A Cassette Approach for the Identification of Intein Insertion Sites

AbstractThe integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.

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Automatic modelling of human musculoskeletal ligaments – Framework overview and model quality evaluation

Technology and Health Care ◽

10.3233/thc-202550 ◽

2021 ◽

pp. 1-14

Author(s):

Noura Hamze ◽

Lukas Nocker ◽

Nikolaus Rauch ◽

Markus Walzthöni ◽

Matthias Harders ◽

...

Keyword(s):

Statistical Model ◽

Soft Tissues ◽

Automatic Generation ◽

Cadaveric Study ◽

Patient Specific ◽

Mean Square ◽

Shape Modelling ◽

Morphological Studies ◽

Insertion Sites ◽

Mean Square Errors

BACKGROUND: Accurate segmentation of connective soft tissues in medical images is very challenging, hampering the generation of geometric models for bio-mechanical computations. Alternatively, one could predict ligament insertion sites and then approximate the shapes, based on anatomical knowledge and morphological studies. OBJECTIVE: In this work, we describe an integrated framework for automatic modelling of human musculoskeletal ligaments. METHOD: We combine statistical shape modelling with geometric algorithms to automatically identify insertion sites, based on which geometric surface/volume meshes are created. As clinical use case, the framework has been applied to generate models of the forearm interosseous membrane. Ligament insertion sites in the statistical model were defined according to anatomical predictions following a published approach. RESULTS: For evaluation we compared the generated sites, as well as the ligament shapes, to data obtained from a cadaveric study, involving five forearms with 15 ligaments. Our framework permitted the creation of models approximating ligaments’ shapes with good fidelity. However, we found that the statistical model trained with the state-of-the-art prediction of the insertion sites was not always reliable. Average mean square errors as well as Hausdorff distances of the meshes could increase by an order of magnitude, as compared to employing known insertion locations of the cadaveric study. Using those, an average mean square error of 0.59 mm and an average Hausdorff distance of less than 7 mm resulted, for all ligaments. CONCLUSIONS: The presented approach for automatic generation of ligament shapes from insertion points appears to be feasible but the detection of the insertion sites with a SSM is too inaccurate, thus making a patient-specific approach necessary.

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The use of retrotransposons as markers for mapping genes responsible for fitness differences between related Drosophila melanogaster strains

Genetics Research ◽

10.1017/s0016672300031712 ◽

1993 ◽

Vol 62 (2) ◽

pp. 125-131 ◽

Cited By ~ 8

Author(s):

Sergey V. Nuzhdin ◽

Peter D. Keightley ◽

Elena G. Pasyukova

Keyword(s):

Drosophila Melanogaster ◽

Molecular Markers ◽

Maximum Likelihood ◽

Quantitative Trait ◽

Pericentromeric Region ◽

Related Strain ◽

Gene Frequencies ◽

Ha Gene ◽

Insertion Sites ◽

Additional Locus

SummaryHitch-hiking of dispersed mobile elements serving as molecular markers was used as a new tool for mapping quantitative trait loci in Drosophila melanogaster. Two Drosophila strains with high fitness (HA) were backcrossed repeatedly to a closely related strain with low fitness (LA) to initiate experimental populations with expected HA gene frequencies of 1/32. The frequencies of 19 insertion sites of the retrotransposons mdg1 and copia were analyzed after 11 to 17 generations. Frequencies of sites from the HA line increased substantially in the pericentromeric region, indicating that one or more loci responsible for the fitness difference between the strains were located there. A maximum likelihood (ML) procedure was applied to estimate selection coefficients associated with the markers, and this indicated a broad, strongly selected region of the chromosome. At least one additional locus was localized in the middle of the 2L arm. Possible applications of this method are discussed.

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Tn5406, a New Staphylococcal Transposon Conferring Resistance to Streptogramin A and Related Compounds Including Dalfopristin

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.46.8.2337-2343.2002 ◽

2002 ◽

Vol 46 (8) ◽

pp. 2337-2343 ◽

Cited By ~ 31

Author(s):

Julien Haroche ◽

Jeanine Allignet ◽

Névine El Solh

Keyword(s):

Staphylococcus Aureus ◽

Insertion Site ◽

Single Copy ◽

Amino Acid Identity ◽

Plasmid Copy ◽

Acid Identity ◽

Abc Protein ◽

Single Plasmid ◽

Insertion Sites ◽

Related Compounds

ABSTRACT We characterized a new transposon, Tn5406 (5,467 bp), in a clinical isolate of Staphylococcus aureus (BM3327). It carries a variant of vgaA, which encodes a putative ABC protein conferring resistance to streptogramin A but not to mixtures of streptogramins A and B. It also carries three putative genes, the products of which exhibit significant similarities (61 to 73% amino acid identity) to the three transposases of the staphylococcal transposon Tn554. Like Tn554, Tn5406 failed to generate target repeats. In BM3327, the single copy of Tn5406 was inserted into the chromosomal att554 site, which is the preferential insertion site of Tn554. In three other independent S. aureus clinical isolates, Tn5406 was either present as a single plasmid copy (BM3318), as two chromosomal copies (BM3252), or both in the chromosome and on a plasmid (BM3385). The Tn5406-carrying plasmids also contain two other genes, vgaB and vatB. The insertion sites of Tn5406 in BM3252 were studied: one copy was in att554, and one copy was in the additional SCCmec element. Amplification experiments revealed circular forms of Tn5406, indicating that this transposon might be active. To our knowledge, a transposon conferring resistance to streptogramin A and related compounds has not been previously described.

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NKBOR, a mini-Tn10-based transposon for random insertion in the chromosome of Gram-negative bacteria and the rapid recovery of sequences flanking the insertion sites in Escherichia coli

Research in Microbiology ◽

10.1016/s0923-2508(01)01221-9 ◽

2001 ◽

Vol 152 (5) ◽

pp. 481-485 ◽

Cited By ~ 21

Author(s):

Michèle Rossignol ◽

Alan Basset ◽

Olivier Espéli ◽

Frédéric Boccard

Keyword(s):

Escherichia Coli ◽

Rapid Recovery ◽

Gram Negative Bacteria ◽

Gram Negative ◽

Insertion Sites ◽

Random Insertion

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Insertion and excision of Caenorhabditis elegans transposable element Tc1

Molecular and Cellular Biology ◽

10.1128/mcb.8.2.737-746.1988 ◽

1988 ◽

Vol 8 (2) ◽

pp. 737-746

Author(s):

D Eide ◽

P Anderson

Keyword(s):

Amino Acid ◽

Caenorhabditis Elegans ◽

Transposable Element ◽

Dna Sequences ◽

Germ Line ◽

Consensus Sequence ◽

Somatic Cells ◽

Chain Gene ◽

Imprecise Excision ◽

Insertion Sites

The transposable element Tc1 is responsible for most spontaneous mutations that occur in Caenorhabditis elegans variety Bergerac. We investigated the genetic and molecular properties of Tc1 transposition and excision. We show that Tc1 insertion into the unc-54 myosin heavy-chain gene was strongly site specific. The DNA sequences of independent Tc1 insertion sites were similar to each other, and we present a consensus sequence for Tc1 insertion that describes these similarities. We show that Tc1 excision was usually imprecise. Tc1 excision was imprecise in both germ line and somatic cells. Imprecise excision generated novel unc-54 alleles that had amino acid substitutions, amino acid insertions, and, in certain cases, probably altered mRNA splicing. The DNA sequences remaining after Tc1 somatic excision were the same as those remaining after germ line excision, but the frequency of somatic excision was at least 1,000-fold higher than that of germ line excision. The genetic properties of Tc1 excision, combined with the DNA sequences of the resulting unc-54 alleles, demonstrated that excision was dependent on Tc1 transposition functions in both germ line and somatic cells. Somatic excision was not regulated in the same strain-specific manner as germ-line excision was. In a genetic background where Tc1 transposition and excision in the germ line was not detectable, Tc1 excision in the soma still occurred at high frequency.

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An unusual cell surface modification: a double plasma membrane

Journal of Cell Science ◽

10.1242/jcs.39.1.355 ◽

1979 ◽

Vol 39 (1) ◽

pp. 355-372

Author(s):

N.J. Lane ◽

J.B. Harrison

Keyword(s):

Plasma Membrane ◽

Membrane Structure ◽

Cell Layer ◽

Peritrophic Membrane ◽

Thin Sections ◽

Double Membrane ◽

Freeze Fracturing ◽

Blood Sucking ◽

Great Pressure ◽

Insertion Sites

The occurrence of an unusual double plasma membrane structure is reported; it has been studied in conventional thin sections, after lanthanum-impregnation and with freeze-fracturing. This modification of the plasmalemma is found where the luminal cell membrane (I membrane) of gut microvilli in the haematophagous insect, Rhodnius prolixus, is surrounded by a second, outer membrane (O membrane), the 2 separated from one another by a highly regular I-O space of about 10 nm. Lanthanum impregnation reveals the presence of columns inclined at an angle, within this I-O space; as in the continuous junctions which link the lateral borders of these cells, these columns may maintain the very precise I-O distance. From the outer microvillar membranes radiate short spoke-like fibrils or sheets which encounter another more extensive system of myelin-like sheets. Freeze-fracturing reveals that the spoke-like sheets and the other ones which lie like a tube, around and parallel to the microvilli, contain linear ridges composed of particles, lying at random within layers of the myelin-like material which also extends into the lumen of the gut. The microvillar membanes, both O and I, fracture into faces containing rows of either PF particles or EF pits arranged as spiral ridges or grooves around the sides and across the tip of each microbillus. These could be the insertion sites of one or both of the I-O columns and spoke-like sheets while the sheets could represent a variant of peritrophic membrane. The double membrane may be a cellular device to increase the strength of the microvillar layer in these blood-sucking animals, since the cell layer must withstand great pressure owing to a sudden massive extension of the gut during a blood meal.

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