The evolutionary emergence of stochastic phenotype switching in bacteria

Stochastic phenotype switching - or bet hedging - is a pervasive feature of living systems and common in bacteria that experience fluctuating (unpredictable) environmental conditions. Under such conditions, the capacity to generate variable offspring spreads the risk of being maladapted in the present environment, against offspring likely to have some chance of survival in the future. While a rich subject for theoretical studies, little is known about the selective causes responsible for the evolutionary emergence of stochastic phenotype switching. Here we review recent work - both theoretical and experimental - that sheds light on ecological factors that favour switching types over non-switching types. Of particular relevance is an experiment that provided evidence for an adaptive origin of stochastic phenotype switching by subjecting bacterial populations to a selective regime that mimicked essential features of the host immune response. Central to the emergence of switching types was frequent imposition of 'exclusion rules' and 'population bottlenecks' - two complementary faces of frequency dependent selection. While features of the immune response, exclusion rules and bottlenecks are likely to operate in many natural environments. Together these factors define a set of selective conditions relevant to the evolution of stochastic switching, including antigenic variation and bacterial persistence.     

Partial protein domains: evolutionary insights and bioinformatics challenges

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.With the rapid expansion in the number of determined protein sequences - over 92 million in UniProt in March 2015 - an ever-increasing number of biologists are using bioinformatics tools for annotation of these sequences. One widely used strategy is to identify occurrences of Pfam families within the sequence of interest [1]. A Pfam family is a multiple sequence alignment of the occurrences of a particular domain both in different species and in different regions of the same protein. The concept underpinning Pfam is that proteins typically comprise one or more domains (regions), each of which is an evolutionary unit that generally has a well-defined biological function. A significant sequence similarity between a query protein and a Pfam family provides the basis for annotations. Two recent articles [2,3] in Genome Biology evaluate the implications of having the query sequence only matching part of a Pfam family, which is an intriguing finding, given that a Pfam family is considered to be an evolutionary unit.     

Balancing contest competition,scramble competition,and social tolerance at feeding sites in wild common marmosets (Callithrix jacchus)

Models of primate sociality focus on the costs and benefits of group living and how factors such as rank, feeding competition, alliance formation, and cooperative behavior shape within‐group social relationships. We conducted a series of controlled field experiments designed to investigate how resource distribution (one or three of four reward platforms) and amount of food on a reward platform affected foraging strategies and individual feeding success in four groups of wild common marmosets (Callithrix jacchus) living in the Caatinga of northeastern Brazil. At our field site, common marmoset groups are characterized by a single breeding female who can produce twin litters twice per year, strong social cohesion, and cooperative infant care provided principally by several adult male helpers. We found that except for the dominant breeding female, rank (based on aggression) was not a strong predictor of feeding success. Although the breeding female in each group occupied the highest rank position and obtained the greatest daily feeding success, all other group members, including adults and juveniles experienced relatively equal feeding success across most experimental conditions. This was accomplished using a balance of behavioral strategies related to contest competition, scramble competition (associated with a finder's advantage), and social tolerance (sharing the same feeding platform). Based on these results, the social structure of common marmosets is best described as “single female dominance,” with the breeding female maximizing food intake needed to offset the energetic costs associated with reproductive twinning and the ability to produce two litters per year. Cooperative infant caregiving, in which the number of helpers is positively correlated with offspring survivorship, requires a set of behavioral strategies that serve to reduce contest competition and promote prosocial behaviors at feeding sites.     

In situ enclosure experiments on the influence of cultured mussels (Perna canaliculus) on phytoplankton at times of high and low ambient nitrogen

The influence of the cultured mussel Perna canaliculus (Gmelin 1791) on the abundance of phytoplankton was investigated in Pelorus Sound, New Zealand. Four in situ enclosure experiments were undertaken, two in summer when ambient nitrogen was low, and two in winter when it was high. Each experiment had four manipulation types: added mussels; added nitrogen; both mussels and nitrogen added; and control (no additions). In summer, there was a significant increase of chlorophyll a in response to added nitrogen, indicating that the phytoplankton were nitrogen-limited. At this time, mussels caused an increase (11-17%) in phytoplankton biomass, possibly by converting particulate nitrogen to ammonium, making the nitrogen available for phytoplankton utilisation. The highest ambient chlorophyll a concentrations coincided with high ambient nitrogen in the winter. At this time, mussel grazing caused a significant decrease (5-14%) in phytoplankton concentration, indicating that within-farm depletion of phytoplankton is most likely to occur in winter. On an annual time scale, the mussels had a stabilising influence on phytoplankton biomass, reducing high ambient levels in winter and slightly increasing low levels in summer.     

Patterns of distribution and abundance of large brown algae and invertebrate herbivores in subtidal regions of northern New Zealand

The distribution and abundance of subtidal laminarian and fucoid algae, echinoids, and four species of herbivorous gastropods were assessed. Line transects and stratified random quadrats were used, encompassing different depths and seven localities ranging over 1000km in northern New Zealand. This sampling was carried out to form a quantitative basis on which to pose hypotheses for later experimental work. Several patterns were apparent, both within and between localities. Fucoid algae were characteristic of depths between 0–6 m, while laminarian algae had peaks of abundance at 3–6 m and from 10–17 m. Intermediate depths were characterized by areas bare of large brown algae, with high densities of echinoids and gastropods. This pattern of a bimodal depth distribution of algae and abundant grazers at intermediate depth was a consistent feature of the northern coastal sites and the semi-exposed offshore islands. Size—frequency distributions for algae at these sites showed that the largest fucoids generally occurred in very shallow water, while the dominant laminarian alga tended to have larger individuals at depths of 10–14 m. In all cases, the biomass distribution with depth of the algal species mirrored their numerical abundance.

Differences between localities were associated both with environmental factors and the unique algal floras of some offshore islands. Echinoids and gastropods were rare at the two most exposed localities, which were also at the extremes of the geographic range. At these sites, depths between 6–10 m were occupied by large brown algae. Deep-water fucoid algae occurred at two offshore localities but the predominant species at one of them was peculiar to that island group.

Because of the general consistency between localities, and the few exceptions to these patterns, hypotheses are considered which could be tested on a local scale to account for echinoid and algal abundances and depth distributions. Our results indicate that the chief questions concerning the structuring of subtidal algal communities are demographic in nature and that an assessment of the status of individual organisms, rather than biomass or productivity, is the appropriate approach to resolve these questions.     

Interleukin-1 beta induces synthesis and secretion of interleukin-6 in human chondrocytes

Increased concentrations of interleukin-6 (IL-6) have been found in the synovial fluid of patients with osteoarthritis, rheumatoid arthritis and crystal-related joint diseases. It is therefore of great interest to identify the cells responsible for the production of IL-6, and to investigate whether IL-6 plays a role in the pathogenesis of degenerative or inflammatory joint diseases. Here we show that human interleukin-1 beta (IL-1 beta) induces IL-6 synthesis and secretion in differentiated human chondrocytes. In organ cultures resembling closely the in vivo system 10(6) chondrocytes incubated with 100 units of interleukin-1 beta per ml of medium led to the release of 6 X 10(3) units of IL-6 within 24 h. Chondrocytes cultured in agarose or as monolayers similarly incubated with IL-1 beta produced even higher amounts of IL-6: 70 X 10(3) units per 10(6) cells within 24 h. The induction of IL-6 synthesis by IL-1 beta was also shown at the mRNA level. IL-6 secreted by stimulated chondrocytes showed heterogeneity upon Western blot analysis.     

A large-subunit mitochondrial ribosomal DNA sequence translocated to the nuclear genome of two stone crabs (Menippe)

Two DNA sequences that appear to be homologous to large-subunit mitochondrial ribosomal RNA genes have been identified in the stone crabs Menippe mercenaria and M. adina. Amplification from whole genomic DNA by polymerase chain reaction (PCR) with oligonucleotide primers based on conserved portions of large-subunit mitochondrial rRNA genes consistently amplified two products of similar length (565 and 567 bp). These products differed at 3% of their nucleotide bases, and could be distinguished by a HindIII site. Only one of these sequences (designated the A sequence) was detected by PCR in purified mitochondrial DNA. The other (designated the B sequence) hybridized to total genomic DNA at a level consistent with a nuclear genome location. It is unlikely that the type B product would have been recognized as a nuclear copy by examination of its sequence alone. This is the first report of a mitochondrial gene sequence translocated into the nuclear genome of a crustacean.