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> Disorders > Cell or Molecular Dysfunction > Inversion, Chromosome

Inversion, Chromosome

Inversion, Chromosome: A chromosomal aberration in which a segment of a chromosome is reversed in its orientation.
This may ocur during meiosis or mitosis and can be detected using banded karyotype analysis.
Chromosomal inversions are associated with certain genetic disorders and cancers, and can impact gene expression and phenotypic traits.
Identifying and understanding chromosomal inversions is an important aspect of cytogenetic analysis and genomic research.

Most cited protocols related to «Inversion, Chromosome»

1
Simulating E. coli Genome Evolution
The complete genome of E. coli K-12 W3110 [112 (link)], was downloaded from RefSeq (AC_000091). This genome was used as the ancestral genome and evolution was simulated along a balanced tree for three evolutionary rates using the Seq-Gen package [113 (link)] with parameters mHKY -t4.0 -l4646332 -n1 -k1 and providing the corresponding binary tree evolved at three evolutionary rates: 0.00001, 0.0001, and 0.001 SNPs per site, per branch. This corresponds to a minimum percent identity of approximately 99%, 99.9%, and 99.99% between the two most divergent genomes, respectively, reflecting the variation seen in typical outbreak analyses. No small (<5 bp) or large Indels were introduced, but an average of 10 1 Kbp rearrangements (inversions and translocations) were added, per genome, using a custom script [114 ]. Paired reads were simulated to model current MiSeq lengths (2 × 150 bp) and error rates (1%). Moderate coverage, two million PE reads (64X coverage), was simulated for each of the 32 samples using wgsim (default parameters, no Indels), from samtools package version 0.1.17 [55 (link)].
Two of the simulated read sets were independently run through iMetAMOS [93 (link)] to automatically determine the best assembler. The consensus pick across both datasets was SPAdes version 3.0 [81 (link)], which was subsequently run on the remaining 30 simulated read sets using default parameters. The final contigs and scaffolds files were used as input to the genome alignment methods. For mapping methods, the raw simulated reads were used. For accuracy comparisons, Indels were ignored and called SNPs were required to be unambiguously aligned across all 32 genomes (that is, not part of a subset relationship; SNPs present but part of a subset relationship were ignored).
Treangen T.J., Ondov B.D., Koren S, & Phillippy A.M. (2014). The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15, 524.
Publication 2014
Biological Evolution Escherichia coli Gene Rearrangement Genome INDEL Mutation Inversion, Chromosome Single Nucleotide Polymorphism Translocation, Chromosomal Trees Vision
2
Calculating Relative Efficiency in CASL
All image data were saved as raw echo intensities and reconstructed offline with custom software. Partial Fourier raw data was acquired at lines –m ≤ u ≤ N/2 (m = 6, N= 64). The low frequency phase map of each coil was estimated from the Fourier transformation of the image generated by Hanning filtering the center portion of the raw data at lines –m ≤ u ≤ m. The final image was combined from each coil image, weighted by the conjugate of the corresponding low resolution phase map. A Region of interest (ROI) for each subject was defined to contain the entire brain.
For the first study, the relative combined inversion efficiency was defined as the ratio of the PCASL average difference signal when control and label are set below the brain to the average CASL difference signal after compensating for the duty cycle difference (dividing the CASL difference signal by dcycle). dcycle is the duty cycle of continuous ASL, which is 53.33% in our study. Previous simulations of adiabatic fast passage demonstrate that the labeling efficiency may not have a linear relationship with the RF duty cycle in the pulsed-form CASL(32 (link)). Simulation was performed to calculate the mean labeling efficiency for the laminar flow across the different time when spin passes through the labeling plane. The simulation result shows that the relative efficiency is within 2% difference with the RF duty cycle. This linearity between the RF duty cycle and labeling efficiency is likely valid because of the long pulse period (375 ms) used in the CASL sequence. This improvement with longer labeling blocks (A pulse period of 100 ms was better approximated by a linear relationship than a pulse period of 20 ms) was suggested in previously reported simulations (32 (link)). The relative efficiency loss of the control pulse was defined as the ratio of the PCASL average difference signal when the control is set below the brain compared with above the brain to the average CASL difference signal after compensating for the duty cycle difference. Because of the very low SNR in the average difference signal between controls in PCASL, we used the low-resolution phase map from the average difference signal between control and label when applied below the brain to phase correct the images from each coil. The relative systematic error between control and label pulses was defined as the ratio of the average PCASL difference signal between control and label when applied above the brain to the average CASL difference signal after compensating for the duty cycle difference. The relative efficiency of labeling pulse was defined as the ratio of the PCASL average difference signal when the label is set below the brain compared with above the brain to the average CASL difference signal after compensating for the duty cycle difference. We used low-resolution phase maps to correct the phase of the image from each coil as in the relative efficiency calculation of control pulse.
For the second study the relative combined efficiency described for the first study was employed. For the third study, frequency-dependent off-resonance saturation effects were analyzed by averaging the difference images (between the control and label images) across the phase direction.
Dai W., Garcia D., de Bazelaire C, & Alsop D.C. (2008). Continuous Flow Driven Inversion for Arterial Spin Labeling Using Pulsed Radiofrequency and Gradient Fields. Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 60(6), 1488-1497.
Publication 2008
Brain ECHO protocol Inversion, Chromosome Microtubule-Associated Proteins Pulse Rate Pulses Spin Labels Vibration
3
Structural Variant Detection in Maize Genomes
Leaves were used to prepare high molecular mass DNA and optical genome maps were constructed as described above for B73. Structural variant calls were generated based on alignment to the reference map B73 v4 chromosomal assembly using the multiple local alignment algorithm (RefSplit)32 (link). A structural variant was identified as an alignment outlier32 (link),49 (link), defined as two well-aligned regions separated by a poorly aligned region with a large size difference between the reference genome and the map or by one or more unaligned sites, or alternatively as a gap between two local alignments. A confidence score was generated by comparing the non-normalized P values of the two well-aligned regions and the non-normalized log-likelihood ratio50 (link) of the unaligned or poorly aligned region. With a confidence score threshold of 3, RefSplit is sensitive to insertions and deletions as small as 100 bp (events smaller than 1 kb are generally compound or substitution and include label changes, not just spacing differences) and other changes such as inversions and complex events which could be balanced. Insertion and deletion calls were based on an alignment outlier P-value threshold of 1 × 10−4. Insertions or deletions that crossed gaps in the B73 pseudomolecules, or that were heterozygous in the optical genome maps, were excluded. Considering the resolution of the BioNano optical map, only insertion and deletions larger than 100 bp were used for subsequent analyses. To obtain high-confidence deletion sequences, sequencing reads from the maize HapMap2 project8 (link) for Ki11 and W22 were aligned to our new B73 v4 reference genome using Bowtie2 (ref. 51 (link)). Read depth (minimum mapping quality >20) was calculated in 10-kb windows with step size of 1 kb. Windows with read depth below 10 in Ki11 and 20 in W22 (sequencing depths for Ki11 and W22 were 2.32× and 4.04×, respectively) in the deleted region were retained for further analysis.
Jiao Y., Peluso P., Shi J., Liang T., Stitzer M.C., Wang B., Campbell M.S., Stein J.C., Wei X., Chin C.S., Guill K., Regulski M., Kumari S., Olson A., Gent J., Schneider K.L., Wolfgruber T.K., May M.R., Springer N.M., Antoniou E., McCombie W.R., Presting G.G., McMullen M., Ross-Ibarra J., Dawe R.K., Hastie A., Rank D.R, & Ware D. (2017). Improved maize reference genome with single-molecule technologies. Nature, 546(7659), 524-527.
Publication 2017
6H,8H-3,4-dihydropyrimido(4,5-c)(1,2)oxazin-7-one BP 100 Chromosomes Deletion Mutation Gene Deletion Genome Heterozygote Inversion, Chromosome Maize Vision
4
SURVIVOR: Simulating and Evaluating Structural Variations
We developed the SURVIVOR tool kit for assessing SVs for short-read data that contains several modules. The first module simulates SVs given a reference genome file (fasta) and the number and size ranges for each SV (insertions, deletions, duplications, inversions and translocations). After reading in the reference genome, SURVIVOR randomly selects the locations and size of SV following the provided parameters. Subsequently, SURVIVOR alters the reference genome accordingly and prints the so altered genome. In addition, SURVIVOR provides an extended bed file to report the locations of the simulated SVs.
The second module evaluates SV calls based on a variant call format (VCF) file56 (link) and any known list of SVs. A SV was identified as correct if (i) they were of same type (for example, deletion); (ii) they were reported on same chromosome and (iii) the start and stop coordinates of the simulated and identified SV were within 1 kb (user definable).
The third module of SURVIVOR was used to filter and combine the calls from three VCF files. In our case, these files were the results of DELLY, LUMPY and Pindel. This module includes methods to convert the method-specific output formats to a VCF format. SVs were filtered out if they were unique to one of the three VCF files. Two SVs were defined as overlapping if they occur on the same chromosome, their start and stop coordinates were within 1 kb, and they were of the same type. In the end, SURVIVOR produced one VCF file containing the so filtered calls. SURVIVOR is available at github.com/fritzsedlazeck/SURVIVOR.
Jeffares D.C., Jolly C., Hoti M., Speed D., Shaw L., Rallis C., Balloux F., Dessimoz C., Bähler J, & Sedlazeck F.J. (2017). Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature Communications, 8, 14061.
Publication 2017
Chromosomes Deletion Mutation Gene Deletion Genome Insertion Mutation Inversion, Chromosome Survivors Translocation, Chromosomal
5
Assembly Quality Evaluation Protocol
We assessed the quality of the assemblies by using several parameters of general use (18 (link)). These include, number of contigs, N50, and genome completeness expressed as the ratio of the observed versus expected assembly size (18 (link)). For assemblies of simulated data the expected assembly size was known. We inferred the presence of redundant contigs/scaffolds if the assembly had a size larger than the reference. On the other hand, a smaller than expected assembly informed about the extent of missing reference genome regions. In addition, we analyzed the accuracy of each assembly by visual inspection of the alignments of its contigs/scaffolds and the reference chromosomes. The pairwise genome alignments were created and visualised using NUCmer v3.1 (19 (link)). The resulting alignments were filtered, keeping only the best alignment for each region from the query sequence, so called many-to-one mode. Subsequently, we counted large rearrangements, namely deletions, inversions or translocations, between every assembly and the respective reference genome. Additionally, we marked the reference sequences missing from each assembly. Finally, we checked by pairwise alignment of the de novo assemblies against the reference chromosomes, whether observed rearrangements originated from the original contigs/scaffolds (SPAdes or SOAPdenovo2) or were introduced during scaffolding. If a particular rearrangement was absent from the respective de novo assembly, we concluded it was introduced during the scaffolding step.
Pryszcz L.P, & Gabaldón T. (2016). Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Research, 44(12), e113.
Publication 2016
Chromosomes Gene Deletion Gene Rearrangement Genome Inversion, Chromosome Translocation, Chromosomal

Most recents protocols related to «Inversion, Chromosome»

1
Pre-Hydrolysis of Infant Formula with Lipase
Not available on PMC !

EXAMPLE 8

Rhizopus oryzae (RO) lipase was covalently bound to acrylic beads and contained in a device resembling a teabag. Enfalac infant formula (25 g) was combined with tap water (88 mL) at 37° C. Reactions were carried out in a glass bottle with 100 mL of infant formula and a tea bag containing either 100, 500, 1000, or 2000 mg of immobilized RO lipase. Each reaction was incubated at 37° C. for 30 minutes with inversion. Samples were taken at the following timepoints: 0, 1, 2, 3, 4, 5, 10, 20, and 30 minutes. Samples were analyzed for DHA and ARA by reverse phase high performance liquid chromatography (RP-HPLC).

At each concentration of immobilized RO lipase, the percent hydrolysis of DHA and ARA increased as the amount of immobilized RO lipase increased (FIGS. 27A-27D). These data demonstrate the feasibility of the tea bag device for pre-hydrolyzing formula with lipase.

US11872191B2. Methods, compositions, and devices for supplying dietary fatty acid needs (2024-01-16). Alcresta Therapeutics, Inc. [US]. Inventors: Alexey L. Margolin [US], Robert Gallotto [US], Bhami Shenoy [US].
Patent 2024
Figs High-Performance Liquid Chromatographies Hydrolysis Infant Formula Inversion, Chromosome Lipase Medical Devices Rhizopus oryzae
2
Polymer Membrane Characterization by SEM
Not available on PMC !

Example 2

A non-filled and a filled polymer membrane were prepared by a different phase inversion process in accordance with U.S. Pat. No. 8,147,732. Scanning electron microscopy images were taken and are shown in FIG. 4 and FIG. 5, respectively. FIG. 4 shows the formation of a porous material. FIG. 5 shows that the fillers are fully covered by the polymer, in other words, there is no exposed surface area of the filler.

US11870058B2. Method of forming a composition and the composition formed therefrom (2024-01-09). TEEBS R&D, LLC [US]. Inventors: Trevor Beard [US].
Patent 2024
Inversion, Chromosome Polymers Scanning Electron Microscopy Tissue, Membrane
3
Cardiac Magnetic Resonance Imaging for LV Function
All participants were scheduled to have CMR-LGE examination just before each CPET. CMR-LGE examination involved a 3.0-Tesla Skyra scanner (Siemens Medical Systems, Erlangen, Germany) operating on the VD13 platform with a 32-channel phased-array receiver body coil. Short-axis (contiguous 8-mm-thick slices) and standard long-axis view (2-, 3- and 4-chamber views) cine images were obtained by steady-state free precession (SSFP) cine imaging with the following parameters: repetition time, 45 ms; echo time, 1.4 ms; matrix, 256 × 256; and field of view, 34 to 40 cm. LV geometry as well as functions, including LV end-diastolic volume (LVEDV), LV end-systolic volume (LVESV), resting CO (COrest), LVEF, LV mass, and left ventricle wall motion (LVWMS) were determined using SSFP cine imaging. The lower the LVWMS is, the better the LV contractility [28 (link)].
Quantitative parametric images of myocardial extracellular volume (ECV) fractions were acquired from longitudinal relaxation time (T1) mapping in short-axis slices before (pre) and after (post) contrast medium enhancement. The ECV was estimated by the following equation: ECV=(1-hematocrit)(1T1myopost-1T1myopre)(1T1bloodpost-1(T1bloodpre)
The CMR-LGE system determines the T1 in each myocardial segment. Myocardial fibrosis was estimated with a modified Look-Locker inversion-recovery (MOLLI) sequence [15 (link)] acquired during the end-expiratory phase in the basal, middle and apical LV myocardial segments at short-axes before (T1myo pre) and approximately 15 to 20 min after (T1myo post) a 0.1 mmol/kg intravenous dose of gadolinium-DOTA (gadoterate meglumine, Dotarem, Guerbet S.A., France). The ECV value was further normalized by the blood T1 mapping image before (T1blood pre) and after (T1blood post) enhancement in the corresponding short-axis slices. The basal slice (Base), mid-cavity slice (Middle), and apical slice (Apex) of LV myocardial segments [29 (link)] were drawn along the epicardial and endocardial surfaces on matched pre- and post-contrast MOLLI images to identify the myocardium for ECV analysis.
Hsu C.C., Wang J.S., Shyu Y.C., Fu T.C., Juan Y.H., Yuan S.S., Wang C.H., Yeh C.H., Liao P.C., Wu H.Y, & Hsu P.H. (2023). Hypermethylation of ACADVL is involved in the high-intensity interval training-associated reduction of cardiac fibrosis in heart failure patients. Journal of Translational Medicine, 21, 187.
Publication 2023
BLOOD Cardiovascular System Clostridium perfringens epsilon-toxin Dental Caries Diastole Dotarem ECHO protocol Endocardium Epistropheus Exhaling Fibrosis Gadolinium gadolinium 1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetate gadoterate meglumine Human Body Inversion, Chromosome Left Ventricles Muscle Contraction Myocardium Sequence Inversion Systole Volumes, Packed Erythrocyte
4
Multimodal Brain Imaging Protocol
A Siemens (Munich, Germany) 3 T Prisma scanner with a standard 64-channel head coil was used to acquire fMRI imaging. All participants were placed in the supine position and tried their best to keep heads as still as possible while acquiring images. The detailed parameters of the multi-slice T2-weighted echo-planar imaging (EPI) sequence were as follows: TR = 2000 ms; TE = 30 ms; FOV = 100 mm; flip angle = 90°; matrix dimensions = 64 × 64; slice thickness = 3.5 mm; and number of slices = 33. Three-dimensional T1-weighted images were acquired with the following parameters: TR = 2,530 ms; TE = 2.98 ms; FOV = 256 × 224 mm2; inversion time = 1,100 ms; flip angle = 7°; matrix size = 224 × 256;, sagittal slices = 192; slice thickness = 1.0 mm; and voxel size = 0.5 × 0.5 × 1 mm3. The BOLD-fMRI gradient EPI sequence acquisition parameters were as follows: TR = 500 ms; TE = 30 ms; matrix dimensions = 64 × 64; FOV = 244 mm × 244 mm; slices thickness = 3.5 mm; voxel size = 3.5 mm × 3.5 mm; number of slices = 960, and scan time = 8 min.
Wu J., Fang Y., Tan X., Kang S., Yue X., Rao Y., Huang H., Liu M., Qiu S, & Yap P.T. (2023). Detecting type 2 diabetes mellitus cognitive impairment using whole-brain functional connectivity. Scientific Reports, 13, 3940.
Publication 2023
fMRI Head Inversion, Chromosome prisma Radionuclide Imaging
5
Comparative Synteny Analysis of Nematode Genomes
For nucleotide-based comparative synteny analysis, we ran lastz77 (version 1.04.00) with the notransition and nogapped options and step = 20 to search for homologous sequences of two genomic sequences, the P. pacificus reference genome versus the P. exspectatus de novo assembly. For P. pacificus, the ‘El_Paco’ reference genome was used36 (link). Only homology at unique sites in the P. exspectatus genome was selected. Pairs of 100 kb non-overlapping sliding windows of the two genome sequences having at least 10 kb sequence homology are visualized in the circos plot (Fig. 2a). To visualize any small homology in the dot-plot analysis, we calculated the P. pacificus genome coordinate homologous to any nucleotides of P. exspectatus as distance from the start site of homology divided by the length of homology. The plot is downsized by 1/100 for visualization. Inversions larger than 100 kb were detected manually from dot-plot analysis, and the position was identified in the 10 kb scale.
For the protein-based comparative synteny analysis, one-to-one orthologues between species were identified as best reciprocal hits with the help of the get_BRH.pl script from the Perl Package for Customized Annotation Computing package73 (link). For C. elegans, the dataset of WormBase ParaSite release 14 (https://parasite.wormbase.org) was used.
Yoshida K., Rödelsperger C., Röseler W., Riebesell M., Sun S., Kikuchi T, & Sommer R.J. (2023). Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. Nature Ecology & Evolution, 7(3), 424-439.
Publication 2023
Caenorhabditis elegans Genome Homologous Sequences Inversion, Chromosome Nucleotides Parasites Proteins Synteny

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More about "Inversion, Chromosome"

Chromosomal Inversion: A Comprehensive Overview Chromosomal inversion is a type of chromosomal aberration where a segment of a chromosome is reversed in its orientation.
This phenomenon can occur during meiosis or mitosis and can be detected through banded karyotype analysis.
Chromosomal inversions are associated with certain genetic disorders, cancers, and can impact gene expression and phenotypic traits.
Understanding chromosomal inversions is crucial in cytogenetic analysis and genomic research.
Identifying and characterizing these structural variations can provide valuable insights into the underlying mechanisms of genetic diseases and inform personalized treatment approaches.
Magnetic resonance imaging (MRI) techniques, such as those utilized in the Discovery MR750, Tim Trio, Ingenia, MAGNETOM Prisma, and MAGNETOM Skyra systems, can be leveraged to support the investigation of chromosomal inversions.
These advanced imaging modalities, equipped with high-performance 32-channel head coils, enable detailed visualization and analysis of chromosomal structures.
Additionally, contrast agents like Gadovist and Dotarem can enhance the visualization of chromosomal features, while the Achieva 12-channel head coil can provide high-resolution imaging to aid in the identification and characterization of chromosomal inversions.
By combining cutting-edge MRI technology, specialized contrast agents, and a thorough understanding of chromosomal inversions, researchers and clinicians can optimize their research protocols, enhance reproducibility, and deliver consistent, high-quality results in the field of cytogenetics and genomics.