Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

<p>Abstract</p> <p>Background</p> <p>In eukaryotes, long terminal repeat (LTR) retrotransposons such as <it>Copia, BEL </it>and <it>Gypsy </it>integrate their DNA copies into the host genome using a particular type of DDE transposase called integrase (INT). The <it>Gypsy </it>INT-like transposase is also conserved in the <it>Polinton/Maverick </it>self-synthesizing DNA transposons and in the 'cut and paste' DNA transposons known as <it>TDD-4 </it>and <it>TDD-5</it>. Moreover, it is known that INT is similar to bacterial transposases that belong to the IS<it>3</it>, IS<it>481</it>, IS<it>30 </it>and IS<it>630 </it>families. It has been suggested that LTR retrotransposons evolved from a non-LTR retrotransposon fused with a DNA transposon in early eukaryotes. In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons.</p> <p>Results</p> <p>A new diverse eukaryotic superfamily of DNA transposons, named <it>Ginger </it>(for '<it>Gypsy </it>INteGrasE Related') DNA transposons is defined and analyzed. Analogously to the IS<it>3 </it>and IS<it>481 </it>bacterial transposons, the <it>Ginger </it>termini resemble those of the <it>Gypsy </it>LTR retrotransposons. Currently, <it>Ginger </it>transposons can be divided into two distinct groups named <it>Ginger1 </it>and <it>Ginger2/Tdd</it>. Elements from the <it>Ginger1 </it>group are characterized by approximately 40 to 270 base pair (bp) terminal inverted repeats (TIRs), and are flanked by CCGG-specific or CCGT-specific target site duplication (TSD) sequences. The <it>Ginger1</it>-encoded transposases contain an approximate 400 amino acid N-terminal portion sharing high amino acid identity to the entire <it>Gypsy</it>-encoded integrases, including the YPYY motif, zinc finger, DDE domain, and, importantly, the GPY/F motif, a hallmark of <it>Gypsy </it>and endogenous retrovirus (ERV) integrases. <it>Ginger1 </it>transposases also contain additional C-terminal domains: ovarian tumor (OTU)-like protease domain or Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from the <it>Gypsy </it>integrases, apparently have evolved from the <it>Ginger1 </it>transposase genes. We also introduce a second <it>Ginger </it>group, designated <it>Ginger2/Tdd</it>, which includes the previously reported DNA transposon <it>TDD-4</it>.</p> <p>Conclusions</p> <p>The <it>Ginger </it>superfamily represents eukaryotic DNA transposons closely related to LTR retrotransposons. <it>Ginger </it>elements provide new insights into the evolution of transposable elements and certain transposable element (TE)-derived genes.</p

From laterally modulated two-dimensional electron gas towards artificial graphene

Cyclotron resonance has been measured in far-infrared transmission of GaAs/Al$_x$Ga$_{1-x}$As heterostructures with an etched hexagonal lateral superlattice. Non-linear dependence of the resonance position on magnetic field was observed as well as its splitting into several modes. Our explanation, based on a perturbative calculation, describes the observed phenomena as a weak effect of the lateral potential on the two-dimensional electron gas. Using this approach, we found a correlation between parameters of the lateral patterning and the created effective potential and obtain thus insights on how the electronic miniband structure has been tuned. The miniband dispersion was calculated using a simplified model and allowed us to formulate four basic criteria that have to be satisfied to reach graphene-like physics in such systems

Magnetotransport in graphene on silicon side of SiC

We have studied the transport properties of graphene grown on silicon side of SiC. Samples under study have been prepared by two different growth methods in two different laboratories. Magnetoresistance and Hall resistance have been measured at temperatures between 4 and 100 K in resistive magnet in magnetic fields up to 22 T. In spite of differences in sample preparation, the field dependence of resistances measured on both sets of samples exhibits two periods of magneto-oscillations indicating two different parallel conducting channels with different concentrations of carriers. The semi-quantitative agreement with the model calculation allows for conclusion that channels are formed by high-density and low-density Dirac carriers. The coexistence of two different groups of carriers on the silicon side of SiC was not reported before.Comment: 5 pages, 6 figures, accepted for publication in the "IOP Journal of Physics: Conference series" as a contribution to the proceedings of the 20th International Conference on "High Magnetic Fields in Semiconductor Physics", HMF 2

Introduction for the Gene special issue dedicated to the meeting Genomic impact of eukaryotic transposable elements at Asilomar

The issues related to \u27Genomic Impact of Eukaryotic Transposable Elements\u27, which took place in Pacific Grove, California between March 31st and April 4th 2006, are discussed. The meeting celebrated the extraordinary contributions of Dr. Carl W. Schmid to the study of repeated DNA sequences and mobile elements. With the advent of recombinant DNA technology, he led the discovery of human Alu elements, and the discovery of their amplification. The idea of the conference was to gather and disseminate information in transposable elements (TEs) on the state-of-the-art tools and approaches. The core sessions from the conference covered research on transposable elements with a strong emphasis on their impact on genomic stability and evolution. The scientific sessions were complemented by after-dinner workshop sessions focusing on Repbase, computer tools used in annotation and analysis of repetitive DNA and open problems related to the field

Informational Theory of Evidence and the Problems of Using the Electronic Means of Proving in Criminal Procedure

Article deals with the topical for modern science of criminal procedural law and law enforcement practice question of use in criminal procedure digital evidence. Authors highlight that development of digital technologies, electronic forms of communication, Internet, transnational and transboundary nature of crimes, which are committed in the sphere of computer information, specific nature of creation of digital tracks, gives the opportunity to state the considerable broadening of the possibilities to use in proving digital evidences, and also cause the necessity of addressing to the solving the problems of proving, which appear in the conditions of digitalization, including the heritage of informational theory of proving, which gives the possibility to adapt the probative activity in criminal procedure to any future innovative discoveries, scientific and technical progress and define the place of the digital evidence among other procedural sources of evidence. During the research, it is found the factors, which influence negatively on the law enforcement practice, lead to recognition the evidence obtained in criminal proceeding as inadmissible. It is emphasized, that the cognitive potential in the aspect of development of the science of criminal procedure has the informational theory of criminal procedural proves. Relying on the fact that digital technologies are based on the methods of coding and transporting information using double code of encryption, which gives the possibility not only transport the information, but also recognize it after that, authors make the conclusion about suitability to use wider concept of «digital information» and «digital evidence » instead of concepts «electronic information» or «computer information». In order to formulate relevant conclusions, the authors refer to the legislation of foreign countries. The results of the study are formulated in the conclusions, where authors suggest definition of the concept of digital evidence and state the need to distinguish the digital evidence as an independent processual source of evidence

Genomic impact of eukaryotic transposable elements

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mobile DNA 3 (2012): 19, doi:10.1186/1759-8753-3-19.The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.The conference was supported in part by the National Institutes of Health grant 5 P41 LM006252

Genomic impact of eukaryotic transposable elements

Abstract The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.http://deepblue.lib.umich.edu/bitstream/2027.42/112619/1/13100_2012_Article_57.pd

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

Miniature inverted-repeat transposable elements (MITEs) are a special type of Class 2 non-autonomous transposable element (TE) that are abundant in the non-coding regions of the genes of many plant and animal species. The accurate identification of MITEs has been a challenge for existing programs because they lack coding sequences and, as such, evolve very rapidly. Because of their importance to gene and genome evolution, we developed MITE-Hunter, a program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets. The output of MITE-Hunter is composed of consensus TE sequences grouped into families that can be used as a library file for homology-based TE detection programs such as RepeatMasker. MITE-Hunter was evaluated by searching the rice genomic database and comparing the output with known rice TEs. It discovered most of the previously reported rice MITEs (97.6%), and found sixteen new elements. MITE-Hunter was also compared with two other MITE discovery programs, FINDMITE and MUST. Unlike MITE-Hunter, neither of these programs can search large genomic data sets including whole genome sequences. More importantly, MITE-Hunter is significantly more accurate than either FINDMITE or MUST as the vast majority of their outputs are false-positives