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Tail

Tail: The posterior, usually flexible, appendage of a vertebrate animal.
Tails vary in shape, size, and function, but often serve as a counterbalance, provide additional locomotion, or play a role in communication and social behavior.
Tails are found in a wide range of species, including mammals, reptiles, amphibians, and some fish.
They can be used for steering, balance, display, and even prehension in certain animals.
The study of tails and their anatomical and functional characteristics is an important area of zoological reseach.

Most cited protocols related to «Tail»

Some sequences, or even entire reads, can be overrepresented in FASTQ data. Analysis of these overrepresented sequences provides an overview of certain sequencing artifacts such as PCR over-duplication, polyG tails and adapter contamination. FASTQC offers an overrepresented sequence analysis module, however, according to the author’s introduction, FASTQC only tracks the first 1 M reads of the input file to conserve memory. We suggest that inferring the overall distribution from the first 1 M reads is not a reliable solution as the initial reads in Illumina FASTQ data usually originate from the edges of flowcell lanes, which may have lower quality and different patterns than the overall distribution.
Unlike FASTQC, fastp samples all reads evenly to evaluate overrepresented sequences and eliminate partial distribution bias. To achieve an efficient implementation of this feature, we designed a two-step method. In the first step, fastp completely analyzes the first 1.5 M base pairs of the input FASTQ to obtain a list of sequences with relatively high occurrence frequency in different sizes. In the second step, fastp samples the entire file and counts the occurrence of each sequence. Finally, the sequences with high occurrence frequency are reported.
Besides the occurrence frequency, fastp also records the positions of overrepresented sequences. This information is quite useful for diagnosing sequence quality issues. Some sequences tend to appear in the read head whereas others appear more often in the read tail. The distribution of overrepresented sequences is visualized in the HTML report. Figure 5 shows a demonstration of overrepresented sequence analysis results.
Publication 2018
Head Memory Poly G Sequence Analysis Tail

fastp supports automatic adapter trimming for both single-end and paired-end Illumina data and uses different algorithms for each of these tasks. For single-end data, adapter sequences are detected by assembling the high-frequency read tails; for paired-end data, adapter sequences are detected by finding the overlap of each pair.
The adapter-sequence detection algorithm is based on two assumptions: the first is that only one adapter exists in the data; the second is that adapter sequences exist only in the read tails. These two assumptions are valid for major next-generation sequencers like Illumina HiSeq series, NextSeq series and NovaSeq series. We compute the k-mer (k = 10) of first N reads (N = 1 M). From this k-mer, the sequences with high occurrence frequencies (>0.0001) are considered as adapter seeds. Low-complexity sequences are removed because they are usually caused by sequencing artifacts. The adapter seeds are sorted by its occurrence frequencies. A tree-based algorithm is applied to extend the adapter seeds to find the real complete adapter, which is described by the pseudo code in Algorithm 1.
In Algorithm 1, the function build_nucleotide_tree() is used to convert a set of sequences to a tree, in which each node is a nucleotide and each path of root to leaf is a sequence. A node’s dominant child is defined as its major child with a dominant percentage (>90%). This algorithm tries to extend an adapter seed in the forward direction to check its validity since a valid adapter can always be extended to the read tails. And if this adapter seed is valid, a backward extension is applied to obtain the complete adapter sequence. The process of extending an adapter seed in forward and backward directions is given in Figure 2.
For paired-end data, fastp seeks the overlap of each pair and considers the bases that fall out of the overlapped regions as adapter contents. The overlapping detection algorithm was derived from our previous work, AfterQC. Compared to sequence-matching-based adapter-trimming tools like Cutadapt and Trimmomatic, a clear advantage of the overlap-analysis-based method is that it can trim adapters with few bases in the read tail. For example, most sequence-matching-based tools require a hatchment of at least three bases and cannot trim adapters with only one or two bases. In contrast, fastp can trim adapters with even only one base in the tail.
Although fastp can detect adapter sequences automatically, it also provides interfaces to set specific adapter sequences for trimming. For SE data, if an adapter sequence is given, then automatic adapter-sequence detection will be disabled. For PE data, the adapter sequence will be used for sequence-matching-based adapter trimming only when fastp fails to detect a good overlap in the pair.
Publication 2018
Child Nucleotides Plant Leaves Plant Roots Tail Trees
The construction of KOGs followed the previously outlined strategy based on sets of consistent BeTs [9 (link),15 (link)], but included additional steps that reflected specific features of eukaryotic proteins. Briefly, the procedure was as follows. 1. Detection and masking of widespread, typically repetitive domains, which was performed by using the RPS-BLAST program and the PSSMs for the respective domains from the CDD collection [40 (link)]. These domains, namely, PPR (pfam01535), WD40 (pfam00400), IG (pfam00047), IGc1, Igv, IG_like, RRM (pfam00076), ANK (pfam00023), myosin tail (pfam01576), Fn3 (pfam00041), CA, (IG), ANK, kelch (pfam01344), OAD_kelch, SH3 (pfam00018), intermediate filaments (pfam00038), C2H2 finger (pfam00096), PDZ (pfam00595), POZ (pfam00651), PH (pfam00169), ZnF-C4 (pfam00105), spectrin (pfam00435), Sushi (pfam00084), TPR (pfam00017), BTB, LRR_CC, LY, ARM, SH2, and CH, were detected and masked prior to applying the COG construction procedure. Masking these domains was required to ensure the robust classification of the eukaryotic orthologous clusters with the KOG detection procedure because hits between these common, "promiscuous" domains resulted in spurious lumping of numerous non-orthologous proteins. 2. All-against-all comparison of protein sequences from the analyzed genomes by using the gapped BLAST program [58 (link)], with filtering for low sequence complexity regions performed using the SEG program [59 (link)]. 3. Detection of triangles of mutually consistent, genome-specific best hits (BeTs). 4. Merging triangles with a common side to form crude, preliminary KOGs. 5. Case by case analysis of each candidate KOG. This analysis serves to eliminate the false-positives that are incorporated in the KOGs during the automatic steps and included, primarily, examination of the domain composition of KOG members, which was determined using the RPS-BLAST program and the CDD collection of position-specific scoring matrices (PSSMs) for individual domains [40 (link)]. Generally, proteins were kept in the same KOG when they shared a conserved core domain architecture. However, in cases when KOGs were artificially bridged by multidomain proteins, the latter were split into individual domains (or arrays of domains) and steps (1)-(4) were repeated with these sequences; this results in the assignment of individual domains to KOGs in accordance with their distinct evolutionary affinities. 6. Assignment of proteins containing promiscuous domains. In cases when a sequence assigned to a KOG contained one or more masked promiscuous domains, these domains were restored and became part of the respective KOG. Proteins containing promiscuous domains but not assigned to any KOG were classified in Fuzzy Orthologous Groups (FOGs) named after the respective domains. 7. Examination of large KOGs, which included multiple members from all or several of the compared genomes by using phylogenetic trees, cluster analysis with the BLASTCLUST program , comparison of domain architectures, and visual inspection of alignments; as a result, some of these protein sets were split into two or more smaller ones that were included in the final set of KOGs.
The KOGs were annotated on the basis of the annotations available through GenBank and other public databases, which were critically assessed against the primary literature. For proteins that are currently annotated as "hypothetical" or "unknown", iterative sequence similarity searches with the PSI-BLAST program [58 (link)], the results of the RPS-BLAST searches, additional domain architecture analysis performed by using the SMART system [60 (link)], and comparison to the COG database by using the COGNITOR program (RLT, unpublished results) were employed to identify distant homologs with experimentally characterized functions and/or structures. The known and predicted functions of KOGs were classified into 23 categories (see legend to Fig. 4); these were modified from the functional classification previously employed for prokaryotic COGs [15 (link)] by including several specific eukaryotic categories.
Publication 2003
Amino Acid Sequence Biological Evolution Eukaryota Fingers Genome Intermediate Filaments Myosin ATPase Prokaryotic Cells Protein Domain Proteins Repetitive Region SET protein, human Spectrin Tail
Once the parcellation has been created, parcellated representations of data from each modality can be generated using either the group parcellation or the individual subject parcellations. For the statistical cross-validation, we created parcellated myelin, cortical thickness, task fMRI, and resting state functional connectivity datasets using the semi-automated multimodal group parcellation (see Supplementary Methods 7.1). For myelin and cortical thickness, we simply averaged the values of the dense individual subject maps within each area. For task fMRI, we averaged the time series within each area prior to computing task statistics (to benefit from the CNR improvements of parcellation demonstrated in Fig. 4e). For the same reason, we averaged resting state time series within each parcel prior to computing functional connectivity to form a parcellated functional connectome.
For each pair of areas that shared a border in the parcellation, we computed a paired samples two-tailed t-test across subjects on these parcellated data for each feature (ignoring tests that involved the diagonal in the resting state parcellated functional connectome). We thresholded these tests at the Bonferroni-corrected significance level of P < 9 × 10−8 (number of area pairs across both hemispheres (1,050) × number of features (266) × number of tails (2) × 0.05) and an effect size threshold of Cohen’s d > 1. We grouped the features into 4 independent categories (cortical thickness, myelin, task fMRI, and resting state fMRI) to determine for each area pair whether it showed robust and statistically significant differences across multiple modalities. For more details, see Supplementary Methods 7.2.
Publication 2016
Connectome Cortex, Cerebral fMRI Microtubule-Associated Proteins Multimodal Imaging Myelin Sheath Tail
Once the parcellation has been created, parcellated representations of data from each modality can be generated using either the group parcellation or the individual subject parcellations. For the statistical cross-validation, we created parcellated myelin, cortical thickness, task fMRI, and resting state functional connectivity datasets using the semi-automated multimodal group parcellation (see Supplementary Methods 7.1). For myelin and cortical thickness, we simply averaged the values of the dense individual subject maps within each area. For task fMRI, we averaged the time series within each area prior to computing task statistics (to benefit from the CNR improvements of parcellation demonstrated in Fig. 4e). For the same reason, we averaged resting state time series within each parcel prior to computing functional connectivity to form a parcellated functional connectome.
For each pair of areas that shared a border in the parcellation, we computed a paired samples two-tailed t-test across subjects on these parcellated data for each feature (ignoring tests that involved the diagonal in the resting state parcellated functional connectome). We thresholded these tests at the Bonferroni-corrected significance level of P < 9 × 10−8 (number of area pairs across both hemispheres (1,050) × number of features (266) × number of tails (2) × 0.05) and an effect size threshold of Cohen’s d > 1. We grouped the features into 4 independent categories (cortical thickness, myelin, task fMRI, and resting state fMRI) to determine for each area pair whether it showed robust and statistically significant differences across multiple modalities. For more details, see Supplementary Methods 7.2.
Publication 2016
Connectome Cortex, Cerebral fMRI Microtubule-Associated Proteins Multimodal Imaging Myelin Sheath Tail

Most recents protocols related to «Tail»

Not available on PMC !

Example 2

In the following experiments, a mouse model of RVO, which induces reproducible retinal edema was used. RVO is the model that was used for testing anti-VEGF therapies for DME. Brown et al., Ophthalmology 117, 1124-1133 el 121 (2010); and Campochiaro et al., Ophthalmology 117, 1102-1112 e1101 (2010). I n this model, Rose Bengal, a photoactivatable dye, is injected into the tail veins of adult C57B16 mice and photoactivated by laser of retinal veins around the optic nerve head. A clot is formed and edema or increased retinal thickness develops rapidly. Inflammation, also seen in diabetes, also develops.

Fluorescein leakage and maximal retinal edema, measured by fluorescein angiography and optical coherence tomography (OCT), respectively, using the Phoenix Micron IV, is observed 24 h after RVO. Retinal edema is maintained over the first 3 days RVO. By day 4 the edema decreases and the retina subsequently thins out. In addition to edema formation there is evidence of cell death in the photoreceptor cell layer by day 2 after RVO.

In this example, mice were anesthetized with intra-peritoneal (IP) injection of ketamine and xylazine. One drop of 0.5% alcaine was added to the eye as topical anesthetic. The retina was imaged with the Phoenix Micron IV to choose veins for laser ablation using the Phoenix Micron IV image guided laser. One to four veins around the optic nerve head were ablated by delivering a laser pulse (power 50 mW, spot size 50 μm, duration 3 seconds) to each vein.

Patent 2024
Adult Alcaine Cell Death Clotrimazole Diabetes Mellitus Edema Fluorescein Fluorescein Angiography Inflammation Injections, Intraperitoneal Ketamine Laser Ablation Mus Neoplasm Metastasis Optic Disk Photoreceptor Cells Pulse Rate Retina Retinal Edema Rose Bengal Tail Tomography, Optical Coherence Topical Anesthetics Vascular Endothelial Growth Factors Veins Veins, Central Retinal Vision Xylazine

Example 4

Through use of a lung metastasis model of mouse breast cancer 4T1 cells, the lung metastasis-suppressing effects of anti-S100A8/A9 monoclonal antibodies were investigated.

In accordance with a protocol illustrated in FIG. 9, 1×105 mouse breast cancer 4T1 cells and 50 μg of each anti-S100A8/A9 monoclonal antibody (Clone Nos.: 45, 85, 235, 258, and 260) were simultaneously injected into the tail vein of five Balb/c nu/nu mice per group, and 2 weeks later, CT scans were performed. FIG. 10 shows the results for comparing typical CT images and the areas of tumor cells calculated from the CT images to those of a negative control group. As a result, it was recognized that Clone No. 45 showed a significant lung metastasis-suppressing effect.

Patent 2024
Breast Clone Cells Lung Lung Cancer Malignant Neoplasm of Breast Mice, Inbred BALB C Mice, Nude Monoclonal Antibodies Mus Neoplasm Metastasis Neoplasms Tail Veins X-Ray Computed Tomography
Not available on PMC !

Example 11

Small molecule agonists of the Liver X Receptor (LXR) have previously been shown to increase Apo E levels. To investigate whether increasing Apo-E levels via LXR activation resulted in therapeutic benefit, assays were carried out to assess the effect of the LXR agonist GW3965 [chemical name: 3-[3-[N-(2-Chloro-3-trifluoromethylbenzyl)-(2,2-diphenylethyl)amino]propyloxy]phenylacetic acid hydrochloride) on Apo-E levels, tumor cell invasion, endothelial recruitment, and in vivo melanoma metastasis (FIG. 10). Incubation of parental MeWo cells in the presence of therapeutic concentrations of GW3965 increased expression of ApoE and DNAJA4 (FIGS. 10A and 10B). Pre-treatment of MeWO cells with GW3965 decreased tumor cell invasion (FIG. 10C) and endothelial recruitment (FIG. 10D). To test whether GW3965 could inhibit metastasis in vivo, mice were administered a grain-based chow diet containing GW3965 (20 mg/kg) or a control diet, and lung metastasis was assayed using bioluminescence after tail-vein injection of 4×104 parental MeWo cells into the mice (FIG. 10E). Oral administration of GW3965 to the mice in this fashion resulted in a significant reduction in in vivo melanoma metastasis (FIG. 10E).

Patent 2024
Administration, Oral agonists Apolipoproteins E Cardiac Arrest Cells Cereals Diet Endothelium GW 3965 Liver X Receptors Lung Malignant Neoplasms Melanoma Mus Neoplasm Invasiveness Neoplasm Metastasis Parent phenylacetic acid Tail Veins
Not available on PMC !

Example 7

ncRNA performance can be modified by adding a cap structure to the 5′ end and/or adding a poly(A) tail at the 3′ end, as depicted in FIG. 55. As shown in FIG. 56, using ncRNA with either or both protection by cap and tail lowered indels as compared uncapped/untailed ncRNAs. In this experiment, a 4 component all-RNA system (RT mRNA+Cas9 mRNA+ncRNA-sgRNA+sgRNA) was delivered to HEK293T cells by Lipofectamine MessengerMAX. All RNA was transfected at a fixed amount RT mRNA 100 ng, ncRNA-sgRNA 400 ng, Cas9 mRNA 100 ng, and sgRNA 5 ng. ncRNA-gRNA fusion was either capped (+cap −tail) or poly-A tailed (−cap +tail) or both capped and poly-A tailed (+cap +tail). Using RNA without end protection (−cap −tail) produced ˜4.5% precise edits and the editing was dependent on retron since the absence of RT abrogated precise editing. Using RNA with either or both protection by cap and tail produced lower precise editing (left graph) but lowered indels (right graph) than without cap and tail.

Patent 2024
Cells INDEL Mutation Lipofectamine RNA, Messenger RNA, Untranslated Tail
Not available on PMC !

Example 14

CD1 mice were fasted for overnight and then administrated with certain amount of peptides through either i.v. or s.c. route. After 6 hours, mice were orally or intraperitoneally administrated with bolus dose of glucose solution at 2 g/kg body mass at concentration of 100 mg/mL and their tail blood glucose levels were measured before (0 min) and after glucose challenge for 2 to 3 hours.

Exemplary data for mTA4 and mTA37 (see Table 6) are shown in FIG. 13 (n=5 for both). Both mTA4 and mTA37 are functional in wild-type mice. The data indicate increased oral glucose tolerance after administration of mTA. OGTT results for mTA4 demonstrated that mTA4 had a greater effect than exendin-4 at 6 hours after a single i.v. dose of mTA.

Patent 2024
Blood Glucose Exenatide Glucose Glucose Tolerance Test Human Body Mice, House Oral Glucose Tolerance Test Peptides Suby's G solution Tail

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D-glucose is a type of monosaccharide, a simple sugar that serves as the primary source of energy for many organisms. It is a colorless, crystalline solid that is soluble in water and other polar solvents. D-glucose is a naturally occurring compound and is a key component of various biological processes.

More about "Tail"

Tails are fascinating appendages found in a diverse array of vertebrate species, including mammals, reptiles, amphibians, and even some fish.
These posterior appendages come in a wide variety of shapes, sizes, and functions, serving as counterbalances, providing additional locomotion, and playing crucial roles in communication and social behavior.
Tails can be used for steering, balance, display, and even prehension in certain animals.
The study of tails and their anatomical and functional characteristics is an important area of zoological research.
Tail-related terms and concepts include vertebrate, appendage, counterbalance, locomotion, communication, social behavior, steering, balance, display, prehension, and zoology.
Specific products and techniques related to tails include STZ (streptozotocin) for inducing diabetes in animal models, Accu-Chek for glucose monitoring, FBS (fetal bovine serum) for cell culture, Rat tail collagen type I for tissue engineering, Matrigel for cell culture and assays, Accu-Chek Performa for continuous glucose monitoring, Pertussis toxin for immune modulation, BP-98A for cardiovascular research, and D-glucose for energy metabolism studies.
The versatility and importance of tails in the animal kingdom make them a fasincating subject of scientific inquiry.