Four Strategies for Whole-Genome Annotation of Transposable Elements and Repeats in Maize.

Transposable elements (TEs) and tandem repeat arrays are ubiquitous components of genomes across all domains of life. Many types of repetitive DNA do not appear to encode for functional proteins, and those that do, typically only code for enzymes involved in their own replication. Nevertheless, repetitive DNA sequences can significantly alter genome structure, and can have a profound impact on an organism's biology at both the molecular and organismal levels.

Navigating the Maze of Maize Genomics: the Impact of Transposable Elements and Tandem Repeats.

Transposable elements (TEs) are abundant and ubiquitous components of eukaryotic genomes. Since TEs were first discovered in maize () by Barbara McClintock in the late 1940s, these elements have been shown to be important agents in shaping genome structure and evolution. Today, maize continues to be an important model organism for molecular and quantitative genetics, and represents a particularly useful system for the study of the interplay between TEs and host genomes.

Multiple horizontal transfers of a Helitron transposon associated with a parasitoid wasp.

In a previous study we described a Helitron transposon that apparently became one of the segments in the symbiotic Cotesia vestalis bracovirus (CvBV) from the parasitoid wasp C. vestalis. We presented evidence that this Helitron, named Hel_c35, invaded the C.

Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons.

Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements.

Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups.

The fact that satellite DNAs (satDNAs) in eukaryotes are abundant genomic components, can perform functional roles, but can also change rapidly across species while being homogenous within a species, makes them an intriguing and fascinating genomic component to study. It is also becoming clear that satDNAs represent an important piece in genome architecture and that changes in their structure, organization, and abundance can affect the evolution of genomes and species in many ways. Since the discovery of satDNAs more than 50 years ago, species from the Drosophila genus have continuously been used as models to study several aspects of satDNA biology.

Identification and characterization of satellite DNAs in two-toed sloths of the genus Choloepus (Megalonychidae, Xenarthra).

Choloepus, the only extant genus of the Megalonychidae family, is composed of two living species of two-toed sloths: Choloepus didactylus and C. hoffmanni. In this work, we identified and characterized the main satellite DNAs (satDNAs) in the sequenced genomes of these two species.

Analysis of silver coins from colonial Brazil by hand held XRF and micro-XRF.

In this work, 960 réis coins from the period when Brazil was a colony of Portugal were analyzed using the x-ray fluorescence (XRF) spectrometry. The history of these coins, dated between the end of the 17th century and the beginning of the 19th century, had a great influence on the immigration of the Portuguese Prince Regent D. João to Brazil, who arrived in 1808.

De novo identification of satellite DNAs in the sequenced genomes of Drosophila virilis and D. americana using the RepeatExplorer and TAREAN pipelines.

Satellite DNAs are among the most abundant repetitive DNAs found in eukaryote genomes, where they participate in a variety of biological roles, from being components of important chromosome structures to gene regulation. Experimental methodologies used before the genomic era were insufficient, too laborious and time-consuming to recover the collection of all satDNAs from a genome. Today, the availability of whole sequenced genomes combined with the development of specific bioinformatic tools are expected to foster the identification of virtually all the "satellitome" of a particular species.

Exploring the Remote Ties between Helitron Transposases and Other Rolling-Circle Replication Proteins.

Rolling-circle replication (RCR) elements constitute a diverse group that includes viruses, plasmids, and transposons, present in hosts from all domains of life. Eukaryotic RCR transposons, also known as Helitrons, are found in species from all eukaryotic kingdoms, sometimes representing a large portion of their genomes. Despite the impact of Helitrons on their hosts, knowledge about their relationship with other RCR elements is still elusive.

A Horizontally Transferred Autonomous Helitron Became a Full Polydnavirus Segment in .

Bracoviruses associate symbiotically with thousands of parasitoid wasp species in the family Braconidae, working as virulence gene vectors, and allowing the development of wasp larvae within hosts. These viruses are composed of multiple DNA circles that are packaged into infective particles, and injected together with wasp's eggs during parasitization. One of the viral segments of bracovirus contains a gene that has been previously described as a helicase of unknown origin.

Monocular denervation of visual nuclei modulates APP processing and sAPPα production: A possible role on neural plasticity.

Amyloid precursor protein (APP) is essential to physiological processes such as synapse formation and neural plasticity. Sequential proteolysis of APP by beta- and gamma-secretases generates amyloid-beta peptide (Aβ), the main component of senile plaques in Alzheimer Disease. Alternative APP cleavage by alpha-secretase occurs within Aβ domain, releasing soluble α-APP (sAPPα), a neurotrophic fragment.

in : Chromatin modulation and tandem insertions.

Although were discovered 15 y ago, they still represent an elusive group of transposable elements (TEs). They are thought to transpose via a rolling-circle mechanism, but no transposition assay has yet been conducted. We have recently characterized a group of in , named , that display interesting features, including pronounced enrichment at β-heterochromatin, multiple tandem insertions (TIs) of the entire TE, and that experienced at least 2 independent expansion events of its internal tandem repeats (TRs) in distant lineages.

Helitrons shaping the genomic architecture of Drosophila: enrichment of DINE-TR1 in α- and β-heterochromatin, satellite DNA emergence, and piRNA expression.

Drosophila INterspersed Elements (DINEs) constitute an abundant but poorly understood group of Helitrons present in several Drosophila species. The general structure of DINEs includes two conserved blocks that may or not contain a region with tandem repeats in between. These central tandem repeats (CTRs) are similar within species but highly divergent between species.