scholarly journals Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes

2013 ◽  
Vol 368 (1626) ◽  
pp. 20120499 ◽  
Author(s):  
Masayuki Horie ◽  
Yuki Kobayashi ◽  
Yoshiyuki Suzuki ◽  
Keizo Tomonaga
Keyword(s):  
Dna Sequences ◽  
Cell Biology ◽  
Evolutionary Biology ◽  
Driving Forces ◽  
Biological Significance ◽  
Comprehensive Analysis ◽  
Retroviral Integration ◽  
Host Interactions ◽  
Mammalian Genomes ◽  
Borna Disease

Bornaviruses are the only animal RNA viruses that establish a persistent infection in their host cell nucleus. Studies of bornaviruses have provided unique information about viral replication strategies and virus–host interactions. Although bornaviruses do not integrate into the host genome during their replication cycle, we and others have recently reported that there are DNA sequences derived from the mRNAs of ancient bornaviruses in the genomes of vertebrates, including humans, and these have been designated endogenous borna-like (EBL) elements. Therefore, bornaviruses have been interacting with their hosts as driving forces in the evolution of host genomes in a previously unexpected way. Studies of EBL elements have provided new models for virology, evolutionary biology and general cell biology. In this review, we summarize the data on EBL elements including what we have newly identified in eukaryotes genomes, and discuss the biological significance of EBL elements, with a focus on EBL nucleoprotein elements in mammalian genomes. Surprisingly, EBL elements were detected in the genomes of invertebrates, suggesting that the host range of bornaviruses may be much wider than previously thought. We also review our new data on non-retroviral integration of Borna disease virus.

An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)

Zootaxa ◽  
2018 ◽  
Vol 4415 (1) ◽  
pp. 45 ◽  
Author(s):  
PIOTR GĄSIOREK ◽  
DANIEL STEC ◽  
WITOLD MOREK ◽  
ŁUKASZ MICHALCZYK
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Model Organism ◽  
Laboratory Strain ◽  
Sensu Stricto ◽  
Nominal Species ◽  
28S Rrna ◽  
The Family ◽  
The 19Th Century ◽  
Hypsibius Dujardini

A laboratory strain identified as “Hypsibius dujardini” is one of the best studied tardigrade strains: it is widely used as a model organism in a variety of research projects, ranging from developmental and evolutionary biology through physiology and anatomy to astrobiology. Hypsibius dujardini, originally described from the Île-de-France by Doyère in the first half of the 19th century, is now the nominal species for the superfamily Hypsibioidea. The species was traditionally considered cosmopolitan despite the fact that insufficient, old and sometimes contradictory descriptions and records prevented adequate delineations of similar Hypsibius species. As a consequence, H. dujardini appeared to occur globally, from Norway to Samoa. In this paper, we provide the first integrated taxonomic redescription of H. dujardini. In addition to classic imaging by light microscopy and a comprehensive morphometric dataset, we present scanning electron photomicrographs, and DNA sequences for three nuclear markers (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial marker (COI) that are characterised by various mutation rates. The results of our study reveal that a commercially available strain that is maintained in many laboratories throughout the world, and assumed to represent H. dujardini sensu stricto, represents, in fact, a new species: H. exemplaris sp. nov. Redescribing the nominal taxon for Hypsibiidae, we also redefine the family and amend the definitions of the subfamily Hypsibiinae and the genus Hypsibius. Moreover, we transfer H. arcticus (Murray, 1907) and Hypsibius conifer Mihelčič, 1938 to the genus Ramazzottius since the species exhibit claws and eggs of the Ramazzottius type. Finally, we designate H. fuhrmanni as subjectively invalid because the extremely poor description precludes identifying neotype material. 

scholarly journals Structures and stability of simple DNA repeats from bacteria

2020 ◽  
Vol 477 (2) ◽  
pp. 325-339 ◽  
Author(s):  
Vaclav Brazda ◽  
Miroslav Fojta ◽  
Richard P. Bowater
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genetic Instability ◽  
Repetitive Sequences ◽  
Biological Significance ◽  
Human Diseases ◽  
Repetitive Dna Sequences ◽  
Dna Repeats ◽  
Diverse Range ◽  
Dna Structures

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

scholarly journals Identification of transmembrane protein 237 as a novel interactor with the intestinal riboflavin transporter-3 (RFVT-3): role in functionality and cell biology

2019 ◽  
Vol 316 (6) ◽  
pp. C805-C814 ◽  
Author(s):  
Subrata Sabui ◽  
Veedamali S. Subramanian ◽  
Quang Pham ◽  
Hamid M. Said
Keyword(s):  
Cell Biology ◽  
Transmembrane Protein ◽  
Biological Significance ◽  
Intestinal Epithelial ◽  
Tnf Α ◽  
Epithelial Cell Lines ◽  
Confocal Images ◽  
Biological Aspects ◽  
Negative Controls ◽  
Function Cell

The apically localized riboflavin (RF) transporter-3 (RFVT-3) is involved in intestinal absorption of vitamin B2. Previous studies have characterized different physiological/biological aspects of the RFVT-3, but there is a lack of knowledge regarding possible existence of interacting partner(s) and consequence of interaction(s) on its function/cell biology. To address the latter, we performed yeast two-hybrid (Y2H) screening of a human colonic cDNA library and have identified transmembrane protein 237 (TMEM237) as a putative interactor with the human (h)RFVT-3; the interaction was further confirmed via “1-by-1” Y2H assay that involved appropriate positive and negative controls. TMEM237 was found to be highly expressed in human native intestine and in human intestinal epithelial cell lines; further, confocal images showed colocalization of the protein with hRFVT-3. The interaction between TMEM237 with hRFVT-3 in human intestinal epithelial HuTu-80 cells was established by coimmunoprecipitation. Expressing TMEM237 in HuTu-80 cells led to a significant induction in RF uptake, while its knockdown (with the use of gene-specific siRNA) led to a significant reduction in uptake. Transfecting TMEM237 into HuTu-80 cells also led to a marked enhancement in hRFVT-3 protein stability (reflected by an increase in the protein half-life). Interestingly, the level of expression of TMEM237 was found to be markedly reduced following treatment with TNF-α (a proinflammatory cytokine that inhibits intestinal RF uptake), while its expression was significantly upregulated following treatment with butyrate (an inducer of intestinal RF uptake). These findings identify TMEM237 as an interactor with the intestinal hRFVT-3 and show that the interaction has physiological/biological significance.

scholarly journals Factors that mold the nuclear landscape of HIV-1 integration

2020 ◽  
Author(s):  
Gregory J Bedwell ◽  
Alan N Engelman
Keyword(s):  
Nuclear Import ◽  
Integration Site ◽  
Preintegration Complex ◽  
Retroviral Integration ◽  
Host Interactions ◽  
Aids Pandemic ◽  
Nuclear Environment ◽  
Site Targeting ◽  
Viral Dna Integration ◽  
Hiv 1

Abstract The integration of retroviral reverse transcripts into the chromatin of the cells that they infect is required for virus replication. Retroviral integration has far-reaching consequences, from perpetuating deadly human diseases to molding metazoan evolution. The lentivirus human immunodeficiency virus 1 (HIV-1), which is the causative agent of the AIDS pandemic, efficiently infects interphase cells due to the active nuclear import of its preintegration complex (PIC). To enable integration, the PIC must navigate the densely-packed nuclear environment where the genome is organized into different chromatin states of varying accessibility in accordance with cellular needs. The HIV-1 capsid protein interacts with specific host factors to facilitate PIC nuclear import, while additional interactions of viral integrase, the enzyme responsible for viral DNA integration, with cellular nuclear proteins and nucleobases guide integration to specific chromosomal sites. HIV-1 integration favors transcriptionally active chromatin such as speckle-associated domains and disfavors heterochromatin including lamina-associated domains. In this review, we describe virus-host interactions that facilitate HIV-1 PIC nuclear import and integration site targeting, highlighting commonalities among factors that participate in both of these steps. We moreover discuss how the nuclear landscape influences HIV-1 integration site selection as well as the establishment of active versus latent virus infection.

scholarly journals Isolation and Analysis of Retroviral Integration Targets by Solo Long Terminal Repeat Inverse PCR

2002 ◽  
Vol 76 (11) ◽  
pp. 5540-5547 ◽  
Author(s):  
Yi Feng Jin ◽  
Toshio Ishibashi ◽  
Akio Nomoto ◽  
Michiaki Masuda
Keyword(s):  
Long Terminal Repeat ◽  
Dna Sequences ◽  
Target Selection ◽  
Terminal Repeat ◽  
Inverse Pcr ◽  
Proviral Integration ◽  
Host Chromosome ◽  
Retroviral Integration ◽  
Integration Sites ◽  
Slip Method

ABSTRACT Upon retroviral infection, the genomic RNA is reverse transcribed to make proviral DNA, which is then integrated into the host chromosome. Although the viral elements required for successful integration have been extensively characterized, little is known about the host DNA structure constituting preferred targets for proviral integration. In order to elucidate the mechanism for the target selection, comparison of host DNA sequences at proviral integration sites may be useful. To achieve simultaneous analysis of the upstream and downstream host DNA sequences flanking each proviral integration site, a Moloney murine leukemia virus-based retroviral vector was designed so that its integrated provirus could be removed by Cre-loxP homologous recombination, leaving a solo long terminal repeat (LTR). Taking advantage of the solo LTR, inverse PCR was carried out to amplify both the upstream and downstream cellular flanking DNA. The method called solo LTR inverse PCR, or SLIP, proved useful for simultaneously cloning the upstream and downstream flanking sequences of individual proviral integration sites from the polyclonal population of cells harboring provirus at different chromosomal sites. By the SLIP method, nucleotide sequences corresponding to 38 independent proviral integration targets were determined and, interestingly, atypical virus-host DNA junction structures were found in more than 20% of the cases. Characterization of retroviral integration sites using the SLIP method may provide useful insights into the mechanism for proviral integration and its target selection.

scholarly journals Resurrecting phenotypes from ancient DNA sequences: promises and perspectives

2015 ◽  
Vol 93 (9) ◽  
pp. 701-710 ◽  
Author(s):  
K.L. Campbell ◽  
M. Hofreiter
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Cell Biology ◽  
Genome Engineering ◽  
Ectopic Expression ◽  
Evolutionary Transitions ◽  
Extinct Species ◽  
Evolutionary Origins ◽  
Structural And Functional Properties

Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller’s sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these “living” processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.

scholarly journals Teaching Real Data Interpretation with Models (TRIM): Analysis of Student Dialogue in a Large-Enrollment Cell and Developmental Biology Course

2016 ◽  
Vol 15 (2) ◽  
pp. ar17 ◽  
Author(s):  
Patricia Zagallo ◽  
Shanice Meddleton ◽  
Molly S. Bolger
Keyword(s):  
Cell Biology ◽  
Biological Significance ◽  
Real Data ◽  
Data Interpretation ◽  
Biological Data ◽  
Scientific Practices ◽  
Student Dialogue ◽  
Audio Recordings ◽  
A Cell ◽  
Large Enrollment

We present our design for a cell biology course to integrate content with scientific practices, specifically data interpretation and model-based reasoning. A 2-yr research project within this course allowed us to understand how students interpret authentic biological data in this setting. Through analysis of written work, we measured the extent to which students’ data interpretations were valid and/or generative. By analyzing small-group audio recordings during in-class activities, we demonstrated how students used instructor-provided models to build and refine data interpretations. Often, students used models to broaden the scope of data interpretations, tying conclusions to a biological significance. Coding analysis revealed several strategies and challenges that were common among students in this collaborative setting. Spontaneous argumentation was present in 82% of transcripts, suggesting that data interpretation using models may be a way to elicit this important disciplinary practice. Argumentation dialogue included frequent co-construction of claims backed by evidence from data. Other common strategies included collaborative decoding of data representations and noticing data patterns before making interpretive claims. Focusing on irrelevant data patterns was the most common challenge. Our findings provide evidence to support the feasibility of supporting students’ data-interpretation skills within a large lecture course.

Mammalian genome evolution as a result of epigenetic regulation of transposable elements

2014 ◽  
Vol 5 (3) ◽  
pp. 183-194 ◽  
Author(s):  
Reuben M. Buckley ◽  
David L. Adelson
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Epigenetic Regulation ◽  
Dna Sequences ◽  
Defense Mechanisms ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Epigenetic Marks ◽  
Rna Molecules ◽  
Mammalian Genomes

AbstractTransposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming – an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.

Well Plate—Coupled Microfluidic Devices Designed for Facile Image-Based Cell Adhesion and Transmigration Assays

2009 ◽  
Vol 15 (1) ◽  
pp. 102-106 ◽  
Author(s):  
Carolyn G. Conant ◽  
Michael A. Schwartz ◽  
Cristian Ionescu-Zanetti
Keyword(s):  
Cell Adhesion ◽  
Shear Flow ◽  
Cell Biology ◽  
Mononuclear Cells ◽  
Biological Significance ◽  
Microfluidic Devices ◽  
Response Curves ◽  
Single Experiment ◽  
Cell Monolayers ◽  
Biological Phenomena

Microfluidic devices have become invaluable tools in recent years to model biological phenomena. Here, the authors present a well plate microfluidic (WPM) device for conducting cell biology assays under shear flow. Physiological shear flow conditions of cell-cell and cell-ligand adhesion within this device produce results with higher biological significance than conventional well plates. The WPM format also produced significant work flow advantages such as faster liquid handling compared to static well plate assays. The authors used the VLA-4—VCAM-1 cell adhesion model as the basis for a rapid, higher throughput adhesion inhibition screen of monoclonal antibodies against VLA-4. Using the WPM device, they generated IC50 dose-response curves 96 times faster than conventional flow cells. The WPM device was also used to study transmigration of mononuclear cells through endothelial cell monolayers. Twenty-four channels of transmigration data were generated in a single experiment.

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