Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass

Citation: Grabowski, Paul P., Geoffrey P. Morris, Michael D. Casler, and Justin O. Borevitz. “Population Genomic Variation Reveals Roles of History, Adaptation and Ploidy in Switchgrass.” Molecular Ecology 23, no. 16 (2014): 4059–73. https://doi.org/10.1111/mec.12845.Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass

Contamination of Domestic Groundwater Systems By Verotoxigenic Escherichia Coli (VTEC), 2003–2019: A global scoping review

Verocytotoxin-producing E. coli (VTEC) are important agents of diarrhoeal disease in humans globally. As a noted waterborne disease, emphasis has been given to the study VTEC in surface waters, readily susceptible to microbial contamination. Conversely, the status of VTEC in potable groundwater sources, generally regarded as a “safe” drinking-water supply remains largely understudied. As such, this investigation presents the first scoping review seeking to determine the global prevalence of VTEC in groundwater supply sources intended for human consumption. Twenty-three peer-reviewed studies were identified and included for data extraction. Groundwater sample and supply detection rates (estimated 0.6 and 1.3%, respectively) indicate VTEC is infrequently present in domestic groundwater sources. However, where generic (fecal indicator) E. coli are present, the VTEC to E. coli ratio was found to be 9.9%, representing a latent health concern for groundwater consumers. Geographically, extracted data indicates higher VTEC detection rates in urban (5.4%) and peri–urban (4.9%) environments than in rural areas (0.9%); however, this finding is confounded by the predominance of research studies in lower income regions. Climate trends indicate local environments classified as ‘temperate’ (14/554; 2.5%) and ‘cold’ (8/392; 2%) accounted for a majority of supply sources with VTEC present, with similar detection rates encountered among supplies sampled during periods typically characterized by ‘high’ precipitation (15/649; 2.3%). Proposed prevalence figures may find application in preventive risk-based catchment and groundwater quality management including development of Quantitative Microbial Risk Assessments (QMRA). Notwithstanding, to an extent, a large geographical disparity in available investigations, lack of standardized reporting, and bias in source selection, restrict the transferability of research findings. Overall, the mechanisms responsible for VTEC transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between hydrogeological and public health research. Key recommendations and guidelines are provided for prospective studies directed at increasingly integrative and multi-disciplinary research

Comparison of methods to estimate ruminal degradation and intestinal digestibility of protein in hydrolyzed feather meal with or without blood

Hydrolyzed feather meal (HFM) is a feedstuff high in rumen undegraded protein (RUP) that can be used as an effective source of metabolizable protein for dairy cattle. Because the production process may vary, the rumen degradability and intestinal digestibility of HFM may also vary. Additionally, some processes may incorporate additional blood into the final product to result in feather meal with poultry blood. To determine the rumen degradability and intestinal digestibility of these products, several laboratory assays can be used; the common assays are the mobile bag (MOB), modified three-step (MTS), and Ross (ROS) assays. Although all 3 assays determine RUP digestibility, they vary in whether they are performed in situ, in vitro, or both. The objective of this study was to evaluate the ruminal degradability and intestinal digestibility of HFM originating from processes that differ in their inclusion of blood, and to compare the MOB, MTS, and ROS assays. Ten samples of HFM, which were identified by the suppliers as HFM with little blood (n = 5) and with more blood (n = 5), were spot-sampled, collected from 10 production plants across the United States, and subjected to all 3 assays. Assay type had an effect on RUP, total-tract crude protein (CP) digestibility, and the amount of RUP digested. A significant effect was observed on RDP and RUP concentrations for blood inclusion; no effect was detected for total-tract CP digestibility. We found no difference in RUP digestibility for assay or blood inclusion. There was also no interaction of the effect of assay or blood inclusion. Results suggest that even though there are differences in chemical composition in HFM associated with the inclusion of blood, such as ash and crude fat, few if any differences are observed in intestinal digestion of protein. Although the assays varied in their estimates of rumen undegraded protein, MOB and MTS yielded the most similar values. However, all 3 assays resulted in similar estimates of RUP digestibility

Additive-Assisted Cerium-Based Electrolytic Coating Process for Corrosion Protection of Aluminum Alloys

The corrosion resistance of an aluminum or aluminum alloy component is enhanced by immersing an aluminum alloy to act as a cathode and an oxygen-evolving anode in an electrolyte comprising water, cerium ions, and an additive selected from among animal gelatin, derivatives of animal gelatin, and amino acids, then passing an electrical current through the electrolyte to deposit a cerium-based coating onto the aluminum-based component

Cerium-Based Spontaneous Coating Process for Corrosion Protection of Aluminum Alloys

A cerium-based coating for corrosion resistance is applied by exposing a cleaned aluminum-based component to a corrosion-inhibiting cerium solution containing cerium ions in the presence of an oxidizing agent. The coating deposits spontaneously without an external source of electrons

How do pediatric anesthesiologists define intraoperative hypotension?

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75736/1/j.1460-9592.2009.03140.x.pd

Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya

Lake Vostok, the 7th largest (by volume) and 4th deepest lake on Earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. The combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. Here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the Vostok 5G ice core. Two sections accreted in the vicinity of an embayment on the southwestern end of the lake, and the other two represented part of the southern main basin. We obtained 3,507 unique gene sequences from concentrates of 500 ml of 0.22 μm-filtered accretion ice meltwater. Taxonomic classifications (to genus and/or species) were possible for 1,623 of the sequences. Species determinations in combination with mRNA gene sequence results allowed deduction of the metabolic pathways represented in the accretion ice and, by extension, in the lake. Approximately 94% of the sequences were from Bacteria and 6% were from Eukarya. Only two sequences were from Archaea. In general, the taxa were similar to organisms previously described from lakes, brackish water, marine environments, soil, glaciers, ice, lake sediments, deep-sea sediments, deep-sea thermal vents, animals and plants. Sequences from aerobic, anaerobic, psychrophilic, thermophilic, halophilic, alkaliphilic, acidophilic, desiccation-resistant, autotrophic and heterotrophic organisms were present, including a number from multicellular eukaryotes. © 2013 Shtarkman et al

Using the CLEANED approach to assess environmental impacts in the dairy value chain in Tanga, Tanzania

Bill & Melinda Gates Foundatio

How Do Different Sources of Partisanship Influence Government Accountability in Europe?

The possibility of holding representatives to account through regular elections is one of the cornerstones of representative democracy. The precise role of partisanship in doing this has not been extensively examined. Using survey data from Europe (2002–2012), we show that partisanship can weaken or strengthen accountability, depending on its sources. If it is an affective-psychological attitude, as the Michigan school suggests, then it weakens accountability because it acts as a perceptual screen. If, however, it is a calculation of party performance which is constantly updated by citizens, then it strengthens accountability. The findings suggest that partisanship in Europe has been quite responsive to performance over the ten-year period. Instead of acting as a screen that inhibits accountability, partisanship appears rooted in calculations of party performance and so enhances accountability. However, the effects are asymmetric with left-leaning partisans more sensitive to the performance of their governments than right-leaning partisans