Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures

Microbial communities are recognized as major drivers of the biogeochemical processes in the oceans. However, the genetic diversity and composition of those communities is poorly understood. The aim of this study is to investigate the composition of bacterial assemblages in three different water layer habitats: surface (2–20 m), deep chlorophyll maximum (DCM; 28–90 m), and deep (100–4600 m) at nine stations along the eastern Atlantic Ocean from 42.8° N to 23.7° S. The sampling of three discrete, predefined habitat types from different depths, Longhurstian provinces, and geographical locations allowed us to investigate whether marine bacterial assemblages show spatial variation and to determine if the observed spatial variation is influenced by current environmental conditions, historical/geographical contingencies, or both. The PCR amplicons of the V6 region of the 16S rRNA from 16 microbial assemblages were pyrosequenced, generating a total of 352 029 sequences; after quality filtering and processing, 257 260 sequences were clustered into 2871 normalized operational taxonomic units (OTU) using a definition of 97% sequence identity. Community ecology statistical analyses demonstrate that the eastern Atlantic Ocean bacterial assemblages are vertically stratified and associated with water layers characterized by unique environmental signals (e.g., temperature, salinity, and nutrients). Genetic compositions of bacterial assemblages from the same water layer are more similar to each other than to assemblages from different water layers. The observed clustering of samples by water layer allows us to conclude that contemporary environments are influencing the observed biogeographic patterns. Moreover, the implementation of a novel Bayesian inference approach that allows a more efficient and explicit use of all the OTU abundance data shows a distance effect suggesting the influence of historical contingencies on the composition of bacterial assemblages. Surface bacterial communities displayed a general congruency with the ecological provinces as defined by Longhurst with modest exceptions usually associated with unique hydrographic and biogeochemical features. Collectively, our findings suggest that vertical (habitat) and latitudinal (distance) biogeographic signatures are present and that both environmental parameters and ecological provinces drive the composition of bacterial assemblages in the eastern Atlantic Ocean

The Test Retest of Internal Reliability of the Bod Pod

Faculty Mentor: Dr. Scott Mur

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Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138269/1/hep29286.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138269/2/hep29286_am.pd

Phi-values in protein folding kinetics have energetic and structural components

Phi-values are experimental measures of how the kinetics of protein folding is changed by single-site mutations. Phi-values measure energetic quantities, but are often interpreted in terms of the structures of the transition state ensemble. Here we describe a simple analytical model of the folding kinetics in terms of the formation of protein substructures. The model shows that Phi-values have both structural and energetic components. In addition, it provides a natural and general interpretation of "nonclassical" Phi-values (i.e., less than zero, or greater than one). The model reproduces the Phi-values for 20 single-residue mutations in the alpha-helix of the protein CI2, including several nonclassical Phi-values, in good agreement with experiments.Comment: 15 pages, 3 figures, 1 tabl

Direct detection of brown adipose tissue thermogenesis in UCP1−/− mice by hyperpolarized 129Xe MR thermometry

Brown adipose tissue (BAT) is a type of fat specialized in non-shivering thermogenesis. While non-shivering thermogenesis is mediated primarily by uncoupling protein 1 (UCP1), the development of the UCP1 knockout mouse has enabled the study of possible UCP1-independent non-shivering thermogenic mechanisms, whose existence has been shown so far only indirectly in white adipose tissue and still continues to be a matter of debate in BAT. In this study, by using magnetic resonance thermometry with hyperpolarized xenon, we produce the first direct evidence of UCP1-independent BAT thermogenesis in knockout mice. We found that, following adrenergic stimulation, the BAT temperature of knockout mice increases more and faster than rectal temperature. While with this study we cannot exclude or separate the physiological effect of norepinephrine on core body temperature, the fast increase of iBAT temperature seems to suggest the existence of a possible UCP1-independent thermogenic mechanism responsible for this temperature increase

Evaluation of the Effect of Hydrated Lime on the Scavenging of Feral Swine (\u3ci\u3eSus Scrofa\u3c/i\u3e) Carcasses and Implications for Managing Carcass-Based Transmission of African Swine Fever Virus

African swine fever (ASF) is a devastating hemorrhagic disease marked by extensive morbidity and mortality in infected swine. The recent global movement of African swine fever virus (ASFV) in domestic and wild swine (Sus scrofa) populations has initiated preparedness and response planning activities within many ASF-free countries. Within the US, feral swine are of utmost concern because they are susceptible to infection, are wide-spread, and are known to interact with domestic swine populations. African swine fever virus is particularly hardy and can remain viable in contaminated carcasses for weeks to months; therefore, carcass-based transmission plays an important role in the epidemiology of ASF. Proper disposal of ASF-infected carcasses has been demonstrated to be paramount to curbing an ASF outbreak in wild boar in Europe; preparedness efforts in the US anticipate carcass management being an essential component of control if an introduction were to occur. Due to environmental conditions, geographic features, or limited personnel, immediately removing every carcass from the landscape may not be viable. Hydrated lime converts to calcium carbonate, forming a sterile crust that may be used to minimize pathogen amplification. Any disturbance by scavenging animals to the sterile crust would nullify the effect of the hydrated lime; therefore, this pilot project aimed to evaluate the behavior of scavenging animals relative to hydrated lime-covered feral swine carcasses on the landscape. At two of the three study sites, hydrated limetreated carcasses were scavenged less frequently compared to the control carcasses. Additionally, the median time to scavenging was 1 d and 6 d for control versus hydrated lime-treated carcasses, respectively. While results of this study are preliminary, hydrated lime may be used to deter carcass disruption via scavenging in the event that the carcass cannot be immediately removed from the landscape

Soil genesis and development, lesson 1: Rocks, minerals, and soils

Most soil parent materials were rocks at some time in their history. The minerals in rocks may contribute to soil fertility and other soil properties long after the original rock is gone. Consequently, it is a valuable skill to be able to identify broad categories of rock. This lesson will discuss igneous, metamorphic, and sedimentary rocks and the minerals found in them. The lesson will also provide opportunities for students to identify rocks based on given characteristics. At the completion of this lesson, students will be able to do the following: 1. Classify rocks based on visual characteristics according to the major types: igneous, metamorphic, and sedimentary. 2. Predict the influence of “parent” rock on soil properties. The lesson uses an interactive approach, embedding questions in each section of the lesson. The lesson is written to target educational needs of lower-level undergraduate students and is open for use by the public and educational institutions

MSH3 polymorphisms and protein levels affect CAG repeat instability in huntington's disease mice

Expansions of trinucleotide CAG/CTG repeats in somatic tissues are thought to contribute to ongoing disease progression through an affected individual's life with Huntington's disease or myotonic dystrophy. Broad ranges of repeat instability arise between individuals with expanded repeats, suggesting the existence of modifiers of repeat instability. Mice with expanded CAG/CTG repeats show variable levels of instability depending upon mouse strain. However, to date the genetic modifiers underlying these differences have not been identified. We show that in liver and striatum the R6/1 Huntington's disease (HD) (CAG)~100 transgene, when present in a congenic C57BL/6J (B6) background, incurred expansion-biased repeat mutations, whereas the repeat was stable in a congenic BALB/cByJ (CBy) background. Reciprocal congenic mice revealed the Msh3 gene as the determinant for the differences in repeat instability. Expansion bias was observed in congenic mice homozygous for the B6 Msh3 gene on a CBy background, while the CAG tract was stabilized in congenics homozygous for the CBy Msh3 gene on a B6 background. The CAG stabilization was as dramatic as genetic deficiency of Msh2. The B6 and CBy Msh3 genes had identical promoters but differed in coding regions and showed strikingly different protein levels. B6 MSH3 variant protein is highly expressed and associated with CAG expansions, while the CBy MSH3 variant protein is expressed at barely detectable levels, associating with CAG stability. The DHFR protein, which is divergently transcribed from a promoter shared by the Msh3 gene, did not show varied levels between mouse strains. Thus, naturally occurring MSH3 protein polymorphisms are modifiers of CAG repeat instability, likely through variable MSH3 protein stability. Since evidence supports that somatic CAG instability is a modifier and predictor of disease, our data are consistent with the hypothesis that variable levels of CAG instability associated with polymorphisms of DNA repair genes may have prognostic implications for various repeat-associated diseases