abuse, criminality, and family violence), four types of maltreatment (physical abuse, sexual abuse, emotional abuse, and neglect), and family economic adversity. Parental death and divorce were assessed only in regards to biological parents, not step-parents or other caregivers. The measure of other loss of contact with parents or caregivers, however, included any disruption of a relationship that lasted for six months or longer that either involved a caregiver leaving the respondent’s home (e.g., the biological mother abandoned the family) or the respondent leaving home (e.g., foster care placement or adoption). Respondents who were born to a single mother and never experienced any further disruption of this parenting arrangement were not coded as experiencing parental loss. We did not code separations from caregivers that involved the respondent being placed in a juvenile detention center or running away from home. We collected information on timing (i.e., the respondent’s age) for all parental loss events.
Physical and emotional abuse of the respondent by parents or caregivers were assessed with a modified version of the Conflict Tactics Scale (CTS).32 Sexual abuse was assessed with questions from the CIDI regarding sexual assault, attempted rape, and rape. Information was also collected on the age at which sexual abuse first occurred. Neglect was assessed with a battery of questions used in studies of child welfare that asked about frequency of not having adequate food, clothing, or medical care, having inadequate supervision, and being required to do chores that were age-inappropriate.33 Parental criminality was assessed with questions in the CIDI and the SAQ about whether a parent either engaged in criminal activities like burglary or selling stolen property or was ever arrested or sent to prison for criminal activity.5 (link) Parental mental illness (major depression, GAD, panic disorder, suicide attempt) and substance abuse were assessed with the Family History Research Diagnostic Criteria (FHRDC) Interview34 and its extensions,35 (link) as well as with items completed by parents in the SAQ. Family violence was assessed with the modified CTS and an item in the trauma section of the CIDI on the respondent’s age when they first observed inter-parental violence. Economic adversity was assessed with questions in the SAQ about whether the respondent’s family received welfare or other government assistance or often did not have enough money to pay for basic necessities of living.
Publication 2012
Abuse, Emotional Abuse, Physical Biopharmaceuticals Brassica napus Childbirth Child Welfare Criminals Diagnosis Food Major Depressive Disorder Mental Disorders Mothers Panic Disorder Parent Physical Examination Sexual Abuse Sexual Assault Step-Parent Substance Abuse Suicide Attempt Supervision Wounds and Injuries

Most recents protocols related to «Brassica napus»

We used a modified version of the Life Events Checklist for DSM-5 to measure exposure to twelve specific, contextually relevant lifetime PTEs. Events of interest included: seeing people hitting or harming one another in your family as a child, physical assault or abuse as a child, sexual assault or rape as a child, physical assault or abuse as an adult from an intimate partner, physical assault or abuse in adulthood from someone other than an intimate partner, sexual assault or rape in adulthood, seeing someone physically assaulted or abused, seeing someone seriously injured or killed, experiencing a natural disaster, experiencing a serious accident or fire, exposure to war, and losing a child through death. One additional question asked individuals to identify any other traumatizing event experienced during childhood or adulthood. We explored the free response text describing any “other” type of experienced lifetime traumatic events and recategorized these events if they fit more appropriately in a pre-defined category (e.g., one individual who reported death of a child through childbirth had not reported loss of a child to death. This event was recoded to loss of a child to death).
For analytic purposes, similar events were further combined such that seven distinct event types were considered: trauma during childhood, experiencing violence in adulthood, witnessing violence in adulthood, accidents, death of a child, war, and any other PTE. We also created a dichotomous variable to represent individuals who were and were not in the top quarter of number of PTEs reported. Individuals in the top quarter reported 6 or more PTEs.
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Publication 2023
Abuse, Child Accidents Adult Brassica napus Child Childbirth Menopause Natural Disasters Physical Examination Sexual Assault
Individuals were asked about exposure to lifetime traumatic events including physical assault or abuse as an adult from an intimate partner and sexual assault or rape in adulthood, as described above. In addition, individuals also completed the Demographic and Health Survey (DHS) domestic violence module which captures four distinct domains of IPV: controlling behavior and emotional, sexual, and physical IPV [37 ]. This tool is a modified version of the Conflict Tactics Scale and asks respondents if they have experienced 15 separate behaviorally-specific types of IPV [38 (link)]. In our prior work, we noted discrepancies between reports of physical and sexual violence on the DHS domestic violence module and the modified version of the Life Events Checklist for DSM-5 used in the assessment of lifetime PTEs in this analysis [39 ]. Thus, we considered individuals who reported physical IPV with their most recent partner on the DHS domestic violence module, but did not report physical assault or abuse from a partner in adulthood on the PTE assessment to have experienced physical assault or abuse in adulthood from a partner in this analysis. Similarly, we considered individuals who reported sexual IPV with their most recent partner on the DHS domestic violence module but did not report sexual assault or rape as an adult on the PTE assessment to have experienced sexual assault or rape in adulthood.
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Publication 2023
Adult Brassica napus Domestic Violence Drug Abuse Emotions Menopause Physical Examination Sexual Assault Sexual Partners Sexual Violence
DELLA protein sequences of pumpkin (7), cucumber (4), melon (4), watermelon (4), Arabidopsis (5), soybean (7), Brassica napus (13), rice (1), tomato (2) and maize (3) were retrieved from cucurbit genomics database, TAIR and Ensembl database (http://plants.ensembl.org/index.html), respectively. Based on multiple sequence alignment, phylogenetic tree was created using the neighbor-joining (NJ) method with MEGA 7.0. The conserved domains were analyzed by the NCBI CDD, and the conserved motifs were predicted by MEME (https://meme-suite.org/meme/). Furthermore, the distribution maps of conserved domains and conserved motifs were visualized using TBtools v 1.0986961. Promoter sequences (2 kp before the start codon) of CmoDELLA genes were analyzed through online PlantCare (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/) to obtain cis-regulatory elements. Interaction networks between CmoDELLA proteins and other proteins were conducted through online STRING (https://string-db.org/), using Arabidopsis as reference species.
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Publication 2023
Amino Acid Sequence Arabidopsis Base Sequence Brassica napus Codon, Initiator Cucumis Genes Lycopersicon esculentum Maize Melons Microtubule-Associated Proteins Plants Proteins Pumpkins Regulatory Sequences, Nucleic Acid Rice Soybeans Watermelon
Protein sequences of AGO1 paralogs and orthologs from Arabidopsis thaliana and representative species were acquired from Uniprot (https://www.uniprot.org/), including 10 Arabidopsis thaliana AGOs, AGO1 (O04379), AGO2 (Q9SHF3), AGO3 (Q9SHF2), AGO4 (Q9ZVD5), AGO5 (Q9SJK3), AGO6 (O48771), AGO7 (Q9C793), AGO8 (Q3E984), AGO9 (Q84VQ0), and AGO10 (Q9XGW1), Arabidopsis lyrata AGO1 (D7KD09), Brassica napus AGO1 (A0A078JMZ3), Glycine max AGO1a (I1MQL3), Oryza sativa AGO1a (Q6EU14), and Zea mays AGO1a (A0A096TTL7). Protein sequence alignments were conducted by MUSCLE [59 (link)] (https://www.ebi.ac.uk/Tools/msa/muscle/) with default settings, and figures were made using ESPript3 [60 (link)] (https://espript.ibcp.fr).
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Publication 2023
Amino Acid Sequence Arabidopsis Arabidopsis thalianas Brassica napus EIF2C2 protein, human Muscle Tissue Oryza sativa Proteins Sequence Alignment Soybeans Zea mays
The cows mainly grazed pasture of perennial ryegrass (Lolium perenne) mixed with red clover (Trifolium pretense) and white clover (Trifolium repens). Besides pasture, cows grazed chicory (Cichorium intybus) in spring. To meet energy requirements and to cope with the seasonal changes in pasture quality and production (Machado et al., 2005 (link)), cows were also fed additional supplements including maize silage (Zea mays) and turnips (Brassica rapa) on various days during the summer and autumn seasons along with main feed (pasture). Supplementary feeds are used when quality pasture is less available, to fill the feed deficits and to support the cows to maintain energy intake and production (DairyNZ, 2022 ). The supplements were only used to provide energy when there was insufficient pasture available especially during summer and autumn. Moreover, the purpose of providing supplements to milking cows in autumn is also to achieve calving body condition score (BCS) targets, if the feeds are not supplemented, cows are more prone to lose as quality pasture is insufficient at that time of the year. Maize silage and turnip stems and leaves as such (in situ) were fed around midday in the paddock. The cows had ad libitum access to drinking water.
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Publication 2023
Brassica napus Brassica rapa Cattle Cichorium intybus Clover Human Body Lolium Silage Stem, Plant Training Programs Trifolium Trifolium pratense Trifolium repens Zea mays

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More about "Brassica napus"

Brassica napus, also known as rapeseed or canola, is a widely cultivated plant species belonging to the Brassicaceae family.
It is an important oilseed crop grown for its edible oil and high-protein meal.
The plant is characterized by its lobed leaves, yellow flowers, and distinctive seed pods.
Brassica napus is native to Europe and is now grown extensively around the world, including in North America, Europe, and Asia.
Research on Brassica napus focuses on improving yield, oil quality, and disease resistance to enhance its agricultural and commercial value.
Researchers can utilize tools like PubCompare.ai to easily locate the most accurate and reproducible protocols from literature, pre-prints, and patents.
This can help optimize their Brassica napus studies and enhance the reliability of their findings.
When conducting Brassica napus research, scientists may use a variety of techniques and materials, such as TRIzol reagent for RNA extraction, the DNeasy Plant Mini Kit for DNA purification, and Sodium hydroxide for sample preparation.
Additionally, they may employ qPCR methods using reagents like FastStart Universal SYBR Green Master or Power SYBR Green PCR Master Mix, and utilize equipment like the Agilent 7900 for gene expression analysis.
For sample cleanup and fractionation, researchers may use Whatman filter paper or Reversed-phase Sep-Pak C18 Plus cartridges.
They may also work with plasmids like the FL10BLB or the PMD18-T vector for genetic engineering and transformation experiments.
By leveraging these tools and techniques, scientists can enhance the accuracy and reliability of their Brassica napus studies, leading to improved understanding and advancements in this important crop species.