Palynological and palaeobotanical investigations in the area of the post-medieval Helsinki Old Town

Pollen, phytolith, and plant macrofossil analyses were carried out on the cultural layers of Helsinki Old Town excavated by the Helsinki City Museum and dated to the 15–17th centuries. Cultural mineral soil layers, a former ditch, a well, one waste pit, one waste heap and three house areas were investigated. The results show that-within certain limits-pollen in the mineral soil reflects the cultural changes of the local settlement from rural to urban. Among the main anthropogenic indicators, the high NAP (non-arboreal pollen) frequencies, the low pollen concentration values, and especially the high frequencies of Cichoriaceae (Liguliflorae) pollen should be emphasized. The macrofossil data were used to determine the species list of the herb pollen and to make a more detailed reconstruction of the local vegetation at Helsinki Old Town.     

A Flexible Approach for Assessing Functional Landscape Connectivity,with Application to Greater Sage-Grouse (Centrocercus urophasianus)

Connectivity of animal populations is an increasingly prominent concern in fragmented landscapes, yet existing methodological and conceptual approaches implicitly assume the presence of, or need for, discrete corridors. We tested this assumption by developing a flexible conceptual approach that does not assume, but allows for, the presence of discrete movement corridors. We quantified functional connectivity habitat for greater sage-grouse (Centrocercus urophasianus) across a large landscape in central western North America. We assigned sample locations to a movement state (encamped, traveling and relocating), and used Global Positioning System (GPS) location data and conditional logistic regression to estimate state-specific resource selection functions. Patterns of resource selection during different movement states reflected selection for sagebrush and general avoidance of rough topography and anthropogenic features. Distinct connectivity corridors were not common in the 5,625 km² study area. Rather, broad areas functioned as generally high or low quality connectivity habitat. A comprehensive map predicting the quality of connectivity habitat across the study area validated well based on a set of GPS locations from independent greater sage-grouse. The functional relationship between greater sage-grouse and the landscape did not always conform to the idea of a discrete corridor. A more flexible consideration of landscape connectivity may improve the efficacy of management actions by aligning those actions with the spatial patterns by which animals interact with the landscape.     

Molecular dipole effects on tuning electron transfer in a porphine–quinone complex: a DFT and TDDFT study

The effect of a strong electric field generated by molecular dipoles on the ground state electronic structure and the Q and B states as well as the lowest charge transfer (CT) excited state of porphine–2,5-dimethyl-1,4-benzoquinone (PQ) complex has been investigated theoretically. Density functional theory DFT and time-dependent DFT (TDDFT) with the BH&HLYP hybrid functional have been applied in these calculations. The molecular dipole effect was generated by imposing one or two helical homopeptides consisting of eight α-aminoisobutyric acid residues (Aib₈) close to the PQ complex. The molecular dipoles in a close proximity to the PQ complex expose it to an electric field of the order of magnitude of 10⁹ V/m. The presence of the ambient molecular dipoles affects mainly the energy of the lowest CT state and barely the energies of the Q and B states. The molecular dipoles affect the energies of the excited states in a similar way as an external electrostatic field. Hence, the electric field induced by the molecular dipoles of the helical peptides could be used analogously to the external electrostatic field to control electron transfer (ET) in the PQ complex.     

Does extraction of DNA and RNA by magnetic fishing work for diverse plant species?

An automated nucleic acid extraction procedure with magnetic particles originally designed for isolation of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from animal tissues was tested for plant material. We isolated genomic DNA and total RNA from taxonomically diverse plant species representing conifers (Scots pine), broad-leaved trees (silver birch and hybrid aspen), dwarf shrubs (bilberry), and both monocotyledonous (regal lily) and dicotyledonous (Saint John's wort, round-leaved sundew, and tobacco) herbaceous plants. Buffers developed for DNA extraction were successfully used in addition to manufacturer's extraction kits. The quality of RNA was appropriate for many applications, but the quality of DNA was not always sufficient for polymerase chain reaction (PCR) amplification. However, we could strikingly improve the quality by eliminating the adherent compounds during the extraction or later in the PCR phase. Our results show that the use of the procedure could be extended to diverse plant species. This procedure is especially suitable for small sample sizes and for simultaneous processing of many samples enabling large-scale plant applications in population genetics, or in the screening of putative transgenic plants.     

Birth of correctly genotyped calves after multiplex marker detection from bovine embryo microblade biopsies

We report a method for multiplex genotyping of bovine embryo microblade biopsies. We have tested the reliability of the method and the viability of the embryos in vitro and in vivo. Two polymorphic gene markers (GHR F279Y and PRLR S18N) associated with milk production traits and one marker for sex diagnosis (ZFX/ZFY) were genotyped simultaneously with a method that combines nested PCR and allelic discrimination. To test the accuracy of genotyping, in the first experiment the genotypes of 134 biopsies from in vitro produced embryos were compared to genotypes determined from the corresponding embryos after biopsy. The method proved to be highly accurate as only in three cases (two for PRLR S18N and one for GHR F279Y) out of 395 genotypes the genotype was in disagreement between the two samples. The viability of similarly biopsied embryos was tested in parallel: after 24-hr culture 94.6% of embryos recovered in vitro. In the second experiment, a total of 150 in vivo-produced embryos were biopsied on Day 7 and genotyped. After the genotyping results were obtained on Day 8, female embryos were selected for transfer. From a total of 57 selected embryos 43 were transferred individually and 14 as pairs. After single embryo transfers, 19 recipients became pregnant and after embryo transfers in pairs one became pregnant. The success of genotyping was tested with the genotypes of donors and bulls and also from the hair samples of born calves. All calves were females and of the same genotypes determined from the biopsy.     

Prioritizing conservation of ungulate calving resources in multiple-use landscapes

Background

Conserving animal populations in places where human activity is increasing is an ongoing challenge in many parts of the world. We investigated how human activity interacted with maternal status and individual variation in behavior to affect reliability of spatially-explicit models intended to guide conservation of critical ungulate calving resources. We studied Rocky Mountain elk (Cervus elaphus) that occupy a region where 2900 natural gas wells have been drilled.

Methodology/Principal Findings

We present novel applications of generalized additive modeling to predict maternal status based on movement, and of random-effects resource selection models to provide population and individual-based inference on the effects of maternal status and human activity. We used a 2×2 factorial design (treatment vs. control) that included elk that were either parturient or non-parturient and in areas either with or without industrial development. Generalized additive models predicted maternal status (parturiency) correctly 93% of the time based on movement. Human activity played a larger role than maternal status in shaping resource use; elk showed strong spatiotemporal patterns of selection or avoidance and marked individual variation in developed areas, but no such pattern in undeveloped areas. This difference had direct consequences for landscape-level conservation planning. When relative probability of use was calculated across the study area, there was disparity throughout 72–88% of the landscape in terms of where conservation intervention should be prioritized depending on whether models were based on behavior in developed areas or undeveloped areas. Model validation showed that models based on behavior in developed areas had poor predictive accuracy, whereas the model based on behavior in undeveloped areas had high predictive accuracy.

Conclusions/Significance

By directly testing for differences between developed and undeveloped areas, and by modeling resource selection in a random-effects framework that provided individual-based inference, we conclude that: 1) amplified selection or avoidance behavior and individual variation, as responses to increasing human activity, complicate conservation planning in multiple-use landscapes, and 2) resource selection behavior in places where human activity is predictable or less dynamic may provide a more reliable basis from which to prioritize conservation action.     

Identifying and prioritizing greater sage-grouse nesting and brood-rearing habitat for conservation in human-modified landscapes

Background

Balancing animal conservation and human use of the landscape is an ongoing scientific and practical challenge throughout the world. We investigated reproductive success in female greater sage-grouse (Centrocercus urophasianus) relative to seasonal patterns of resource selection, with the larger goal of developing a spatially-explicit framework for managing human activity and sage-grouse conservation at the landscape level.

Methodology/Principal Findings

We integrated field-observation, Global Positioning Systems telemetry, and statistical modeling to quantify the spatial pattern of occurrence and risk during nesting and brood-rearing. We linked occurrence and risk models to provide spatially-explicit indices of habitat-performance relationships. As part of the analysis, we offer novel biological information on resource selection during egg-laying, incubation, and night. The spatial pattern of occurrence during all reproductive phases was driven largely by selection or avoidance of terrain features and vegetation, with little variation explained by anthropogenic features. Specifically, sage-grouse consistently avoided rough terrain, selected for moderate shrub cover at the patch level (within 90 m²), and selected for mesic habitat in mid and late brood-rearing phases. In contrast, risk of nest and brood failure was structured by proximity to anthropogenic features including natural gas wells and human-created mesic areas, as well as vegetation features such as shrub cover.

Conclusions/Significance

Risk in this and perhaps other human-modified landscapes is a top-down (i.e., human-mediated) process that would most effectively be minimized by developing a better understanding of specific mechanisms (e.g., predator subsidization) driving observed patterns, and using habitat-performance indices such as those developed herein for spatially-explicit guidance of conservation intervention. Working under the hypothesis that industrial activity structures risk by enhancing predator abundance or effectiveness, we offer specific recommendations for maintaining high-performance habitat and reducing low-performance habitat, particularly relative to the nesting phase, by managing key high-risk anthropogenic features such as industrial infrastructure and water developments.     

Effect of the inseminate and the site of insemination on the uterus and pregnancy rates of mares

In this review, effects of the composition of the inseminate on uterine response and pregnancy rates in mares are discussed. The inseminate can differ for volume, sperm concentration, total sperm numbers, presence, absence, or proportion of seminal plasma, and extender composition. Semen can be used as fresh, cooled, or frozen. The site of semen deposition also plays a role; semen is deposited either into the uterine body (standard artificial insemination (AI)) or into the tip of the uterine horn ipsilateral to the preovulatory follicle (deep AI) using the hysterocopical or transrectally guided techniques. In addition to pregnancy rates, some uterine responses to the inseminate are considered including myometrial contractions, transport and elimination of sperm, and uterine inflammation, which is reflected as numbers of polymorphonuclear leukocytes, enzyme levels, and presence of intrauterine fluid. Reproductively normal and abnormal mares are compared.