scholarly journals Spatial Structure and Lamarckian Adaptation Explain Extreme Genetic Diversity at CRISPR Locus

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Jan O. Haerter ◽  
Kim Sneppen
Keyword(s):  
Genetic Diversity ◽  
Numerical Model ◽  
Spatial Structure ◽  
Spatial Correlations ◽  
Bacterial Strains ◽  
Large Variability ◽  
Crispr Locus ◽  
Virulent Phage ◽  
Short Palindromic Repeat ◽  
Different Levels

ABSTRACT Even within similar bacterial strains, it has been found that the clustered, regularly interspaced short palindromic repeat (CRISPR) shows a large variability of spacers. Modeling bacterial strains with different levels of immunity to infection by a single virulent phage, we find that coexistence in a well-mixed environment is possible only when these levels are distinctly different. When bacterial strains are similar, one subpopulation collapses. In the case of bacteria with various levels of CRISPR immunity to a range of phages, small differences in spacer composition will accordingly be suppressed under well-mixed conditions. Using a numerical model of populations spreading in space, we predict that it is the Lamarckian nature of CRISPR evolution that combines with spatial correlations to sustain the experimentally observed distribution of spacer diversity.

scholarly journals Genetic Diversity and Aggressiveness of Ralstonia solanacearum Strains Causing Bacterial Wilt of Potato in Uruguay

Plant Disease ◽  
2011 ◽  
Vol 95 (10) ◽  
pp. 1292-1301 ◽  
Author(s):  
M. I. Siri ◽  
A. Sanabria ◽  
M. J. Pianzzola
Keyword(s):  
Genetic Diversity ◽  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Potato Tubers ◽  
Bacterial Strains ◽  
Potato Plants ◽  
Polymerase Chain ◽  
First Time ◽  
Different Levels

Bacterial wilt, caused by Ralstonia solanacearum, is a major disease affecting potato (Solanum tuberosum) production worldwide. Although local reports suggest that the disease is widespread in Uruguay, characterization of prevalent R. solanacearum strains in that country has not been done. In all, 28 strains of R. solanacearum isolated from major potato-growing areas in Uruguay were evaluated, including 26 strains isolated from potato tubers and 2 from soil samples. All strains belonged to phylotype IIB, sequevar 1 (race 3, biovar 2). Genetic diversity of strains was assessed by repetitive-sequence polymerase chain reaction, which showed that the Uruguayan strains constituted a homogeneous group. In contrast, inoculation of the strains on tomato and potato plants showed, for the first time, different levels of aggressiveness among R. solanacearum strains belonging to phylotype IIB, sequevar 1. Aggressiveness assays were also performed on accessions of S. commersonii, a wild species native to Uruguay that is a source of resistance for potato breeding. No significant interactions were found between bacterial strains and potato and S. commersonii genotypes, and differences in aggressiveness among R. solanacearum strains were consistent with previously identified groups based on tomato and potato inoculations. Moreover, variation in responses to R. solanacearum was observed among the S. commersonii accessions tested.

scholarly journals The CARF Protein MM_0565 Affects Transcription of the Casposon-Encoded cas1-solo Gene in Methanosarcina mazei Gö1

Biomolecules ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1161
Author(s):  
Andrea Ulbricht ◽  
Lisa Nickel ◽  
Katrin Weidenbach ◽  
Herman Vargas Gebauer ◽  
Claudia Kießling ◽  
...  
Keyword(s):  
Specific Binding ◽  
Type I ◽  
Crispr Locus ◽  
Methanosarcina Mazei ◽  
Methanosarcina Mazei Gö1 ◽  
Molecular Machinery ◽  
Short Palindromic Repeat ◽  
High Salt Stress ◽  
Different Levels

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci are found in bacterial and archaeal genomes where they provide the molecular machinery for acquisition of immunity against foreign DNA. In addition to the cas genes fundamentally required for CRISPR activity, a second class of genes is associated with the CRISPR loci, of which many have no reported function in CRISPR-mediated immunity. Here, we characterize MM_0565 associated to the type I-B CRISPR-locus of Methanosarcina mazei Gö1. We show that purified MM_0565 composed of a CRISPR-Cas Associated Rossmann Fold (CARF) and a winged helix-turn-helix domain forms a dimer in solution; in vivo, the dimeric MM_0565 is strongly stabilized under high salt stress. While direct effects on CRISPR-Cas transcription were not detected by genetic approaches, specific binding of MM_0565 to the leader region of both CRISPR-Cas systems was observed by microscale thermophoresis and electromobility shift assays. Moreover, overexpression of MM_0565 strongly induced transcription of the cas1-solo gene located in the recently reported casposon, the gene product of which shows high similarity to classical Cas1 proteins. Based on our findings, and taking the absence of the expressed CRISPR locus-encoded Cas1 protein into account, we hypothesize that MM_0565 might modulate the activity of the CRISPR systems on different levels.

scholarly journals Defining Urban Science

2021 ◽  
pp. 15-28
Author(s):  
Michael Batty
Keyword(s):  
Spatial Structure ◽  
Spatial Interaction ◽  
Urban Informatics ◽  
Form And Function ◽  
Urban Science ◽  
Operational Models ◽  
And Function ◽  
The City ◽  
Different Levels

AbstractThis introductory chapter provides a brief overview of the theories and models that constitute what has come to be called urban science. Explaining and measuring the spatial structure of the city in terms of its form and function is one of the main goals of this science. It provides links between the way various theories about how the city is formed, in terms of its economy and social structure, and how these theories might be transformed into models that constitute the operational tools of urban informatics. First the idea of the city as a system is introduced, and then various models pertaining to the forces that determine what is located where in the city are presented. How these activities are linked to one another through flows and networks are then introduced. These models relate to formal models of spatial interaction, the distribution of the sizes of different cities, and the qualitative changes that take place as cities grow and evolve to different levels. Scaling is one of the major themes uniting these different elements grounding this science within the emerging field of complexity. We then illustrate how we might translate these ideas into operational models which are at the cutting edge of the new tools that are being developed in urban informatics, and which are elaborated in various chapters dealing with modeling and mobility throughout this book.

VNTR typing of the bacterial rice pathogen Burkholderia glumae reveals the coexistence of several diverging lineages in a single field in Colombia.

Plant Disease ◽  
2021 ◽  
Author(s):  
Gilles Bena ◽  
Paola Fory ◽  
Johanna Echeverri ◽  
Gloria Mosquera
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Tandem Repeats ◽  
Genetic Relationships ◽  
Rice Paddy ◽  
Rice Cultivar ◽  
Bacterial Strains ◽  
Burkholderia Glumae ◽  
Significant Drop ◽  
Origin And Evolution

Bulkholderia glumae is responsible for the panicle blight disease of rice. This disease is present worldwide and can result in significant drop in yields. In order to estimate the genetic diversity of the bacterial strains present in a rice paddy field in Colombia, we sampled 109 strains from infected panicles. In order to detect fine genetic relationships among related haplotypes, and to overcome a very low nucleotide diversity detected in previous studies, we designed primers to amplify and sequence several highly variable minisatellite loci, or Variable Number Tandem Repeats, as well as part of the Toxoflavin toxA gene, in all strains. Results show that (i) the toxA nucleotide diversity defined four lineages and was similar to that detected in several fields in Japan, (ii) data suggest that B. glumae has spread from Asia to America without major loss of genetic diversity, (iii) five VNTR loci discriminated the strains within the field revealing single and multi-infections of the rice panicles with a wide distribution of the haplotypes among the different plots. Even though disease levels vary considerably from year to year, the bacterial genetic diversity is maintained within a field. We do not detect any geographical structuring within the field, nor any effect of the rice cultivar on the observed diversity. The consequences on the origin and evolution of the bacteria are discussed.

scholarly journals Origins and Assembly of Malesian Rainforests

2019 ◽  
Vol 50 (1) ◽  
pp. 119-143 ◽  
Author(s):  
Robert M. Kooyman ◽  
Robert J. Morley ◽  
Darren M. Crayn ◽  
Elizabeth M. Joyce ◽  
Maurizio Rossetto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Spatial Structure ◽  
Fossil Record ◽  
Functional Trait ◽  
Indian Plate ◽  
Evolutionary Origins ◽  
Australian Plate ◽  
Floristic Elements ◽  
Adaptive Radiations ◽  
Abundance And Diversity

Unraveling the origins of Malesia's once vast, hyperdiverse rainforests is a perennial challenge. Major contributions to rainforest assembly came from floristic elements carried on the Indian Plate and montane elementsfrom the Australian Plate (Sahul). The Sahul component is now understood to include substantial two-way exchanges with Sunda inclusive of lowland taxa. Evidence for the relative contributions of the great Asiatic floristic interchanges (GAFIs) with India and Sahul, respectively, to the flora of Malesia comes from contemporary lineage distributions, the fossil record, time-calibrated phylogenies, functional traits, and the spatial structure of genetic diversity. Functional-trait and biome conservatism are noted features of montane austral lineages from Sahul (e.g., diverse Podocarpaceae), whereas the abundance and diversity of lowland lineages, including Syzygium (Myrtaceae) and the Asian dipterocarps (Dipterocarpoideae), reflect a less well understood combination of dispersal, ecology, and adaptive radiations. Thus, Malesian rainforest assembly has been shaped by sharply contrasting evolutionary origins and biogeographic histories.

scholarly journals Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Edward W. Davis ◽  
Javier F. Tabima ◽  
Alexandra J. Weisberg ◽  
Lucas Dantas Lopes ◽  
Michele S. Wiseman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Adaptive Immune System ◽  
The United States ◽  
Genomic Diversity ◽  
Data Set ◽  
Important Species ◽  
Content Type ◽  
Low Genetic Diversity ◽  
History Of ◽  
Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

scholarly journals Spatial Structure and Antimicrobial Activity of Cyclopropane Derivative of Limonene

2018 ◽  
Vol 13 (4) ◽  
pp. 1934578X1801300
Author(s):  
Daniyar Sadyrbekov ◽  
Timur Saliev ◽  
Yuri Gatilov ◽  
Ivan Kulakov ◽  
Roza Seidakhmetova ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Pseudomonas Aeruginosa ◽  
Antimicrobial Activity ◽  
Bacillus Subtilis ◽  
Spatial Structure ◽  
Bacterial Strains ◽  
Gram Negative ◽  
X Ray ◽  
Cyclopropane Derivative

A cyclopropane derivative of limonene, (1 S, 4 S, 6 R)-7,7-dichloro-4-[(1 S)-2,2-dichloro-1-methylcyclopropyl]-1-methylbicyclo [4.1.0] heptane (compound 2), was synthesized and its structure was determined by NMR and X-ray crystallographic methods. In addition, an antimicrobial activity of the compound against Gram-positive ( Staphylococcus aureus, Bacillus subtilis) and Gram-negative ( Escherichia coli, Pseudomonas aeruginosa) bacterial strains was also scrutinized.

Evaluation of populations of Dactylis glomerata L. native to Mediterranean environments

2012 ◽  
Vol 63 (12) ◽  
pp. 1124 ◽  
Author(s):  
V. Copani ◽  
G. Testa ◽  
A. Lombardo ◽  
S. L. Cosentino
Keyword(s):  
Genetic Diversity ◽  
Biomass Yield ◽  
Agronomic Traits ◽  
Dactylis Glomerata ◽  
Leaf Length ◽  
Mediterranean Environment ◽  
Summer Dormancy ◽  
Low Levels ◽  
Dactylis Glomerata L ◽  
Different Levels

Several morphological and agronomic traits and the genetic diversity of nine Dactylis glomerata L. populations collected throughout Sicily (semi-arid Mediterranean environment) were evaluated for two successive years. Significant differences were recorded for morphological traits (plant height, leaf length, leaf width). In relation to the measurement of summer dormancy, the results suggest the expression of different levels of dormancy (completely dormant, semi-dormant, and non-dormant). For biomass yield, some Sicilian populations (SD63 and SD56) characterised by low levels of summer dormancy show production levels similar to the summer-active control varieties (Medly and Porto). However, SD46, with a much higher level of dormancy, gave biomass yield higher than the summer-dormant control variety (Kasbah). The genetic diversity evaluated by fAFLP analysis confirms the observed morphological and agronomic variability.

Sign in / Sign up

Export Citation Format

Share Document