Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value≤10-5) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies

Long-term and realistic global change manipulations had low impact on diversity of soil biota in temperate heathland

In a dry heathland ecosystem we manipulated temperature (warming), precipitation (drought) and atmospheric concentration of CO(2) in a full-factorial experiment in order to investigate changes in below-ground biodiversity as a result of future climate change. We investigated the responses in community diversity of nematodes, enchytraeids, collembolans and oribatid mites at two and eight years of manipulations. We used a structural equation modelling (SEM) approach analyzing the three manipulations, soil moisture and temperature, and seven soil biological and chemical variables. The analysis revealed a persistent and positive effect of elevated CO(2) on litter C:N ratio. After two years of treatment, the fungi to bacteria ratio was increased by warming, and the diversities within oribatid mites, collembolans and nematode groups were all affected by elevated CO(2) mediated through increased litter C:N ratio. After eight years of treatment, however, the CO(2)-increased litter C:N ratio did not influence the diversity in any of the four fauna groups. The number of significant correlations between treatments, food source quality, and soil biota diversities was reduced from six to three after two and eight years, respectively. These results suggest a remarkable resilience within the soil biota against global climate change treatments in the long term

Effectiveness of Teriparatide in Women Over 75 Years of Age with Severe Osteoporosis: 36-Month Results from the European Forsteo Observational Study (EFOS)

This predefined analysis of the European Forsteo Observational Study (EFOS) aimed to describe clinical fracture incidence, back pain, and health-related quality of life (HRQoL) during 18 months of teriparatide treatment and 18 months post-teriparatide in the subgroup of 589 postmenopausal women with osteoporosis aged ≥75 years. Data on clinical fractures, back pain (visual analogue scale, VAS), and HRQoL (EQ-5D) were collected over 36 months. Fracture data were summarized in 6-month intervals and analyzed using logistic regression with repeated measures. A repeated-measures model analyzed changes from baseline in back pain VAS and EQ-VAS. During the 36-month observation period, 87 (14.8 %) women aged ≥75 years sustained a total of 111 new fractures: 37 (33.3 %) vertebral fractures and 74 (66.7 %) nonvertebral fractures. Adjusted odds of fracture was decreased by 80 % in the 30 to <36–month interval compared with the first 6-month interval (P < 0.009). Although the older subgroup had higher back pain scores and poorer HRQoL at baseline than the younger subgroup, both age groups showed significant reductions in back pain and improvements in HRQoL postbaseline. In conclusion, women aged ≥75 years with severe postmenopausal osteoporosis treated with teriparatide in normal clinical practice showed a reduced clinical fracture incidence by 30 months compared with baseline. An improvement in HRQoL and, possibly, an early and significant reduction in back pain were also observed, which lasted for at least 18 months after teriparatide discontinuation when patients were taking other osteoporosis medication. The results should be interpreted in the context of an uncontrolled observational study

Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases

Dataset: Accelerated Retreat of Coastal Glaciers in the Western Prince William Sound, Alaska

Analysis of historical maps and Landsat imagery suggests coastal glaciers in the western Prince William Sound have retreated since the end of the Little Ice Age, with a period of accelerated retreat after 2004/06. I develop a multi-temporal inventory of 43 glaciers based on historical field observations, topographic maps, and Landsat imagery. Area and length measurements are derived from digitized outlines, and center lines calculated using a semi-automatic, geographic information system-based algorithm. Land-based glaciers retreated at a rate of 22 m a-1 from ~1950 to 2004/06 and peaked to 48 m a-1 after 2004/06. From ~1950 to 2018, the total area of land-based glaciers decreased by 228 km2, with 36% of the glacier loss occurring after 2004/06. Tidewater glaciers reacted asynchronously compared to land-based glaciers, with differing rates of area and length loss. Evaluation of climate trends indicates increasing temperatures and decreasing winter precipitation in the study area. Historical topographic maps of the study area provide the spatial data needed to extend glacier length change and area chronologies to the 1950s. The 21 maps I obtained for this study are available for download in a georeferenced format from the USGS (https://ngmdb.usgs.gov/topoview/viewer/#4/40.00/-100.00), allowing for use in geographical information systems (GIS) without further processing. The maps span 1951-1960 and are produced at the 1:63,360 scale from aerial photographs acquired from 1948-1957. I access Landsat images from an online service portal (ESRI, 2019). The images are georeferenced and orthorectified by USGS, allowing for direct integration into GIS. The images, at 30-60 m resolution, provide the spatial data for the repeat measurement of glacier outlines spanning 1973-2018. Previous studies provided Little Ice Age maximums for eight of the land-based glaciers analyzed in this study (Barclay et al., 2003; Wiles et al., 1999). I manually digitize outlines from historical maps, topographic maps, and Landsat images for glaciers 10 km2 or larger. Each study glacier is identified by a project identification number; Global Land Ice Measurements (GLIMS) and Randolph Glacier Inventory (RGI) identification numbers; and glacier name, if available. I manually digitize and adjust glacier boundaries based on the interpretation of 1950/57 topographic maps and Landsat images acquired in 1973/75, 1986, 1994, 2004/06, and 2018. Glacier length changes are measured from the intersection of the center line with each glacier terminus. I repeat measurements for 1950/57 topographic maps and the Landsat images acquired in 1973/75, 1986, 1994, 2004/06, and 2018, resulting in a glacier length change chronology for each glacier. For a subset of eight glaciers, I measure length changes to the digitized LIA maximum terminus positions identified in previous studies

Dataset: Accelerated Retreat of Coastal Glaciers in the Western Prince William Sound, Alaska

Analyzing historical maps and Landsat imagery indicates that coastal glaciers in the western Prince William Sound (PWS) have retreated since the end of the Little Ice Age, exhibiting accelerated retreat after the mid-2000s. A multi-temporal inventory of 43 glaciers was developed using historical field observations, topographic maps, and Landsat imagery. Area and length measurements are derived from digitized outlines, and center lines are derived from a semi-automatic, GIS-based algorithm. Land-based glaciers retreated at a peak rate of 48 m a-1 from the mid-2000s to 2018, more than doubling the average rate of retreat (22 m a-1) for the preceding 50-year period. From ~1950 to 2018, the total area of land-based glaciers decreased by 228 km2, with 36% of the glacier loss occurring after the mid-2000s. Simple upscaling of area and volume changes to unmeasured glaciers across the entire PWS resulted in an estimated aggregate glacier mass loss of 379 Gt, equivalent to a 1.047 mm rise in sea level from the 1950s to 2018. Tidewater glaciers respond asynchronously with differing periods of peak area and length loss and lower average rate of retreat compared to land-based glaciers. Glacier retreat correlates with increased summer and winter temperatures and decreased winter precipitation. I manually digitize outlines from historical maps, topographic maps, and Landsat images for glaciers 10 km2 or larger. Each study glacier is identified by a project identification number; Global Land Ice Measurements (GLIMS) and Randolph Glacier Inventory (RGI) identification numbers; and glacier name, if available. I manually digitize and adjust glacier boundaries based on the interpretation of 1950/57 topographic maps and Landsat images acquired in 1973/75, 1986, 1994, 2004/06, and 2018. Glacier length changes are measured from the intersection of the centerline with each glacier terminus. I repeat measurements for 1950/57 topographic maps and the Landsat images acquired in 1973/75, 1986, 1994, 2004/06, and 2018, resulting in a glacier length change chronology for each glacier. Glacier outlines are available from the GLIMS database (www.glims.org). See disclaimer in the "Data" section

Dataset: Accelerated Retreat of Coastal Glaciers in the Western Prince William Sound, Alaska

Analysis of historical maps and Landsat imagery suggests coastal glaciers in the western Prince William Sound have retreated since the end of the Little Ice Age, with a period of accelerated retreat after 2004/06. I develop a multi-temporal inventory of 43 glaciers based on historical field observations, topographic maps, and Landsat imagery. Area and length measurements are derived from digitized outlines, and center lines calculated using a semi-automatic, geographic information system-based algorithm. Land-based glaciers retreated at a rate of 22 m a-1 from ~1950 to 2004/06 and peaked to 48 m a-1 after 2004/06. From ~1950 to 2018, the total area of land-based glaciers decreased by 228 km2, with 36% of the glacier loss occurring after 2004/06. Tidewater glaciers reacted asynchronously compared to land-based glaciers, with differing rates of area and length loss. Evaluation of climate trends indicates increasing temperatures and decreasing winter precipitation in the study area. Historical topographic maps of the study area provide the spatial data needed to extend glacier length change and area chronologies to the 1950s. The 21 maps I obtained for this study are available for download in a georeferenced format from the USGS (https://ngmdb.usgs.gov/topoview/viewer/#4/40.00/-100.00), allowing for use in geographical information systems (GIS) without further processing. The maps span 1951-1960 and are produced at the 1:63,360 scale from aerial photographs acquired from 1948-1957. I access Landsat images from an online service portal (ESRI, 2019). The images are georeferenced and orthorectified by USGS, allowing for direct integration into GIS. The images, at 30-60 m resolution, provide the spatial data for the repeat measurement of glacier outlines spanning 1973-2018. Previous studies provided Little Ice Age maximums for eight of the land-based glaciers analyzed in this study (Barclay et al., 2003; Wiles et al., 1999). I manually digitize outlines from historical maps, topographic maps, and Landsat images for glaciers 10 km2 or larger. Each study glacier is identified by a project identification number; Global Land Ice Measurements (GLIMS) and Randolph Glacier Inventory (RGI) identification numbers; and glacier name, if available. I manually digitize and adjust glacier boundaries based on the interpretation of 1950/57 topographic maps and Landsat images acquired in 1973/75, 1986, 1994, 2004/06, and 2018. Glacier length changes are measured from the intersection of the center line with each glacier terminus. I repeat measurements for 1950/57 topographic maps and the Landsat images acquired in 1973/75, 1986, 1994, 2004/06, and 2018, resulting in a glacier length change chronology for each glacier. For a subset of eight glaciers, I measure length changes to the digitized LIA maximum terminus positions identified in previous studies. See disclaimer under &quot;Experimental Data File&quot; section

Dataset: Accelerated Retreat of Coastal Glaciers in the Western Prince William Sound, Alaska

Analyzing historical maps and Landsat imagery indicates that coastal glaciers in the western Prince William Sound (PWS) have retreated since the end of the Little Ice Age, exhibiting accelerated retreat after the mid-2000s. A multi-temporal inventory of 43 glaciers was developed using historical field observations, topographic maps, and Landsat imagery. Area and length measurements are derived from digitized outlines, and center lines are derived from a semi-automatic, GIS-based algorithm. Land-based glaciers retreated at a peak rate of 48 m a-1 from the mid-2000s to 2018, more than doubling the average rate of retreat (22 m a-1) for the preceding 50-year period. From ~1950 to 2018, the total area of land-based glaciers decreased by 228 km2, with 36% of the glacier loss occurring after the mid-2000s. Simple upscaling of area and volume changes to unmeasured glaciers across the entire PWS resulted in an estimated aggregate glacier mass loss of 379 Gt, equivalent to a 1.047 mm rise in sea level from the 1950s to 2018. Tidewater glaciers respond asynchronously with differing periods of peak area and length loss and lower average rate of retreat compared to land-based glaciers. Glacier retreat correlates with increased summer and winter temperatures and decreased winter precipitation. I manually digitize outlines from historical maps, topographic maps, and Landsat images for glaciers 10 km2 or larger. Each study glacier is identified by a project identification number; Global Land Ice Measurements (GLIMS) and Randolph Glacier Inventory (RGI) identification numbers; and glacier name, if available. I manually digitize and adjust glacier boundaries based on the interpretation of 1950/57 topographic maps and Landsat images acquired in 1973/75, 1986, 1994, 2004/06, and 2018. Glacier length changes are measured from the intersection of the centerline with each glacier terminus. I repeat measurements for 1950/57 topographic maps and the Landsat images acquired in 1973/75, 1986, 1994, 2004/06, and 2018, resulting in a glacier length change chronology for each glacier. Glacier outlines are available from the GLIMS database (www.glims.org). See disclaimer in the "Data" section