scholarly journals Large-scale dynamics of horizontal transfers

2012 ◽  
Vol 2 (3) ◽  
pp. 163-167 ◽  
Author(s):  
Luigi Grassi ◽  
Jacopo Grilli ◽  
Marco Cosentino Lagomarsino
Keyword(s):  
Large Scale ◽  
Horizontal Transfers

scholarly journals An updated assembly strategy helps parsing the cryptic mitochondrial genome evolution in plants

2021 ◽  
Author(s):  
Yanlei Feng ◽  
Xiaoguo Xiang ◽  
Zhixi Fu ◽  
Xiaohua Jin
Keyword(s):  
Large Scale ◽  
Gc Content ◽  
Comparative Genomic ◽  
Genomic Analyses ◽  
Evolutionary Trajectories ◽  
Mitochondrial Genome Evolution ◽  
Foreign Dna ◽  
Almost All ◽  
Horizontal Transfers ◽  
Main Chromosome

AbstractAlthough plant mitogenomes are small in size, their variations are no less than any other complex genomes. They are under rapid structure and size changes. These characters make the assembly a great challenge. This caused two intertwined problems, a slow growth of known mitogenomes and a poor knowledge of their evolution. In many species, mitogenome becomes the last genome that undeciphered. To have a better understanding of these two questions, we developed a strategy using short sequencing reads and combining current tools and manual steps to get high quality mitogenomes. This strategy allowed us to assembled 23 complete mitogenomes from 5 families in Fagales. Our large-scale comparative genomic analyses indicated the composition of mitogenomes is very mosaic that “horizontal transfers” can be from almost all taxa in seed plants. The largest mitogenome contains more homologous DNA with other Fagales, rather than unique sequences. Besides of real HGTs, sometimes mitovirus, nuclear insertions and other third-part DNA could also produce HGT-like sequences, accounting partially for the unusual evolutionary trajectories, including the cryptic size expansion in Carpinus. Mitochondrial plasmid was also found. Its lower GC content indicates that it may be only an interphase of a foreign DNA before accepting by the main chromosome. Our methods and results provide new insights into the assembly and mechanisms of mitogenome evolution.

scholarly journals High frequency of horizontal transfer in Jockey families (LINE order) of drosophilids

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Izabella L. Tambones ◽  
Annabelle Haudry ◽  
Maryanna C. Simão ◽  
Claudia M. A. Carareto
Keyword(s):  
Transposable Element ◽  
Horizontal Transfer ◽  
Large Scale ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Genetic Material ◽  
Long Terminal Repeat Retrotransposons ◽  
Spatio Temporal ◽  
Line Elements ◽  
Horizontal Transfers

Abstract Background The use of large-scale genomic analyses has resulted in an improvement of transposable element sampling and a significant increase in the number of reported HTT (horizontal transfer of transposable elements) events by expanding the sampling of transposable element sequences in general and of specific families of these elements in particular, which were previously poorly sampled. In this study, we investigated the occurrence of HTT events in a group of elements that, until recently, were uncommon among the HTT records in Drosophila – the Jockey elements, members of the LINE (long interspersed nuclear element) order of non-LTR (long terminal repeat) retrotransposons. The sequences of 111 Jockey families deposited in Repbase that met the criteria of the analysis were used to identify Jockey sequences in 48 genomes of Drosophilidae (genus Drosophila, subgenus Sophophora: melanogaster, obscura and willistoni groups; subgenus Drosophila: immigrans, melanica, repleta, robusta, virilis and grimshawi groups; subgenus Dorsilopha: busckii group; genus/subgenus Zaprionus and genus Scaptodrosophila). Results Phylogenetic analyses revealed 72 Jockey families in 41 genomes. Combined analyses revealed 15 potential HTT events between species belonging to different genera and species groups of Drosophilidae, providing evidence for the flow of genetic material favoured by the spatio-temporal sharing of these species present in the Palaeartic or Afrotropical region. Conclusions Our results provide phylogenetic, biogeographic and temporal evidence of horizontal transfers of the Jockey elements, increase the number of rare records of HTT in specific families of LINE elements, increase the number of known occurrences of these events, and enable a broad understanding of the evolutionary dynamics of these elements and the host species.

scholarly journals Large scale genome reconstructions illuminate Wolbachia evolution

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Matthias Scholz ◽  
Davide Albanese ◽  
Kieran Tuohy ◽  
Claudio Donati ◽  
Nicola Segata ◽  
...  
Keyword(s):  
Gene Function ◽  
Large Scale ◽  
Core Genome ◽  
Evolutionary Dynamics ◽  
Cytoplasmic Incompatibility ◽  
Horizontal Transmission ◽  
Model Organisms ◽  
Future Studies ◽  
Horizontal Transfers ◽  
Gains And Losses

Abstract Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling over 1000 Wolbachia genomes, we provide a substantial increase in host representation. Our phylogenies based on both core-genome and gene content provide a robust reference for future studies, support new strains in model organisms, and reveal recent horizontal transfers amongst distantly related hosts. We find various instances of gene function gains and losses in different super-groups and in cytoplasmic incompatibility inducing strains. Our Wolbachia-host co-phylogenies indicate that horizontal transmission is widespread at the host intraspecific level and that there is no support for a general Wolbachia-mitochondrial synchronous divergence.

Some comments about observations and image processing of comet 29P/Schwassmann-Wachmann 1

1999 ◽  
Vol 173 ◽  
pp. 243-248
Author(s):  
D. Kubáček ◽  
A. Galád ◽  
A. Pravda
Keyword(s):  
Image Processing ◽  
Large Scale ◽  
Harvard College ◽  
Oak Ridge ◽  
Large Scale Structures ◽  
Short Period Comet ◽  
Short Period ◽  
Scale Structures ◽  
Harvard College Observatory ◽  
Period Comet

AbstractUnusual short-period comet 29P/Schwassmann-Wachmann 1 inspired many observers to explain its unpredictable outbursts. In this paper large scale structures and features from the inner part of the coma in time periods around outbursts are studied. CCD images were taken at Whipple Observatory, Mt. Hopkins, in 1989 and at Astronomical Observatory, Modra, from 1995 to 1998. Photographic plates of the comet were taken at Harvard College Observatory, Oak Ridge, from 1974 to 1982. The latter were digitized at first to apply the same techniques of image processing for optimizing the visibility of features in the coma during outbursts. Outbursts and coma structures show various shapes.

Evolution of Large-Scale Coronal Structures

1994 ◽  
Vol 144 ◽  
pp. 29-33
Author(s):  
P. Ambrož
Keyword(s):  
Magnetic Field ◽  
Field Line ◽  
Large Scale ◽  
Coronal Magnetic Field ◽  
Source Surface ◽  
Solar Cycles ◽  
Characteristic Relationship ◽  
The Magnetic Field ◽  
Coronal Structures

AbstractThe large-scale coronal structures observed during the sporadically visible solar eclipses were compared with the numerically extrapolated field-line structures of coronal magnetic field. A characteristic relationship between the observed structures of coronal plasma and the magnetic field line configurations was determined. The long-term evolution of large scale coronal structures inferred from photospheric magnetic observations in the course of 11- and 22-year solar cycles is described.Some known parameters, such as the source surface radius, or coronal rotation rate are discussed and actually interpreted. A relation between the large-scale photospheric magnetic field evolution and the coronal structure rearrangement is demonstrated.

Large-scale Motion of Solar Filaments

2000 ◽  
Vol 179 ◽  
pp. 205-208
Author(s):  
Pavel Ambrož ◽  
Alfred Schroll
Keyword(s):  
Magnetic Flux ◽  
Proper Motion ◽  
Time Scale ◽  
Large Scale ◽  
Accuracy Of Measurements ◽  
Solar Filaments ◽  
General Movement ◽  
Scale Motion ◽  
Velocity Scatter

AbstractPrecise measurements of heliographic position of solar filaments were used for determination of the proper motion of solar filaments on the time-scale of days. The filaments have a tendency to make a shaking or waving of the external structure and to make a general movement of whole filament body, coinciding with the transport of the magnetic flux in the photosphere. The velocity scatter of individual measured points is about one order higher than the accuracy of measurements.

Some applications of electron beam microanalysis techniques in VLSI process evaluation

1983 ◽  
Vol 41 ◽  
pp. 160-161
Author(s):  
Simon Thomas
Keyword(s):  
Integrated Circuits ◽  
Process Evaluation ◽  
Large Scale ◽  
Technology Development ◽  
Analytical Techniques ◽  
Successful Implementation ◽  
Analysis Of Failures ◽  
Characterization Of Materials ◽  
Circuits Vlsi

Trends in the technology development of very large scale integrated circuits (VLSI) have been in the direction of higher density of components with smaller dimensions. The scaling down of device dimensions has been not only laterally but also in depth. Such efforts in miniaturization bring with them new developments in materials and processing. Successful implementation of these efforts is, to a large extent, dependent on the proper understanding of the material properties, process technologies and reliability issues, through adequate analytical studies. The analytical instrumentation technology has, fortunately, kept pace with the basic requirements of devices with lateral dimensions in the micron/ submicron range and depths of the order of nonometers. Often, newer analytical techniques have emerged or the more conventional techniques have been adapted to meet the more stringent requirements. As such, a variety of analytical techniques are available today to aid an analyst in the efforts of VLSI process evaluation. Generally such analytical efforts are divided into the characterization of materials, evaluation of processing steps and the analysis of failures.

Electron microscopy study of reactively sputter-deposited Ti/N films on silicon

1992 ◽  
Vol 50 (2) ◽  
pp. 1362-1363
Author(s):  
V. C. Kannan ◽  
A. K. Singh ◽  
R. B. Irwin ◽  
S. Chittipeddi ◽  
F. D. Nkansah ◽  
...  
Keyword(s):  
Integrated Circuits ◽  
Large Scale ◽  
Hexagonal Phase ◽  
Microscopy Study ◽  
Electron Microscopy Study ◽  
Process Conditions ◽  
Tin Films ◽  
Wide Range ◽  
Fcc Phase ◽  
Circuits Vlsi

Titanium nitride (TiN) films have historically been used as diffusion barrier between silicon and aluminum, as an adhesion layer for tungsten deposition and as an interconnect material etc. Recently, the role of TiN films as contact barriers in very large scale silicon integrated circuits (VLSI) has been extensively studied. TiN films have resistivities on the order of 20μ Ω-cm which is much lower than that of titanium (nearly 66μ Ω-cm). Deposited TiN films show resistivities which vary from 20 to 100μ Ω-cm depending upon the type of deposition and process conditions. TiNx is known to have a NaCl type crystal structure for a wide range of compositions. Change in color from metallic luster to gold reflects the stabilization of the TiNx (FCC) phase over the close packed Ti(N) hexagonal phase. It was found that TiN (1:1) ideal composition with the FCC (NaCl-type) structure gives the best electrical property.

Evolution of the microstructure of Cu(Ti)/SiO2 layers annealed in NH3

1995 ◽  
Vol 53 ◽  
pp. 452-453
Author(s):  
J. Liu ◽  
N. D. Theodore ◽  
D. Adams ◽  
S. Russell ◽  
T. L. Alford ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Titanium Nitride ◽  
Large Scale ◽  
Standard Procedure ◽  
Alloy Film ◽  
Electron Beam Evaporation ◽  
Copper Metallization ◽  
Nominal Composition ◽  
Ti Alloy ◽  
Thermally Grown

Copper-based metallization has recently attracted extensive research because of its potential application in ultra-large-scale integration (ULSI) of semiconductor devices. The feasibility of copper metallization is, however, limited due to its thermal stability issues. In order to utilize copper in metallization systems diffusion barriers such as titanium nitride and other refractory materials, have been employed to enhance the thermal stability of copper. Titanium nitride layers can be formed by annealing Cu(Ti) alloy film evaporated on thermally grown SiO2 substrates in an ammonia ambient. We report here the microstructural evolution of Cu(Ti)/SiO2 layers during annealing in NH3 flowing ambient.The Cu(Ti) films used in this experiment were prepared by electron beam evaporation onto thermally grown SiO2 substrates. The nominal composition of the Cu(Ti) alloy was Cu73Ti27. Thermal treatments were conducted in NH3 flowing ambient for 30 minutes at temperatures ranging from 450°C to 650°C. Cross-section TEM specimens were prepared by the standard procedure.

Immunogold labeling of CMP-KDO synthetase produced by recombinant E. Coli cells

1987 ◽  
Vol 45 ◽  
pp. 924-925
Author(s):  
F. A. Durum ◽  
R. G. Goldman ◽  
T. J. Bolling ◽  
M. F. Miller
Keyword(s):  
Inclusion Bodies ◽  
Large Scale ◽  
Recombinant Dna ◽  
Test System ◽  
Cell Protein ◽  
Gram Negative Bacteria ◽  
Cytoplasmic Inclusions ◽  
Isolation And Purification ◽  
E Coli ◽  
Low Concentrations

CMP-KDO synthetase (CKS) is an enzyme which plays a key role in the synthesis of LPS, an outer membrane component unique to gram negative bacteria. CKS activates KDO to CMP-KDO for incorporation into LPS. The enzyme is normally present in low concentrations (0.02% of total cell protein) which makes it difficult to perform large scale isolation and purification. Recently, the gene for CKS from E. coli was cloned and various recombinant DNA constructs overproducing CKS several thousandfold (unpublished data) were derived. Interestingly, no cytoplasmic inclusions of overproduced CKS were observed by EM (Fig. 1) which is in contrast to other reports of large proteinaceous inclusion bodies in various overproducing recombinant strains. The present immunocytochemical study was undertaken to localize CKS in these cells.Immune labeling conditions were first optimized using a previously described cell-free test system. Briefly, this involves soaking small blocks of polymerized bovine serum albumin in purified CKS antigen and subjecting them to various fixation, embedding and immunochemical conditions.

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