Initial and future stand development following mountain pine beetle in harvested and uncut lodgepole pine forests

2010 Spring.Covers not scanned.Includes bibliographical references.The extent and severity of over tory lodgepole pine (Pinus contorta Dougl.) mortality from mountain pine beetle (Dendroctonus ponderosae Hopkins) has created management concerns associated with forest regeneration, wildfire risk, human safety, and scenic, wildlife and watershed resources in western North America. In northern Colorado and southern Wyoming the long-term ecological and socioeconomic consequences of the outbreak hinge upon the response of tree regeneration in both harvested and untreated forests. To characterize initial and future forest development following mountain pine beetle mortality I conducted two studies. First, I used historic U.S. Forest Service stand and seedling survey records to compare the density and species composition of advance regeneration in uncut stands and post-harvest recruits in clearcut harvest units during pre-outbreak (1980-1996) and outbreak (2002-2007) period. Second, I compared the effects of various intensities of forest management on site conditions, seedling establishment and growth of advance regeneration to uncut areas in beetle-infested lodgepole pine stands. Advance regeneration averaged 3,953 stems ha-1 and was at least as high in beetle-infested stands compared to the pre-outbreak period. Lodgepole pine advance regeneration showed increased leader growth from 2008 to 2009 in harvested and untreated stands in response to canopy removal and decreased canopy foliage following overstory mortality. The density of seedling recruitment was three times higher in harvested than untreated stands (6,487 versus 2,021 seedlings ha-1), and did not differ between outbreak and pre-outbreak stands. Growth simulations showed uncut and partial cut stands will be dominated by subalpine fir (Abies lasiocarpa), while clearcut stand will be dominated by lodgepole pine and have attributes similar to pre-outbreak stands within a century

Genetic diversity among populations of Antarctic springtails (Collembola) within the Mackay Glacier ecotone

Climate changes are likely to have major influences on the distribution and abundance of Antarctic terrestrial biota. To assess arthropod distribution and diversity within the Ross Sea region, we examined mitochondrial DNA (COI) sequences for three currently recognized species of springtail (Collembola) collected from sites in the vicinity, and to the north of, the Mackay Glacier (77°S). This area acts as a transition between two biogeographic regions (northern and southern Victoria Land). We found populations of highly divergent individuals (5%–11.3% intraspecific sequence divergence) for each of the three putative springtail species, suggesting the possibility of cryptic diversity. Based on molecular clock estimates, these divergent lineages are likely to have been isolated for 3–5 million years. It was during this time that the Western Antarctic Ice Sheet (WAIS) was likely to have completely collapsed, potentially facilitating springtail dispersal via rafting on running waters and open seaways. The reformation of the WAIS would have isolated newly established populations, with subsequent dispersal restricted by glaciers and ice-covered areas. Given the currently limited distributions for these genetically divergent populations, any future changes in species’ distributions can be easily tracked through the DNA barcoding of springtails from within the Mackay Glacier ecotone

Biogeography and genetic diversity of terrestrial mites in the Ross Sea region, Antarctica

Free-living terrestrial mites (Acari) have persisted through numerous glacial cycles in Antarctica. Very little is known, however, of their genetic diversity and distribution, particularly within the Ross Sea region. To redress this gap, we sampled mites throughout the Ross Sea region, East Antarctica, including Victoria Land and the Queen Maud Mountains (QMM), covering a latitudinal range of 72–85 °S, as well as Lauft Island near Mt. Siple (73 °S) in West Antarctica and Macquarie Island (54oS) in the sub-Antarctic. We assessed genetic diversity using mitochondrial cytochrome c oxidase subunit I gene sequences (COI-5P DNA barcode region), and also morphologically identified voucher specimens. We obtained 130 sequences representing four genera: Nanorchestes (n = 30 sequences), Stereotydeus (n = 46), Coccorhagidia (n = 18) and Eupodes (n = 36). Tree-based analyses (maximum likelihood) revealed 13 genetic clusters, representing as many as 23 putative species indicated by barcode index numbers (BINs) from the Barcode of Life Datasystems (BOLD) database. We found evidence for geographically-isolated cryptic species, e.g., within Stereotydeus belli and S. punctatus, as well as unique genetic groups occurring in sympatry (e.g., Nanorchestes spp. in QMM). Collectively, these data confirm high genetic divergence as a consequence of geographic isolation over evolutionary timescales. From a conservation perspective, additional targeted sampling of understudied areas in the Ross Sea region should be prioritised, as further diversity is likely to be found in these short-range endemic mites

Genetic diversity of soil invertebrates corroborates timing estimates for past collapses of the West Antarctic Ice Sheet

During austral summer field seasons between 1999 and 2018, we sampled at 91 locations throughout southern Victoria Land and along the Transantarctic Mountains for six species of endemic microarthropods (Collembola), covering a latitudinal range from 76.0°S to 87.3°S. We assembled individual mitochondrial cytochrome oxidase subunit 1 (COI) sequences (= 866) and found high levels of sequence divergence at both small (600 km) spatial scales for four of the six Collembola species. We applied molecular clock estimates and assessed genetic divergences relative to the timing of past glacial cycles, including collapses of the West Antarctic Ice Sheet (WAIS). We found that genetically distinct lineages within three species have likely been isolated for at least 5.54 My to 3.52 My, while the other three species diverged more recently (<2 My). We suggest that Collembola had greater dispersal opportunities under past warmer climates, via flotation along coastal margins. Similarly increased opportunities for dispersal may occur under contemporary climate warming scenarios, which could influence the genetic structure of extant populations. As Collembola are a living record of past landscape evolution within Antarctica, these findings provide biological evidence to support geological and glaciological estimates of historical WAIS dynamics over the last ca. 5 My

Ligand-induced epitope masking. Dissociation of integrin α5β1-fibronectin complexes only by monoclonal antibodies with an allosteric mode of action.

We previously demonstrated that Arg-Gly-Asp (RGD)-containing ligand-mimetic inhibitors of integrins are unable to dissociate pre-formed integrin-fibronectin complexes (IFCs). These observations suggested that amino acid residues involved in integrin-fibronectin binding become obscured in the ligand-occupied state. Because the epitopes of some function-blocking anti-integrin monoclonal antibodies (mAbs) lie near the ligand-binding pocket, it follows that the epitopes of these mAbs may become shielded in the ligand-occupied state. Here, we tested whether function-blocking mAbs directed against α5β1 can interact with the integrin after it forms a complex with an RGD-containing fragment of fibronectin. We showed that the anti-α5 subunit mAbs JBS5, SNAKA52, 16, and P1D6 failed to disrupt IFCs and hence appeared unable to bind to the ligand-occupied state. In contrast, the allosteric anti-β1 subunit mAbs 13, 4B4, and AIIB2 could dissociate IFCs and therefore were able to interact with the ligand-bound state. However, another class of function-blocking anti-β1 mAbs, exemplified by Lia1/2, could not disrupt IFCs. This second class of mAbs was also distinguished from 13, 4B4, and AIIB2 by their ability to induce homotypic cell aggregation. Although the epitope of Lia1/2 was closely overlapping with those of 13, 4B4, and AIIB2, it appeared to lie closer to the ligand-binding pocket. A new model of the α5β1-fibronectin complex supports our hypothesis that the epitopes of mAbs that fail to bind to the ligand-occupied state lie within, or very close to, the integrin-fibronectin interface. Importantly, our findings imply that the efficacy of some therapeutic anti-integrin mAbs could be limited by epitope masking

Womens' opinions on antenatal care in developing countries: results of a study in Cuba, Thailand, Saudi Arabia and Argentina

BACKGROUND: The results of a qualitative study carried out in four developing countries (Cuba, Thailand, Saudi Arabia and Argentina) are presented. The study was conducted in the context of a randomised controlled trial to test the benefits of a new antenatal care protocol that reduced the number of visits to the doctor, rationalised the application of technology, and improved the provision of information to women in relation to the traditional protocol applied in each country. METHODS: Through focus groups discussions we were able to assess the concepts and expectations underlying women's evaluation of concepts and experiences of the care received in antenatal care clinics. 164 women participated in 24 focus groups discussion in all countries. RESULTS: Three areas are particularly addressed in this paper: a) concepts about pregnancy and health care, b) experience with health services and health providers, and c) opinions about the modified Antenatal Care (ANC) programme. In all three topics similarities were identified as well as particular opinions related to country specific social and cultural values. In general women have a positive view of the new ANC protocol, particularly regarding the information they receive. However, controversial issues emerged such as the reduction in the number of visits, particularly in Cuba where women are used to have 18 ANC visits in one pregnancy period. CONCLUSION: Recommendations to improve ANC services performance are being proposed. Any country interested in the application of a new ANC protocol should regard the opinion and acceptability of women towards changes

The mechanisms of boronate ester formation and fluorescent turn-on in ortho-aminomethylphenylboronic acids

ortho-Aminomethylphenylboronic acids are used in receptors for carbohydrates and various other compounds containing vicinal diols. The presence of the o-aminomethyl group enhances the affinity towards diols at neutral pH, and the manner in which this group plays this role has been a topic of debate. Further, the aminomethyl group is believed to be involved in the turn-on of the emission properties of appended fluorophores upon diol binding. In this treatise, a uniform picture emerges for the role of this group: it primarily acts as an electron-withdrawing group that lowers the pK(a) of the neighbouring boronic acid thereby facilitating diol binding at neutral pH. The amine appears to play no role in the modulation of the fluorescence of appended fluorophores in the protic-solvent-inserted form of the boronic acid/boronate ester. Instead, fluorescence turn-on can be consistently tied to vibrational-coupled excited-state relaxation (a loose-bolt effect). Overall, this Review unifies and discusses the existing data as of 2019 whilst also highlighting why o-aminomethyl groups are so widely used, and the role they play in carbohydrate sensing using phenylboronic acids

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

Advances in the technologies and informatics used to generate and process large biological data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches generating monothematic rather than integrated knowledge. As other areas of biomedical sciences, including metabolomics, epigenomics and pharmacogenomics, are moving towards the omics scale, we are witnessing the rise of inter-disciplinary data integration strategies to support a better understanding of biological systems and eventually the development of successful precision medicine. This review cuts across the boundaries between genomics, transcriptomics and proteomics, summarizing how omics data are generated, analysed and shared, and provides an overview of the current strengths and weaknesses of this global approach. This work intends to target students and researchers seeking knowledge outside of their field of expertise and fosters a leap from the reductionist to the global-integrative analytical approach in research

Erratum to: Methods for evaluating medical tests and biomarkers

[This corrects the article DOI: 10.1186/s41512-016-0001-y.]