An <Emphasis Type="Italic">Escherichia coli aer</Emphasis> mutant exhibits a reduced ability to colonize the streptomycin-treated mouse large intestine

The oxygen sensor Aer of Escherichia coli affects the expression level of genes that are involved in sugar acid degradation. Phenotypes of Aer mediated gene regulation, namely growth on sugar acids was tested ‘in vitro’ with Phenotype MicroArrays and colonization of the mouse large intestine was tested ‘in vivo’. The aer mutant did not grow on the sugar acids d-gluconate, d-glucuronate, d-galacturonate, as well as the sugar alcohol d-mannitol. Since sugar acids are the predominant carbon source for E. coli in the intestinal mucosa, the ability of the aer mutant to colonize the streptomycin-treated mouse large intestine was tested. The mutant exhibited a decreased ability to colonize the intestine when compared to wild-type cells. This effect was more pronounced under competitive conditions. The colonization phenotype of the aer mutant was complemented with either of two plasmids. One of them expressed the Aer protein, whereas the other one expressed the sugar acid degradation enzymes that are encoded by edd and eda. The data support the interpretation that decreased expression of edd and eda along with the decreased ability to grow on sugar acids may contribute to the reduced capacity of the aer mutant to colonize the mouse intestine. While Aer seems to be important during the initiation phase of colonization, FlhD/FlhC appears to be of disadvantage during maintenance phase. FlhD/FlhC is the master regulator of all flagellar genes and required for Aer expression. Mutants in flhD exhibited an initial competitive disadvantage during the first 3 days of colonization, but recovered lateron.     

Livelihood Dynamics Across a Variable Flooding Regime

Variability in environmental phenomena such as fire, flooding, and weather-related events can have significant impacts for social and environmental systems and their coupled interactions. Livelihoods systems reliant on the natural environment can be disrupted or eliminated, while associated governance regimes require negotiation to ensure equitable and sustainable management responses. These patterns can be particularly pronounced within areas prone to flooding, as these sites can experience variability in the location, timing, amount, and duration of flooding events. While research within the social and natural sciences has evaluated these dynamics within flooding regimes, the coupled interactions can be underemphasized even though they are integral in producing livelihood systems and possibilities for environmental management. This paper details research conducted from 2011 to 2016 in five villages located in different locations within the Okavango Delta of Botswana. We report the findings from qualitative interviewing and livelihood mapping activities that are integrated with remote sensing analysis to provide concrete empirical detail on the variability of flooding and resulting variations in perception and livelihood responses. The paper demonstrates that flooding dynamics vary at discrete locations and produce diverse perceptions that are tied to livelihood adjustments in place-specific ways. These patterns are also embedded in regional and global processes that have significant implications for household vulnerability within socio-ecological systems strongly impacted by local and distant climatic and hydrological drivers of change.     

Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure

Genome-wide chromatin immunoprecipitation (ChIP) studies have brought significant insight into the genomic localization of chromatin-associated proteins and histone modifications. The large amount of data generated by these analyses, however, require approaches that enable rapid validation and analysis of biological relevance. Furthermore, there are still protein and modification targets that are difficult to detect using standard ChIP methods. To address these issues, we developed an immediate chromatin immunoprecipitation procedure which we call ZipChip. ZipChip significantly reduces the time and increases sensitivity allowing for rapid screening of multiple loci. Here we describe how ZipChIP enables detection of histone modifications (H3K4 mono- and trimethylation) and two yeast histone demethylases, Jhd2 and Rph1, which were previously difficult to detect using standard methods. Furthermore, we demonstrate the versatility of ZipChIP by analyzing the enrichment of the histone deacetylase Sir2 at heterochromatin in yeast and enrichment of the chromatin remodeler, PICKLE, at euchromatin in Arabidopsis thaliana.     

Bloody‐minded parasites and sex: the effects of fluctuating virulence

Asexual lineages can grow at a faster rate than sexual lineages. Why then is sexual reproduction so widespread? Much empirical evidence supports the Red Queen hypothesis. Under this hypothesis, coevolving parasites favour sexual reproduction by adapting to infect common asexual clones and driving them down in frequency. One limitation, however, seems to challenge the generality of the Red Queen: in theoretical models, parasites must be very virulent to maintain sex. Moreover, experiments show virulence to be unstable, readily shifting in response to environmental conditions. Does variation in virulence further limit the ability of coevolving parasites to maintain sex? To address this question, we simulated temporal variation in virulence and evaluated the outcome of competition between sexual and asexual females. We found that variation in virulence did not limit the ability of coevolving parasites to maintain sex. In fact, relatively high variation in virulence promoted parasite‐mediated maintenance of sex. With sufficient variation, sexual females persisted even when mean virulence fell well below the threshold virulence required to maintain sex under constant conditions. We conclude that natural variation in virulence does not limit the relevance of the Red Queen hypothesis for natural populations; on the contrary, it could expand the range of conditions over which coevolving parasites can maintain sex.     

Cryptic invaders: nonindigenous and cryptogenic freshwater Bryozoa and Entoprocta in the St. Lawrence River

The distributions of most cosmopolitan invertebrate species are assumed to result from natural processes. Cryptic invertebrates with obscure biogeographic origins are often considered native by default, resulting in potentially severe underestimation of the extent of human-assisted invasions. This problem is exemplified by freshwater Bryozoa (Ectoprocta) and Entoprocta—small and widely distributed invertebrates commonly found in lakes and rivers. A benthic survey of a thermally modified section of the St. Lawrence River revealed the presence of two nonindigenous bryozoans: Carter’s moss animal Lophopodella carteri (Hyatt) and the crystal moss animal Lophopus crystallinus Pallas. Also discovered was a cryptogenic entoproct, the goblet worm Urnatella gracilis Leidy. These species were collected as statoblasts and (in the case of U. gracilis) colonial fragments downstream of the Gentilly-2 nuclear power plant at Bécancoeur, Quebec. Local densities of both U. gracilis and L. carteri increased by an order of magnitude at sites closer to the power plant. The occurrence of Lophopus crystallinus statoblasts in St. Lawrence River sediments is the first documented physical evidence of the species in North America. Contrary to the presumed natural Holarctic distribution of L. crystallinus, our literature review found that published historical records of L. crystallinus in the United States are erroneous or unsubstantiated. We propose that L. crystallinus is a western Palearctic species recently introduced to the St. Lawrence River, most likely as statoblasts discharged with ballast water from transoceanic ships.     

Relationship between cardiac performance and environment across populations of Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis>): a common garden experiment implicates local adaptation

Cardiac performance in fishes is predicted to be shaped by environmental factors such as temperature and river flow rate through natural selection for local adaptations, but few studies have explored these relationships. Using a common garden breeding design, we collected heart rate data from three populations of Atlantic salmon (Salmo salar) to measure peak heart rate and estimate optimal and upper critical temperatures for cardiac performance. We found that peak heart rate across populations matched the variation in natural river flow rates, such that the population that experienced the highest flow rate had the highest peak heart rate. Moreover, all populations showed evidence of local adaptation to summer water temperatures, with optimal temperatures (inferred from the Arrhenius breakpoint temperature) consistently falling 2.2–3.8 °C below the water temperature averaged for the summer months for each population. Also, upper critical temperatures (inferred from the temperature at which heart rates became arrhythmic) were nearly identical to peak summer water temperatures (0–0.3 °C above the peak). These results are consistent with heritable differences in cardiac performance among populations and suggest local adaptation to temperature and river flow.     

Type IV‐pili dependent motility is co‐regulated by PilSR and PilS2R2 two‐component systems via distinct pathways in Myxococcus xanthus

Myxococcus xanthus is an environmental bacterium with two forms of motility. One type, known as social motility, is dependent on extension and retraction of Type‐IV pili (T4P) and production of extracellular polysaccharides (EPS). Several signaling systems have been linked to regulation of T4P‐dependent motility. In particular, expression of the pilin subunit pilA requires the PilSR two‐component signaling system (TCS). A second TCS, PilS2R2, encoded within the same locus that encodes PilSR, has also been linked to M. xanthus T4P‐dependent motility. We demonstrate that PilSR and PilS2R2 regulate M. xanthus T4P‐dependent motility through distinct pathways. Consistent with known roles of PilSR, our results indicate that the primary function of PilSR is to regulate expression of pilA. In contrast, PilS2 and PilR2 have little to no affect on PilA protein levels. However, deletion of pilR2 resulted in a reduction of assembled pili, significant decreases in EPS production and loss of T4P‐dependent motility. Furthermore, the pilR2 mutation led to increased production of outer membrane vesicles (OMV). Collectively, we propose that PilS2R2 is required for proper assembly of T4P and regulation of OMV production, and hypothesize that production of these vesicles is related to M. xanthus motility.     

Running with the Red Queen: the role of biotic conflicts in evolution

What are the causes of natural selection? Over 40 years ago, Van Valen proposed the Red Queen hypothesis, which emphasized the primacy of biotic conflict over abiotic forces in driving selection. Species must continually evolve to survive in the face of their evolving enemies, yet on average their fitness remains unchanged. We define three modes of Red Queen coevolution to unify both fluctuating and directional selection within the Red Queen framework. Empirical evidence from natural interspecific antagonisms provides support for each of these modes of coevolution and suggests that they often operate simultaneously. We argue that understanding the evolutionary forces associated with interspecific interactions requires incorporation of a community framework, in which new interactions occur frequently. During their early phases, these newly established interactions are likely to drive fast evolution of both parties. We further argue that a more complete synthesis of Red Queen forces requires incorporation of the evolutionary conflicts within species that arise from sexual reproduction. Reciprocally, taking the Red Queen''s perspective advances our understanding of the evolution of these intraspecific conflicts.     

The Mitochondrial Genomes of the Nudibranch Mollusks,Melibe leonina and Tritonia diomedea,and Their Impact on Gastropod Phylogeny

The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group.