The application of strand invasion phenomenon,directed by peptide nucleic acid (PNA) and single‐stranded DNA binding protein (SSB) for the recognition of specific sequences of human endogenous retroviral HERV‐W family

The HERV‐W family of human endogenous retroviruses represents a group of numerous sequences that show close similarity in genetic composition. It has been documented that some members of HERV‐W–derived expression products are supposed to play significant role in humans' pathology, such as multiple sclerosis or schizophrenia. Other members of the family are necessary to orchestrate physiological processes (eg, ERVWE1 coding syncytin‐1 that is engaged in syncytiotrophoblast formation). Therefore, an assay that would allow the recognition of particular form of HERV‐W members is highly desirable. A peptide nucleic acid (PNA)–mediated technique for the discrimination between multiple sclerosis‐associated retrovirus and ERVWE1 sequence has been developed. The assay uses a PNA probe that, being fully complementary to the ERVWE1 but not to multiple sclerosis‐associated retrovirus (MSRV) template, shows high selective potential. Single‐stranded DNA binding protein facilitates the PNA‐mediated, sequence‐specific formation of strand invasion complex and, consequently, local DNA unwinding. The target DNA may be then excluded from further analysis in any downstream process such as single‐stranded DNA‐specific exonuclease action. Finally, the reaction conditions have been optimized, and several PNA probes that are targeted toward distinct loci along whole HERV‐W env sequences have been evaluated. We believe that PNA/single‐stranded DNA binding protein–based application has the potential to selectively discriminate particular HERV‐W molecules as they are at least suspected to play pathogenic role in a broad range of medical conditions, from psycho‐neurologic disorders (multiple sclerosis and schizophrenia) and cancers (breast cancer) to that of an auto‐immunologic background (psoriasis and lupus erythematosus).     

Hatchery selection promotes boldness in newly hatched brown trout (Salmo trutta): implications for dominance

By using newly hatched (approximately 2 weeks old) brown trout(Salmo trutta) from six families of wild and six families ofsea-ranched origin (seventh generation), we tested the hypothesesthat (1) the hatchery environment selects for increased boldness,and (2) boldness predicts dominance status. Sea-ranched troutspend their first 2 years in the hatchery before being releasedinto the wild at the onset of seaward migration. Trout werepresented with a novel object (tack) and with food (brine shrimp),and their responses were measured and scored in terms of boldness.Siblings with increasing difference in boldness were then pairedin dyadic contests. Fish of sea-ranged origin were on averagebolder than were fish of wild origin, and bolder individualswere more likely to become dominant regardless of origin. Boldnesswas not related to RNA levels, indicating that bold behaviorwas not a consequence of higher metabolism or growth rate. Neitherwas size a predictor of bold behavior or the outcome of dyadiccontests. These results are consistent with studies on olderlife stages showing increased boldness toward predators in hatchery-selectedfish, which suggests that behavioral consequences of hatcheryselection are manifested very early in life. The concordancebetween boldness and dominance may suggest that these behaviorsare linked in a risk prone-aggressive phenotype, which may bepromoted by hatchery selection. However, we also found significantvariation in behavioral and growth-related traits among families,suggesting that heritable variation has not been exhausted bysea-ranching procedures.     

Isomeric lipid signatures reveal compartmentalized fatty acid metabolism in cancer

The cellular energy and biomass demands of cancer drive a complex dynamic between uptake of extracellular FAs and their de novo synthesis. Given that oxidation of de novo synthesized FAs for energy would result in net-energy loss, there is an implication that FAs from these two sources must have distinct metabolic fates; however, hitherto, all FAs have been considered part of a common pool. To probe potential metabolic partitioning of cellular FAs, cancer cells were supplemented with stable isotope-labeled FAs. Structural analysis of the resulting glycerophospholipids revealed that labeled FAs from uptake were largely incorporated to canonical (sn-) positions on the glycerol backbone. Surprisingly, labeled FA uptake also disrupted canonical isomer patterns of the unlabeled lipidome and induced repartitioning of n-3 and n-6 PUFAs into glycerophospholipid classes. These structural changes support the existence of differences in the metabolic fates of FAs derived from uptake or de novo sources and demonstrate unique signaling and remodeling behaviors usually hidden from conventional lipidomics.     

Effects of local density and flower colour polymorphism on pollination and reproduction in the rewardless orchid Dactylorhiza sambucina (L.) Soò

The rewardless orchid Dactylorhiza sambucina shows a stable flower colour polymorphism, with both yellow- and red-flowered morphs growing sympatrically. Pollination biology and breeding system were investigated to examine the effects of density of plants, colour polymorphism, inflorescence dimension, and flower position within inflorescence on male and female reproductive success in three natural populations of D. sambucina. There were significant differences among sites in the number of pollinia removed and in fruit set per inflorescence. Number of removed pollinia and capsule production in D. sambucina were independent from flower and inflorescence size or flower position. As a whole, the red morphs showed the highest number of capsules produced, while the yellow morphs had the greatest male success. The relative male and female reproductive success were independent from plant density but were significantly correlated with the yellow morph frequency at the population level. Overall, our findings show that the contribution to the total reproductive success deriving from the two colour morphs does not conform with the predictions of negative frequency-dependent selection.     

An assay for the detection of specific binding of 3-methylcholanthrene to rat liver cytosolic proteins using DEAE-cellulose

A method for the detection of the specific binding of 3-methylcholanthrene to rat liver cytosolic proteins is described. The separation of the protein-bound 3-methylcholanthrene from the free 3-methylcholanthrene was achieved using a batch DEAE-cellulose technique. Extraction of the DEAE-cellulose with 0.3 M KCl allowed the selective release and measurement of the amount of protein-bound 3-methylcholanthrene. The assay was optimized for the following parameters: time of incubation with DEAE-cellulose, time required for salt extraction, protein concentration, the concentration of KCl required to elute the specific binding proteins, the amount of DEAE-cellulose required to bind the specific binding proteins, and ligand specificity. The sedimentation properties of those 3-methylcholanthrene-binding proteins which were extracted with salt from DEAE-cellulose were examined on 5 to 20% sucrose gradients; the major binding species sedimented as a broad peak at 4.5 S.     

Optimization of speed and accuracy of decoding in translation

The speed and accuracy of protein synthesis are fundamental parameters for understanding the fitness of living cells, the quality control of translation, and the evolution of ribosomes. In this study, we analyse the speed and accuracy of the decoding step under conditions reproducing the high speed of translation in vivo. We show that error frequency is close to 10⁻³, consistent with the values measured in vivo. Selectivity is predominantly due to the differences in k_cat values for cognate and near-cognate reactions, whereas the intrinsic affinity differences are not used for tRNA discrimination. Thus, the ribosome seems to be optimized towards high speed of translation at the cost of fidelity. Competition with near- and non-cognate ternary complexes reduces the rate of GTP hydrolysis in the cognate ternary complex, but does not appreciably affect the rate-limiting tRNA accommodation step. The GTP hydrolysis step is crucial for the optimization of both the speed and accuracy, which explains the necessity for the trade-off between the two fundamental parameters of translation.     

Influence of rainfall on sleeping site choice by a group of anubis baboons (Papio anubis)

For diurnal nonhuman primates, shifting among different sleeping sites may provide multiple benefits such as better protection from predators, reduced risk of parasitic infection, and closer proximity to spatially and temporally heterogeneous food and water. This last benefit may be particularly important in sleeping site selection by primates living in savanna‐woodlands where rainfall is more limited and more seasonally pronounced than in rainforests. Here, we examined the influence of rainfall, a factor that affects food and water availability, on the use of sleeping sites by anubis baboons (Papio anubis) over two 13‐month study periods that differed in rainfall patterns. We predicted that during wet periods, when food and water availability should be higher, the study group would limit the number of sleeping sites and would stay at each one for more consecutive nights than during dry periods. Conversely, we predicted that during dry periods the group would increase the number of sleeping sites and stay at each one for fewer consecutive nights as they searched more widely for food and water. We also predicted that the group would more often choose sleeping sites closer to the center of the area used during daytime (between 07:00 and 19:00) during wet months than during dry months. Using Global Positioning System data from collared individuals, we found that our first prediction was not supported on either monthly or yearly timescales, although past monthly rainfall predicted the use of the main sleeping site in the second study period. Our second prediction was supported only on a yearly timescale. This study suggests that baboons’ choice of sleeping sites is fluid over time while being sensitive to local environmental conditions, one of which may be rainfall.     

Microhabitat nest‐site selection by ducks in the boreal forest

The boreal forest is one of the North America’s most important breeding areas for ducks, but information about the nesting ecology of ducks in the region is limited. We collected microhabitat data related to vegetation structure and composition at 157 duck nests and paired random locations in Alberta’s boreal forest region from 2016 to 2018. We identified fine‐scale vegetation features selected by ducks for all nests, between nesting guilds, and among five species using conditional logistic regression. Ducks in the boreal forest selected nest sites with greater overhead and graminoid cover, but less forb cover than random sites. Characteristics of the nest sites of upland‐ and overwater‐nesting guilds differed, with species nesting in upland habitat selecting nests that provided greater shrub cover and less lateral concealment and species nesting over water selecting nests with less shrub cover. We examined the characteristics of nest sites of American Wigeon (Mareca americana), Blue‐winged Teal (Spatula discors), Green‐winged Teal (Anas crecca), Mallards (Anas platyrhynchos), and Ring‐necked Ducks (Aythya collaris), and found differences among species that may facilitate species coexistence at a regional scale. Our results suggest that females of species nesting in upland habitat selected nest sites that optimized concealment from aerial predators while also allowing detection of and escape from terrestrial predators. Consequently, alteration in the composition and heterogeneity of vegetation and predator communities caused by climate change and industrial development in the boreal forest of Canada may affect the nest‐site selection strategies of boreal ducks.