Somatic DNA recombination in a mouse genomic region, BC-1, in brain and non-brain tissueThis paper is one of a selection of papers published in this Special Issue, entitled The Nucleus: A Cell Within A Cell.

2006 ◽  
Vol 84 (3-4) ◽  
pp. 443-449
Author(s):  
Toyoki Maeda ◽  
Ryuzo Mizuno ◽  
Masahiro Sugano ◽  
Shinji Satoh ◽  
Junichi Oyama ◽  
...  
Keyword(s):  
Dna Recombination ◽  
Perinatal Period ◽  
Genomic Region ◽  
Homologous Region ◽  
Circular Dna ◽  
Late Embryogenesis ◽  
Dna Production ◽  
A Cell ◽  
Selection Of

The genomic region BC-1 (GenBank acc. No. AB075899 ) on mouse chromosome 16 has been reported as a genomic region undergoing somatic DNA recombination producing circular DNA and genomic deletion in brain during late embryogenesis. The present study shows that the BC-1 circular DNA production had already started on the 13th day of embryonic age, earlier than the previous observation that the circular DNA production started on the 15th through 17th embryonic day. The BC-1 deletion was also observed in the spleen and ocular lens. In situ hybridization analysis indicated that a human-homologous region in the BC-1 sequence was expressed in the lens at a perinatal period. These data suggest that the somatic DNA recombination in the BC-1 region is not restricted to brain tissue, and that the BC-1 DNA recombination relates to lens development.

Somatic DNA recombination yielding circular DNA and deletion of a genomic region in embryonic brain

2004 ◽  
Vol 319 (4) ◽  
pp. 1117-1123 ◽  
Author(s):  
Toyoki Maeda ◽  
Yoshiharu Chijiiwa ◽  
Hideo Tsuji ◽  
Saburo Sakoda ◽  
Kenzaburo Tani ◽  
...  
Keyword(s):  
Dna Recombination ◽  
Genomic Region ◽  
Embryonic Brain ◽  
Circular Dna

Somatic DNA recombination in the brainThis paper is one of a selection of papers published in this Special Issue, entitled The Nucleus: A Cell Within A Cell.

2006 ◽  
Vol 84 (3-4) ◽  
pp. 319-324
Author(s):  
Toyoki Maeda ◽  
Saburo Sakoda ◽  
Tomokazu Suzuki ◽  
Naoki Makino
Keyword(s):  
Dna Recombination ◽  
Biological Significance ◽  
Indirect Evidence ◽  
Dna Rearrangement ◽  
Special Issue ◽  
Recombination Activity ◽  
A Cell ◽  
The Brain ◽  
Oriented Approach ◽  
Selection Of

Possible somatic DNA recombination in the brain has been investigated by attempting to capture direct or indirect evidence of it. Until recently, the biological significance of the DNA event, the genes is involved in the recombination, or even whether the event actually occurs in the brain has remained unclear. The DNA-rearranged locus-oriented approach and the recombination activity-oriented approach have mutually contributed to the elucidation of the biological features of extra-immune system somatic DNA recombination. There have been only 2 loci proposed for the candidate, one is a repetitive sequence and the other DNA recombination is nonrepetitive locus. This review states conventional concepts and discussions chronologically and finally to the newest aspects of DNA rearrangement in the brain.

Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments

2019 ◽  
pp. 27-33
Author(s):  
YuE Kravchenko ◽  
SV Ivanov ◽  
DS Kravchenko ◽  
EI Frolova ◽  
SP Chumakov
Keyword(s):  
Phage Display ◽  
Selection Procedure ◽  
Free System ◽  
Phage Displays ◽  
High Affinity ◽  
Binding Domains ◽  
A Cell ◽  
Vhh Antibodies ◽  
Efficiency Of Selection ◽  
Selection Of

Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.

scholarly journals 3D reconstruction of genomic regions from sparse interaction data

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Julen Mendieta-Esteban ◽  
Marco Di Stefano ◽  
David Castillo ◽  
Irene Farabella ◽  
Marc A Marti-Renom
Keyword(s):  
3D Models ◽  
Genomic Region ◽  
Gene Promoters ◽  
Chromosome Conformation ◽  
The Matrix ◽  
Chromatin Structural ◽  
A Cell ◽  
Similar Accuracy ◽  
Genomic Regions ◽  
Interaction Matrices

Abstract Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions involving non-contiguous sets of loci, resulting in sparse interaction matrices. One of such 3C technologies is Promoter Capture Hi-C (pcHi-C) that is tailored to probe only interactions involving gene promoters. As such, pcHi-C provides sparse interaction matrices that are suitable to characterize short- and long-range enhancer–promoter interactions. Here, we introduce a new method to reconstruct the chromatin structural (3D) organization from sparse 3C-based datasets such as pcHi-C. Our method allows for data normalization, detection of significant interactions and reconstruction of the full 3D organization of the genomic region despite of the data sparseness. Specifically, it builds, with as low as the 2–3% of the data from the matrix, reliable 3D models of similar accuracy of those based on dense interaction matrices. Furthermore, the method is sensitive enough to detect cell-type-specific 3D organizational features such as the formation of different networks of active gene communities.

Suitability of Natural Geomedia for Radwaste Storage

1982 ◽  
Vol 15 ◽  
Author(s):  
W. S. Fyfe
Keyword(s):  
Rock Properties ◽  
Fracture Flow ◽  
Time Prediction ◽  
Sedimentary Sequences ◽  
Rock Types ◽  
Direct Observations ◽  
Long Time ◽  
Mining Disturbance ◽  
Selection Of

ABSTRACTSelection of the best rock types for radwaste disposal will depend on their having minimal permeability, maximal flow dispersion, minimal chance of forming new wide aperture fractures, maximal ion retention, and minimal thermal and mining disturbance. While no rock is perfect, thinly bedded complex sedimentary sequences may have good properties, either as repository rocks, or as cover to a repository.Long time prediction of such favorable properties of a rock at a given site may be best modelled from studies of in situ rock properties. Fracture flow, dispersion history, and geological stability can be derived from direct observations of rocks themselves, and can provide the parameters needed for convincing demonstration of repository security for appropriate times.

scholarly journals An in situ near-ambient pressure X-ray Photoelectron Spectroscopy study of Mn polarised anodically in a cell with solid oxide electrolyte

2015 ◽  
Vol 174 ◽  
pp. 532-541 ◽  
Author(s):  
Benedetto Bozzini ◽  
Matteo Amati ◽  
Patrizia Bocchetta ◽  
Simone Dal Zilio ◽  
Axel Knop-Gericke ◽  
...  
Keyword(s):  
Photoelectron Spectroscopy ◽  
Ambient Pressure ◽  
Solid Oxide ◽  
Spectroscopy Study ◽  
Solid Oxide Electrolyte ◽  
X Ray ◽  
A Cell ◽  
Oxide Electrolyte

scholarly journals Order and stochasticity in the folding of individual Drosophila genomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sergey V. Ulianov ◽  
Vlada V. Zakharova ◽  
Aleksandra A. Galitsyna ◽  
Pavel I. Kos ◽  
Kirill E. Polovnikov ◽  
...  
Keyword(s):  
Random Walk ◽  
High Resolution ◽  
3D Genome ◽  
Topologically Associating Domains ◽  
Chromatin Folding ◽  
A Cell ◽  
Single Nucleus ◽  
High Level ◽  
Cell To Cell Variability

AbstractMammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.

scholarly journals Strategic selection of an optimal sorbent mixture for in-situ remediation of heavy metal contaminated sediments: Framework and case study

2012 ◽  
Vol 105 ◽  
pp. 1-11 ◽  
Author(s):  
Y.W. Chiang ◽  
R.M. Santos ◽  
K. Ghyselbrecht ◽  
V. Cappuyns ◽  
J.A. Martens ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Contaminated Sediments ◽  
In Situ Remediation ◽  
Selection Of

scholarly journals Prilog poznavanju djelovanja Mateja Andrijina Moronzona*

Ars Adriatica ◽  
2016 ◽  
pp. 103
Author(s):  
Barbara Španjol-Pandelo
Keyword(s):  
Comparative Analysis ◽  
Virgin Mary ◽  
Main Role ◽  
Huge Number ◽  
General Acceptance ◽  
Parish Church ◽  
Archival Documents ◽  
First Time ◽  
Selection Of

Matteo Moronzon, a member of the Venetian family of woodcarvers, was mentioned for the first time in 1407 according to the present known archival documents. Probably after being trained in his father's workshop in Venice, he moved to Zadar with his family – his wife Francisca and sons Pietro and Francesco. In 1418 he undertook the commission of furnishing carved choir stalls for the cathedral of St. Anastasia in Zadar. Various archival documents testify that Matteo lived and worked in Zadar for many years. Therefore it can be assumed that he probably founded his own workshop in Zadar where his son Francesco was trained too. Apart from the attempt to reconstruct Matteo's life and career, the aim of this paper is to interpret one important woodcarving work of art preserved in situ: choir stalls in the former cathedral of Rab, today the arch parish church of the Assumption of the Blessed Virgin Mary in Rab. Without doubt Matteo was the master carver in the production of the choir stalls in Zadar. Since he lived in Zadar it was not unusual that he had the main role in carving the stalls. In Zadar the selection of motives is more balanced and there are no significant differences in the modelling of decorative elements. However, the question whether Matteo carved absolutely everything or he had assistants arises. Considering the amount of work that had to be done it must be assumed that he had assistants who participated in work and helped him to shape the stalls. However, in literature Matteo was considered the only and undisputed author of the choir stalls in Zadar, mostly because of the preserved document. The analysis of the choir stalls in Rab by Ivo Petricioli as well as their evident formal and stylistic similarities with the stalls from the cathedral in Zadar have led to the general acceptance of the hypothesis that they were carved at the workshop of Matteo Moronzon. However, a comprehensive comparative analysis that could confirm that hypothesis was still missing. The analysis of the details and the whole led to the overall conclusion that there were a huge number of similarities between the choir stalls in Rab and Zadar. Therefore it was concluded that Matteo was the principal designer of the choir stalls in Rab who also carved the best parts in Rab, while others, less successful parts, were made by his apprentices and assistants who at the time lived on the island of Rab. In this respect, if Matteo was accepted as the author of the choir stalls of the cathedral in Zadar he must also be accepted as the author of the choir stalls from the excathedral in Rab.

scholarly journals The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Mohammed Kaplan ◽  
Debnath Ghosal ◽  
Poorna Subramanian ◽  
Catherine M Oikonomou ◽  
Andreas Kjaer ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Pathogenic Bacteria ◽  
Bioinformatics Analysis ◽  
Cell Envelope ◽  
Shewanella Oneidensis ◽  
Flagellar Motor ◽  
Flagellar Motors ◽  
A Cell ◽  
Animal Hosts

The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis, providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor’s stator system and its structural elaboration. Motors with a single H+-driven stator have only the core periplasmic P- and L-rings; those with dual H+-driven stators have an elaborated P-ring; and motors with Na+ or Na+/H+-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts.

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