scholarly journals Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria

2021 ◽  
Author(s):  
Anna K. Simonsen
Keyword(s):  
Environmental Change ◽  
Environmental Stress ◽  
High Stress ◽  
Spatial Proximity ◽  
Accessory Gene ◽  
Entire Genome ◽  
Bacterial Populations ◽  
Selection Gene ◽  
Close Spatial Proximity ◽  
Core Genes

AbstractBacteria have highly flexible pangenomes, which are thought to facilitate evolutionary responses to environmental change, but the impacts of environmental stress on pangenome evolution remain unclear. Using a landscape pangenomics approach, I demonstrate that environmental stress leads to consistent, continuous reduction in genome content along four environmental stress gradients (acidity, aridity, heat, salinity) in naturally occurring populations of Bradyrhizobium diazoefficiens (widespread soil-dwelling plant mutualists). Using gene-level network and duplication functional traits to predict accessory gene distributions across environments, genes predicted to be superfluous are more likely lost in high stress, while genes with multi-functional roles are more likely retained. Genes with higher probabilities of being lost with stress contain significantly higher proportions of codons under strong purifying and positive selection. Gene loss is widespread across the entire genome, with high gene-retention hotspots in close spatial proximity to core genes, suggesting Bradyrhizobium has evolved to cluster essential-function genes (accessory genes with multifunctional roles and core genes) in discrete genomic regions, which may stabilise viability during genomic decay. In conclusion, pangenome evolution through genome streamlining are important evolutionary responses to environmental change. This raises questions about impacts of genome streamlining on the adaptive capacity of bacterial populations facing rapid environmental change.

scholarly journals 4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments

2015 ◽  
Author(s):  
Ramya Raviram ◽  
Pedro P. Rocha ◽  
Christian L. Müller ◽  
Emily R. Miraldi ◽  
Sana Badri ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
Cell Types ◽  
Single Locus ◽  
Spatial Proximity ◽  
Experimental Conditions ◽  
Entire Genome ◽  
Chromosome Conformation ◽  
Genome Wide ◽  
The Many ◽  
Close Spatial Proximity

ABSTRACT4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or “bait”) that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.AUTHORS SUMMARYCircularized chromosome conformation capture, or 4C-Seq is a technique developed to identify regions of the genome that are in close spatial proximity to a single locus of interest (‘bait’). This technique is used to detect regulatory interactions between promoters and enhancers and to characterize the nuclear environment of different regions within and across different cell types. So far, existing methods for 4C-Seq data analysis do not comprehensively identify interactions across the entire genome due to biases in the technique that are related to the decrease in 4C signal that results from increased 3D distance from the bait. To compensate for these weaknesses in existing methods we developed 4C-ker, a method that explicitly models these biases to improve the analysis of 4C-Seq to better understand the genome wide interaction profile of an individual locus.

scholarly journals Involvement of loop 5 lysine residues and the N-terminal β-hairpin of the ribotoxin hirsutellin A on its insecticidal activity

2016 ◽  
Vol 397 (2) ◽  
pp. 135-145 ◽  
Author(s):  
Miriam Olombrada ◽  
Lucía García-Ortega ◽  
Javier Lacadena ◽  
Mercedes Oñaderra ◽  
José G. Gavilanes ◽  
...  
Keyword(s):  
Active Sites ◽  
Structural Changes ◽  
The Other ◽  
Spatial Proximity ◽  
Ribonucleolytic Activity ◽  
The Family ◽  
Lysine Residues ◽  
Hirsutella Thompsonii ◽  
Close Spatial Proximity ◽  
High Degree

Abstract Ribotoxins are cytotoxic members of the family of fungal extracellular ribonucleases best represented by RNase T1. They share a high degree of sequence identity and a common structural fold, including the geometric arrangement of their active sites. However, ribotoxins are larger, with a well-defined N-terminal β-hairpin, and display longer and positively charged unstructured loops. These structural differences account for their cytotoxic properties. Unexpectedly, the discovery of hirsutellin A (HtA), a ribotoxin produced by the invertebrate pathogen Hirsutella thompsonii, showed how it was possible to accommodate these features into a shorter amino acid sequence. Examination of HtA N-terminal β-hairpin reveals differences in terms of length, charge, and spatial distribution. Consequently, four different HtA mutants were prepared and characterized. One of them was the result of deleting this hairpin [Δ(8-15)] while the other three affected single Lys residues in its close spatial proximity (K115E, K118E, and K123E). The results obtained support the general conclusion that HtA active site would show a high degree of plasticity, being able to accommodate electrostatic and structural changes not suitable for the other previously known larger ribotoxins, as the variants described here only presented small differences in terms of ribonucleolytic activity and cytotoxicity against cultured insect cells.

scholarly journals ‘They Eat Potatoes, I Eat Rice’: Symbolic Boundary Making and Space in Neighbour Relations

2011 ◽  
Vol 16 (4) ◽  
pp. 22-33 ◽  
Author(s):  
Gwen Van Eijk
Keyword(s):  
Personal Information ◽  
Spatial Proximity ◽  
Easy Access ◽  
Symbolic Boundaries ◽  
Personal Privacy ◽  
Social Mixing ◽  
Boundary Making ◽  
Close Spatial Proximity ◽  
Depth Interviews ◽  
Symbolic Boundary

This article examines ‘neighbouring’ as the setting in which cross-category relations develop and symbolic boundaries are constructed. The study is based on thirty in-depth interviews with residents living in a multi-ethnic and a mono-ethnic neighbourhood in Rotterdam, the Netherlands. The findings challenge the hoped-for outcomes of social mixing in neighbourhoods, as well as the view that boundary making is something inherent to multi-ethnic neighbourhoods only. Neighbour relations are often setting-specific (relations are interchangeable, scripted and bounded, and passively maintained), which is relevant for understanding the spatiality of neighbouring and the limited exchange of personal information between neighbours. Because neighbouring involves the balancing of personal privacy and close spatial proximity, the exchange of personal information is limited, while spatial proximity ensures easy access to observable (through seeing, hearing and smelling) categorical markers that signify class, ethnicity, lifestyle, etc. In this way, neighbour interaction reconstructs symbolic boundaries rather than breaking them down.

Ontogeny of spatial relationships and social behaviour in juvenile Richardson's ground squirrels

1981 ◽  
Vol 59 (9) ◽  
pp. 1666-1676 ◽  
Author(s):  
Gail R. Michener
Keyword(s):  
Social Interactions ◽  
Social Behaviour ◽  
Ground Squirrels ◽  
Spatial Proximity ◽  
Family Unit ◽  
Social Patterns ◽  
Rapid Acquisition ◽  
The Family ◽  
Core Areas ◽  
Close Spatial Proximity

The development of spatial and social patterns by juvenile Richardson's ground squirrels, from first emergence from the natal burrow to entry into hibernation, is described. Juveniles enter the aboveground population at [Formula: see text] weeks of age. During the next 4 weeks juveniles remain in close spatial proximity to family members with whom they engage in frequent amicable social interactions. Thereafter, juveniles become increasingly independent from the family unit, establishing their own spatially distinct core areas and exhibiting site-dependent dominance toward nonkin. Typically juveniles remain physically closer to and more amicable with littermates and mother than other conspecifics such that they compose kin clusters, the members of which are agonistic toward members of adjacent kin clusters. Daughters are more likely to continue to reside close to kin as adults than are sons. At 9–10 weeks of age juveniles exhibit the majority of spatial and social patterns characteristic of adults, and at 12 weeks they are behaviourally indistinguishable from adults. Similar rapid acquisition of adult patterns occurs in four other species of ground-dwelling sciurids that are also obligate hibernators and that breed immediately following emergence from their first hibernation.

Effects of Continents and Supercontinents on Organic Evolution

2004 ◽  
Author(s):  
John J. W. Rogers ◽  
M. Santosh
Keyword(s):  
Environmental Change ◽  
Environmental Stress ◽  
Tectonic Activity ◽  
Continental Margins ◽  
Organic Evolution ◽  
Ocean Ridges ◽  
Large Numbers ◽  
Local Species ◽  
Orogenic Belts ◽  
Shallow Seas

The earth’s organic life has changed continually for more than 3.5 billion years. This evolution may have resulted partly from environmental stress generated by tectonic activity within the earth and partly from processes independent of the earth’s interior. This chapter investigates these different effects in an attempt to determine the role that continents played in the evolution of organisms. Continents and tectonics associated with them may have influenced organic evolution in both active and passive ways. Active effects include several processes that partly controlled the earth’s surface environment. Climate change was caused partly by movements of continents and construction of orogenic belts. Continental rifting increased the area of shallow seas as new continental margins subsided. Changes in volume of ocean ridges and epeiric movements of continents caused marine transgressions and regressions. Temperatures of water in shallow seas increased or decreased as continents moved across latitudes. The major passive effects of continents and supercontinents result from their influence on diversity of organisms. When continents were broadly dispersed and occupied most latitudes, as on the present earth, this isolation resulted in shallow-water and subaerial families that contained numerous genera, genera with large numbers of species, and species divided among many different varieties. This diversity was clearly smaller at times when continents were aggregated into a few landmasses and particularly low when supercontinents permitted exchange of organisms throughout most of the world’s land and shallow seas. During times of major environmental stress, these differences would have restricted extinction of organisms to local species and genera during times of high diversity but might have permitted disappearance of whole orders and classes when diversity was low. Organic evolution was almost certainly affected by species diversity, but it may have occurred without any active control by tectonic processes. Although evolution probably occurs only when changing environments place stresses on organisms that enhance the competition among them, it is also possible that competition between organisms can cause evolution even without significant environmental change. Furthermore, some environmental change probably resulted from processes that are not related to the tectonics of the solid earth.

scholarly journals Adenine DNA methylation, 3D genome organization, and gene expression in the parasiteTrichomonas vaginalis

2020 ◽  
Vol 117 (23) ◽  
pp. 13033-13043
Author(s):  
Ayelen Lizarraga ◽  
Zach Klapholz O’Brown ◽  
Konstantinos Boulias ◽  
Lara Roach ◽  
Eric Lieberman Greer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Trichomonas Vaginalis ◽  
Three Dimensional ◽  
Wide Distribution ◽  
Spatial Proximity ◽  
Regulation Of Transcription ◽  
3D Genome ◽  
Intergenic Regions ◽  
Close Spatial Proximity

Trichomonas vaginalisis a common sexually transmitted parasite that colonizes the human urogenital tract causing infections that range from asymptomatic to highly inflammatory. Recent works have highlighted the importance of histone modifications in the regulation of transcription and parasite pathogenesis. However, the nature of DNA methylation in the parasite remains unexplored. Using a combination of immunological techniques and ultrahigh-performance liquid chromatography (UHPLC), we analyzed the abundance of DNA methylation in strains with differential pathogenicity demonstrating that N6-methyladenine (6mA), and not 5‐methylcytosine (5mC), is the main DNA methylation mark inT. vaginalis. Genome-wide distribution of 6mA reveals that this mark is enriched at intergenic regions, with a preference for certain superfamilies of DNA transposable elements. We show that 6mA inT. vaginalisis associated with silencing when present on genes. Interestingly, bioinformatics analysis revealed the presence of transcriptionally active or repressive intervals flanked by 6mA-enriched regions, and results from chromatin conformation capture (3C) experiments suggest these 6mA flanked regions are in close spatial proximity. These associations were disrupted when parasites were treated with the demethylation activator ascorbic acid. This finding revealed a role for 6mA in modulating three-dimensional (3D) chromatin structure and gene expression in this divergent member of the Excavata.

Spatiotemporal factors influence sound-source segregation in localization behavior

2020 ◽  
Author(s):  
Guus Christian van Bentum ◽  
Marc Mathijs van Wanrooij ◽  
A. John Van Opstal
Keyword(s):  
Temporal Order ◽  
Weighted Average ◽  
Spatial Separation ◽  
Stimulus Location ◽  
Spatial Proximity ◽  
Sound Source Segregation ◽  
Close Spatial Proximity ◽  
Inhibitory Interactions ◽  
Localization Behavior ◽  
Sensorimotor Map

To program a goal-directed response in the presence of acoustic reflections, the audio-motor system should suppress the detection of time-delayed sources. We examined the effects of spatial separation and inter-stimulus delay on the ability of human listeners to localize a pair of broadband sounds in the horizontal plane. Participants indicated how many sounds were heard and where these were perceived by making one or two head-orienting localization responses. Results suggest that perceptual fusion of the two sounds depends on delay and spatial separation. Leading and lagging stimuli in close spatial proximity required longer stimulus delays to be perceptually separated than those further apart. Whenever participants heard one sound, their localization responses for synchronous sounds were oriented to a weighted average of both source locations. For short delays, responses were directed towards the leading stimulus location. Increasing spatial separation enhanced this effect. For longer delays, responses were again directed towards a weighted average. When participants perceived two sounds, the first and the second response were directed to either of the leading and lagging source locations. Perceived locations were interchanged often in their temporal order (in ~40% of trials). We show that the percept of two sounds occurring requires sufficient spatiotemporal separation, after which localization can be performed with high accuracy. We propose that the percept of temporal order of two concurrent sounds results from a different process than localization, and discuss how dynamic lateral excitatory-inhibitory interactions within a spatial sensorimotor map could explain the findings.

scholarly journals Plasmid carriage can limit bacteria–phage coevolution

2015 ◽  
Vol 11 (8) ◽  
pp. 20150361 ◽  
Author(s):  
Ellie Harrison ◽  
Julie Truman ◽  
Rosanna Wright ◽  
Andrew J. Spiers ◽  
Steve Paterson ◽  
...  
Keyword(s):  
Conjugative Plasmid ◽  
Phage Resistance ◽  
Resistance Mutations ◽  
Accessory Gene ◽  
Bacterial Populations ◽  
High Frequencies ◽  
Qualitative Resistance ◽  
Selection For ◽  
Evolutionary Consequences ◽  
Plasmid Carriage

Coevolution with bacteriophages is a major selective force shaping bacterial populations and communities. A variety of both environmental and genetic factors has been shown to influence the mode and tempo of bacteria–phage coevolution. Here, we test the effects that carriage of a large conjugative plasmid, pQBR103, had on antagonistic coevolution between the bacterium Pseudomonas fluorescens and its phage, SBW25 ϕ 2. Plasmid carriage limited bacteria–phage coevolution; bacteria evolved lower phage-resistance and phages evolved lower infectivity in plasmid-carrying compared with plasmid-free populations. These differences were not explained by effects of plasmid carriage on the costs of phage resistance mutations. Surprisingly, in the presence of phages, plasmid carriage resulted in the evolution of high frequencies of mucoid bacterial colonies. Mucoidy can provide weak partial resistance against SBW25 ϕ 2, which may have limited selection for qualitative resistance mutations in our experiments. Taken together, our results suggest that plasmids can have evolutionary consequences for bacteria that go beyond the direct phenotypic effects of their accessory gene cargo.

scholarly journals Social structure and residency in aggregations of male sperm whales

2002 ◽  
Vol 80 (7) ◽  
pp. 1189-1196 ◽  
Author(s):  
Erland Lettevall ◽  
Christoph Richter ◽  
Nathalie Jaquet ◽  
Elizabeth Slooten ◽  
Steve Dawson ◽  
...  
Keyword(s):  
Social Structure ◽  
Social Structures ◽  
Spatial Proximity ◽  
Residence Times ◽  
Physeter Macrocephalus ◽  
Sperm Whales ◽  
Apparent Lack ◽  
Male Sperm ◽  
Close Spatial Proximity

Sperm whales (Physeter macrocephalus) are sexually dimorphic in several respects, including size, latitudinal distribution, and social structure. Females are known to have complex social structures, including long-term bonds, but the social structures of sexually mature or maturing males have received much less attention. Using data from aggregations of males off Norway, Nova Scotia, New Zealand, and the Galápagos Islands, we examined aggregation size, residence times within aggregations, clustering at the surface, and long-term bonds. Results were generally consistent among study areas. The aggregations found in each area contained around 10–30 males at any time, and were usually a few tens of kilometres across. Mean residence times within aggregations ranged from a few days to a few weeks. Close clustering at the surface was rare, but present at each site. There was no evidence for preferred companionship between individuals at any temporal scale in any of the study areas. The rarity of clustering and the apparent lack of long-term relationships amongst male sperm whales contrast strongly with results of studies on females, suggesting that both close spatial proximity at the surface and permanent bonds between individuals may be a consequence of the need for care of the young.

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