Purification, crystallization, and preliminary X-ray data for porcine fumarase

Single crystals of fumarase purified from pig heart have been prepared from solutions containing polyethylene glycol. The crystals give diffraction data corresponding to Bragg spacings of 2.0 A and contain a single subunit of the enzyme in the asymmetric unit of the C222 unit cell. Therefore, the subunits of this tetrameric molecule are arranged with the point symmetry group 222. The present purification scheme and studies of the NH2-terminal amino acid sequences suggest that only a single form of the enzyme is present, and it is thought to be the mitochondrial enzyme.     

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.     

Assessment of Acropora palmata in the Mesoamerican Reef System

The once-dominant shallow reef-building coral Acropora palmata has suffered drastic geographical declines in the wider Caribbean from a disease epidemic that began in the late 1970s. At present there is a lack of quantitative data to determine whether this species is recovering over large spatial scales. Here, we use quantitative surveys conducted in 107 shallow-water reef sites between 2010 and 2012 to investigate the current distribution and abundance of A. palmata along the Mesoamerican Reef System (MRS). Using historical data we also explored how the distribution and abundance of this species has changed in the northern portion of the MRS between 1985 and 2010–2012. A. palmata was recorded in only a fifth of the surveyed reef sites in 2010–2012. In the majority of these reef sites the presence of A. palmata was patchy and rare. Only one site (Limones reef), in the northernmost portion of the MRS, presented considerably high A. palmata cover (mean: 34.7%, SD: 24.5%). At this site, the size-frequency distribution of A. palmata colonies was skewed towards small colony sizes; 84% of the colonies were healthy, however disease prevalence increased with colony size. A comparison with historical data showed that in the northern portion of the MRS, in 1985, A. palmata occurred in 74% of the 31 surveyed sites and had a mean cover of 7.7% (SD = 9.0), whereas in 2010–2012 this species was recorded in 48% of the sites with a mean cover of 2.9% (SD = 7.5). A. palmata populations along the MRS are failing to recover the distribution and abundance they had prior to the 1980s. Investigating the biological (e.g., population genetics) and environmental conditions (e.g., sources of stress) of the few standing reefs with relatively high A. palmata cover is crucial for the development of informed restoration models for this species.     

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.     

Scats and den contents as indicators of the diet of stoats (Mustela erminea) in the Tasman Valley,South Canterbury,New Zealand

Stoats are significant predators of native fauna in New Zealand. They occur in many habitat types and consume a wide range of prey. The diet of stoats in the Tasman River, South Canterbury, was studied by analysis of scats and den contents. Analysis of 206 scats showed that stoats ate mainly lagomorphs, birds and invertebrates. Minor components included mice, lizards, fish and hedgehogs. Stoats ate more birds in spring than in autumn, and female stoats ate more invertebrates than did males. The contents of 219 dens collected in the same area at the same time provided further information. Birds and lagomorphs occurred at high frequency in dens, and other components were minor. Remains in dens were larger than in scats and allowed identification of many more prey items to species level. Den contents revealed a potentially substantial impact of stoats on threatened shorebirds locally; this impact was not detected by analysis of scats.     

Genetic relationships of the hydrocoral Millepora alcicornis and its symbionts within and between locations across the Atlantic

Although the hydrocoral Millepora alcicornis is a prominent and ecologically relevant amphi-Atlantic reef builder, little attention has been given to its endosymbionts which are also involved in the survival and adaptation success of the species in different environments. In this study, we resolve the genetic relationships between M. alcicornis and its symbionts (Symbiodiniaceae) within both sides and across the Atlantic. The COI and 16S-rDNA regions were selected for the host tissues, and the 23S-rDNA and ITS regions were chosen for the symbionts. Phylogenetic networks consistently showed that host populations from the eastern Atlantic archipelagos (Canary and Cape Verde Islands) were more related to western Atlantic populations than they were between them. However, results for Symbiodiniaceae species varied according to the molecular marker used. Samples from Mexico were grouped as Symbiodinium sp. (formerly Symbiodinium clade A) by both markers. Specimens from Puerto Rico were grouped as either Symbiodinium sp. or Breviolum sp. (formerly Symbiodinium clade B), according to the molecular marker used. Most samples from the eastern Atlantic were identified as Breviolum sp. by both markers, except for one sample from the Canary Islands and two samples from the Cape Verde Islands, which were identified as Cladocopium sp. (formerly Symbiodinium clade C) using ITS-rDNA. These results suggest that these two genera of Symbiodiniaceae may cohabit the same M. alcicornis colony. Because hydrocorals from the Canary Islands were phylogenetically related to the western Atlantic, but symbionts were more related to those of the Cape Verde Islands, the origin of the coral and its symbionts is probably different. This may be explained either by “horizontal” transmission, i.e. acquisition from the environment, or by a change in the dominant symbiont composition within the host. The flexibility of this hydrocoral to select symbionts, depending on environmental conditions, can provide new insight to understand how this coral may face ongoing climate change.

     

Symbiotic Association Between Symbiodinium and the Gastropod Strombus gigas: Larval Acquisition of Symbionts

The importance of the dinoflagellate Symbiodinium sp. was studied in the early life stages of the gastropod Strombus gigas. This dinoflagellate was not found in the eggs or the gelatinous mass surrounding the eggs of the mollusk; therefore, Symbiodinium is not inherited directly. To determine whether the planktonic veligers can acquire these algae from the environment, they were exposed to freshly isolated Symbiodinium from adult S. gigas (homologous). The optimal stage for Symbiodinium inoculation was found at 48 h post-hatching. Survival and growth rates of veligers and juveniles were higher when inoculated with freshly isolated Symbiodinium in conjunction with daily feeding of Isochrysis spp. Veligers inoculated with Symbiodinium freshly isolated from three host species elicited distinct responses: (1) veligers did not take up Symbiodinium isolated from the hydrozoan Millepora alcicornis suggesting that there is discrimination on contact prior to ingestion, (2) veligers did take up Symbiodinium isolated from the anemone Bartholomea annulata, but the algae did not persist in the host tissue suggesting that selection against this type took place after ingestion or that the algae did not divide in the host, and (3) veligers did take up Symbiodinium isolated from Pterogorgia anceps where it persisted and was associated with metamorphosis of the larvae. In contrast, the Symbiodinium freshly isolated from S. gigas were not associated with metamorphosis and required an inducer such as the red alga Laurencia poitei. These data present a significant advancement for the establishment of a new approach in the aquaculture of this important but declining Caribbean species.