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.     

Rhythm generation through period concatenation in rat somatosensory cortex

Rhythmic voltage oscillations resulting from the summed activity of neuronal populations occur in many nervous systems. Contemporary observations suggest that coexistent oscillations interact and, in time, may switch in dominance. We recently reported an example of these interactions recorded from in vitro preparations of rat somatosensory cortex. We found that following an initial interval of coexistent gamma ( approximately 25 ms period) and beta2 ( approximately 40 ms period) rhythms in the superficial and deep cortical layers, respectively, a transition to a synchronous beta1 ( approximately 65 ms period) rhythm in all cortical layers occurred. We proposed that the switch to beta1 activity resulted from the novel mechanism of period concatenation of the faster rhythms: gamma period (25 ms)+beta2 period (40 ms) = beta1 period (65 ms). In this article, we investigate in greater detail the fundamental mechanisms of the beta1 rhythm. To do so we describe additional in vitro experiments that constrain a biologically realistic, yet simplified, computational model of the activity. We use the model to suggest that the dynamic building blocks (or motifs) of the gamma and beta2 rhythms combine to produce a beta1 oscillation that exhibits cross-frequency interactions. Through the combined approach of in vitro experiments and mathematical modeling we isolate the specific components that promote or destroy each rhythm. We propose that mechanisms vital to establishing the beta1 oscillation include strengthened connections between a population of deep layer intrinsically bursting cells and a transition from antidromic to orthodromic spike generation in these cells. We conclude that neural activity in the superficial and deep cortical layers may temporally combine to generate a slower oscillation.     

A new species of Asthenocotyle Robinson, 1961 (Monogenea: Microbothriidae), a skin parasite of the great lanternshark Etmopterus princeps Collett from the Azores, with a redescription of A. kaikourensis Robinson, 1961 and observations on A. taranakiensis Beverley-Burton, Klassen & Lester, 1987

Asthenocotyle azorensis n. sp. (Monogenea: Microbothriidae) is described from the dermal denticles of the great lanternshark Etmopterus princeps Collett off the Azores. The type-species of the genus, A. kaikourensis Robinson, 1961, is redescribed and additional observations are made on A. taranakiensis Beverley-Burton, Klassen & Lester, 1987. The generic diagnosis is revised. The new species is distinguished from its two congeners by the large size of the pharynx and fewer testes. The ejaculatory bulb of A. kaikourensis is much larger than those of A. taranakiensis and A. azorensis and is supplied with many ducts from an extensive field of male accessory gland-cells located outside the genital pouch and extending posteriorly to the region of the germarium and external seminal vesicle. Asthenocotyle taranakiensis is distinguished from the other two species by its copulatory sclerite, which forms a double loop, although this may not be the case when the copulatory organ is extended. The bodies of A. azorensis and A. kaikourensis are similar in shape, with the maximum width approximately 37% and 25%, respectively, of the total length from the anterior end. In addition to the relatively small size of the genital pouch and ejaculatory bulb in A. azorensis and A. taranakiensis, the vaginal opening is adjacent to the common genital opening. In A. kaikourensis, the vaginal opening is distant from and posterior to the common genital opening. The functional morphology of the copulatory organ of A. azorensis is considered. The relative importance, for the taxonomy of microbothriids, of the number of testes versus the anatomy of the copulatory complex is discussed.     

Growth responses, biomass partitioning, and nitrogen isotopes of prairie legumes in response to elevated temperature and varying nitrogen source in a growth chamber experiment

? Premise of the Study: Because legumes can add nitrogen (N) to ecosystems through symbiotic fixation, they play important roles in many plant communities, such as prairies and grasslands. However, very little research has examined the effect of projected climate change on legume growth and function. Our goal was to study the effects of temperature on growth, nodulation, and N chemistry of prairie legumes and determine whether these effects are mediated by source of N. ? Methods: We grew seedlings of Amorpha canescens, Dalea purpurea, Lespedeza capitata, and Lupinus perennis at 25/20°C (day/night) or 28/23°C with and without rhizobia and mineral N in controlled-environment growth chambers. Biomass, leaf area, nodule number and mass, and shoot N concentration and δ(15)N values were measured after 12 wk of growth. ? Key Results: Both temperature and N-source affected responses in a species-specific manner. Lespedeza showed increased growth and higher shoot N content at 28°C. Lupinus showed decreases in nodulation and lower shoot N concentration at 28°C. The effect of temperature on shoot N concentration occurred only in individuals whose sole N source was N(2)-fixation, but there was no effect of temperature on δ(15)N values in these plants. ? Conclusions: Elevated temperature enhanced seedling growth of some species, while inhibiting nodulation in another. Temperature-induced shifts in legume composition or nitrogen dynamics may be another potential mechanism through which climate change affects unmanaged ecosystems.     

Hatching strategies in monogenean (platyhelminth) parasites that facilitate host infection

In parasites, environmental cues may influence hatching of eggs and enhance the success of infections. The two major endoparasitic groups of parasitic platyhelminths, cestodes (tapeworms) and digeneans (flukes), typically have high fecundity, infect more than one host species, and transmit trophically. Monogeneans are parasitic flatworms that are among the most host specific of all parasites. Most are ectoparasites with relatively low fecundity and direct life cycles tied to water. They infect a single host species, usually a fish, although some are endoparasites of amphibians and aquatic chelonian reptiles. Monogenean eggs have strong shells and mostly release ciliated larvae, which, against all odds, must find, identify, and infect a suitable specific host. Some monogeneans increase their chances of finding a host by greatly extending the hatching period (possible bet-hedging). Others respond to cues for hatching such as shadows, chemicals, mechanical disturbance, and osmotic changes, most of which may be generated by the host. Hatching may be rhythmical, larvae emerging at times when the host is more vulnerable to invasion, and this may be combined with responses to other environmental cues. Different monogenean species that infect the same host species may adopt different strategies of hatching, indicating that tactics may be more complex than first thought. Control of egg assembly and egg-laying, possibly by host hormones, has permitted colonization of frogs and toads by polystomatid monogeneans. Some monogeneans further improve the chances of infection by attaching eggs to the host or by retaining eggs on, or in, the body of the parasite. The latter adaptation has led ultimately to viviparity in gyrodactylid monogeneans.     

A 12 000-year record of environmental change in the Lomond Hills, Fife, Scotland: Vegetational and climatic variability

The Lomond Hills of Fife, an isolated upland area rising to over 500 m, provide an opportunity to investigate the effect of altitude on vegetation and climate in an area otherwise dominated by lower-lying land. The West Lomond site contains sediments of the Devensian Late-glacial period; they reveal a well-defined sequence of Bolling-Older Dryas-Allerod-Younger Dryas events, commencing ca. 12 190 radiocarbon years B.P. and a probable Amphi-Atlantic Oscillation between ca. 11 040 and 10 800 B.P. The Holocene record is constrained by low sediment input but does reveal a woodland presence at this altitude, dominated byBetula andCorylus. Size statistics forBetula pollen are presented and the implications of the vegetational and climatic record are discussed. The traditional view of a smooth progress towards more temperate conditions following the Younger Dryas is not supported; between 10 180 and 9120 B.P., three cooler periods are inferred, the earliest of which may belong to a terminal phase of the Younger Dryas. Comparative pollen ‘influx’ data strongly suggest thatQuercus,Ulmus andAlnus were not present locally. As a working hypothesis, it is suggested that the demise of woodland, from ca. 5950 B.P., was a result of exposure. Pollen indicative of human impact was probably derived from areas of lowland agricultural activity from ca. 5330 B.P. onwards.     

King penguin demography since the last glaciation inferred from genome-wide data

How natural climate cycles, such as past glacial/interglacial patterns, have shaped species distributions at the high-latitude regions of the Southern Hemisphere is still largely unclear. Here, we show how the post-glacial warming following the Last Glacial Maximum (ca 18 000 years ago), allowed the (re)colonization of the fragmented sub-Antarctic habitat by an upper-level marine predator, the king penguin Aptenodytes patagonicus. Using restriction site-associated DNA sequencing and standard mitochondrial data, we tested the behaviour of subsets of anonymous nuclear loci in inferring past demography through coalescent-based and allele frequency spectrum analyses. Our results show that the king penguin population breeding on Crozet archipelago steeply increased in size, closely following the Holocene warming recorded in the Epica Dome C ice core. The following population growth can be explained by a threshold model in which the ecological requirements of this species (year-round ice-free habitat for breeding and access to a major source of food such as the Antarctic Polar Front) were met on Crozet soon after the Pleistocene/Holocene climatic transition.     

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.     

The influence of vertical mixing on the photoinhibition of variable chlorophyll a fluorescence and its inclusion in a model of phytoplankton photosynthesis

The maximum effective quantum yield of photosystem II was estimatedfrom measurements of variable chlorophyll a fluorescence [(F'_m- F'_o)/F'_m = F'_v/F'_m] in samples of phytoplankton collectedfrom various depths in Chaffey Reservoir, Australia. Duringstratified conditions, F'_v/F'_m showed depth-dependent decreasesas irradiance increased during the morning, and increases asirradiancereduced in the afternoon. Wind-induced mixing disrupted thediel pattern, but even under well-mixed conditions a verticalgradient in F'_v/F'_m remained. Differences in F'_v/F'_m valuesbetween samples incubated at fixed depths and unconstrainedlake samples enabled identification of the phytoplankton mixingdepth. Recovery of F'_v/F'_m was modelled as a function of timeand the degree of F'_v/F'_m inhibition, while damage was considereda function of photon dose. A combined, numerical model was fittedto diel sequences of F'_v/F'_m to estimate rate constants fordamage and repair. Recovery rate constants ranged from r = 0.7x 10^-4 to 9.1 x 10^-4 s^-1, while damage rate constants rangedfrom k = 0.03 to 0.22 m² mol photon^-1. A fluorescence-basedmodel of photosynthesis was used to investigate the effectsof wind speed, euphotic depth and mixed layer depth on photoinhibition.At different mixing rates, depth-integrated photosynthesis wasenhanced by up to 16% under the conditions tested, while increasesof 9% occurred between phytoplankton with different measureddamage and repair characteristics.     

Effect of DMSO on the dielectric properties of canine kidney tissue

The dielectric permittivity and conductivity of canine kidney tissue samples were measured at R_f frequencies between ?20 °C and +20 °C. Some of the kidneys had been perfused with DMSO (10%) in canine plasma, others with physiological saline alone. The DMSO greatly increases the conductivity of frozen tissue above that of tissue not treated with this cryoprotectant. Apparently, the chief reason for nonuniform heating of a partially frozen organ in a microwave field is the great change in tissue conductivity as it thaws. We suggest that the effect on the conductivity of tissue should be considered in the choice of a cryoprotectant for tissues which are to be thawed by microwave or radiofrequency irradiation.