Molecular docking of alkaloid compounds with the matrix metalloproteinase 2

Matrix metalloproteinase protein-2 (MMP-2) is linked to the human oral squamous cell carcinoma. Therefore, it is of interest to design new inhibitors for MMP-2 to combat the disease. Thus, we document the molecular docking features of Aristolochic acid, Cryptopleurine, Epipodophyllotoxin, and Fagaronine with MMP-2 for further consideration.     

The importance of willow thickets for ptarmigan and hares in shrub tundra: the more the better?

In patchy habitats, the relationship between animal abundance and cover of a preferred habitat may change with the availability of that habitat, resulting in a functional response in habitat use. Here, we investigate the relationship of two specialized herbivores, willow ptarmigan (Lagopus lagopus) and mountain hare (Lepus timidus), to willows (Salix spp.) in three regions of the shrub tundra zone-northern Norway, northern European Russia and western Siberia. Shrub tundra is a naturally patchy habitat where willow thickets represent a major structural element and are important for herbivores both as food and shelter. Habitat use was quantified using feces counts in a hierarchical spatial design and related to several measures of willow thicket configuration. We document a functional response in the use of willow thickets by ptarmigan, but not by hares. For hares, whose range extends into forested regions, occurrence increased overall with willow cover. The occurrence of willow ptarmigan showed a strong positive relationship to willow cover and a negative relationship to thicket fragmentation in the region with lowest willow cover at landscape scale, where willow growth may be limited by reindeer browsing. In regions with higher cover, in contrast, such relationships were not observed. Differences in predator communities among the regions may contribute to the observed pattern, enhancing the need for cover where willow thickets are scarce. Such region-specific relationships reflecting regional characteristics of the ecosystem highlight the importance of large-scale investigations to understand the relationships of habitat availability and use, which is a critical issue considering that habitat availability changes quickly with climate change and human impact.     

Rough-Legged Buzzards,Arctic Foxes and Red Foxes in a Tundra Ecosystem without Rodents

Small rodents with multi-annual population cycles strongly influence the dynamics of food webs, and in particular predator-prey interactions, across most of the tundra biome. Rodents are however absent from some arctic islands, and studies on performance of arctic predators under such circumstances may be very instructive since rodent cycles have been predicted to collapse in a warming Arctic. Here we document for the first time how three normally rodent-dependent predator species—rough-legged buzzard, arctic fox and red fox – perform in a low-arctic ecosystem with no rodents. During six years (in 2006-2008 and 2011-2013) we studied diet and breeding performance of these predators in the rodent-free Kolguev Island in Arctic Russia. The rough-legged buzzards, previously known to be a small rodent specialist, have only during the last two decades become established on Kolguev Island. The buzzards successfully breed on the island at stable low density, but with high productivity based on goslings and willow ptarmigan as their main prey – altogether representing a novel ecological situation for this species. Breeding density of arctic fox varied from year to year, but with stable productivity based on mainly geese as prey. The density dynamic of the arctic fox appeared to be correlated with the date of spring arrival of the geese. Red foxes breed regularly on the island but in very low numbers that appear to have been unchanged over a long period – a situation that resemble what has been recently documented from Arctic America. Our study suggests that the three predators found breeding on Kolguev Island possess capacities for shifting to changing circumstances in low-arctic ecosystem as long as other small - medium sized terrestrial herbivores are present in good numbers.     

Manometric and spectrophotometric procedures for measurement of procaine hydrolysis by mouse liver in vitro

A decrease in absorbance at 313 nm was used to determine procaine hydrolysis by mouse liver. Results suggested that procaine hydrolysis was not linearly dependent upon the amount of tissue added to the incubate. This resulted from the fact that p-aminobenzoic acid, one of procaine's hydrolysis products, also absorbed at 313 nm. A dual wavelength analysis procedure is described which permitted accurate measurement of procaine hydrolysis by mouse liver without physical separation of procaine from its hydrolysis products. Measurements by the dual wavelength and manometric methods of inhibition of procaine hydrolysis in livers from mice treated with triorthotolyl phosphate indicated that both methods yielded quantitatively comparable results. The dual wavelength procedure is recommended for future studies of procaine hydrolysis by mammalian tissues.     

Implications of the Circumpolar Genetic Structure of Polar Bears for Their Conservation in a Rapidly Warming Arctic

We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1–3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.     

Vaso-occlusion in Schimke-immuno-osseous dysplasia: is the NO pathway involved?

Schimke-immuno-osseous dysplasia (SIOD) is an autosomal recessive disorder with the main clinical findings of spondyloepiphyseal dysplasia, nephrotic syndrome, and defective cellular immunity. Vaso-occlusive processes, especially generalized atherosclerosis, are a life-limiting complication in patients with severe SIOD. The nitric oxide synthase (NOS) oxidizes L-arginine to nitric oxide (NO). NO is a potent vasodilator with inhibitory effects on platelet aggregation and the development of atherosclerosis. We hypothesized that reduced NO production due to antagonism of NOS by asymmetric dimethylarginine (ADMA) would be a possible pathophysiological mechanism for vaso-occlusion in SIOD. We tested this hypothesis in 10 patients with SIOD and 10 age-matched healthy controls. Plasma and urine levels of nitrite and nitrate, the indicators of NO synthesis, and of ADMA, an endogenous NOS inhibitor, in children suffering from SIOD were not significantly different from those in the age-matched healthy controls. Our results suggest that the L-arginine/NO pathway is not altered in SIOD. Antagonism of NOS by ADMA does not seem to be the cause of premature general atherosclerosis in SIOD. The underlying pathology of vaso-occlusion in SIOD still remains unclear.     

Solution-based targeted genomic enrichment for precious DNA samples

ABSTRACT: BACKGROUND: Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1) modifying or eliminating time consuming steps; 2) increasing yield to reduce input DNA and excessive PCR cycling; and 3) enhancing reproducible. RESULTS: We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company. CONCLUSIONS: This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.