Using hydrogeochemical and ecohydrologic responses to understand epikarst process in semi-arid systems, Edwards plateau, Texas, USA

The epikarst is a permeable boundary between surface and subsurface environments and can be conceptualized as the vadose critical zone of epigenic karst systems which have not developed under insoluble cover. From a hydrologic perspective, this boundary is often thought of as being permeable in one direction only (down), but connectivity between the flow paths of water through the epikarst and the root systems of woody plants means that water moves both up and down across the epikarst. However, the dynamics of these flows are complex and highly dependent on variability in the spatial structure of the epikarst, vegetation characteristics, as well as temporal variability in precipitation and evaporative demand. Here we summarize insights gained from working at several sites on the Edwards Plateau of Central Texas, combining isotopic, hydrogeochemical, and ecophysiological methodologies. 1) Dense woodland vegetation at sites with thin to absent soils (0-30 cm) is in part supported by water uptake from the epikarst. 2) However, tree transpiration typically becomes water-limited in dry summers, suggesting that the plant-available fraction of stored water in the epikarst depletes quickly, even when sustained cave drip rates indicate that water is still present in the epikarst. 3) Flow paths for water that feeds cave drips become rapidly disconnected from the evaporation zone of the epikarst and out of reach for plant roots. 4) Deep infiltration and recharge does not occur in these systems without heavy or continuous precipitation that exceeds some threshold value. Thresholds are strongly correlated with antecedent potential evapotranspiration and rainfall, suggesting control by the moisture status of the epikarst evapotranspiration zone. The epikarst and unsaturated zone in this region can be conceptualized as a variably saturated system with storage in fractures, matrix porosity, and in shallow perched aquifers, most of which is inaccessible to the root systems of trees, although woody vegetation may control recharge thresholds.Keywords: hydraulic disconnection, precipitation thresholds, root zone, plant water use, recharge, epikarst storage, barometric pressure.DOI: 10.3986/ac.v42i2-3.67

Differentially expressed alternatively spliced genes in Malignant Pleural Mesothelioma identified using massively parallel transcriptome sequencing

<p>Abstract</p> <p>Background</p> <p>Analyses of Expressed Sequence Tags (ESTs) databases suggest that most human genes have multiple alternative splice variants. The alternative splicing of pre-mRNA is tightly regulated during development and in different tissue types. Changes in splicing patterns have been described in disease states. Recently, we used whole-transcriptome shotgun pryrosequencing to characterize 4 malignant pleural mesothelioma (MPM) tumors, 1 lung adenocarcinoma and 1 normal lung. We hypothesized that alternative splicing profiles might be detected in the sequencing data for the expressed genes in these samples.</p> <p>Methods</p> <p>We developed a software pipeline to map the transcriptome read sequences of the 4 MPM samples and 1 normal lung sample onto known exon junction sequences in the comprehensive AceView database of expressed sequences and to count how many reads map to each junction. 13,274,187 transcriptome reads generated by the Roche/454 sequencing platform for 5 samples were compared with 151,486 exon junctions from the AceView database. The exon junction expression index (EJEI) was calculated for each exon junction in each sample to measure the differential expression of alternative splicing events. Top ten exon junctions with the largest EJEI difference between the 4 mesothelioma and the normal lung sample were then examined for differential expression using Quantitative Real Time PCR (qRT-PCR) in the 5 sequenced samples. Two of the differentially expressed exon junctions (ACTG2.aAug05 and CDK4.aAug05) were further examined with qRT-PCR in additional 18 MPM and 18 normal lung specimens.</p> <p>Results</p> <p>We found 70,953 exon junctions covered by at least one sequence read in at least one of the 5 samples. All 10 identified most differentially expressed exon junctions were validated as present by RT-PCR, and 8 were differentially expressed exactly as predicted by the sequence analysis. The differential expression of the AceView exon junctions for the ACTG2 and CDK4 genes were also observed to be statistically significant in an additional 18 MPM and 18 normal lung samples examined using qRT-PCR. The differential expression of these two junctions was shown to successfully classify these mesothelioma and normal lung specimens with high sensitivity (89% and 78%, respectively).</p> <p>Conclusion</p> <p>Whole-transcriptome shotgun sequencing, combined with a downstream bioinformatics pipeline, provides powerful tools for the identification of differentially expressed exon junctions resulting from alternative splice variants. The alternatively spliced genes discovered in the study could serve as useful diagnostic markers as well as potential therapeutic targets for MPM.</p

Structure, Function, and Evolution of the Thiomonas spp. Genome

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live

Finding friends online: Online activities by deaf students and their well-being

Contains fulltext : 125129.pdf (publisher's version ) (Open Access)Generally, deaf and hard of hearing (D/HH) children have fewer friends than hearing peers and their friendships are of a lower quality. The research hypothesis was that using the computer to communicate with new online friends through social network sites or playing games with offline friends is associated with D/HH friendship qualities, because it removes certain communication barriers D/HH face in offline communication settings. With online questionnaires the relation between computer use and online, mixed (offline friend who you also speak in online settings), and offline friendship quality of D/HH and hearing students (18–25 years) was compared in both the Netherlands (n = 100) and the United States (n = 122). In addition, the study examined whether the different friendship qualities were related to the participants' well-being. Results showed that, in general, D/HH students' friendship qualities and levels of well-being were similar to their hearing peers. The quality of the mixed friendships was positively related to well-being. Furthermore, the frequency of pc use with both online and offline friends was positively related to friendships qualities in both hearing and D/HH students. A combination of the online and offline friendship seems to be the most important friendship type for both hearing and D/HH students and it is worthwhile to encourage this friendship type.10 p

Keratinocyte-Macrophage Crosstalk by the Nrf2/Ccl2/EGF Signaling Axis Orchestrates Tissue Repair

Unveiling the molecular mechanisms underlying tissue regeneration provides new opportunities to develop treatments for diabetic ulcers and other chronic skin lesions. Here, we show that Ccl2 secretion by epidermal keratinocytes is directly orchestrated by Nrf2, a prominent transcriptional regulator of tissue regeneration that is activated early after cutaneous injury. Through a unique feedback mechanism, we find that Ccl2 from epidermal keratinocytes not only drives chemotaxis of macrophages into the wound but also triggers macrophage expression of EGF, which in turn activates basal epidermal keratinocyte proliferation. Notably, we find dysfunctional activation of Nrf2 in epidermal keratinocytes of diabetic mice after wounding, which partly explains regenerative impairments associated with diabetes. These findings provide mechanistic insight into the critical relationship between keratinocyte and macrophage signaling during tissue repair, providing the basis for continued investigation of the therapeutic value of Nrf2