Notes on the ground-squirrel, Callospermophilus

http://deepblue.lib.umich.edu/bitstream/2027.42/56624/1/OP185.pd

The mammals of Iraq.

http://deepblue.lib.umich.edu/bitstream/2027.42/56350/1/MP106.pd

Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps

Microbial communities thriving in hypersaline brines of solar salterns are highly resistant and resilient to environmental changes, and salinity is a major factor that deterministically influences community structure. Here, we demonstrate that this resilience occurs even after rapid osmotic shocks caused by a threefold change in salinity (a reduction from 34 to 12% salts) leading to massive amounts of archaeal cell lysis. Specifically, our temporal metagenomic datasets identified two co-occurring ecotypes within the most dominant archaeal population of the brines Haloquadratum walsbyi that exhibited different salt concentration preferences. The dominant ecotype was generally more abundant and occurred in high-salt conditions (34%); the low abundance ecotype always co-occurred but was enriched at salinities around 20% or lower and carried unique gene content related to solute transport and gene regulation. Despite their apparent distinct ecological preferences, the ecotypes did not outcompete each other presumably due to weak functional differentiation between them. Further, the osmotic shock selected for a temporal increase in taxonomic and functional diversity at both the Hqr. walsbyi population and whole-community levels supporting the specialization-disturbance hypothesis, that is, the expectation that disturbance favors generalists. Altogether, our results provide new insights into how intraspecies diversity is maintained in light of substantial gene-content differences and major environmental perturbations

Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

Background Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae. Results Sequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE-dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker) for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase) homologs and a putative conjugative pilus system. Despite the loss of many c-type cytochrome and oxidative-stress-responsive genes, strain SZ retained the majority of Geobacter core metabolic capabilities, including U(VI) respiration. Conclusions Gene acquisitions have expanded strain SZ’s respiratory capabilities to include PCE and TCE as electron acceptors. Respiratory processes core to the Geobacter genus, such as metal reduction, were retained despite a substantially reduced number of c-type cytochrome genes. pSZ77 is stably maintained within its host strains SZ and KB-1, likely because the replicon carries essential genes including genes involved in cobalamin biosynthesis and possibly corrinoid transport. Lateral acquisition of the plasmid replicon and the RDase genomic island represent unique genome features of the PCE-respiring G. lovleyi strains SZ and KB-1, and at least the latter signifies adaptation to PCE contamination

Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

Background Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae. Results Sequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE-dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker) for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase) homologs and a putative conjugative pilus system. Despite the loss of many c-type cytochrome and oxidative-stress-responsive genes, strain SZ retained the majority of Geobacter core metabolic capabilities, including U(VI) respiration. Conclusions Gene acquisitions have expanded strain SZ’s respiratory capabilities to include PCE and TCE as electron acceptors. Respiratory processes core to the Geobacter genus, such as metal reduction, were retained despite a substantially reduced number of c-type cytochrome genes. pSZ77 is stably maintained within its host strains SZ and KB-1, likely because the replicon carries essential genes including genes involved in cobalamin biosynthesis and possibly corrinoid transport. Lateral acquisition of the plasmid replicon and the RDase genomic island represent unique genome features of the PCE-respiring G. lovleyi strains SZ and KB-1, and at least the latter signifies adaptation to PCE contamination

imGLAD: accurate detection and quantification of target organisms in metagenomes

Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets. imGLAD achieves high accuracy because it uses the sequence-discrete population concept for discriminating between metagenomic reads originating from the target organism compared to reads from co-occurring close relatives, masks regions of the genome that are not informative using the MyTaxa engine, and models both the sequencing breadth and depth to determine relative abundance and limit of detection. We validated imGLAD by analyzing metagenomic datasets derived from spinach leaves inoculated with the enteric pathogen Escherichia coli O157:H7 and showed that its limit of detection can be comparable to that of PCR-based approaches for these samples (∼1 cell/gram)

Tools to Assess Behavioral and Social Science Competencies in Medical Education: A Systematic Review

Behavioral and social science (BSS) competencies are needed to provide quality health care, but psychometrically validated measures to assess these competencies are difficult to find. Moreover, they have not been mapped to existing frameworks, like those from the Liaison Committee on Medical Education (LCME) and Accreditation Council for Graduate Medical Education (ACGME). This systematic review aimed to identify and evaluate the quality of assessment tools used to measure BSS competencies

Predicted asteroseismic detection yield for solar-like oscillating stars with PLATO

Aims: In this work, we determine the expected yield of detections of solar-like oscillations for the targets of the foreseen PLATO ESA mission. Our estimates are based on a study of the detection probability, which takes into account the properties of the target stars, using the information available in the PIC 1.1.0, including the current best estimate of the signal-to-noise ratio (S/N). The stellar samples, as defined for this mission, include those with the lowest noise level (P1 and P2 samples) and the P5 sample, which has a higher noise level. For the P1 and P2 samples, the S/N is high enough (by construction) that we can assume that the individual mode frequencies can be measured. For these stars, we estimate the expected uncertainties in mass, radius, and age due to statistical errors induced by uncertainties from the observations only.Methods: We used a formulation from the literature to calculate the detection probability. We validated this formulation and the underlying assumptions with Kepler data. Once validated, we applied this approach to the PLATO samples. Using again Kepler data as a calibration set, we also derived relations to estimate the uncertainties of seismically inferred stellar mass, radius, and age. We then applied those relations to the main sequence stars with masses equal to or below 1.2 M⊙ belonging to the PLATO P1 and P2 samples and for which we predict a positive seismic detection.Results: We found that we can expect positive detections of solar-like oscillations for more than 15 000 FGK stars in one single field after a two-year observation run. Among them, 1131 main sequence stars with masses of ≤1.2 M⊙ satisfy the PLATO requirements for the uncertainties of the seismically inferred stellar masses, radii, and ages. The baseline observation programme of PLATO consists of observing two fields of similar size (one in the southern hemisphere and one in the northern hemisphere) for two years apiece. Accordingly, the expected seismic yields of the mission amount to over 30 000 FGK dwarfs and subgiants, with positive detections of solar-like oscillations. This sample of expected solar-like oscillating stars is large enough to enable the PLATO mission's stellar objectives to be amply satisfied.Conclusions: The PLATO mission is expected to produce a catalog sample of extremely well seismically characterized stars of a quality that is equivalent to the Kepler Legacy sample, but containing a number that is about 80 times greater, when observing two PLATO fields for two years apiece. These stars are a gold mine that will make it possible to make significant advances in stellar modelling

Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities

While the dynamics of microbial community assembly driven by environmental perturbations have been extensively studied, our understanding is far from complete, particularly for light‐induced perturbations. Extremely halophilic communities thriving in coastal solar salterns are mainly influenced by two environmental factors—salt concentrations and high sunlight irradiation. By experimentally manipulating light intensity through the application of shading, we showed that light acts as a deterministic factor that ultimately drives the establishment of recurrent microbial communities under near‐saturation salt concentrations. In particular, the stable and highly change‐resistant communities that established under high‐light intensities were dominated (>90% of metagenomic reads) by Haloquadratum spp. and Salinibacter spp. On the other hand, under 37‐fold lower light intensity, different, less stable and change‐resistant communities were established, mainly dominated by yet unclassified haloarchaea and relatively diverse photosynthetic microorganisms. These communities harboured, in general, much lower carotenoid pigment content than their high‐irradiation counterparts. Both assemblage types appeared to be highly resilient, re‐establishing when favourable conditions returned after perturbation (i.e. high‐irradiation for the former communities and low‐irradiation for the latter ones). Overall, our results revealed that stochastic processes were of limited significance to explain these patterns.This study was funded by the Spanish Ministry of Economy projects CGL2012-39627-C03-03 CLG2015_66686-C3-1-P and PGC2018-096956-B-C41 (to R.R.M.), CGL2015_66686-C3-3-P (to J.A.) and CGL2015_66686-C3-2-P (to J.E.G.P.), which were also supported with European Regional Development Fund (FEDER) funds. R.A. was funded by the Max Planck Society. KTK’s research was supported, in part, by the U.S. National Science Foundation (Award No. 1831582). T.V.P. received a pre-doctoral fellowship (No. BES-2013-064420) from the Spanish Government Ministry for Finance and Competition. R.R.M. acknowledges the financial support of the sabbatical stay at Georgia Tech supported by the Grant PRX18/00048 of the Ministry of Sciences, Innovation and Universities