scholarly journals Integrative and conjugative elements and their hosts: composition, distribution, and organization

2017 ◽  
Author(s):  
Jean Cury ◽  
Marie Touchon ◽  
Eduardo P. C. Rocha
Keyword(s):  
Large Scale ◽  
Functional Organization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Model Systems ◽  
Integrative And Conjugative Elements ◽  
Scale Characterization ◽  
And Function ◽  
Sequence Similarity Networks

AbstractConjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species’ pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses show that ICEs are modular and that their gene repertoires can be grouped in function of their conjugation types, even if integrases were shown to be paraphyletic relative to the latter. We show that there are general trends in the functional organization of genes within ICEs and of ICEs within the bacterial chromosome paving the way for future functional and evolutionary analyses.

scholarly journals Remote Sensing Methods for the Biophysical Characterization of Protected Areas Globally: Challenges and Opportunities

2021 ◽  
Vol 10 (6) ◽  
pp. 384
Author(s):  
Javier Martínez-López ◽  
Bastian Bertzky ◽  
Simon Willcock ◽  
Marine Robuchon ◽  
María Almagro ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Protected Areas ◽  
Large Scale ◽  
Anthropogenic Activities ◽  
Global Scale ◽  
Area Network ◽  
Biophysical Characterization ◽  
Challenges And Opportunities ◽  
Scale Characterization

Protected areas (PAs) are a key strategy to reverse global biodiversity declines, but they are under increasing pressure from anthropogenic activities and concomitant effects. Thus, the heterogeneous landscapes within PAs, containing a number of different habitats and ecosystem types, are in various degrees of disturbance. Characterizing habitats and ecosystems within the global protected area network requires large-scale monitoring over long time scales. This study reviews methods for the biophysical characterization of terrestrial PAs at a global scale by means of remote sensing (RS) and provides further recommendations. To this end, we first discuss the importance of taking into account the structural and functional attributes, as well as integrating a broad spectrum of variables, to account for the different ecosystem and habitat types within PAs, considering examples at local and regional scales. We then discuss potential variables, challenges and limitations of existing global environmental stratifications, as well as the biophysical characterization of PAs, and finally offer some recommendations. Computational and interoperability issues are also discussed, as well as the potential of cloud-based platforms linked to earth observations to support large-scale characterization of PAs. Using RS to characterize PAs globally is a crucial approach to help ensure sustainable development, but it requires further work before such studies are able to inform large-scale conservation actions. This study proposes 14 recommendations in order to improve existing initiatives to biophysically characterize PAs at a global scale.

A widespread pathway for substitution of adenine by diaminopurine in phage genomes

Science ◽  
2021 ◽  
Vol 372 (6541) ◽  
pp. 512-516
Author(s):  
Yan Zhou ◽  
Xuexia Xu ◽  
Yifeng Wei ◽  
Yu Cheng ◽  
Yu Guo ◽  
...  
Keyword(s):  
Large Scale ◽  
Restriction Enzymes ◽  
Diverse Range ◽  
Host Restriction ◽  
Form And Function ◽  
Multienzyme System ◽  
Dna Modifications ◽  
Dna Production ◽  
And Function

DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Z-genome synthesis. We identified dozens of globally widespread phages harboring such enzymes, and we further verified the Z genome in one of these phages, Acinetobacter phage SH-Ab 15497, by using liquid chromatography with ultraviolet and mass spectrometry. The Z genome endows phages with evolutionary advantages for evading the attack of host restriction enzymes, and the characterization of its biosynthetic pathway enables Z-DNA production on a large scale for a diverse range of applications.

Large scale characterization of plant plasma membrane proteins

Biochimie ◽  
1999 ◽  
Vol 81 (6) ◽  
pp. 655-661 ◽  
Author(s):  
Véronique Santoni ◽  
Patrick Doumas ◽  
David Rouquié ◽  
Monique Mansion ◽  
Thierry Rabilloud ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Large Scale ◽  
Plasma Membrane Proteins ◽  
Scale Characterization ◽  
Plant Plasma Membrane

Cardiac physiology at the cellular level: use of cultured HL-1 cardiomyocytes for studies of cardiac muscle cell structure and function

2004 ◽  
Vol 286 (3) ◽  
pp. H823-H829 ◽  
Author(s):  
Steven M. White ◽  
Phillip E. Constantin ◽  
William C. Claycomb
Keyword(s):  
Cell Line ◽  
Cell Structure ◽  
Ischemia Reperfusion ◽  
Cellular Level ◽  
Model Systems ◽  
Cardiac Physiology ◽  
Cardiac Phenotype ◽  
Pathological Conditions ◽  
And Function

HL-1 cells are currently the only cardiomyocyte cell line available that continuously divides and spontaneously contracts while maintaining a differentiated cardiac phenotype. Extensive characterization using microscopic, genetic, immunohistochemical, electrophysiological, and pharmacological techniques has demonstrated how similar HL-1 cells are to primary cardiomyocytes. In the few years that HL-1 cells have been available, they have been used in a variety of model systems designed to answer important questions regarding cardiac biology at the cellular and molecular levels. Whereas HL-1 cells have been used to study normal cardiomyocyte function with regard to signaling, electrical, metabolic, and transcriptional regulation, they have also been used to address pathological conditions such as hypoxia, hyperglycemia-hyperinsulinemia, apoptosis, and ischemia-reperfusion. The availability of an immortalized, contractile cardiac cell line has provided investigators with a tool for probing the intricacies of cardiomyocyte function. In this review, we describe the culture and characterization of HL-1 cardiomyocytes as well as various model systems that have been developed using these cells to gain a better understanding of cardiac biology at the cellular and molecular levels.

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